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[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "Recently, one of the interferon-induced transmembrane IFITM family proteins, IFITM3, has become an important target for the activity against influenza A H1N1 virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop.", "IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane TM1 domain and in the cytoplasmic CP loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes.", "IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 FKBP11 to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3.", "Our investigations using an established reporter, 17-octadecynoic acid 17-ODYA , and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP , revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP.", "Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11.", "These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule.", "The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation. Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A .", "Text: The interferon-induced transmembrane IFITM protein family also known as the Fragilis family in mice is a part of the dispanin family and is composed of double-transmembrane α-helices connected by a cytoplasmic CP loop and extracellular EC amino-and carboxyl-terminal polypeptide sequences Figure 1-A . The IFITM proteins are evolutionarily conserved in vertebrates . Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 .", "Recent genomic research has revealed that there are 5 IFITM members in humans IFITM1, 2, 3, 5 and 10 and 7 members in mice IFITM1, 2, 3, 5, 6, 7, and 10 . These proteins play roles in diverse biological processes, such as germ cell maturation during gastrulation IFITM1-3 , cell-to-cell adhesion IFITM1 , antiviral activity IFITM1-3 , and bone formation IFITM5 , although the detailed functions of IFITM6, 7, and 10 are unknown at present. In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization .", "In particular, IFITM3 has been a target of intensive studies on its activity against influenza A H1N1 virus infection and internalization . In 2010, Dr. Yount and co-workers reported that the antiviral activity of IFITM3 is dependent on S-palmitoylation on the protein . The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B .", "The S-palmitoylation is a post-translational modification on proteins by C 16 saturated-fatty acids palmitic acids covalently attached to certain cysteine residues via a thioester linkage Figure 1-B . The modification is reversibly catalyzed by protein acyltransferases and acylprotein thioesterases, and confers unique properties to the protein, such as membrane binding and targeting, immunoreactivity, Amino-acid sequence alignment of IFITM5, IFITM1, IFITM2, and IFITM3 derived from mice. The conserved residues are highlighted in black.", "The conserved residues are highlighted in black. The three conserved cysteines are highlighted in red and numbered based on the sequence of IFITM5 top and IFITM3 bottom . The residues unique in IFITM5 are highlighted in gray.", "The residues unique in IFITM5 are highlighted in gray. The first and the second transmembrane domains, the extracellular sequences, and the cytoplasmic loop are indicated by arrows and denoted as TM1 and TM2, EC, and the CP loop, respectively. The TM domains were predicted by SOSUI.", "The TM domains were predicted by SOSUI. The aspartates at the C-terminal region in IFITM5 are shown in blue. B The schematic illustration of the protein S-palmitoylation. The C 16 -palmitic acid is attached to cysteine via a thioester linkage. The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively.", "The palmitoylation and depalmitoylation are catalyzed by protein acyltransferases and acylprotein thioesterases, respectively. In this study, hydroxylamine, NH 2 OH, was used to reduce the thioester linkage. C The amino acid sequence identity similarity among IFITM5, IFITM1, IFITM2, and IFITM3 is summarized. .1371/journal.pone.0075831.g001 and protein-protein interaction.", ".1371/journal.pone.0075831.g001 and protein-protein interaction. The authors revealed that IFITM3 is S-palmitoylated on three membrane proximal cysteines, Cys71 and Cys72 in the first transmembrane TM1 domain, and Cys105 in the CP loop Figure 1-A . In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity.", "In addition, IFITM3 lacking the S-palmitoylation is not clustered in the cell membrane and significantly diminishes the antiviral activity. Moreover, the cysteines in IFITM2, Cys70, Cys71, and Cys104 are also palmitoylated in the same manner, which affects the intracellular localization . A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability .", "A resent study has revealed that murine IFITM1 has four cysteine residues Cys49, Cys50, Cys83, and Cys103 for the S-palmitoylation, which is required for the antiviral activity and the protein stability . The other IFITM family members also possess these cysteines Figure 1-A , and thus the role of the Spalmitoylation on the cysteines should be significant for the functions of IFITM proteins. Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein .", "Here, we focused on IFITM5, which is also known as bonerestricted IFITM-like BRIL protein . Among the IFITM family proteins, IFITM5 is unique. i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements .", "i Expression of IFITM5: Unlike the other IFITM family proteins, the expression of IFITM5 is not induced by interferons because the region upstream of the ifitm5 gene lacks the interferon regulatory elements . Furthermore, the expression of IFITM5 is mostly restricted to osteoblast cells , while the other IFITM proteins are expressed ubiquitously ii . Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C .", "Amino-acid sequence similarity: The amino acid sequence of IFITM5 is relatively dissimilar to IFITM1-3 proteins ~ 65% similarity , while IFITM1-3 proteins share ~ 85% similarity with each other Figure 1 -C . In addition, IFITM5 has an aspartate-rich domain in the C-terminal region, which could be involved in calcium binding Figure 1 -A . iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells .", "iii Role of IFITM5 in bone formation: The expression of IFITM5 is associated with mineralization during the bone formation process in osteoblast cells . Previous studies have confirmed the expression of IFITM5 in bone tissues in mice, rats, humans and tammar wallabies . The ifitm5-gene knockout mice have smaller bones .", "The ifitm5-gene knockout mice have smaller bones . Moreover, the knockdown of the ifitm5 gene by small hairpin RNA induces a decrease in bone nodule formation, whereas overexpression of the gene in UMR106 cells has been shown to increase calcium uptake and bone nodule formation . iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex .", "iv Role of IFITM5 for immune activity: Recent studies have revealed that IFITM5 interacts with the FK506-binding protein 11 FKBP11 to form IFITM5-FKBP11-CD81-the prostaglandin F2 receptor negative regulator FPRP complex . When the complex is formed, the expressions of 5 interferon-induced genes are induced, including bone marrow stromal cell antigen 2 Bst2 , interferon inducible protein 1 Irgm , interferoninduced protein with tetratricopeptide repeats 3 Ifit3 , b.microglobulin B2m , and MHC class I antigen gene. Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity.", "Consequently, these results indicate that IFITM5 is involved not only in the bone formation but also in the immune system activity. In this study, we investigated the S-palmitoylation of IFITM5 and its role in the interaction with FKBP11 in mouse osteoblast cells. Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP .", "Cells transfected by a plasmid DNA encoding mouse IFITM5 were grown in the presence of an established chemical reporter, 17-octadecynoic acid 17-ODYA , or an inhibitor for the S-palmitoylation, 2-bromopalmitic acid 2BP . The biochemical assays using these compounds revealed that the wild-type IFITM5 is S-palmitoylated. To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less .", "To identify the Spalmitoylation site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C86A, -C52A/C53A, and -C52A/53A/86A Cys-less . The chemical reporter assay suggested that at least two out of three cysteines in IFITM5 are S-palmitoylated. The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP.", "The interaction of IFITM5 with FKBP11 was examined by immunoprecipitation assay, resulting in the loss of the interaction in the presence of 2BP. The same result was obtained in the two mutants, C52A/C53A and Cys-less. These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11.", "These results suggested that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain of IFITM5 is necessary for the interaction with FKBP11. On the other hand, Cys86 in the CP loop of IFITM5 was S-palmitoylated but not involved in the interaction. Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells.", "Because this interaction is important for the immunologically relevant gene expression, it was indicated that the role of the S-palmitoylation is to promote the interaction of IFITM5 with FKBP11 and to regulate the immune activity in the osteoblast cells. The possible interaction mechanism and the effect of the S-palmitoylation on the bone nodule formation will be discussed. For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan .", "For mammalian cell expression, plasmid vectors of wild-type IFITM5 IFITM5-WT and FLAG-fused FKBP11 FKBP11-FLAG were constructed by inserting the cloned genes into a pBApo-CMV Neo expression vector Takara Bio, Shiga, Japan . The details of the recombinant DNA constructs were the same as described previously . The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA .", "The genes of IFITM5 mutants IFITM5-C86A, -C52A/53A, and -C52A/C53A/C86A Cys-less were prepared using a QuikChange site-directed mutagenesis kit Stratagene, La Jolla, CA . The plasmid vectors of FLAG-fused IFITM5-WT, -C52A/53A, and Cys-less were constructed by inserting the cloned genes into the pBApo-CMV Neo expression vector. For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector.", "For E. coli cell expression, the plasmid vector of IFITM5-WT was constructed by inserting the cloned gene into a pET22b Novagen, Madison, WI expression vector. The forward primer 5'-GGAATTCCATATGGACACTTCATATCCCCGTG-3' and the reverse primer 5'-CCGCTCGAGGTTATAGTCCTCCTCATCAAACTTGG-3' were used to amplify the gene encoding the entire IFITM5 from the plasmid vector for mammalian cell expression described above. The underlined letters denote an NdeI and an XhoI cleavage site, respectively.", "The underlined letters denote an NdeI and an XhoI cleavage site, respectively. The plasmids of IFITM5 mutants were prepared using a QuikChange site-directed mutagenesis kit. The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO .", "The sense and anti-sense primers used were 5'-GGCAGTATGGCTCCAAAGCCAAGGCGTACAACATCCTGG CTGC-3' and 5'-GCAGCCAGGATGTTGTACGCCTTGGCTTTGGAGCCATACT GCC-3' for IFITM5-C86A; and 5'-GCACGATGTACCTGAATCTGGCGGCGCTTGGATTCCTGG CGC-3' and 5'-GCGCCAGGAATCCAAGCGCCGCCAGATTCAGGTACATCG TGC-3' for IFITM5-C52A/C53A, respectively Sigma-Aldrich, St. Louis, MO . Osteoblast-like MC3T3 cells were provided by the RIKEN, Cell Bank RCB 1126 . The procedures for cell culture, transfection, and protein expression were the same as reported previously.", "The procedures for cell culture, transfection, and protein expression were the same as reported previously. When necessary, 2-bromopalmitic acid 2BP; Wako, Osaka, Japan and 17-octadecynoic acid 17-ODYA; Sigma-Aldrich were dissolved in 99.5% dimethyl sulfoxide DMSO; Wako and added to differentiation medium at concentrations of 100 μM and 50 μM in less than 0.1% DMSO, respectively . Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system.", "Wild-type and mutant IFITM5 proteins were also produced using an E. coli recombinant expression system. E. coli BL21 DE3 cells transformed by the expression plasmid were grown at 37°C in LB medium containing 50 μg/mL ampicillin. After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C .", "After four-hour induction by 1 mM isopropyl β-Dthiogalactopyranoside IPTG , cells were harvested by centrifugation 6,400 × g for 10 min at 4°C . The cells were suspended in 50 mM Tris-HCl buffer pH 8 and disrupted by a French press Ohtake, Tokyo, Japan 100 MPa × 4 times . The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C .", "The crude membrane fraction was collected by ultracentrifugation 178,000 × g for 90 min at 4°C . The collected fraction was solubilized with 1.5% n-dodecyl-β-Dmaltopyranoside DDM Dojindo Lab, Kumamoto, Japan in 50 mM Tris-HCl, pH 8, containing 0.3 M NaCl and 5 mM imidazole. After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany .", "After the ultracentrifugation, the supernatant was incubated with Ni 2+ -NTA agarose resin Qiagen, Hilden, Germany . The resin was applied to a chromatography column and washed with 50 mM imidazole containing 50 mM Tris-HCl pH 8 , 0.3 M NaCl and 0.1% DDM. The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole.", "The DDM-solubilized IFITM5 was collected by elution with the same buffer containing 0.3 M imidazole. The sample media were replaced by the appropriate buffer solution by two passages over a PD-10 column GE Healthcare UK, Ltd., Amersham Place, England . The experimental details are described in previous reports .", "The experimental details are described in previous reports . Briefly, total proteins were extracted from the osteoblast cells which co-expressed IFITM5 and FKBP11-FLAG using a total protein extraction kit BioChain Institute Inc., Newark, CA . Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot.", "Then, the cell lysate was incubated with anti-FLAG M2 agarose gel Sigma-Aldrich at 4°C for 2 h. To recover FKBP11-FLAG, 500 ng/μL 3 × FLAG peptide Sigma-Aldrich dissolved in Tris-buffered saline was added to the collected gel at 4°C for 1 h. The recovered proteins and the cell lysate containing total proteins were analyzed by SDS-PAGE 15% ePAGEL; ATTO, Tokyo, Japan and western blot. The anti-IFITM5 polyclonal antibody, which was prepared from the amino-terminal peptide sequence TSYPREDPRAPSSRC , and anti-FLAG monoclonal antibody Sigma-Aldrich were used as primary antibodies. The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively.", "The HRP-conjugated goat anti-rabbit IgG H+L Zymed Laboratories, San Francisco, CA and goat anti-mouse IgG H+L Sigma-Aldrich antibodies were used as secondary antibodies for the anti-IFITM5 and anti-FLAG primary antibodies, respectively. The proteins were detected by chemiluminescent reaction MercK-Millipore, Billerica, MA . The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins.", "The cell lysate extracted from the osteoblast cells metabolically labeled by 17-ODYA was incubated with anti-FLAG M2 agarose gel to obtain purified FLAG-fused IFITM5 proteins. The 17-ODYA-labeled proteins were chemically labeled with azide-PEG 3 -5.-carboxytetramethylrhodamine TAMRA-azide; Click Chemistry Tools, Scottsdale, AZ with reference to previous studies and the manufacturer's guide. The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare .", "The proteins separated by SDS-PAGE were visualized using a 532-nm laser for excitation and the fluorescence by TAMRA 565 nm was detected using a 575nm long-path filter Typhoon FLA 9000; GE Healthcare . The subcultured osteoblast MC3T3 cells were seeded at a density of 5,000 cells/cm 2 in 40 mm dishes and cultured in α-Modified Eagle's Medium α-MEM; Sigma-Aldrich containing 10% v/v fetal bovine serum FBS; Nichirei Biosciences Inc., Tokyo, Japan . On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation.", "On the next day, this was replaced with differentiation medium, containing 2 mM glycerophosphate and 50 μg/mL sodium ascorbate at final concentrations, to induce osteoblast differentiation. When necessary, 100 μM 2BP in less than 0.1% DMSO, or 0.1% DMSO alone was added to the differentiation medium at final concentrations. All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days.", "All cultures were incubated at 37°C in a humidified atmosphere containing 5% CO 2 for 27 days. Mineralized nodules were stained with Alizarin Red S Sigma-Aldrich . The standard staining procedure was used. The mineralized nodules were checked every three days.", "The standard staining procedure was used. The mineralized nodules were checked every three days. To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A .", "To identify the S-palmitoylation on IFITM5, the osteoblast cells harboring the plasmid DNA encoding IFITM5-WT were cultured in the absence and presence of 2BP, which inhibits the S-palmitoylation Figure 2-A . Then, the cell lysate containing total protein was extracted for use in the SDS-PAGE and western blot analyses. For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted.", "For purposes of comparison, E. coli cells were also cultured in the absence of 2BP and the cell lysate was extracted. Figure 2 -B shows the results of the western blot assay for IFITM5-WT expressed in the osteoblast and the E. coli cells. In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP.", "In the osteoblast cells, IFITM5-WT exhibited a single band near the 17.4 kDa molecular-mass marker see lane 1 in the absence of 2BP. However, in the presence of 2BP see lane 4 , the band appeared at a lower position than that in the absence of 2BP lane 1 . These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively.", "These results suggested that IFITM5-WT has high and low molecular-mass forms in the absence and presence of 2BP, respectively. The S-palmitoylation is a reversible reaction, and therefore is depalmitoylated by a strong reductant such as hydroxylamine . Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 .", "Following hydroxylamine treatment see lane 2 , the band appeared at the same position as in the presence of 2BP lane 4 . In prokaryote E. coli cells, the post-translational modification S-Palmitoylation on IFITM5 PLOS ONE | does not occur. Hence, the band was also observed at the same lower position see lane 3 .", "Hence, the band was also observed at the same lower position see lane 3 . In the case of IFITM3, the palmitoylation was also reported to induce a change in mobility on electrophoresis, just as in our present results . For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used.", "For direct observation of the S-palmitoylation, an established chemical reporter, 17-ODYA Figure 2-C , was used. The osteoblast cells harboring the plasmid encoding IFITM5-WT were cultured in the presence of 17-ODYA to label the protein metabolically. Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 .", "Following the extraction and the purification of the cell lysate, the labeled IFITM5-WT was ligated with TAMRA-azide according to the Cu I -catalyzed 3+2 azidealkyne cycloaddition method 10, 29, 30, 32 . An in-gel fluorescence image of the 17-ODYA-TAMRA-labeled IFITM5-WT see lane 2 in Figure 2 -D showed that IFITM5 was Spalmitoylated in the osteoblast cells. The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 .", "The FLAG-tag attached to IFITM5 has no influence on the modification and chemical labeling lanes 1 and 5 . In addition, after the hydroxylamine treatment see lane 6 , the fluorescence became weak because of the dissociation of 17-ODYA from IFITM5, which was the same mechanism as the dissociation of the palmitic acid from IFITM5 by reduction as described above lane 2 of Figure 2-B . Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated.", "Therefore, we concluded that the IFITM5 expressed in the native osteoblast cells is S-palmitoylated. In addition, the bands corresponding to the high and the low molecular-mass forms shown in western blot analysis were tentatively assigned to the S-palmitoylated and the depalmitoylated forms, respectively. As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation.", "As described above in the Introduction, cysteine residues are the substrate for S-palmitoylation. IFITM5 possesses three cysteines, Cys52 and Cys53 in the TM1 domain, and Cys86 in the CP loop Figure 1-A . All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A .", "All of these cysteines are highly conserved among the mammalian IFITM family proteins Figure 3-A . To identify the modification site in IFITM5, we prepared cysteine-substituted mutants, IFITM5-C52A/C53A, -C86A, and -C52A/C53A/C86A Cys-less . The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted.", "The osteoblast cells harboring each plasmid were cultured in the absence of 2BP, and then the cell lysate was extracted. Figure 3 -B shows the results of the western blot detecting the expression of all the mutants in the osteoblast cells. In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected.", "In the C52A/C53A and Cys-less mutants see lanes 2 and 4 , the low molecular-mass form was detected. This result indicates that either Cys52 or Cys53 is involved in the S-palmitoylation. In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 .", "In addition, as shown in Figure 2 -D, strong and weak fluorescence were detected in the C52A/ C53A mutant in the absence and presence of hydroxylamine lanes 3 and 7 , respectively, but not in the Cys-less mutant lanes 4 and 8 . These results suggested that the rest of the cysteine in the C52A/C53A mutant, Cys86, is S-palmitoylated and the Cys-less mutant completely lost the S-palmitoylation because all the cysteines were substituted. Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated.", "Therefore, we concluded that Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated. In addition, it was found that the S-palmitoylation on the TM1 domain has a major effect on the mobility in the gel lower panel of Figure 2 -D and Figure 3-B . Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively.", "Therefore, we hereafter refer to the high and low molecular-mass forms as the TM1palmitoylated and the TM1-depalmitoylated forms, respectively. Finally, we reassigned the bands shown in the western blot analysis as follows: IFITM5-WT is fully palmitoylated, the C86A mutant is partially palmitoylated at Cys52 and/or Cys53, the C52A/C53A mutant is partially palmitoylated at Cys86, and the Cys-less mutant is completely depalmitoylated. Previous studies have revealed that IFITM5 interacts with FKBP11 .", "Previous studies have revealed that IFITM5 interacts with FKBP11 . FKBP11 belongs to the FK506-binding protein family and has a transmembrane domain. The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene .", "The interaction between IFITM5 and FKBP11 is important for the immune activity because formation of the IFITM5-FKBP11-CD81-FPRP complex induces the expression of interferon-induced genesnamely, the Bst2, Irgm, Ifit3, B2m, and MHC class I antigen gene . To investigate the effect of the S-palmitoylation on the interaction of IFITM5 with FKBP11, we carried out an immunoprecipitation assay. The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP.", "The osteoblast cells co-transfected by the plasmids encoding IFITM5-WT and FKBP11-FLAG were cultured in the absence and the presence of 2BP. Then, the extracted cell-lysate was incubated with anti-FLAG agarose gel. The gel was washed several times. Finally, the proteins were competitively eluted by the addition of FLAG peptide.", "Finally, the proteins were competitively eluted by the addition of FLAG peptide. If IFITM5 interacted with FKBP11, it was expected that IFITM5 The conserved cysteines are highlighted in orange and numbered. In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2.", "In the lower panel, the numbers given in parenthesis correspond to the residual number for IFITM2. For the calculation of probability, a total of 23 IFITM2, 23 IFITM3, and 17 IFITM5 sequences derived from mammalian species in the Kyoto Encyclopedia of Genes and Genomes KEGG database were used. Sequence alignment was carried out using CLUSTALW.", "Sequence alignment was carried out using CLUSTALW. Sequence logos were generated using WEBLOGO 3. B Western blot for the wild-type and cysteine-substituted mutants of IFITM5 expressed in the osteoblast cells. For detection, the anti-IFITM5 antibody was used as a primary antibody.", "For detection, the anti-IFITM5 antibody was used as a primary antibody. The upper arrow indicates that C52 and/or C53 in the TM1 domain is Spalmitoylated lanes 1 and 3 . The C52A/C53A lane 2 and Cys-less lane 4 mutants are partially and completely depalmitoylated. The experiment was carried out 2 times.", "The experiment was carried out 2 times. .1371/journal.pone.0075831.g003 would be obtained during this step and detected by immunoblotting. Figure 4 -A shows the results of the western blot for the co-immunoprecipitation of IFITM5-WT with FKBP-FLAG. The band corresponding to FKBP11 appeared in all the lanes upper panel .", "The band corresponding to FKBP11 appeared in all the lanes upper panel . Lanes 1 and 2 are controls to ensure that IFITM5 and FKBP11 are both contained in the cell lysate before the immunoprecipitation. The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 .", "The controls also ensured that IFITM5 was S-palmitoylated in the absence of 2BP see lane 1 , whereas IFITM5 was not S-palmitoylated in the presence of 2BP see lane 2 . After the immunoprecipitation, a single band corresponding to the S-palmitoylated IFITM5 appeared in the absence of 2BP see lane 3 , indicating the interaction of the Spalmitoylated IFITM5 with FKBP11. However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other.", "However, in the presence of 2BP, no band corresponding to IFITM5 appeared see lane 4 , indicating that the two molecules do not interact with each other. These results suggest that the S-palmitoylation on IFITM5 contributes to the interaction with FKBP11. Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above.", "Next, we further investigated the relationship between the Spalmitoylation and the interaction with FKBP11 by using the IFITM5 mutants described above. The osteoblast cells cotransfected by the plasmids encoding IFITM5 mutants C52A/ C53A, C86A, and Cys-less and FKBP11-FLAG were cultured. The immunoprecipitation assay was carried out in the same way as described above.", "The immunoprecipitation assay was carried out in the same way as described above. Figure 4 -B shows the results of the western blot for the co-immunoprecipitation of the wild-type and the IFITM5 mutants with FKBP11. Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation.", "Figure 4 -C shows the results of the control experiment using the cell lysate before the immunoprecipitation. As described in the previous section 3-3, the band corresponding to FKBP11 appeared in all the lanes upper panels because the immunoprecipitation was carried out using the anti-FLAG agarose gel. In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 .", "In the lower panel of Figure 4 -B, single bands were observed for the IFITM5-WT and -C86A mutant lanes 1 and 3 but not for the -C52A/C53A and Cys-less mutants lanes 2 and 4 . This result indicates that the wild-type and the C86A mutant interact with FKBP11, whereas the other two mutants do not. Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C .", "Interestingly, this tendency mirrored the trend for the S-palmitoylation profiles, which means that Cys52 and/or Cys53 in the TM1 domain of the IFITM5-WT and -C86A mutants is S-palmitoylated, whereas these residues are not S-palmitoylated in the C52A/C53A and Cys-less mutants see Figures 2-D, 3 -B and the lower panel of Figure 4 -C . Because the S-palmitoylation contributes to the IFITM5-FKBP11 interaction, as described in the previous section 3-3 also in Figure 4-A , the results of Figure 4 -B suggest that the mutants which lost the S-palmitoylation site s , Cys52 and/or Cys53, are not able to interact with FKBP11. In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11.", "In other words, the S-palmitoylation on these cysteines is necessary for the interaction of IFITM5 with FKBP11. As described above in the Introduction, previous studies have revealed that IFITM5 also contributes to bone formation . Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed.", "Therefore, we investigated the influence of Spalmitoylation on the bone nodule formation in osteoblast cells, in which native IFITM5 is expressed. Figure 5 shows the time-dependent nodule formation in the absence and the presence of 2BP Figure 5-A and -B . Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation.", "Figure 5 -C shows the results of the control trial to verify the effect of DMSO, which was used as the solvent for 2BP, on the nodule formation. The mineralized nodule was stained with Alizarin Red, which reacts with deposited calcium. In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time.", "In Figure 5 -D, the area of the mineralized nodule was plotted against experimental time. In the absence of 2BP Figure 5-A, -C, and -D , the mineralization was started 15 days after the initiation of the cell differentiation Day 0 . On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12.", "On the other hand, in the presence of 2BP Figure 5-B and -D , the nodule was formed on Day 12. The halftime for the maximum mineralization in the presence of 2BP was estimated to be 7 days earlier than that in the absence of 2BP Figure 5-D . In addition, differences in the form of the mineralized nodules were observed.", "In addition, differences in the form of the mineralized nodules were observed. Figure 5 -E shows an enlarged view of each nodule on Day 21. The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c .", "The stained nodules were diffused in the presence of 2BP panel b , whereas in the absence of 2BP the nodules formed a large cluster panels a and c . Therefore, our observations in this study suggested that the S-palmitoylation affects the bone nodule formation in the osteoblast cells. In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2.", "In this study, we confirmed the S-palmitoylation on IFITM5 in the osteoblast cells, which was the same as that previously reported for IFITM3 and IFITM2. As reported previously, in IFITM3 and IFITM2, which share 85% sequence similarity Figure 1-C , two cysteines in the TM1 domain Cys71 and Cys72 for IFITM3, Cys70 and Cys71 for IFITM2 and one cysteine in the CP loop Cys105 for IFITM3, Cys104 for IFITM2 are all S-palmitoylated in cells . On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated.", "On the other hand, although IFITM5 shares 68% and 66% sequence similarity to IFITM3 and IFITM2, respectively, more than one cysteine in the TM1 domain Cys52 or Cys53 and one cysteine in the CP loop Cys86 are S-palmitoylated. Taking into account the high conservation of three cysteines in the IFITM proteins Figures 1-A and 3-A , all the cysteines in IFITM5 may be involved in the S-palmitoylation just as in the case of IFITM3 and IFITM2 . The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below .", "The roles of the S-palmitoylation on IFITM3 have been studied intensively, and the S-palmitoylation has been shown to be crucial for the correct positioning in the membrane and the resistance to viral infection and internalization the roles are summarized in Figure 6 -A and discussed in detail below . A recent study has revealed that the S-palmitoylation on IFITM2 is also important for the protein clustering in the membrane . However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies.", "However, we do not know the role of the Spalmitoylation of IFITM5 for the clustering in the membrane at present because we have not yet succeeded in obtaining a proper antibody for immunohistochemistry, despite our allocating much time to the search and considering a considerable number of antibodies. Dr. Hanagata and co-workers previously reported that IFITM5 lacking the TM1 domain and the CP loop, which and IFITM5 lower panels , the anti-FLAG and the anti-IFITM5 antibodies were used as primary antibodies, respectively. Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5.", "Arrows indicate the existence of each protein and the S-palmitoylation on IFITM5. A Western blot for the co-immunoprecipitation of the wild-type IFITM5 with the FLAG-fused FKBP11 FKBP11-FLAG in the osteoblast cells in the absence and the presence of 2BP denoted as \"-\" and \"+\", respectively . Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation.", "Lanes 1 and 2 are the results for the control trials used to verify the existence of IFITM5 and FKBP11 before the immunoprecipitation, and Lanes 3 and 4 show the results after the immunoprecipitation. The experiment was repeated 3 times. B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells.", "B Western blot for the co-immunoprecipitation of the wild-type and the cysteine-substituted mutants of IFITM5 with FKBP11-FLAG in the osteoblast cells. The band corresponding to FLAG peptide is not shown because of the smaller molecular-mass of FLAG peptide relative to FKBP11-FLAG. C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation.", "C The control experiment of Figure 4 -B used to verify that IFITM5 and FKBP11 were both present in the cell lysate before the immunoprecipitation. The experiment was repeated 2 times. A The functional mechanism of IFITM3 is summarized from previous studies.", "A The functional mechanism of IFITM3 is summarized from previous studies. i IFITM3 is S-palmitoylated at Cys71, Cys72, and Cys105, ii which induces clustering and correct positioning in the membrane, iii resulting in the antiviral activity against influenza virus. B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies.", "B The functional mechanism of IFITM5 is summarized by combining the results from the present and the previous studies. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii .", "The S-palmitoylation allows IFITM5 to interact with FKBP11 in the osteoblast cells iii . The dissociation of CD9 from the FKBP11-CD81-FPRP/CD9 complex is induced by formation of the IFITM5-FKBP11-CD81-FPRP complex and leads to the immunologically relevant gene expression. IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2.", "IFITM5 also contributes to the bone formation, but it is unknown which states as described in i - iii are important for the bone formation at present.At present, no interactive protein has been identified in IFITM3 and IFITM2. On the other hand, IFITM5 interacts with the partner protein, FKBP11, and the S-palmitoylation clearly makes a significant contribution to the interaction. Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function.", "Therefore, IFITM5 forms a hetero-oligomer in the cell membrane for its physiological function. contain the relevant modification sites, lost the ability to interact with FKBP11 . In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction.", "In the present study, we determined that the S-palmitoylation on Cys52 and/or Cys53 in the TM1 domain is necessary for the interaction. From these results, we speculate that Cys52 and Cys53 face toward the interaction surface with FKBP11, and therefore IFITM5 and FKBP11 interact with each other through the palmitic acid s attached to the cysteine s summarized in Figure 6 -B, discussed in detail later . Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11.", "Our investigation revealed that Cys86 is involved in the Spalmitoylation but does not contribute to the interaction with FKBP11. We speculate that some other residues in the CP loop located near the TM1 domain make some contribution to the interaction. Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 .", "Previous investigations also revealed that IFITM5 expressed in the heterologous fibroblast NIH3T3 cells exhibited direct interactions with CD81, the B cell receptor-associated protein 31 BCAP31 , and the hydroxysteroid 17-beta dehydrogenase 7 HSD17b7 . These three proteins bind to the IFITM5 without the S-palmitoylation low molecular-mass form; see Figure 3 -b in ref . and Figure 1 -B in ref .", "and Figure 1 -B in ref . . In the fibroblast cells, the S-palmitoylation on IFITM5 is insufficient . These interactions are not observed in the native osteoblast cells, and therefore are nonspecific. Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells.", "Taking these facts into consideration, we speculate that the S-palmitoylation on IFITM5 promotes the specific interaction with FKBP11 in the osteoblast cells. The role played by the S-palmitoylation of IFITM5 in immune activity of the osteoblast cells will be discussed by combining the results from the present and the previous studies. A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex.", "A specific interaction between IFITM5 and FKBP11 should be necessary to form the IFITM5-FKBP11-CD81-FPRP complex. CD81, also known as TAPA-1, is a member of the tetraspanin membrane protein family and a component of the B-cell coreceptor complex which mediates the B-cell signaling for immune responses. When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene .", "When forming this complex, CD9, a partner protein with CD81, dissociates from the FKBP11-CD81-FPRP/CD9 complex and consequently induces the osteoblastspecific expression of the interferon-induced genes, Bst2, Irgm, Ifit3, B2m, and the MHC class I antigen gene . If the Spalmitoylation-mediated specific interaction of IFITM5 with FKBP11 were lost, the IFITM5-FKBP11-CD81-FPRP complex would not be formed, and consequently the interferon-induced gene expression would be inhibited because CD9 would remain associated with the FKBP11-CD81-FPRP/CD9 complex. In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity.", "In this respect, we speculate that IFITM5 is involved in the immune system activity in the osteoblast cells and the interaction of the S-palmitoylated IFITM5 with FKBP11 regulates the immune activity. In addition, it was suggested that the S-palmitoylation on IFITM5 contributes to the bone nodule formation, including morphology and time for mineralization, in the osteoblast cells Figure 5 . It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP.", "It is difficult to conclude at present that the lack of the S-palmitoylation on IFITM5 causes the diffusion of the bone nodules panel b of Figure 5 -E ; we can say, however, that IFITM5 will probably not be S-palmitoylated in the cells in the presence of 2BP. While 2BP is commonly used as an inhibitor of palmitoylation, it also targets many metabolic enzymes . Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP.", "Thus, it is also difficult to interpret the results of the long-term incubation of the osteoblast cells in the presence of 2BP. In any case, these are interesting and key observations in terms of clarifying the role played by the S-palmitoylation of IFITM5 in bone formation, and further studies are required. Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3.", "Figure 6 describes a possible mechanism of the interaction of IFITM5 with FKBP11 and the role of IFITM5 in the osteoblast cell function by means of a comparison with IFITM3. In the case of IFITM3, as shown in Figure 6 -A, the following are observed. i The three cysteines are all S-palmitoylated ii .", "i The three cysteines are all S-palmitoylated ii . The S-palmitoylation leads to the clustering and the correct positioning of IFITM3 molecules in the membrane iii . The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus.", "The Spalmitoylation and the following clustering are crucial for the resistance to the influenza virus. When IFITM3 lacks the Spalmitoylation, the IFITM3 molecules do not cluster, which leads to the significant decrease in the antiviral activity. On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5.", "On the other hand, Figure 6 -B shows that the following observations are made in the case of IFITM5. i Cys86, plus one or two other cysteine residues in IFITM5, i.e., Cys52 and/or Cys53, are S-palmitoylated ii . The S-palmitoylated IFITM5 is able to interact specifically with FKBP11.", "The S-palmitoylated IFITM5 is able to interact specifically with FKBP11. The interaction is presumed to be mediated by the palmitic acid s attached to the cysteine s facing toward the interaction surface on FKBP11. Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11.", "Cys86 is involved in the S-palmitoylation but not in the interaction of IFITM5 with FKBP11. At present, however, little is known about the role of the S-palmitoylation of IFITM5 for the localization in the membrane. When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized.", "When the S-palmitoylation affects the localization of IFITM5 as in the case of IFITM3 , the S-palmitoylated IFITM5 molecules should be localized in the membrane or the depalmitoylated molecules should be delocalized. The loss of the interaction between IFITM5 and FKBP11 could be due to a relocalization of the depalmitoylated IFITM5 that prevents its association with FKBP11 iii . The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes.", "The Spalmitoylated IFITM5 interacts with the FKBP11-CD81-FPRP/CD9 complex through FKBP11, which induces the dissociation of CD9 from the complex and the expression of 5 immunologically relevant genes. Finally, IFITM5 forms the IFITM5-FKBP11-CD81-FPRP complex. It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells.", "It is unknown at present which of the three states i ~ iii illustrated in Figure 6 -B is important for the bone mineralization of the osteoblast cells. The lack of the S-palmitoylation influences the interaction with FKBP11, which could account for the following complex formation and gene expression. In addition, the bone nodule formation is also affected.", "In addition, the bone nodule formation is also affected. Note that the role of the Spalmitoylation has been involved in the bone formation . It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation.", "It is indicated that the S-palmitoylation on IFITM5 plays roles not only for the regulation of the immune activity but also for the bone formation. In conclusion, we have revealed the S-palmitoylation on IFITM5 and its role in the interaction with FKBP11. Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation.", "Not only the immune activity but also the bone mineralization in the osteoblast cells is affected by the S-palmitoylation. In general, the functional role of the S-palmitoylation is different for each protein . For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes.", "For many proteins, the palmitoylation and depalmitoylation cycle is constitutive and regulated by enzymes. Based on the present results, it is difficult to address i whether the S-palmitoylation on IFITM5 is constitutive or regulated, or ii when and where IFITM5 is S-palmitoylated in the osteoblast cells. Further studies are required and are currently underway." ]

[ "We sequenced the first Bovine coronavirus BCoV complete genome sequence from France. This BCoV was directly sequenced from a fecal sample collected from a calf in Normandy in 2014. Text: B ovine coronavirus BCoV belongs to the Nidovirales order, the Coronaviridae family, the Coronavirinae subfamily, and the Betacoronavirus ICTV/proposals/2008.085-122V.v4.Coronaviridae.pdf .", "Text: B ovine coronavirus BCoV belongs to the Nidovirales order, the Coronaviridae family, the Coronavirinae subfamily, and the Betacoronavirus ICTV/proposals/2008.085-122V.v4.Coronaviridae.pdf . Its genome is a single-stranded, linear, and nonsegmented RNA of around 31 kb. BCoV is responsible for respiratory and enteric diseases in cattle, particularly during winter . .", "BCoV is responsible for respiratory and enteric diseases in cattle, particularly during winter . . To date, the 19 complete BCoV genome sequences available in GenBank databases consulted on 17 January 2017 originated from the United States or Asia. Here, we report the first complete genome sequence of a BCoV detected in France.", "Here, we report the first complete genome sequence of a BCoV detected in France. The BCoV/FRA-EPI/CAEN/2014/13 strain was obtained from a fecal sample collected from a 1-week-old calf in Normandy in 2014. The presence of BCoV in the fecal sample was assessed using an in-house reverse transcription-PCR RT-PCR targeting the M gene .. A cDNA library was synthesized using SuperScript III Invitrogen, Carlsbad, CA, USA and hexamers.", "The presence of BCoV in the fecal sample was assessed using an in-house reverse transcription-PCR RT-PCR targeting the M gene .. A cDNA library was synthesized using SuperScript III Invitrogen, Carlsbad, CA, USA and hexamers. The complete genome sequencing of overlapping PCR products was carried out in both directions, using original primers and Sanger's dideoxy sequencing. Sequencing reactions were performed as previously described .. Sequences were assembled and annotated using the Geneious software version 5.1.6 .", "Sequencing reactions were performed as previously described .. Sequences were assembled and annotated using the Geneious software version 5.1.6 . We obtained a sequence counting 30,847 nucleotides. The orf1ab, HE, S, ns5, E, M, and N genes of the obtained BCoV were submitted to a Blastn analysis.", "The orf1ab, HE, S, ns5, E, M, and N genes of the obtained BCoV were submitted to a Blastn analysis. According to these analyses, the orf1ab 20kb nucleotides, located at the 5= side of the genome gene is closely related to the Dromedary camel coronavirus DcCoV HKU23-23-362F strain from the United Arab Emirates accession no. KF906251 , with a nucleotide identity of 99.19%.", "KF906251 , with a nucleotide identity of 99.19%. Conversely, the NS2, HE, S, ns5, and M genes are closely related to the BCoV Bubalus/Italy/179/07-11 strain accession no. EU019216 , with nucleotide identities of 99.88%, 99.45%, 99.02%, 98.79%, and 99.28%, respectively.", "EU019216 , with nucleotide identities of 99.88%, 99.45%, 99.02%, 98.79%, and 99.28%, respectively. The E gene is closely related to the Chinese Bovine coronavirus strain BCV-AKS-01 accession no. KU886219 , with a nucleotide identity of 100%.", "KU886219 , with a nucleotide identity of 100%. Finally, the highest Blastn score for the N gene was found with the American enteric BCoV-ENT accession no. AF391541 , associated with a nucleotide identity of 100%.", "AF391541 , associated with a nucleotide identity of 100%. Multiple-sequence alignment, including 20 BCoVs and 10 clade A betacoronaviruses closely related to BCoV from North America, two DcCoVs from the United Arab Emirates, and two Human coronavirus OC43 HCoV-OC43 strains from France, was performed using the Muscle algorithm implemented in MEGA7 . .", ". The phylogenetic analysis on the orf1ab confirms that BCoV/FRA-EPI/CAEN/2014/13 is closely related to the Dromedary camel coronavirus DcCoV HKU23-23-362F. The orf1ab gene of these two viruses together clustered separately from that of BCoV and BCoV-like viruses from North America and Asia.", "The orf1ab gene of these two viruses together clustered separately from that of BCoV and BCoV-like viruses from North America and Asia. This finding also confirms the results from our previous analysis on partial genomes in which nsp12, S, and N genes of American and Asian BCoVs group together in a cluster tentatively named C 1 . The nsp12 and N coding regions of BCoVs from France and DcCoVs from the United Arab Emirates clustered together in C 2 .", "The nsp12 and N coding regions of BCoVs from France and DcCoVs from the United Arab Emirates clustered together in C 2 . The DcCoV S gene individualized from both HCoV-OC43 and BCoV S genes. Potential recombination events could be at the origin of DcCoV. Accession number s .", "Potential recombination events could be at the origin of DcCoV. Accession number s . The complete genome sequence sequence of the BCoV/FRA-EPI/CAEN/2014/13 isolate has been deposited in GenBank under the accession number KX982264." ]

[ "We sequenced the first Bovine coronavirus BCoV complete genome sequence from France. This BCoV was directly sequenced from a fecal sample collected from a calf in Normandy in 2014. Text: B ovine coronavirus BCoV belongs to the Nidovirales order, the Coronaviridae family, the Coronavirinae subfamily, and the Betacoronavirus ICTV/proposals/2008.085-122V.v4.Coronaviridae.pdf .", "Text: B ovine coronavirus BCoV belongs to the Nidovirales order, the Coronaviridae family, the Coronavirinae subfamily, and the Betacoronavirus ICTV/proposals/2008.085-122V.v4.Coronaviridae.pdf . Its genome is a single-stranded, linear, and nonsegmented RNA of around 31 kb. BCoV is responsible for respiratory and enteric diseases in cattle, particularly during winter . .", "BCoV is responsible for respiratory and enteric diseases in cattle, particularly during winter . . To date, the 19 complete BCoV genome sequences available in GenBank databases consulted on 17 January 2017 originated from the United States or Asia. Here, we report the first complete genome sequence of a BCoV detected in France.", "Here, we report the first complete genome sequence of a BCoV detected in France. The BCoV/FRA-EPI/CAEN/2014/13 strain was obtained from a fecal sample collected from a 1-week-old calf in Normandy in 2014. The presence of BCoV in the fecal sample was assessed using an in-house reverse transcription-PCR RT-PCR targeting the M gene .. A cDNA library was synthesized using SuperScript III Invitrogen, Carlsbad, CA, USA and hexamers.", "The presence of BCoV in the fecal sample was assessed using an in-house reverse transcription-PCR RT-PCR targeting the M gene .. A cDNA library was synthesized using SuperScript III Invitrogen, Carlsbad, CA, USA and hexamers. The complete genome sequencing of overlapping PCR products was carried out in both directions, using original primers and Sanger's dideoxy sequencing. Sequencing reactions were performed as previously described .. Sequences were assembled and annotated using the Geneious software version 5.1.6 .", "Sequencing reactions were performed as previously described .. Sequences were assembled and annotated using the Geneious software version 5.1.6 . We obtained a sequence counting 30,847 nucleotides. The orf1ab, HE, S, ns5, E, M, and N genes of the obtained BCoV were submitted to a Blastn analysis.", "The orf1ab, HE, S, ns5, E, M, and N genes of the obtained BCoV were submitted to a Blastn analysis. According to these analyses, the orf1ab 20kb nucleotides, located at the 5= side of the genome gene is closely related to the Dromedary camel coronavirus DcCoV HKU23-23-362F strain from the United Arab Emirates accession no. KF906251 , with a nucleotide identity of 99.19%.", "KF906251 , with a nucleotide identity of 99.19%. Conversely, the NS2, HE, S, ns5, and M genes are closely related to the BCoV Bubalus/Italy/179/07-11 strain accession no. EU019216 , with nucleotide identities of 99.88%, 99.45%, 99.02%, 98.79%, and 99.28%, respectively.", "EU019216 , with nucleotide identities of 99.88%, 99.45%, 99.02%, 98.79%, and 99.28%, respectively. The E gene is closely related to the Chinese Bovine coronavirus strain BCV-AKS-01 accession no. KU886219 , with a nucleotide identity of 100%.", "KU886219 , with a nucleotide identity of 100%. Finally, the highest Blastn score for the N gene was found with the American enteric BCoV-ENT accession no. AF391541 , associated with a nucleotide identity of 100%.", "AF391541 , associated with a nucleotide identity of 100%. Multiple-sequence alignment, including 20 BCoVs and 10 clade A betacoronaviruses closely related to BCoV from North America, two DcCoVs from the United Arab Emirates, and two Human coronavirus OC43 HCoV-OC43 strains from France, was performed using the Muscle algorithm implemented in MEGA7 . .", ". The phylogenetic analysis on the orf1ab confirms that BCoV/FRA-EPI/CAEN/2014/13 is closely related to the Dromedary camel coronavirus DcCoV HKU23-23-362F. The orf1ab gene of these two viruses together clustered separately from that of BCoV and BCoV-like viruses from North America and Asia.", "The orf1ab gene of these two viruses together clustered separately from that of BCoV and BCoV-like viruses from North America and Asia. This finding also confirms the results from our previous analysis on partial genomes in which nsp12, S, and N genes of American and Asian BCoVs group together in a cluster tentatively named C 1 . The nsp12 and N coding regions of BCoVs from France and DcCoVs from the United Arab Emirates clustered together in C 2 .", "The nsp12 and N coding regions of BCoVs from France and DcCoVs from the United Arab Emirates clustered together in C 2 . The DcCoV S gene individualized from both HCoV-OC43 and BCoV S genes. Potential recombination events could be at the origin of DcCoV. Accession number s .", "Potential recombination events could be at the origin of DcCoV. Accession number s . The complete genome sequence sequence of the BCoV/FRA-EPI/CAEN/2014/13 isolate has been deposited in GenBank under the accession number KX982264." ]

[ "We sequenced the first Bovine coronavirus BCoV complete genome sequence from France. This BCoV was directly sequenced from a fecal sample collected from a calf in Normandy in 2014. Text: B ovine coronavirus BCoV belongs to the Nidovirales order, the Coronaviridae family, the Coronavirinae subfamily, and the Betacoronavirus ICTV/proposals/2008.085-122V.v4.Coronaviridae.pdf .", "Text: B ovine coronavirus BCoV belongs to the Nidovirales order, the Coronaviridae family, the Coronavirinae subfamily, and the Betacoronavirus ICTV/proposals/2008.085-122V.v4.Coronaviridae.pdf . Its genome is a single-stranded, linear, and nonsegmented RNA of around 31 kb. BCoV is responsible for respiratory and enteric diseases in cattle, particularly during winter . .", "BCoV is responsible for respiratory and enteric diseases in cattle, particularly during winter . . To date, the 19 complete BCoV genome sequences available in GenBank databases consulted on 17 January 2017 originated from the United States or Asia. Here, we report the first complete genome sequence of a BCoV detected in France.", "Here, we report the first complete genome sequence of a BCoV detected in France. The BCoV/FRA-EPI/CAEN/2014/13 strain was obtained from a fecal sample collected from a 1-week-old calf in Normandy in 2014. The presence of BCoV in the fecal sample was assessed using an in-house reverse transcription-PCR RT-PCR targeting the M gene .. A cDNA library was synthesized using SuperScript III Invitrogen, Carlsbad, CA, USA and hexamers.", "The presence of BCoV in the fecal sample was assessed using an in-house reverse transcription-PCR RT-PCR targeting the M gene .. A cDNA library was synthesized using SuperScript III Invitrogen, Carlsbad, CA, USA and hexamers. The complete genome sequencing of overlapping PCR products was carried out in both directions, using original primers and Sanger's dideoxy sequencing. Sequencing reactions were performed as previously described .. Sequences were assembled and annotated using the Geneious software version 5.1.6 .", "Sequencing reactions were performed as previously described .. Sequences were assembled and annotated using the Geneious software version 5.1.6 . We obtained a sequence counting 30,847 nucleotides. The orf1ab, HE, S, ns5, E, M, and N genes of the obtained BCoV were submitted to a Blastn analysis.", "The orf1ab, HE, S, ns5, E, M, and N genes of the obtained BCoV were submitted to a Blastn analysis. According to these analyses, the orf1ab 20kb nucleotides, located at the 5= side of the genome gene is closely related to the Dromedary camel coronavirus DcCoV HKU23-23-362F strain from the United Arab Emirates accession no. KF906251 , with a nucleotide identity of 99.19%.", "KF906251 , with a nucleotide identity of 99.19%. Conversely, the NS2, HE, S, ns5, and M genes are closely related to the BCoV Bubalus/Italy/179/07-11 strain accession no. EU019216 , with nucleotide identities of 99.88%, 99.45%, 99.02%, 98.79%, and 99.28%, respectively.", "EU019216 , with nucleotide identities of 99.88%, 99.45%, 99.02%, 98.79%, and 99.28%, respectively. The E gene is closely related to the Chinese Bovine coronavirus strain BCV-AKS-01 accession no. KU886219 , with a nucleotide identity of 100%.", "KU886219 , with a nucleotide identity of 100%. Finally, the highest Blastn score for the N gene was found with the American enteric BCoV-ENT accession no. AF391541 , associated with a nucleotide identity of 100%.", "AF391541 , associated with a nucleotide identity of 100%. Multiple-sequence alignment, including 20 BCoVs and 10 clade A betacoronaviruses closely related to BCoV from North America, two DcCoVs from the United Arab Emirates, and two Human coronavirus OC43 HCoV-OC43 strains from France, was performed using the Muscle algorithm implemented in MEGA7 . .", ". The phylogenetic analysis on the orf1ab confirms that BCoV/FRA-EPI/CAEN/2014/13 is closely related to the Dromedary camel coronavirus DcCoV HKU23-23-362F. The orf1ab gene of these two viruses together clustered separately from that of BCoV and BCoV-like viruses from North America and Asia.", "The orf1ab gene of these two viruses together clustered separately from that of BCoV and BCoV-like viruses from North America and Asia. This finding also confirms the results from our previous analysis on partial genomes in which nsp12, S, and N genes of American and Asian BCoVs group together in a cluster tentatively named C 1 . The nsp12 and N coding regions of BCoVs from France and DcCoVs from the United Arab Emirates clustered together in C 2 .", "The nsp12 and N coding regions of BCoVs from France and DcCoVs from the United Arab Emirates clustered together in C 2 . The DcCoV S gene individualized from both HCoV-OC43 and BCoV S genes. Potential recombination events could be at the origin of DcCoV. Accession number s .", "Potential recombination events could be at the origin of DcCoV. Accession number s . The complete genome sequence sequence of the BCoV/FRA-EPI/CAEN/2014/13 isolate has been deposited in GenBank under the accession number KX982264." ]

[ "We sequenced the first Bovine coronavirus BCoV complete genome sequence from France. This BCoV was directly sequenced from a fecal sample collected from a calf in Normandy in 2014. Text: B ovine coronavirus BCoV belongs to the Nidovirales order, the Coronaviridae family, the Coronavirinae subfamily, and the Betacoronavirus ICTV/proposals/2008.085-122V.v4.Coronaviridae.pdf .", "Text: B ovine coronavirus BCoV belongs to the Nidovirales order, the Coronaviridae family, the Coronavirinae subfamily, and the Betacoronavirus ICTV/proposals/2008.085-122V.v4.Coronaviridae.pdf . Its genome is a single-stranded, linear, and nonsegmented RNA of around 31 kb. BCoV is responsible for respiratory and enteric diseases in cattle, particularly during winter . .", "BCoV is responsible for respiratory and enteric diseases in cattle, particularly during winter . . To date, the 19 complete BCoV genome sequences available in GenBank databases consulted on 17 January 2017 originated from the United States or Asia. Here, we report the first complete genome sequence of a BCoV detected in France.", "Here, we report the first complete genome sequence of a BCoV detected in France. The BCoV/FRA-EPI/CAEN/2014/13 strain was obtained from a fecal sample collected from a 1-week-old calf in Normandy in 2014. The presence of BCoV in the fecal sample was assessed using an in-house reverse transcription-PCR RT-PCR targeting the M gene .. A cDNA library was synthesized using SuperScript III Invitrogen, Carlsbad, CA, USA and hexamers.", "The presence of BCoV in the fecal sample was assessed using an in-house reverse transcription-PCR RT-PCR targeting the M gene .. A cDNA library was synthesized using SuperScript III Invitrogen, Carlsbad, CA, USA and hexamers. The complete genome sequencing of overlapping PCR products was carried out in both directions, using original primers and Sanger's dideoxy sequencing. Sequencing reactions were performed as previously described .. Sequences were assembled and annotated using the Geneious software version 5.1.6 .", "Sequencing reactions were performed as previously described .. Sequences were assembled and annotated using the Geneious software version 5.1.6 . We obtained a sequence counting 30,847 nucleotides. The orf1ab, HE, S, ns5, E, M, and N genes of the obtained BCoV were submitted to a Blastn analysis.", "The orf1ab, HE, S, ns5, E, M, and N genes of the obtained BCoV were submitted to a Blastn analysis. According to these analyses, the orf1ab 20kb nucleotides, located at the 5= side of the genome gene is closely related to the Dromedary camel coronavirus DcCoV HKU23-23-362F strain from the United Arab Emirates accession no. KF906251 , with a nucleotide identity of 99.19%.", "KF906251 , with a nucleotide identity of 99.19%. Conversely, the NS2, HE, S, ns5, and M genes are closely related to the BCoV Bubalus/Italy/179/07-11 strain accession no. EU019216 , with nucleotide identities of 99.88%, 99.45%, 99.02%, 98.79%, and 99.28%, respectively.", "EU019216 , with nucleotide identities of 99.88%, 99.45%, 99.02%, 98.79%, and 99.28%, respectively. The E gene is closely related to the Chinese Bovine coronavirus strain BCV-AKS-01 accession no. KU886219 , with a nucleotide identity of 100%.", "KU886219 , with a nucleotide identity of 100%. Finally, the highest Blastn score for the N gene was found with the American enteric BCoV-ENT accession no. AF391541 , associated with a nucleotide identity of 100%.", "AF391541 , associated with a nucleotide identity of 100%. Multiple-sequence alignment, including 20 BCoVs and 10 clade A betacoronaviruses closely related to BCoV from North America, two DcCoVs from the United Arab Emirates, and two Human coronavirus OC43 HCoV-OC43 strains from France, was performed using the Muscle algorithm implemented in MEGA7 . .", ". The phylogenetic analysis on the orf1ab confirms that BCoV/FRA-EPI/CAEN/2014/13 is closely related to the Dromedary camel coronavirus DcCoV HKU23-23-362F. The orf1ab gene of these two viruses together clustered separately from that of BCoV and BCoV-like viruses from North America and Asia.", "The orf1ab gene of these two viruses together clustered separately from that of BCoV and BCoV-like viruses from North America and Asia. This finding also confirms the results from our previous analysis on partial genomes in which nsp12, S, and N genes of American and Asian BCoVs group together in a cluster tentatively named C 1 . The nsp12 and N coding regions of BCoVs from France and DcCoVs from the United Arab Emirates clustered together in C 2 .", "The nsp12 and N coding regions of BCoVs from France and DcCoVs from the United Arab Emirates clustered together in C 2 . The DcCoV S gene individualized from both HCoV-OC43 and BCoV S genes. Potential recombination events could be at the origin of DcCoV. Accession number s .", "Potential recombination events could be at the origin of DcCoV. Accession number s . The complete genome sequence sequence of the BCoV/FRA-EPI/CAEN/2014/13 isolate has been deposited in GenBank under the accession number KX982264." ]

[ "We sequenced the first Bovine coronavirus BCoV complete genome sequence from France. This BCoV was directly sequenced from a fecal sample collected from a calf in Normandy in 2014. Text: B ovine coronavirus BCoV belongs to the Nidovirales order, the Coronaviridae family, the Coronavirinae subfamily, and the Betacoronavirus ICTV/proposals/2008.085-122V.v4.Coronaviridae.pdf .", "Text: B ovine coronavirus BCoV belongs to the Nidovirales order, the Coronaviridae family, the Coronavirinae subfamily, and the Betacoronavirus ICTV/proposals/2008.085-122V.v4.Coronaviridae.pdf . Its genome is a single-stranded, linear, and nonsegmented RNA of around 31 kb. BCoV is responsible for respiratory and enteric diseases in cattle, particularly during winter . .", "BCoV is responsible for respiratory and enteric diseases in cattle, particularly during winter . . To date, the 19 complete BCoV genome sequences available in GenBank databases consulted on 17 January 2017 originated from the United States or Asia. Here, we report the first complete genome sequence of a BCoV detected in France.", "Here, we report the first complete genome sequence of a BCoV detected in France. The BCoV/FRA-EPI/CAEN/2014/13 strain was obtained from a fecal sample collected from a 1-week-old calf in Normandy in 2014. The presence of BCoV in the fecal sample was assessed using an in-house reverse transcription-PCR RT-PCR targeting the M gene .. A cDNA library was synthesized using SuperScript III Invitrogen, Carlsbad, CA, USA and hexamers.", "The presence of BCoV in the fecal sample was assessed using an in-house reverse transcription-PCR RT-PCR targeting the M gene .. A cDNA library was synthesized using SuperScript III Invitrogen, Carlsbad, CA, USA and hexamers. The complete genome sequencing of overlapping PCR products was carried out in both directions, using original primers and Sanger's dideoxy sequencing. Sequencing reactions were performed as previously described .. Sequences were assembled and annotated using the Geneious software version 5.1.6 .", "Sequencing reactions were performed as previously described .. Sequences were assembled and annotated using the Geneious software version 5.1.6 . We obtained a sequence counting 30,847 nucleotides. The orf1ab, HE, S, ns5, E, M, and N genes of the obtained BCoV were submitted to a Blastn analysis.", "The orf1ab, HE, S, ns5, E, M, and N genes of the obtained BCoV were submitted to a Blastn analysis. According to these analyses, the orf1ab 20kb nucleotides, located at the 5= side of the genome gene is closely related to the Dromedary camel coronavirus DcCoV HKU23-23-362F strain from the United Arab Emirates accession no. KF906251 , with a nucleotide identity of 99.19%.", "KF906251 , with a nucleotide identity of 99.19%. Conversely, the NS2, HE, S, ns5, and M genes are closely related to the BCoV Bubalus/Italy/179/07-11 strain accession no. EU019216 , with nucleotide identities of 99.88%, 99.45%, 99.02%, 98.79%, and 99.28%, respectively.", "EU019216 , with nucleotide identities of 99.88%, 99.45%, 99.02%, 98.79%, and 99.28%, respectively. The E gene is closely related to the Chinese Bovine coronavirus strain BCV-AKS-01 accession no. KU886219 , with a nucleotide identity of 100%.", "KU886219 , with a nucleotide identity of 100%. Finally, the highest Blastn score for the N gene was found with the American enteric BCoV-ENT accession no. AF391541 , associated with a nucleotide identity of 100%.", "AF391541 , associated with a nucleotide identity of 100%. Multiple-sequence alignment, including 20 BCoVs and 10 clade A betacoronaviruses closely related to BCoV from North America, two DcCoVs from the United Arab Emirates, and two Human coronavirus OC43 HCoV-OC43 strains from France, was performed using the Muscle algorithm implemented in MEGA7 . .", ". The phylogenetic analysis on the orf1ab confirms that BCoV/FRA-EPI/CAEN/2014/13 is closely related to the Dromedary camel coronavirus DcCoV HKU23-23-362F. The orf1ab gene of these two viruses together clustered separately from that of BCoV and BCoV-like viruses from North America and Asia.", "The orf1ab gene of these two viruses together clustered separately from that of BCoV and BCoV-like viruses from North America and Asia. This finding also confirms the results from our previous analysis on partial genomes in which nsp12, S, and N genes of American and Asian BCoVs group together in a cluster tentatively named C 1 . The nsp12 and N coding regions of BCoVs from France and DcCoVs from the United Arab Emirates clustered together in C 2 .", "The nsp12 and N coding regions of BCoVs from France and DcCoVs from the United Arab Emirates clustered together in C 2 . The DcCoV S gene individualized from both HCoV-OC43 and BCoV S genes. Potential recombination events could be at the origin of DcCoV. Accession number s .", "Potential recombination events could be at the origin of DcCoV. Accession number s . The complete genome sequence sequence of the BCoV/FRA-EPI/CAEN/2014/13 isolate has been deposited in GenBank under the accession number KX982264." ]

[ "BACKGROUND: Exhaled breath condensate EBC sampling has been considered an inventive and novel method for the isolation of respiratory viruses. METHODS: In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses.", "Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection.", "The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive.", "RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.", "CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections. Text: Human respiratory tract infections represent the most commonly encountered infections worldwide. In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection.", "In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection. Respiratory tract infections in healthy adults can be caused by a variety of pathogens and the detection of these agents is currently based on their isolation from nasal swabs NS , bronchoalveolar lavages BAL , nasopharyngeal aspirates and sputum samples. The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient.", "The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient. Therefore, exhaled breath condensate EBC analysis has recently been explored as a new and non-invasive method to monitor lung inflammation and pulmonary disease such as chronic obstructive pulmonary disease COPD , asthma, cystic fibrosis, lung cancer etc. EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid .", "EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid . This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid.", "At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid. However, the effect of the turbulent airflow is limited to the upper airways since the turbulent airflow becomes laminar as it reaches the smaller bronchial airways and alveoli. Recently, the bronchiole fluid film burst model has been described .", "Recently, the bronchiole fluid film burst model has been described . This model suggests that aerosols are produced during inhalation by the bursting of fluid bubbles present in the bronchioles. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate.", "The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. Therefore we screened the EBC samples with virus specific PCR assays targeting 14 In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms defined in Table 1 , using a commercially available condenser RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA . The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes.", "The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes. No nose clips were used during collection and saliva contamination was avoided by the presence of a one-way valve and the T-shaped section of the mouthpiece. In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory.", "In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory. The majority of these volunteers were students that responded to the information leaflet, distributed in the university buildings of the Catholic University of Leuven. The samples were collected with the aluminium cooler sleeve chilled at -80°C.", "The samples were collected with the aluminium cooler sleeve chilled at -80°C. In the fall and first half of the winter of 2009/2010, 32 condensates were collected from patients who presented themselves to their general practitioner. Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C.", "Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C. For 13 out of 32 collections, the RTube™ was connected by a custom made connectingpiece to the ECoVent Jaeger, Germany . This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume.", "This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume. Additionally, a NS was obtained in parallel with the condensate collection from each patient. All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated.", "All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated. After viral DNA and RNA extraction, EBC samples and nasal swabs were stored at -80°C. Three specimens were excluded from the study due to incorrect condensate collection.", "Three specimens were excluded from the study due to incorrect condensate collection. A short questionnaire was used to document the date of birth, the severity of respiratory complaints and to record the days of symptomatic illness from all volunteers. This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants.", "This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants. Viral DNA and RNA were isolated with the QIAamp MinElute Virus kit Qiagen, Westburg, The Netherlands according to the instruction manual. EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer.", "EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer. The breath condensates were screened for 11 respiratory RNA viruses CoV NL63, E229 and OC43, RV, HMPV, InfA&B and PIV1-4 using a OneStep RT-PCR Kit Qiagen, Westburg, The Netherlands in a 50 μl reaction containing 10 μl of the extracted RNA, 0.6 μM of forward and reverse primers Table 2 , 1.5 μl One Step Enzyme Mix, 10 μl 5 × One Step RT-PCR Buffer and 400 μM of each dNTP. For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl.", "For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl. The PCR primers used were located in conserved regions of the genomes of the respiratory pathogens Table 2 . The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C.", "The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C. The DNA amplification program was initiated with a denaturation step at 94°C for 3 min, followed by 45 cycles of 94°C for 30 s, 55°C for 30 s and a final extension step at 72°C for 1 min. The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide.", "The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide. PCR products were purified using the Invitek MSB Spin PCRapace Kit and cycle sequenced in forward and reverse direction using the ABI PRISM Big-Dye Termination Cycle Sequencing Ready Reaction kit Applied Biosystems, Foster City, CA, USA . Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA .", "Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA . Consensus sequences were obtained using the SeqMan II software DNASTAR, Madison, Wis. . For samples from HRSV was detected using a RT-PCR assay as previously described .", "For samples from HRSV was detected using a RT-PCR assay as previously described . In brief, a multiplex mix was prepared in a final volume of 25 μl using 5 μl extracted RNA, 12.5 μl of Eurogentec One-Step Reverse Transcriptase qPCR Master Mix containing ROX as a passive reference, 0.125 μl Euroscript + RT & RNase inhibitor Eurogentec, Seraing, Belgium 200 nM of HRSV-A and -B specific forward and reverse primers and 100 nM of HRSV-A and -B MGB probes. cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified.", "cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified. The viral load of RV positive samples were quantified by qRT-PCR as described in the manuscript published by Lu and coworkers . The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above.", "The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above. The primerset HRSV-AF F 669-695 ctgtgatagarttccaacaaaagaaca HRSV-AF F 718-745 agttacacctgcattaacactaaattcc HRSV-BN N 435-458 ggctccagaatataggcatgattc HRSV-BN N 480-508 tggttattacaagaagagcagctatacacagt MGB probes and probe, located in 5'UTR, were added to a final concentration of 1 μM and 0.1 μM, respectively. cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA .", "cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA . Quantification was performed with a spectrophotometer at 260 nm and converted to the molecule number . Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used.", "Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used. The RT-PCR assays were carried out on a ABI PRISM 7500 Sequence Detection System Applied Biosystems, Foster City, CA, USA . An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min.", "An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min. Finally, an amplification step of 45 cycli at 95°C for 15 sec and 1 min at 60°C was completed. 37.5% men, with a median age of 29 range 9 -46 years .", "37.5% men, with a median age of 29 range 9 -46 years . Age and gender was missing for 2 participants of the second group. In total, 52% of the participants were between 20-30 years old. Only 6% were younger than 20 years old and 3% were older than 70 years.", "Only 6% were younger than 20 years old and 3% were older than 70 years. In totality, 80 patients 78.4% were already feeling ill for 1 to 7 days at the day the sample was obtained. Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection.", "Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection. Data on the duration of symptoms was lacking for 6 patients. Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 .", "Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 . Forty-seven 46.1% volunteers complained about a constant runny or stuffy nose, 43 42.2% had frequent sneezing events and 38 37.3% participants had a serious sore throat Table 1 . In a first part of the study, we collected 70 EBCs.", "In a first part of the study, we collected 70 EBCs. Screening of the EBCs for 14 respiratory viruses Table 2 , showed 5 RV 7.1% positive samples Table 3 . In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner.", "In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner. Two of these EBCs were positive for one of the 14 investigated respiratory viruses, 1 for RV and 1 for InfB. To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison.", "To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison. In 15 out of 32 NS 46.8% , one or more viral pathogens were isolated. Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B.", "Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B. Quantification of the HRSV-B viral load demonstrated for samples 72 and 101 viral titers of 8.0 × 10 4 RNA copies/ml and 6.8 × 10 7 RNA copies/ml respectively. The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 .", "The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 . Presence of the same pathogen in both the EBC and the NS was confirmed for only 1 sample: sample 71, which tested positive for RV in both the EBC and the NS. For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection.", "For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection. For EBC samples that were collected in the fall and winter of 2009/2010, measurements with the ECoVent in Table 3 , sample 81 was positive for InfB when using the RTube™ in combination with the EcoVent. In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load.", "In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load. Then, an estimation of the RNA copies per litre exhaled air or per minute can be calculated. Quantification of the exhaled InfB would allow us to predict the generation rate for this virus.", "Quantification of the exhaled InfB would allow us to predict the generation rate for this virus. Due to insufficient sample volume, we could not determine the number of RNA copies in the sample. Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract.", "Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. The collection of EBC is easy to perform and can be conducted in a home environment. This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc.", "This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc. This aspect renders the method very attractive for routine laboratory diagnostics of viral infections. Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact .", "Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact . With the RTube™ collection device, aerosolized particles of the airway lining fluid are precipitated into a condensate when the breath is cooled which serves as an immediate starting point for molecular testing. Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses.", "Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses. Previous studies reported the inclusion of a limited subset of participants and investigated the presence of a limited number of viruses in the breath samples. The study performed by Fabian and colleagues, included 12 volunteers .", "The study performed by Fabian and colleagues, included 12 volunteers . Huynh and co-workers recruited 9 volunteers for exhaled breath sampling . In the study by Stelzer-Braid et al., 50 EBCs were analysed and St-George et al. report the participation of 12 adults .", "report the participation of 12 adults . These studies have focused on the detection of InfA and -B, PIV1-3, HRSV and HMPV, while we have screened the samples for a panel of 14 commonly circulating respiratory viruses. Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples.", "Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples. Since many of the volunteers had already been experiencing symptoms for 1 to 7 days, we initially presumed that they were already recovering from the infection and were no longer exhaling the virus. For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms.", "For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms. However, in a second part of our study we started collecting EBCs in parallel with nasal swabs from patients presenting themselves to their medical doctor, 1 to 3 days after onset of symptoms. Only for 1 condensate the same pathogen was detected in both the EBC and the NS.", "Only for 1 condensate the same pathogen was detected in both the EBC and the NS. The detection rate for respiratory viral pathogens in the NS was 46.8% which is much higher than the 7% detection rate in the EBCs. The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious.", "The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious. The discrepant detection rate between samples may also be explained by different severity of respiratory infection, since comparator samples were of different parts of the respiratory tract. Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection.", "Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection. However, the effect of nasal inhalation on EBC collection, guiding formed particles in the upper respiratory tract to the lower compartments, in stead of oral inhalation was not investigated. Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection.", "Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection. However, this was not different for 7 patients with positive NS. Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 .", "Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 . In the group of volunteers that provided an EBC negative or EBC and NS negative sample, the manifestation of symptoms were reported ranging from 1 day to more than two weeks. When reported symptoms were compared between EBC positive patients .", "When reported symptoms were compared between EBC positive patients . and NS positive patients . , 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group.", ", 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group. In all groups fever, headache, watering eyes, stuffed nose, frequent sneezing, sore throat and coughing were reported. Volunteers were not diagnosed with other pathogens before participation in the study.", "Volunteers were not diagnosed with other pathogens before participation in the study. Since we did not test these samples for other than viral pathogens, we can not exclude the possibility that some of the negative NS are positive for bacteria or other pathogens causing respiratory illness. Recently, one study reported a detection rate of 5% for influenza in EBC .", "Recently, one study reported a detection rate of 5% for influenza in EBC . This is in the same range of the detection rate that we report for respiratory viruses in general. Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included .", "Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included . Remarkably, the studies reporting this higher detection rate used collections masks, while the study using the RTube™ reported comparable findings. Face masks consist of electret which trap viruses based on permanently charged fibres .", "Face masks consist of electret which trap viruses based on permanently charged fibres . In addition, the Teflon filter has 2 μm pores which will retain all larger particles. Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials.", "Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials. The qRT-PCR developed by Lu and coworkers for the detection of RV, did not allow the assessment of the viral load present in the EBC samples . Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay.", "Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay. For diagnosis, more sensitive methods might be necessary to detect respiratory viruses present in EBC since it is unpredictable how diluted the viral particles in the specimen are. Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols .", "Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols . Also person-dependent factors, such as the number of particles produced, the exhaled volume and the age of the patient, have been suggested to play an important role for exhalation of viral particles. The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older .", "The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older . For hospitalized children a much higher rate of virus positive samples is reported . In our study, the majority of volunteers were between 20 and 30 years old.", "In our study, the majority of volunteers were between 20 and 30 years old. Only two children less than 10 years and 3 elderly people > 70 years were included. One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC.", "One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC. For influenza, an exhaled generation rate of <3.2 to 20 influenza RNA copies per minute was predicted by quantifying the virus aerosols that impacted on a removable Teflon filter of a collection mask . We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume.", "We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume. In this way, when the number of RNA copies in the EBC is quantified, the amount of viral particles that are exhaled per litre or per minute can be estimated. Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined.", "Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined. Although an inventive, new and promising method, EBC collected by the RTube™ does not appear to be appropriate for diagnosis of respiratory infections. Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses.", "Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses. This technique also confirms the observation that viruses are able to disseminate through normal breathing, particularly RV. In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns.", "In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns. In calves that were experimentally infected with bovine RSV, an increase in leukotriene B 4 , indicating oxidative stress, was observed. This increased level was also associated with the development of bronchial hyperresponsiveness .", "This increased level was also associated with the development of bronchial hyperresponsiveness . In humans, a transiently elevated H 2 O 2 level was observed during common cold infection. This marker returned to baseline values when volunteers recovered from infection.", "This marker returned to baseline values when volunteers recovered from infection. H 2 O 2 has also been recognized as an interesting marker in asthma, where it is associated with chronic lower airway inflammation . In InfA infected volunteers, an increased CO level was observed during upper respiratory infection.", "In InfA infected volunteers, an increased CO level was observed during upper respiratory infection. This observation might imply that CO is an indicator of airway inflammation or represents one of the host defence mechanisms against viral infection . Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection.", "Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection. This may contribute to the biomarker profiles established for diseases like asthma and COPD, for which viral infections are suggested to trigger or exacerbate symptoms ." ]

[ "BACKGROUND: Exhaled breath condensate EBC sampling has been considered an inventive and novel method for the isolation of respiratory viruses. METHODS: In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses.", "Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection.", "The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive.", "RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.", "CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections. Text: Human respiratory tract infections represent the most commonly encountered infections worldwide. In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection.", "In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection. Respiratory tract infections in healthy adults can be caused by a variety of pathogens and the detection of these agents is currently based on their isolation from nasal swabs NS , bronchoalveolar lavages BAL , nasopharyngeal aspirates and sputum samples. The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient.", "The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient. Therefore, exhaled breath condensate EBC analysis has recently been explored as a new and non-invasive method to monitor lung inflammation and pulmonary disease such as chronic obstructive pulmonary disease COPD , asthma, cystic fibrosis, lung cancer etc. EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid .", "EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid . This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid.", "At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid. However, the effect of the turbulent airflow is limited to the upper airways since the turbulent airflow becomes laminar as it reaches the smaller bronchial airways and alveoli. Recently, the bronchiole fluid film burst model has been described .", "Recently, the bronchiole fluid film burst model has been described . This model suggests that aerosols are produced during inhalation by the bursting of fluid bubbles present in the bronchioles. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate.", "The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. Therefore we screened the EBC samples with virus specific PCR assays targeting 14 In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms defined in Table 1 , using a commercially available condenser RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA . The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes.", "The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes. No nose clips were used during collection and saliva contamination was avoided by the presence of a one-way valve and the T-shaped section of the mouthpiece. In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory.", "In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory. The majority of these volunteers were students that responded to the information leaflet, distributed in the university buildings of the Catholic University of Leuven. The samples were collected with the aluminium cooler sleeve chilled at -80°C.", "The samples were collected with the aluminium cooler sleeve chilled at -80°C. In the fall and first half of the winter of 2009/2010, 32 condensates were collected from patients who presented themselves to their general practitioner. Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C.", "Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C. For 13 out of 32 collections, the RTube™ was connected by a custom made connectingpiece to the ECoVent Jaeger, Germany . This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume.", "This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume. Additionally, a NS was obtained in parallel with the condensate collection from each patient. All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated.", "All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated. After viral DNA and RNA extraction, EBC samples and nasal swabs were stored at -80°C. Three specimens were excluded from the study due to incorrect condensate collection.", "Three specimens were excluded from the study due to incorrect condensate collection. A short questionnaire was used to document the date of birth, the severity of respiratory complaints and to record the days of symptomatic illness from all volunteers. This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants.", "This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants. Viral DNA and RNA were isolated with the QIAamp MinElute Virus kit Qiagen, Westburg, The Netherlands according to the instruction manual. EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer.", "EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer. The breath condensates were screened for 11 respiratory RNA viruses CoV NL63, E229 and OC43, RV, HMPV, InfA&B and PIV1-4 using a OneStep RT-PCR Kit Qiagen, Westburg, The Netherlands in a 50 μl reaction containing 10 μl of the extracted RNA, 0.6 μM of forward and reverse primers Table 2 , 1.5 μl One Step Enzyme Mix, 10 μl 5 × One Step RT-PCR Buffer and 400 μM of each dNTP. For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl.", "For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl. The PCR primers used were located in conserved regions of the genomes of the respiratory pathogens Table 2 . The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C.", "The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C. The DNA amplification program was initiated with a denaturation step at 94°C for 3 min, followed by 45 cycles of 94°C for 30 s, 55°C for 30 s and a final extension step at 72°C for 1 min. The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide.", "The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide. PCR products were purified using the Invitek MSB Spin PCRapace Kit and cycle sequenced in forward and reverse direction using the ABI PRISM Big-Dye Termination Cycle Sequencing Ready Reaction kit Applied Biosystems, Foster City, CA, USA . Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA .", "Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA . Consensus sequences were obtained using the SeqMan II software DNASTAR, Madison, Wis. . For samples from HRSV was detected using a RT-PCR assay as previously described .", "For samples from HRSV was detected using a RT-PCR assay as previously described . In brief, a multiplex mix was prepared in a final volume of 25 μl using 5 μl extracted RNA, 12.5 μl of Eurogentec One-Step Reverse Transcriptase qPCR Master Mix containing ROX as a passive reference, 0.125 μl Euroscript + RT & RNase inhibitor Eurogentec, Seraing, Belgium 200 nM of HRSV-A and -B specific forward and reverse primers and 100 nM of HRSV-A and -B MGB probes. cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified.", "cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified. The viral load of RV positive samples were quantified by qRT-PCR as described in the manuscript published by Lu and coworkers . The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above.", "The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above. The primerset HRSV-AF F 669-695 ctgtgatagarttccaacaaaagaaca HRSV-AF F 718-745 agttacacctgcattaacactaaattcc HRSV-BN N 435-458 ggctccagaatataggcatgattc HRSV-BN N 480-508 tggttattacaagaagagcagctatacacagt MGB probes and probe, located in 5'UTR, were added to a final concentration of 1 μM and 0.1 μM, respectively. cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA .", "cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA . Quantification was performed with a spectrophotometer at 260 nm and converted to the molecule number . Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used.", "Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used. The RT-PCR assays were carried out on a ABI PRISM 7500 Sequence Detection System Applied Biosystems, Foster City, CA, USA . An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min.", "An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min. Finally, an amplification step of 45 cycli at 95°C for 15 sec and 1 min at 60°C was completed. 37.5% men, with a median age of 29 range 9 -46 years .", "37.5% men, with a median age of 29 range 9 -46 years . Age and gender was missing for 2 participants of the second group. In total, 52% of the participants were between 20-30 years old. Only 6% were younger than 20 years old and 3% were older than 70 years.", "Only 6% were younger than 20 years old and 3% were older than 70 years. In totality, 80 patients 78.4% were already feeling ill for 1 to 7 days at the day the sample was obtained. Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection.", "Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection. Data on the duration of symptoms was lacking for 6 patients. Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 .", "Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 . Forty-seven 46.1% volunteers complained about a constant runny or stuffy nose, 43 42.2% had frequent sneezing events and 38 37.3% participants had a serious sore throat Table 1 . In a first part of the study, we collected 70 EBCs.", "In a first part of the study, we collected 70 EBCs. Screening of the EBCs for 14 respiratory viruses Table 2 , showed 5 RV 7.1% positive samples Table 3 . In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner.", "In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner. Two of these EBCs were positive for one of the 14 investigated respiratory viruses, 1 for RV and 1 for InfB. To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison.", "To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison. In 15 out of 32 NS 46.8% , one or more viral pathogens were isolated. Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B.", "Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B. Quantification of the HRSV-B viral load demonstrated for samples 72 and 101 viral titers of 8.0 × 10 4 RNA copies/ml and 6.8 × 10 7 RNA copies/ml respectively. The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 .", "The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 . Presence of the same pathogen in both the EBC and the NS was confirmed for only 1 sample: sample 71, which tested positive for RV in both the EBC and the NS. For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection.", "For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection. For EBC samples that were collected in the fall and winter of 2009/2010, measurements with the ECoVent in Table 3 , sample 81 was positive for InfB when using the RTube™ in combination with the EcoVent. In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load.", "In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load. Then, an estimation of the RNA copies per litre exhaled air or per minute can be calculated. Quantification of the exhaled InfB would allow us to predict the generation rate for this virus.", "Quantification of the exhaled InfB would allow us to predict the generation rate for this virus. Due to insufficient sample volume, we could not determine the number of RNA copies in the sample. Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract.", "Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. The collection of EBC is easy to perform and can be conducted in a home environment. This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc.", "This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc. This aspect renders the method very attractive for routine laboratory diagnostics of viral infections. Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact .", "Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact . With the RTube™ collection device, aerosolized particles of the airway lining fluid are precipitated into a condensate when the breath is cooled which serves as an immediate starting point for molecular testing. Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses.", "Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses. Previous studies reported the inclusion of a limited subset of participants and investigated the presence of a limited number of viruses in the breath samples. The study performed by Fabian and colleagues, included 12 volunteers .", "The study performed by Fabian and colleagues, included 12 volunteers . Huynh and co-workers recruited 9 volunteers for exhaled breath sampling . In the study by Stelzer-Braid et al., 50 EBCs were analysed and St-George et al. report the participation of 12 adults .", "report the participation of 12 adults . These studies have focused on the detection of InfA and -B, PIV1-3, HRSV and HMPV, while we have screened the samples for a panel of 14 commonly circulating respiratory viruses. Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples.", "Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples. Since many of the volunteers had already been experiencing symptoms for 1 to 7 days, we initially presumed that they were already recovering from the infection and were no longer exhaling the virus. For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms.", "For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms. However, in a second part of our study we started collecting EBCs in parallel with nasal swabs from patients presenting themselves to their medical doctor, 1 to 3 days after onset of symptoms. Only for 1 condensate the same pathogen was detected in both the EBC and the NS.", "Only for 1 condensate the same pathogen was detected in both the EBC and the NS. The detection rate for respiratory viral pathogens in the NS was 46.8% which is much higher than the 7% detection rate in the EBCs. The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious.", "The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious. The discrepant detection rate between samples may also be explained by different severity of respiratory infection, since comparator samples were of different parts of the respiratory tract. Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection.", "Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection. However, the effect of nasal inhalation on EBC collection, guiding formed particles in the upper respiratory tract to the lower compartments, in stead of oral inhalation was not investigated. Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection.", "Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection. However, this was not different for 7 patients with positive NS. Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 .", "Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 . In the group of volunteers that provided an EBC negative or EBC and NS negative sample, the manifestation of symptoms were reported ranging from 1 day to more than two weeks. When reported symptoms were compared between EBC positive patients .", "When reported symptoms were compared between EBC positive patients . and NS positive patients . , 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group.", ", 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group. In all groups fever, headache, watering eyes, stuffed nose, frequent sneezing, sore throat and coughing were reported. Volunteers were not diagnosed with other pathogens before participation in the study.", "Volunteers were not diagnosed with other pathogens before participation in the study. Since we did not test these samples for other than viral pathogens, we can not exclude the possibility that some of the negative NS are positive for bacteria or other pathogens causing respiratory illness. Recently, one study reported a detection rate of 5% for influenza in EBC .", "Recently, one study reported a detection rate of 5% for influenza in EBC . This is in the same range of the detection rate that we report for respiratory viruses in general. Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included .", "Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included . Remarkably, the studies reporting this higher detection rate used collections masks, while the study using the RTube™ reported comparable findings. Face masks consist of electret which trap viruses based on permanently charged fibres .", "Face masks consist of electret which trap viruses based on permanently charged fibres . In addition, the Teflon filter has 2 μm pores which will retain all larger particles. Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials.", "Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials. The qRT-PCR developed by Lu and coworkers for the detection of RV, did not allow the assessment of the viral load present in the EBC samples . Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay.", "Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay. For diagnosis, more sensitive methods might be necessary to detect respiratory viruses present in EBC since it is unpredictable how diluted the viral particles in the specimen are. Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols .", "Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols . Also person-dependent factors, such as the number of particles produced, the exhaled volume and the age of the patient, have been suggested to play an important role for exhalation of viral particles. The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older .", "The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older . For hospitalized children a much higher rate of virus positive samples is reported . In our study, the majority of volunteers were between 20 and 30 years old.", "In our study, the majority of volunteers were between 20 and 30 years old. Only two children less than 10 years and 3 elderly people > 70 years were included. One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC.", "One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC. For influenza, an exhaled generation rate of <3.2 to 20 influenza RNA copies per minute was predicted by quantifying the virus aerosols that impacted on a removable Teflon filter of a collection mask . We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume.", "We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume. In this way, when the number of RNA copies in the EBC is quantified, the amount of viral particles that are exhaled per litre or per minute can be estimated. Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined.", "Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined. Although an inventive, new and promising method, EBC collected by the RTube™ does not appear to be appropriate for diagnosis of respiratory infections. Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses.", "Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses. This technique also confirms the observation that viruses are able to disseminate through normal breathing, particularly RV. In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns.", "In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns. In calves that were experimentally infected with bovine RSV, an increase in leukotriene B 4 , indicating oxidative stress, was observed. This increased level was also associated with the development of bronchial hyperresponsiveness .", "This increased level was also associated with the development of bronchial hyperresponsiveness . In humans, a transiently elevated H 2 O 2 level was observed during common cold infection. This marker returned to baseline values when volunteers recovered from infection.", "This marker returned to baseline values when volunteers recovered from infection. H 2 O 2 has also been recognized as an interesting marker in asthma, where it is associated with chronic lower airway inflammation . In InfA infected volunteers, an increased CO level was observed during upper respiratory infection.", "In InfA infected volunteers, an increased CO level was observed during upper respiratory infection. This observation might imply that CO is an indicator of airway inflammation or represents one of the host defence mechanisms against viral infection . Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection.", "Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection. This may contribute to the biomarker profiles established for diseases like asthma and COPD, for which viral infections are suggested to trigger or exacerbate symptoms ." ]

[ "BACKGROUND: Exhaled breath condensate EBC sampling has been considered an inventive and novel method for the isolation of respiratory viruses. METHODS: In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses.", "Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection.", "The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive.", "RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.", "CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections. Text: Human respiratory tract infections represent the most commonly encountered infections worldwide. In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection.", "In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection. Respiratory tract infections in healthy adults can be caused by a variety of pathogens and the detection of these agents is currently based on their isolation from nasal swabs NS , bronchoalveolar lavages BAL , nasopharyngeal aspirates and sputum samples. The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient.", "The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient. Therefore, exhaled breath condensate EBC analysis has recently been explored as a new and non-invasive method to monitor lung inflammation and pulmonary disease such as chronic obstructive pulmonary disease COPD , asthma, cystic fibrosis, lung cancer etc. EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid .", "EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid . This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid.", "At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid. However, the effect of the turbulent airflow is limited to the upper airways since the turbulent airflow becomes laminar as it reaches the smaller bronchial airways and alveoli. Recently, the bronchiole fluid film burst model has been described .", "Recently, the bronchiole fluid film burst model has been described . This model suggests that aerosols are produced during inhalation by the bursting of fluid bubbles present in the bronchioles. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate.", "The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. Therefore we screened the EBC samples with virus specific PCR assays targeting 14 In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms defined in Table 1 , using a commercially available condenser RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA . The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes.", "The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes. No nose clips were used during collection and saliva contamination was avoided by the presence of a one-way valve and the T-shaped section of the mouthpiece. In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory.", "In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory. The majority of these volunteers were students that responded to the information leaflet, distributed in the university buildings of the Catholic University of Leuven. The samples were collected with the aluminium cooler sleeve chilled at -80°C.", "The samples were collected with the aluminium cooler sleeve chilled at -80°C. In the fall and first half of the winter of 2009/2010, 32 condensates were collected from patients who presented themselves to their general practitioner. Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C.", "Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C. For 13 out of 32 collections, the RTube™ was connected by a custom made connectingpiece to the ECoVent Jaeger, Germany . This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume.", "This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume. Additionally, a NS was obtained in parallel with the condensate collection from each patient. All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated.", "All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated. After viral DNA and RNA extraction, EBC samples and nasal swabs were stored at -80°C. Three specimens were excluded from the study due to incorrect condensate collection.", "Three specimens were excluded from the study due to incorrect condensate collection. A short questionnaire was used to document the date of birth, the severity of respiratory complaints and to record the days of symptomatic illness from all volunteers. This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants.", "This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants. Viral DNA and RNA were isolated with the QIAamp MinElute Virus kit Qiagen, Westburg, The Netherlands according to the instruction manual. EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer.", "EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer. The breath condensates were screened for 11 respiratory RNA viruses CoV NL63, E229 and OC43, RV, HMPV, InfA&B and PIV1-4 using a OneStep RT-PCR Kit Qiagen, Westburg, The Netherlands in a 50 μl reaction containing 10 μl of the extracted RNA, 0.6 μM of forward and reverse primers Table 2 , 1.5 μl One Step Enzyme Mix, 10 μl 5 × One Step RT-PCR Buffer and 400 μM of each dNTP. For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl.", "For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl. The PCR primers used were located in conserved regions of the genomes of the respiratory pathogens Table 2 . The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C.", "The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C. The DNA amplification program was initiated with a denaturation step at 94°C for 3 min, followed by 45 cycles of 94°C for 30 s, 55°C for 30 s and a final extension step at 72°C for 1 min. The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide.", "The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide. PCR products were purified using the Invitek MSB Spin PCRapace Kit and cycle sequenced in forward and reverse direction using the ABI PRISM Big-Dye Termination Cycle Sequencing Ready Reaction kit Applied Biosystems, Foster City, CA, USA . Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA .", "Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA . Consensus sequences were obtained using the SeqMan II software DNASTAR, Madison, Wis. . For samples from HRSV was detected using a RT-PCR assay as previously described .", "For samples from HRSV was detected using a RT-PCR assay as previously described . In brief, a multiplex mix was prepared in a final volume of 25 μl using 5 μl extracted RNA, 12.5 μl of Eurogentec One-Step Reverse Transcriptase qPCR Master Mix containing ROX as a passive reference, 0.125 μl Euroscript + RT & RNase inhibitor Eurogentec, Seraing, Belgium 200 nM of HRSV-A and -B specific forward and reverse primers and 100 nM of HRSV-A and -B MGB probes. cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified.", "cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified. The viral load of RV positive samples were quantified by qRT-PCR as described in the manuscript published by Lu and coworkers . The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above.", "The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above. The primerset HRSV-AF F 669-695 ctgtgatagarttccaacaaaagaaca HRSV-AF F 718-745 agttacacctgcattaacactaaattcc HRSV-BN N 435-458 ggctccagaatataggcatgattc HRSV-BN N 480-508 tggttattacaagaagagcagctatacacagt MGB probes and probe, located in 5'UTR, were added to a final concentration of 1 μM and 0.1 μM, respectively. cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA .", "cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA . Quantification was performed with a spectrophotometer at 260 nm and converted to the molecule number . Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used.", "Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used. The RT-PCR assays were carried out on a ABI PRISM 7500 Sequence Detection System Applied Biosystems, Foster City, CA, USA . An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min.", "An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min. Finally, an amplification step of 45 cycli at 95°C for 15 sec and 1 min at 60°C was completed. 37.5% men, with a median age of 29 range 9 -46 years .", "37.5% men, with a median age of 29 range 9 -46 years . Age and gender was missing for 2 participants of the second group. In total, 52% of the participants were between 20-30 years old. Only 6% were younger than 20 years old and 3% were older than 70 years.", "Only 6% were younger than 20 years old and 3% were older than 70 years. In totality, 80 patients 78.4% were already feeling ill for 1 to 7 days at the day the sample was obtained. Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection.", "Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection. Data on the duration of symptoms was lacking for 6 patients. Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 .", "Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 . Forty-seven 46.1% volunteers complained about a constant runny or stuffy nose, 43 42.2% had frequent sneezing events and 38 37.3% participants had a serious sore throat Table 1 . In a first part of the study, we collected 70 EBCs.", "In a first part of the study, we collected 70 EBCs. Screening of the EBCs for 14 respiratory viruses Table 2 , showed 5 RV 7.1% positive samples Table 3 . In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner.", "In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner. Two of these EBCs were positive for one of the 14 investigated respiratory viruses, 1 for RV and 1 for InfB. To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison.", "To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison. In 15 out of 32 NS 46.8% , one or more viral pathogens were isolated. Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B.", "Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B. Quantification of the HRSV-B viral load demonstrated for samples 72 and 101 viral titers of 8.0 × 10 4 RNA copies/ml and 6.8 × 10 7 RNA copies/ml respectively. The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 .", "The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 . Presence of the same pathogen in both the EBC and the NS was confirmed for only 1 sample: sample 71, which tested positive for RV in both the EBC and the NS. For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection.", "For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection. For EBC samples that were collected in the fall and winter of 2009/2010, measurements with the ECoVent in Table 3 , sample 81 was positive for InfB when using the RTube™ in combination with the EcoVent. In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load.", "In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load. Then, an estimation of the RNA copies per litre exhaled air or per minute can be calculated. Quantification of the exhaled InfB would allow us to predict the generation rate for this virus.", "Quantification of the exhaled InfB would allow us to predict the generation rate for this virus. Due to insufficient sample volume, we could not determine the number of RNA copies in the sample. Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract.", "Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. The collection of EBC is easy to perform and can be conducted in a home environment. This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc.", "This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc. This aspect renders the method very attractive for routine laboratory diagnostics of viral infections. Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact .", "Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact . With the RTube™ collection device, aerosolized particles of the airway lining fluid are precipitated into a condensate when the breath is cooled which serves as an immediate starting point for molecular testing. Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses.", "Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses. Previous studies reported the inclusion of a limited subset of participants and investigated the presence of a limited number of viruses in the breath samples. The study performed by Fabian and colleagues, included 12 volunteers .", "The study performed by Fabian and colleagues, included 12 volunteers . Huynh and co-workers recruited 9 volunteers for exhaled breath sampling . In the study by Stelzer-Braid et al., 50 EBCs were analysed and St-George et al. report the participation of 12 adults .", "report the participation of 12 adults . These studies have focused on the detection of InfA and -B, PIV1-3, HRSV and HMPV, while we have screened the samples for a panel of 14 commonly circulating respiratory viruses. Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples.", "Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples. Since many of the volunteers had already been experiencing symptoms for 1 to 7 days, we initially presumed that they were already recovering from the infection and were no longer exhaling the virus. For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms.", "For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms. However, in a second part of our study we started collecting EBCs in parallel with nasal swabs from patients presenting themselves to their medical doctor, 1 to 3 days after onset of symptoms. Only for 1 condensate the same pathogen was detected in both the EBC and the NS.", "Only for 1 condensate the same pathogen was detected in both the EBC and the NS. The detection rate for respiratory viral pathogens in the NS was 46.8% which is much higher than the 7% detection rate in the EBCs. The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious.", "The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious. The discrepant detection rate between samples may also be explained by different severity of respiratory infection, since comparator samples were of different parts of the respiratory tract. Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection.", "Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection. However, the effect of nasal inhalation on EBC collection, guiding formed particles in the upper respiratory tract to the lower compartments, in stead of oral inhalation was not investigated. Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection.", "Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection. However, this was not different for 7 patients with positive NS. Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 .", "Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 . In the group of volunteers that provided an EBC negative or EBC and NS negative sample, the manifestation of symptoms were reported ranging from 1 day to more than two weeks. When reported symptoms were compared between EBC positive patients .", "When reported symptoms were compared between EBC positive patients . and NS positive patients . , 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group.", ", 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group. In all groups fever, headache, watering eyes, stuffed nose, frequent sneezing, sore throat and coughing were reported. Volunteers were not diagnosed with other pathogens before participation in the study.", "Volunteers were not diagnosed with other pathogens before participation in the study. Since we did not test these samples for other than viral pathogens, we can not exclude the possibility that some of the negative NS are positive for bacteria or other pathogens causing respiratory illness. Recently, one study reported a detection rate of 5% for influenza in EBC .", "Recently, one study reported a detection rate of 5% for influenza in EBC . This is in the same range of the detection rate that we report for respiratory viruses in general. Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included .", "Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included . Remarkably, the studies reporting this higher detection rate used collections masks, while the study using the RTube™ reported comparable findings. Face masks consist of electret which trap viruses based on permanently charged fibres .", "Face masks consist of electret which trap viruses based on permanently charged fibres . In addition, the Teflon filter has 2 μm pores which will retain all larger particles. Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials.", "Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials. The qRT-PCR developed by Lu and coworkers for the detection of RV, did not allow the assessment of the viral load present in the EBC samples . Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay.", "Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay. For diagnosis, more sensitive methods might be necessary to detect respiratory viruses present in EBC since it is unpredictable how diluted the viral particles in the specimen are. Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols .", "Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols . Also person-dependent factors, such as the number of particles produced, the exhaled volume and the age of the patient, have been suggested to play an important role for exhalation of viral particles. The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older .", "The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older . For hospitalized children a much higher rate of virus positive samples is reported . In our study, the majority of volunteers were between 20 and 30 years old.", "In our study, the majority of volunteers were between 20 and 30 years old. Only two children less than 10 years and 3 elderly people > 70 years were included. One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC.", "One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC. For influenza, an exhaled generation rate of <3.2 to 20 influenza RNA copies per minute was predicted by quantifying the virus aerosols that impacted on a removable Teflon filter of a collection mask . We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume.", "We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume. In this way, when the number of RNA copies in the EBC is quantified, the amount of viral particles that are exhaled per litre or per minute can be estimated. Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined.", "Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined. Although an inventive, new and promising method, EBC collected by the RTube™ does not appear to be appropriate for diagnosis of respiratory infections. Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses.", "Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses. This technique also confirms the observation that viruses are able to disseminate through normal breathing, particularly RV. In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns.", "In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns. In calves that were experimentally infected with bovine RSV, an increase in leukotriene B 4 , indicating oxidative stress, was observed. This increased level was also associated with the development of bronchial hyperresponsiveness .", "This increased level was also associated with the development of bronchial hyperresponsiveness . In humans, a transiently elevated H 2 O 2 level was observed during common cold infection. This marker returned to baseline values when volunteers recovered from infection.", "This marker returned to baseline values when volunteers recovered from infection. H 2 O 2 has also been recognized as an interesting marker in asthma, where it is associated with chronic lower airway inflammation . In InfA infected volunteers, an increased CO level was observed during upper respiratory infection.", "In InfA infected volunteers, an increased CO level was observed during upper respiratory infection. This observation might imply that CO is an indicator of airway inflammation or represents one of the host defence mechanisms against viral infection . Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection.", "Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection. This may contribute to the biomarker profiles established for diseases like asthma and COPD, for which viral infections are suggested to trigger or exacerbate symptoms ." ]

[ "BACKGROUND: Exhaled breath condensate EBC sampling has been considered an inventive and novel method for the isolation of respiratory viruses. METHODS: In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses.", "Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection.", "The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive.", "RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.", "CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections. Text: Human respiratory tract infections represent the most commonly encountered infections worldwide. In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection.", "In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection. Respiratory tract infections in healthy adults can be caused by a variety of pathogens and the detection of these agents is currently based on their isolation from nasal swabs NS , bronchoalveolar lavages BAL , nasopharyngeal aspirates and sputum samples. The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient.", "The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient. Therefore, exhaled breath condensate EBC analysis has recently been explored as a new and non-invasive method to monitor lung inflammation and pulmonary disease such as chronic obstructive pulmonary disease COPD , asthma, cystic fibrosis, lung cancer etc. EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid .", "EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid . This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid.", "At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid. However, the effect of the turbulent airflow is limited to the upper airways since the turbulent airflow becomes laminar as it reaches the smaller bronchial airways and alveoli. Recently, the bronchiole fluid film burst model has been described .", "Recently, the bronchiole fluid film burst model has been described . This model suggests that aerosols are produced during inhalation by the bursting of fluid bubbles present in the bronchioles. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate.", "The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. Therefore we screened the EBC samples with virus specific PCR assays targeting 14 In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms defined in Table 1 , using a commercially available condenser RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA . The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes.", "The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes. No nose clips were used during collection and saliva contamination was avoided by the presence of a one-way valve and the T-shaped section of the mouthpiece. In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory.", "In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory. The majority of these volunteers were students that responded to the information leaflet, distributed in the university buildings of the Catholic University of Leuven. The samples were collected with the aluminium cooler sleeve chilled at -80°C.", "The samples were collected with the aluminium cooler sleeve chilled at -80°C. In the fall and first half of the winter of 2009/2010, 32 condensates were collected from patients who presented themselves to their general practitioner. Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C.", "Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C. For 13 out of 32 collections, the RTube™ was connected by a custom made connectingpiece to the ECoVent Jaeger, Germany . This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume.", "This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume. Additionally, a NS was obtained in parallel with the condensate collection from each patient. All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated.", "All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated. After viral DNA and RNA extraction, EBC samples and nasal swabs were stored at -80°C. Three specimens were excluded from the study due to incorrect condensate collection.", "Three specimens were excluded from the study due to incorrect condensate collection. A short questionnaire was used to document the date of birth, the severity of respiratory complaints and to record the days of symptomatic illness from all volunteers. This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants.", "This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants. Viral DNA and RNA were isolated with the QIAamp MinElute Virus kit Qiagen, Westburg, The Netherlands according to the instruction manual. EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer.", "EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer. The breath condensates were screened for 11 respiratory RNA viruses CoV NL63, E229 and OC43, RV, HMPV, InfA&B and PIV1-4 using a OneStep RT-PCR Kit Qiagen, Westburg, The Netherlands in a 50 μl reaction containing 10 μl of the extracted RNA, 0.6 μM of forward and reverse primers Table 2 , 1.5 μl One Step Enzyme Mix, 10 μl 5 × One Step RT-PCR Buffer and 400 μM of each dNTP. For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl.", "For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl. The PCR primers used were located in conserved regions of the genomes of the respiratory pathogens Table 2 . The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C.", "The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C. The DNA amplification program was initiated with a denaturation step at 94°C for 3 min, followed by 45 cycles of 94°C for 30 s, 55°C for 30 s and a final extension step at 72°C for 1 min. The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide.", "The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide. PCR products were purified using the Invitek MSB Spin PCRapace Kit and cycle sequenced in forward and reverse direction using the ABI PRISM Big-Dye Termination Cycle Sequencing Ready Reaction kit Applied Biosystems, Foster City, CA, USA . Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA .", "Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA . Consensus sequences were obtained using the SeqMan II software DNASTAR, Madison, Wis. . For samples from HRSV was detected using a RT-PCR assay as previously described .", "For samples from HRSV was detected using a RT-PCR assay as previously described . In brief, a multiplex mix was prepared in a final volume of 25 μl using 5 μl extracted RNA, 12.5 μl of Eurogentec One-Step Reverse Transcriptase qPCR Master Mix containing ROX as a passive reference, 0.125 μl Euroscript + RT & RNase inhibitor Eurogentec, Seraing, Belgium 200 nM of HRSV-A and -B specific forward and reverse primers and 100 nM of HRSV-A and -B MGB probes. cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified.", "cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified. The viral load of RV positive samples were quantified by qRT-PCR as described in the manuscript published by Lu and coworkers . The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above.", "The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above. The primerset HRSV-AF F 669-695 ctgtgatagarttccaacaaaagaaca HRSV-AF F 718-745 agttacacctgcattaacactaaattcc HRSV-BN N 435-458 ggctccagaatataggcatgattc HRSV-BN N 480-508 tggttattacaagaagagcagctatacacagt MGB probes and probe, located in 5'UTR, were added to a final concentration of 1 μM and 0.1 μM, respectively. cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA .", "cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA . Quantification was performed with a spectrophotometer at 260 nm and converted to the molecule number . Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used.", "Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used. The RT-PCR assays were carried out on a ABI PRISM 7500 Sequence Detection System Applied Biosystems, Foster City, CA, USA . An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min.", "An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min. Finally, an amplification step of 45 cycli at 95°C for 15 sec and 1 min at 60°C was completed. 37.5% men, with a median age of 29 range 9 -46 years .", "37.5% men, with a median age of 29 range 9 -46 years . Age and gender was missing for 2 participants of the second group. In total, 52% of the participants were between 20-30 years old. Only 6% were younger than 20 years old and 3% were older than 70 years.", "Only 6% were younger than 20 years old and 3% were older than 70 years. In totality, 80 patients 78.4% were already feeling ill for 1 to 7 days at the day the sample was obtained. Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection.", "Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection. Data on the duration of symptoms was lacking for 6 patients. Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 .", "Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 . Forty-seven 46.1% volunteers complained about a constant runny or stuffy nose, 43 42.2% had frequent sneezing events and 38 37.3% participants had a serious sore throat Table 1 . In a first part of the study, we collected 70 EBCs.", "In a first part of the study, we collected 70 EBCs. Screening of the EBCs for 14 respiratory viruses Table 2 , showed 5 RV 7.1% positive samples Table 3 . In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner.", "In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner. Two of these EBCs were positive for one of the 14 investigated respiratory viruses, 1 for RV and 1 for InfB. To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison.", "To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison. In 15 out of 32 NS 46.8% , one or more viral pathogens were isolated. Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B.", "Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B. Quantification of the HRSV-B viral load demonstrated for samples 72 and 101 viral titers of 8.0 × 10 4 RNA copies/ml and 6.8 × 10 7 RNA copies/ml respectively. The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 .", "The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 . Presence of the same pathogen in both the EBC and the NS was confirmed for only 1 sample: sample 71, which tested positive for RV in both the EBC and the NS. For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection.", "For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection. For EBC samples that were collected in the fall and winter of 2009/2010, measurements with the ECoVent in Table 3 , sample 81 was positive for InfB when using the RTube™ in combination with the EcoVent. In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load.", "In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load. Then, an estimation of the RNA copies per litre exhaled air or per minute can be calculated. Quantification of the exhaled InfB would allow us to predict the generation rate for this virus.", "Quantification of the exhaled InfB would allow us to predict the generation rate for this virus. Due to insufficient sample volume, we could not determine the number of RNA copies in the sample. Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract.", "Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. The collection of EBC is easy to perform and can be conducted in a home environment. This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc.", "This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc. This aspect renders the method very attractive for routine laboratory diagnostics of viral infections. Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact .", "Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact . With the RTube™ collection device, aerosolized particles of the airway lining fluid are precipitated into a condensate when the breath is cooled which serves as an immediate starting point for molecular testing. Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses.", "Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses. Previous studies reported the inclusion of a limited subset of participants and investigated the presence of a limited number of viruses in the breath samples. The study performed by Fabian and colleagues, included 12 volunteers .", "The study performed by Fabian and colleagues, included 12 volunteers . Huynh and co-workers recruited 9 volunteers for exhaled breath sampling . In the study by Stelzer-Braid et al., 50 EBCs were analysed and St-George et al. report the participation of 12 adults .", "report the participation of 12 adults . These studies have focused on the detection of InfA and -B, PIV1-3, HRSV and HMPV, while we have screened the samples for a panel of 14 commonly circulating respiratory viruses. Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples.", "Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples. Since many of the volunteers had already been experiencing symptoms for 1 to 7 days, we initially presumed that they were already recovering from the infection and were no longer exhaling the virus. For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms.", "For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms. However, in a second part of our study we started collecting EBCs in parallel with nasal swabs from patients presenting themselves to their medical doctor, 1 to 3 days after onset of symptoms. Only for 1 condensate the same pathogen was detected in both the EBC and the NS.", "Only for 1 condensate the same pathogen was detected in both the EBC and the NS. The detection rate for respiratory viral pathogens in the NS was 46.8% which is much higher than the 7% detection rate in the EBCs. The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious.", "The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious. The discrepant detection rate between samples may also be explained by different severity of respiratory infection, since comparator samples were of different parts of the respiratory tract. Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection.", "Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection. However, the effect of nasal inhalation on EBC collection, guiding formed particles in the upper respiratory tract to the lower compartments, in stead of oral inhalation was not investigated. Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection.", "Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection. However, this was not different for 7 patients with positive NS. Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 .", "Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 . In the group of volunteers that provided an EBC negative or EBC and NS negative sample, the manifestation of symptoms were reported ranging from 1 day to more than two weeks. When reported symptoms were compared between EBC positive patients .", "When reported symptoms were compared between EBC positive patients . and NS positive patients . , 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group.", ", 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group. In all groups fever, headache, watering eyes, stuffed nose, frequent sneezing, sore throat and coughing were reported. Volunteers were not diagnosed with other pathogens before participation in the study.", "Volunteers were not diagnosed with other pathogens before participation in the study. Since we did not test these samples for other than viral pathogens, we can not exclude the possibility that some of the negative NS are positive for bacteria or other pathogens causing respiratory illness. Recently, one study reported a detection rate of 5% for influenza in EBC .", "Recently, one study reported a detection rate of 5% for influenza in EBC . This is in the same range of the detection rate that we report for respiratory viruses in general. Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included .", "Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included . Remarkably, the studies reporting this higher detection rate used collections masks, while the study using the RTube™ reported comparable findings. Face masks consist of electret which trap viruses based on permanently charged fibres .", "Face masks consist of electret which trap viruses based on permanently charged fibres . In addition, the Teflon filter has 2 μm pores which will retain all larger particles. Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials.", "Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials. The qRT-PCR developed by Lu and coworkers for the detection of RV, did not allow the assessment of the viral load present in the EBC samples . Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay.", "Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay. For diagnosis, more sensitive methods might be necessary to detect respiratory viruses present in EBC since it is unpredictable how diluted the viral particles in the specimen are. Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols .", "Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols . Also person-dependent factors, such as the number of particles produced, the exhaled volume and the age of the patient, have been suggested to play an important role for exhalation of viral particles. The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older .", "The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older . For hospitalized children a much higher rate of virus positive samples is reported . In our study, the majority of volunteers were between 20 and 30 years old.", "In our study, the majority of volunteers were between 20 and 30 years old. Only two children less than 10 years and 3 elderly people > 70 years were included. One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC.", "One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC. For influenza, an exhaled generation rate of <3.2 to 20 influenza RNA copies per minute was predicted by quantifying the virus aerosols that impacted on a removable Teflon filter of a collection mask . We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume.", "We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume. In this way, when the number of RNA copies in the EBC is quantified, the amount of viral particles that are exhaled per litre or per minute can be estimated. Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined.", "Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined. Although an inventive, new and promising method, EBC collected by the RTube™ does not appear to be appropriate for diagnosis of respiratory infections. Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses.", "Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses. This technique also confirms the observation that viruses are able to disseminate through normal breathing, particularly RV. In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns.", "In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns. In calves that were experimentally infected with bovine RSV, an increase in leukotriene B 4 , indicating oxidative stress, was observed. This increased level was also associated with the development of bronchial hyperresponsiveness .", "This increased level was also associated with the development of bronchial hyperresponsiveness . In humans, a transiently elevated H 2 O 2 level was observed during common cold infection. This marker returned to baseline values when volunteers recovered from infection.", "This marker returned to baseline values when volunteers recovered from infection. H 2 O 2 has also been recognized as an interesting marker in asthma, where it is associated with chronic lower airway inflammation . In InfA infected volunteers, an increased CO level was observed during upper respiratory infection.", "In InfA infected volunteers, an increased CO level was observed during upper respiratory infection. This observation might imply that CO is an indicator of airway inflammation or represents one of the host defence mechanisms against viral infection . Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection.", "Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection. This may contribute to the biomarker profiles established for diseases like asthma and COPD, for which viral infections are suggested to trigger or exacerbate symptoms ." ]

[ "BACKGROUND: Exhaled breath condensate EBC sampling has been considered an inventive and novel method for the isolation of respiratory viruses. METHODS: In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses.", "Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection.", "The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive.", "RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.", "CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections. Text: Human respiratory tract infections represent the most commonly encountered infections worldwide. In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection.", "In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection. Respiratory tract infections in healthy adults can be caused by a variety of pathogens and the detection of these agents is currently based on their isolation from nasal swabs NS , bronchoalveolar lavages BAL , nasopharyngeal aspirates and sputum samples. The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient.", "The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient. Therefore, exhaled breath condensate EBC analysis has recently been explored as a new and non-invasive method to monitor lung inflammation and pulmonary disease such as chronic obstructive pulmonary disease COPD , asthma, cystic fibrosis, lung cancer etc. EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid .", "EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid . This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid.", "At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid. However, the effect of the turbulent airflow is limited to the upper airways since the turbulent airflow becomes laminar as it reaches the smaller bronchial airways and alveoli. Recently, the bronchiole fluid film burst model has been described .", "Recently, the bronchiole fluid film burst model has been described . This model suggests that aerosols are produced during inhalation by the bursting of fluid bubbles present in the bronchioles. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate.", "The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. Therefore we screened the EBC samples with virus specific PCR assays targeting 14 In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms defined in Table 1 , using a commercially available condenser RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA . The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes.", "The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes. No nose clips were used during collection and saliva contamination was avoided by the presence of a one-way valve and the T-shaped section of the mouthpiece. In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory.", "In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory. The majority of these volunteers were students that responded to the information leaflet, distributed in the university buildings of the Catholic University of Leuven. The samples were collected with the aluminium cooler sleeve chilled at -80°C.", "The samples were collected with the aluminium cooler sleeve chilled at -80°C. In the fall and first half of the winter of 2009/2010, 32 condensates were collected from patients who presented themselves to their general practitioner. Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C.", "Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C. For 13 out of 32 collections, the RTube™ was connected by a custom made connectingpiece to the ECoVent Jaeger, Germany . This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume.", "This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume. Additionally, a NS was obtained in parallel with the condensate collection from each patient. All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated.", "All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated. After viral DNA and RNA extraction, EBC samples and nasal swabs were stored at -80°C. Three specimens were excluded from the study due to incorrect condensate collection.", "Three specimens were excluded from the study due to incorrect condensate collection. A short questionnaire was used to document the date of birth, the severity of respiratory complaints and to record the days of symptomatic illness from all volunteers. This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants.", "This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants. Viral DNA and RNA were isolated with the QIAamp MinElute Virus kit Qiagen, Westburg, The Netherlands according to the instruction manual. EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer.", "EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer. The breath condensates were screened for 11 respiratory RNA viruses CoV NL63, E229 and OC43, RV, HMPV, InfA&B and PIV1-4 using a OneStep RT-PCR Kit Qiagen, Westburg, The Netherlands in a 50 μl reaction containing 10 μl of the extracted RNA, 0.6 μM of forward and reverse primers Table 2 , 1.5 μl One Step Enzyme Mix, 10 μl 5 × One Step RT-PCR Buffer and 400 μM of each dNTP. For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl.", "For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl. The PCR primers used were located in conserved regions of the genomes of the respiratory pathogens Table 2 . The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C.", "The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C. The DNA amplification program was initiated with a denaturation step at 94°C for 3 min, followed by 45 cycles of 94°C for 30 s, 55°C for 30 s and a final extension step at 72°C for 1 min. The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide.", "The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide. PCR products were purified using the Invitek MSB Spin PCRapace Kit and cycle sequenced in forward and reverse direction using the ABI PRISM Big-Dye Termination Cycle Sequencing Ready Reaction kit Applied Biosystems, Foster City, CA, USA . Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA .", "Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA . Consensus sequences were obtained using the SeqMan II software DNASTAR, Madison, Wis. . For samples from HRSV was detected using a RT-PCR assay as previously described .", "For samples from HRSV was detected using a RT-PCR assay as previously described . In brief, a multiplex mix was prepared in a final volume of 25 μl using 5 μl extracted RNA, 12.5 μl of Eurogentec One-Step Reverse Transcriptase qPCR Master Mix containing ROX as a passive reference, 0.125 μl Euroscript + RT & RNase inhibitor Eurogentec, Seraing, Belgium 200 nM of HRSV-A and -B specific forward and reverse primers and 100 nM of HRSV-A and -B MGB probes. cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified.", "cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified. The viral load of RV positive samples were quantified by qRT-PCR as described in the manuscript published by Lu and coworkers . The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above.", "The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above. The primerset HRSV-AF F 669-695 ctgtgatagarttccaacaaaagaaca HRSV-AF F 718-745 agttacacctgcattaacactaaattcc HRSV-BN N 435-458 ggctccagaatataggcatgattc HRSV-BN N 480-508 tggttattacaagaagagcagctatacacagt MGB probes and probe, located in 5'UTR, were added to a final concentration of 1 μM and 0.1 μM, respectively. cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA .", "cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA . Quantification was performed with a spectrophotometer at 260 nm and converted to the molecule number . Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used.", "Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used. The RT-PCR assays were carried out on a ABI PRISM 7500 Sequence Detection System Applied Biosystems, Foster City, CA, USA . An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min.", "An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min. Finally, an amplification step of 45 cycli at 95°C for 15 sec and 1 min at 60°C was completed. 37.5% men, with a median age of 29 range 9 -46 years .", "37.5% men, with a median age of 29 range 9 -46 years . Age and gender was missing for 2 participants of the second group. In total, 52% of the participants were between 20-30 years old. Only 6% were younger than 20 years old and 3% were older than 70 years.", "Only 6% were younger than 20 years old and 3% were older than 70 years. In totality, 80 patients 78.4% were already feeling ill for 1 to 7 days at the day the sample was obtained. Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection.", "Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection. Data on the duration of symptoms was lacking for 6 patients. Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 .", "Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 . Forty-seven 46.1% volunteers complained about a constant runny or stuffy nose, 43 42.2% had frequent sneezing events and 38 37.3% participants had a serious sore throat Table 1 . In a first part of the study, we collected 70 EBCs.", "In a first part of the study, we collected 70 EBCs. Screening of the EBCs for 14 respiratory viruses Table 2 , showed 5 RV 7.1% positive samples Table 3 . In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner.", "In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner. Two of these EBCs were positive for one of the 14 investigated respiratory viruses, 1 for RV and 1 for InfB. To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison.", "To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison. In 15 out of 32 NS 46.8% , one or more viral pathogens were isolated. Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B.", "Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B. Quantification of the HRSV-B viral load demonstrated for samples 72 and 101 viral titers of 8.0 × 10 4 RNA copies/ml and 6.8 × 10 7 RNA copies/ml respectively. The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 .", "The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 . Presence of the same pathogen in both the EBC and the NS was confirmed for only 1 sample: sample 71, which tested positive for RV in both the EBC and the NS. For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection.", "For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection. For EBC samples that were collected in the fall and winter of 2009/2010, measurements with the ECoVent in Table 3 , sample 81 was positive for InfB when using the RTube™ in combination with the EcoVent. In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load.", "In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load. Then, an estimation of the RNA copies per litre exhaled air or per minute can be calculated. Quantification of the exhaled InfB would allow us to predict the generation rate for this virus.", "Quantification of the exhaled InfB would allow us to predict the generation rate for this virus. Due to insufficient sample volume, we could not determine the number of RNA copies in the sample. Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract.", "Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. The collection of EBC is easy to perform and can be conducted in a home environment. This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc.", "This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc. This aspect renders the method very attractive for routine laboratory diagnostics of viral infections. Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact .", "Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact . With the RTube™ collection device, aerosolized particles of the airway lining fluid are precipitated into a condensate when the breath is cooled which serves as an immediate starting point for molecular testing. Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses.", "Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses. Previous studies reported the inclusion of a limited subset of participants and investigated the presence of a limited number of viruses in the breath samples. The study performed by Fabian and colleagues, included 12 volunteers .", "The study performed by Fabian and colleagues, included 12 volunteers . Huynh and co-workers recruited 9 volunteers for exhaled breath sampling . In the study by Stelzer-Braid et al., 50 EBCs were analysed and St-George et al. report the participation of 12 adults .", "report the participation of 12 adults . These studies have focused on the detection of InfA and -B, PIV1-3, HRSV and HMPV, while we have screened the samples for a panel of 14 commonly circulating respiratory viruses. Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples.", "Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples. Since many of the volunteers had already been experiencing symptoms for 1 to 7 days, we initially presumed that they were already recovering from the infection and were no longer exhaling the virus. For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms.", "For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms. However, in a second part of our study we started collecting EBCs in parallel with nasal swabs from patients presenting themselves to their medical doctor, 1 to 3 days after onset of symptoms. Only for 1 condensate the same pathogen was detected in both the EBC and the NS.", "Only for 1 condensate the same pathogen was detected in both the EBC and the NS. The detection rate for respiratory viral pathogens in the NS was 46.8% which is much higher than the 7% detection rate in the EBCs. The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious.", "The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious. The discrepant detection rate between samples may also be explained by different severity of respiratory infection, since comparator samples were of different parts of the respiratory tract. Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection.", "Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection. However, the effect of nasal inhalation on EBC collection, guiding formed particles in the upper respiratory tract to the lower compartments, in stead of oral inhalation was not investigated. Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection.", "Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection. However, this was not different for 7 patients with positive NS. Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 .", "Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 . In the group of volunteers that provided an EBC negative or EBC and NS negative sample, the manifestation of symptoms were reported ranging from 1 day to more than two weeks. When reported symptoms were compared between EBC positive patients .", "When reported symptoms were compared between EBC positive patients . and NS positive patients . , 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group.", ", 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group. In all groups fever, headache, watering eyes, stuffed nose, frequent sneezing, sore throat and coughing were reported. Volunteers were not diagnosed with other pathogens before participation in the study.", "Volunteers were not diagnosed with other pathogens before participation in the study. Since we did not test these samples for other than viral pathogens, we can not exclude the possibility that some of the negative NS are positive for bacteria or other pathogens causing respiratory illness. Recently, one study reported a detection rate of 5% for influenza in EBC .", "Recently, one study reported a detection rate of 5% for influenza in EBC . This is in the same range of the detection rate that we report for respiratory viruses in general. Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included .", "Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included . Remarkably, the studies reporting this higher detection rate used collections masks, while the study using the RTube™ reported comparable findings. Face masks consist of electret which trap viruses based on permanently charged fibres .", "Face masks consist of electret which trap viruses based on permanently charged fibres . In addition, the Teflon filter has 2 μm pores which will retain all larger particles. Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials.", "Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials. The qRT-PCR developed by Lu and coworkers for the detection of RV, did not allow the assessment of the viral load present in the EBC samples . Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay.", "Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay. For diagnosis, more sensitive methods might be necessary to detect respiratory viruses present in EBC since it is unpredictable how diluted the viral particles in the specimen are. Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols .", "Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols . Also person-dependent factors, such as the number of particles produced, the exhaled volume and the age of the patient, have been suggested to play an important role for exhalation of viral particles. The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older .", "The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older . For hospitalized children a much higher rate of virus positive samples is reported . In our study, the majority of volunteers were between 20 and 30 years old.", "In our study, the majority of volunteers were between 20 and 30 years old. Only two children less than 10 years and 3 elderly people > 70 years were included. One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC.", "One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC. For influenza, an exhaled generation rate of <3.2 to 20 influenza RNA copies per minute was predicted by quantifying the virus aerosols that impacted on a removable Teflon filter of a collection mask . We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume.", "We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume. In this way, when the number of RNA copies in the EBC is quantified, the amount of viral particles that are exhaled per litre or per minute can be estimated. Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined.", "Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined. Although an inventive, new and promising method, EBC collected by the RTube™ does not appear to be appropriate for diagnosis of respiratory infections. Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses.", "Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses. This technique also confirms the observation that viruses are able to disseminate through normal breathing, particularly RV. In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns.", "In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns. In calves that were experimentally infected with bovine RSV, an increase in leukotriene B 4 , indicating oxidative stress, was observed. This increased level was also associated with the development of bronchial hyperresponsiveness .", "This increased level was also associated with the development of bronchial hyperresponsiveness . In humans, a transiently elevated H 2 O 2 level was observed during common cold infection. This marker returned to baseline values when volunteers recovered from infection.", "This marker returned to baseline values when volunteers recovered from infection. H 2 O 2 has also been recognized as an interesting marker in asthma, where it is associated with chronic lower airway inflammation . In InfA infected volunteers, an increased CO level was observed during upper respiratory infection.", "In InfA infected volunteers, an increased CO level was observed during upper respiratory infection. This observation might imply that CO is an indicator of airway inflammation or represents one of the host defence mechanisms against viral infection . Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection.", "Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection. This may contribute to the biomarker profiles established for diseases like asthma and COPD, for which viral infections are suggested to trigger or exacerbate symptoms ." ]

[ "BACKGROUND: Exhaled breath condensate EBC sampling has been considered an inventive and novel method for the isolation of respiratory viruses. METHODS: In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses.", "Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection.", "The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive.", "RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.", "CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections. Text: Human respiratory tract infections represent the most commonly encountered infections worldwide. In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection.", "In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection. Respiratory tract infections in healthy adults can be caused by a variety of pathogens and the detection of these agents is currently based on their isolation from nasal swabs NS , bronchoalveolar lavages BAL , nasopharyngeal aspirates and sputum samples. The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient.", "The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient. Therefore, exhaled breath condensate EBC analysis has recently been explored as a new and non-invasive method to monitor lung inflammation and pulmonary disease such as chronic obstructive pulmonary disease COPD , asthma, cystic fibrosis, lung cancer etc. EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid .", "EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid . This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid.", "At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid. However, the effect of the turbulent airflow is limited to the upper airways since the turbulent airflow becomes laminar as it reaches the smaller bronchial airways and alveoli. Recently, the bronchiole fluid film burst model has been described .", "Recently, the bronchiole fluid film burst model has been described . This model suggests that aerosols are produced during inhalation by the bursting of fluid bubbles present in the bronchioles. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate.", "The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. Therefore we screened the EBC samples with virus specific PCR assays targeting 14 In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms defined in Table 1 , using a commercially available condenser RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA . The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes.", "The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes. No nose clips were used during collection and saliva contamination was avoided by the presence of a one-way valve and the T-shaped section of the mouthpiece. In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory.", "In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory. The majority of these volunteers were students that responded to the information leaflet, distributed in the university buildings of the Catholic University of Leuven. The samples were collected with the aluminium cooler sleeve chilled at -80°C.", "The samples were collected with the aluminium cooler sleeve chilled at -80°C. In the fall and first half of the winter of 2009/2010, 32 condensates were collected from patients who presented themselves to their general practitioner. Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C.", "Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C. For 13 out of 32 collections, the RTube™ was connected by a custom made connectingpiece to the ECoVent Jaeger, Germany . This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume.", "This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume. Additionally, a NS was obtained in parallel with the condensate collection from each patient. All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated.", "All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated. After viral DNA and RNA extraction, EBC samples and nasal swabs were stored at -80°C. Three specimens were excluded from the study due to incorrect condensate collection.", "Three specimens were excluded from the study due to incorrect condensate collection. A short questionnaire was used to document the date of birth, the severity of respiratory complaints and to record the days of symptomatic illness from all volunteers. This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants.", "This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants. Viral DNA and RNA were isolated with the QIAamp MinElute Virus kit Qiagen, Westburg, The Netherlands according to the instruction manual. EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer.", "EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer. The breath condensates were screened for 11 respiratory RNA viruses CoV NL63, E229 and OC43, RV, HMPV, InfA&B and PIV1-4 using a OneStep RT-PCR Kit Qiagen, Westburg, The Netherlands in a 50 μl reaction containing 10 μl of the extracted RNA, 0.6 μM of forward and reverse primers Table 2 , 1.5 μl One Step Enzyme Mix, 10 μl 5 × One Step RT-PCR Buffer and 400 μM of each dNTP. For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl.", "For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl. The PCR primers used were located in conserved regions of the genomes of the respiratory pathogens Table 2 . The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C.", "The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C. The DNA amplification program was initiated with a denaturation step at 94°C for 3 min, followed by 45 cycles of 94°C for 30 s, 55°C for 30 s and a final extension step at 72°C for 1 min. The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide.", "The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide. PCR products were purified using the Invitek MSB Spin PCRapace Kit and cycle sequenced in forward and reverse direction using the ABI PRISM Big-Dye Termination Cycle Sequencing Ready Reaction kit Applied Biosystems, Foster City, CA, USA . Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA .", "Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA . Consensus sequences were obtained using the SeqMan II software DNASTAR, Madison, Wis. . For samples from HRSV was detected using a RT-PCR assay as previously described .", "For samples from HRSV was detected using a RT-PCR assay as previously described . In brief, a multiplex mix was prepared in a final volume of 25 μl using 5 μl extracted RNA, 12.5 μl of Eurogentec One-Step Reverse Transcriptase qPCR Master Mix containing ROX as a passive reference, 0.125 μl Euroscript + RT & RNase inhibitor Eurogentec, Seraing, Belgium 200 nM of HRSV-A and -B specific forward and reverse primers and 100 nM of HRSV-A and -B MGB probes. cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified.", "cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified. The viral load of RV positive samples were quantified by qRT-PCR as described in the manuscript published by Lu and coworkers . The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above.", "The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above. The primerset HRSV-AF F 669-695 ctgtgatagarttccaacaaaagaaca HRSV-AF F 718-745 agttacacctgcattaacactaaattcc HRSV-BN N 435-458 ggctccagaatataggcatgattc HRSV-BN N 480-508 tggttattacaagaagagcagctatacacagt MGB probes and probe, located in 5'UTR, were added to a final concentration of 1 μM and 0.1 μM, respectively. cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA .", "cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA . Quantification was performed with a spectrophotometer at 260 nm and converted to the molecule number . Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used.", "Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used. The RT-PCR assays were carried out on a ABI PRISM 7500 Sequence Detection System Applied Biosystems, Foster City, CA, USA . An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min.", "An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min. Finally, an amplification step of 45 cycli at 95°C for 15 sec and 1 min at 60°C was completed. 37.5% men, with a median age of 29 range 9 -46 years .", "37.5% men, with a median age of 29 range 9 -46 years . Age and gender was missing for 2 participants of the second group. In total, 52% of the participants were between 20-30 years old. Only 6% were younger than 20 years old and 3% were older than 70 years.", "Only 6% were younger than 20 years old and 3% were older than 70 years. In totality, 80 patients 78.4% were already feeling ill for 1 to 7 days at the day the sample was obtained. Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection.", "Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection. Data on the duration of symptoms was lacking for 6 patients. Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 .", "Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 . Forty-seven 46.1% volunteers complained about a constant runny or stuffy nose, 43 42.2% had frequent sneezing events and 38 37.3% participants had a serious sore throat Table 1 . In a first part of the study, we collected 70 EBCs.", "In a first part of the study, we collected 70 EBCs. Screening of the EBCs for 14 respiratory viruses Table 2 , showed 5 RV 7.1% positive samples Table 3 . In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner.", "In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner. Two of these EBCs were positive for one of the 14 investigated respiratory viruses, 1 for RV and 1 for InfB. To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison.", "To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison. In 15 out of 32 NS 46.8% , one or more viral pathogens were isolated. Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B.", "Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B. Quantification of the HRSV-B viral load demonstrated for samples 72 and 101 viral titers of 8.0 × 10 4 RNA copies/ml and 6.8 × 10 7 RNA copies/ml respectively. The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 .", "The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 . Presence of the same pathogen in both the EBC and the NS was confirmed for only 1 sample: sample 71, which tested positive for RV in both the EBC and the NS. For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection.", "For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection. For EBC samples that were collected in the fall and winter of 2009/2010, measurements with the ECoVent in Table 3 , sample 81 was positive for InfB when using the RTube™ in combination with the EcoVent. In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load.", "In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load. Then, an estimation of the RNA copies per litre exhaled air or per minute can be calculated. Quantification of the exhaled InfB would allow us to predict the generation rate for this virus.", "Quantification of the exhaled InfB would allow us to predict the generation rate for this virus. Due to insufficient sample volume, we could not determine the number of RNA copies in the sample. Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract.", "Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. The collection of EBC is easy to perform and can be conducted in a home environment. This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc.", "This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc. This aspect renders the method very attractive for routine laboratory diagnostics of viral infections. Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact .", "Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact . With the RTube™ collection device, aerosolized particles of the airway lining fluid are precipitated into a condensate when the breath is cooled which serves as an immediate starting point for molecular testing. Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses.", "Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses. Previous studies reported the inclusion of a limited subset of participants and investigated the presence of a limited number of viruses in the breath samples. The study performed by Fabian and colleagues, included 12 volunteers .", "The study performed by Fabian and colleagues, included 12 volunteers . Huynh and co-workers recruited 9 volunteers for exhaled breath sampling . In the study by Stelzer-Braid et al., 50 EBCs were analysed and St-George et al. report the participation of 12 adults .", "report the participation of 12 adults . These studies have focused on the detection of InfA and -B, PIV1-3, HRSV and HMPV, while we have screened the samples for a panel of 14 commonly circulating respiratory viruses. Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples.", "Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples. Since many of the volunteers had already been experiencing symptoms for 1 to 7 days, we initially presumed that they were already recovering from the infection and were no longer exhaling the virus. For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms.", "For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms. However, in a second part of our study we started collecting EBCs in parallel with nasal swabs from patients presenting themselves to their medical doctor, 1 to 3 days after onset of symptoms. Only for 1 condensate the same pathogen was detected in both the EBC and the NS.", "Only for 1 condensate the same pathogen was detected in both the EBC and the NS. The detection rate for respiratory viral pathogens in the NS was 46.8% which is much higher than the 7% detection rate in the EBCs. The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious.", "The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious. The discrepant detection rate between samples may also be explained by different severity of respiratory infection, since comparator samples were of different parts of the respiratory tract. Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection.", "Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection. However, the effect of nasal inhalation on EBC collection, guiding formed particles in the upper respiratory tract to the lower compartments, in stead of oral inhalation was not investigated. Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection.", "Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection. However, this was not different for 7 patients with positive NS. Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 .", "Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 . In the group of volunteers that provided an EBC negative or EBC and NS negative sample, the manifestation of symptoms were reported ranging from 1 day to more than two weeks. When reported symptoms were compared between EBC positive patients .", "When reported symptoms were compared between EBC positive patients . and NS positive patients . , 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group.", ", 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group. In all groups fever, headache, watering eyes, stuffed nose, frequent sneezing, sore throat and coughing were reported. Volunteers were not diagnosed with other pathogens before participation in the study.", "Volunteers were not diagnosed with other pathogens before participation in the study. Since we did not test these samples for other than viral pathogens, we can not exclude the possibility that some of the negative NS are positive for bacteria or other pathogens causing respiratory illness. Recently, one study reported a detection rate of 5% for influenza in EBC .", "Recently, one study reported a detection rate of 5% for influenza in EBC . This is in the same range of the detection rate that we report for respiratory viruses in general. Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included .", "Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included . Remarkably, the studies reporting this higher detection rate used collections masks, while the study using the RTube™ reported comparable findings. Face masks consist of electret which trap viruses based on permanently charged fibres .", "Face masks consist of electret which trap viruses based on permanently charged fibres . In addition, the Teflon filter has 2 μm pores which will retain all larger particles. Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials.", "Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials. The qRT-PCR developed by Lu and coworkers for the detection of RV, did not allow the assessment of the viral load present in the EBC samples . Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay.", "Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay. For diagnosis, more sensitive methods might be necessary to detect respiratory viruses present in EBC since it is unpredictable how diluted the viral particles in the specimen are. Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols .", "Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols . Also person-dependent factors, such as the number of particles produced, the exhaled volume and the age of the patient, have been suggested to play an important role for exhalation of viral particles. The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older .", "The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older . For hospitalized children a much higher rate of virus positive samples is reported . In our study, the majority of volunteers were between 20 and 30 years old.", "In our study, the majority of volunteers were between 20 and 30 years old. Only two children less than 10 years and 3 elderly people > 70 years were included. One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC.", "One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC. For influenza, an exhaled generation rate of <3.2 to 20 influenza RNA copies per minute was predicted by quantifying the virus aerosols that impacted on a removable Teflon filter of a collection mask . We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume.", "We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume. In this way, when the number of RNA copies in the EBC is quantified, the amount of viral particles that are exhaled per litre or per minute can be estimated. Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined.", "Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined. Although an inventive, new and promising method, EBC collected by the RTube™ does not appear to be appropriate for diagnosis of respiratory infections. Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses.", "Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses. This technique also confirms the observation that viruses are able to disseminate through normal breathing, particularly RV. In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns.", "In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns. In calves that were experimentally infected with bovine RSV, an increase in leukotriene B 4 , indicating oxidative stress, was observed. This increased level was also associated with the development of bronchial hyperresponsiveness .", "This increased level was also associated with the development of bronchial hyperresponsiveness . In humans, a transiently elevated H 2 O 2 level was observed during common cold infection. This marker returned to baseline values when volunteers recovered from infection.", "This marker returned to baseline values when volunteers recovered from infection. H 2 O 2 has also been recognized as an interesting marker in asthma, where it is associated with chronic lower airway inflammation . In InfA infected volunteers, an increased CO level was observed during upper respiratory infection.", "In InfA infected volunteers, an increased CO level was observed during upper respiratory infection. This observation might imply that CO is an indicator of airway inflammation or represents one of the host defence mechanisms against viral infection . Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection.", "Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection. This may contribute to the biomarker profiles established for diseases like asthma and COPD, for which viral infections are suggested to trigger or exacerbate symptoms ." ]

[ "BACKGROUND: Exhaled breath condensate EBC sampling has been considered an inventive and novel method for the isolation of respiratory viruses. METHODS: In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses.", "Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection.", "The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive.", "RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.", "CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections. Text: Human respiratory tract infections represent the most commonly encountered infections worldwide. In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection.", "In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection. Respiratory tract infections in healthy adults can be caused by a variety of pathogens and the detection of these agents is currently based on their isolation from nasal swabs NS , bronchoalveolar lavages BAL , nasopharyngeal aspirates and sputum samples. The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient.", "The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient. Therefore, exhaled breath condensate EBC analysis has recently been explored as a new and non-invasive method to monitor lung inflammation and pulmonary disease such as chronic obstructive pulmonary disease COPD , asthma, cystic fibrosis, lung cancer etc. EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid .", "EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid . This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid.", "At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid. However, the effect of the turbulent airflow is limited to the upper airways since the turbulent airflow becomes laminar as it reaches the smaller bronchial airways and alveoli. Recently, the bronchiole fluid film burst model has been described .", "Recently, the bronchiole fluid film burst model has been described . This model suggests that aerosols are produced during inhalation by the bursting of fluid bubbles present in the bronchioles. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate.", "The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. Therefore we screened the EBC samples with virus specific PCR assays targeting 14 In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms defined in Table 1 , using a commercially available condenser RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA . The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes.", "The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes. No nose clips were used during collection and saliva contamination was avoided by the presence of a one-way valve and the T-shaped section of the mouthpiece. In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory.", "In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory. The majority of these volunteers were students that responded to the information leaflet, distributed in the university buildings of the Catholic University of Leuven. The samples were collected with the aluminium cooler sleeve chilled at -80°C.", "The samples were collected with the aluminium cooler sleeve chilled at -80°C. In the fall and first half of the winter of 2009/2010, 32 condensates were collected from patients who presented themselves to their general practitioner. Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C.", "Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C. For 13 out of 32 collections, the RTube™ was connected by a custom made connectingpiece to the ECoVent Jaeger, Germany . This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume.", "This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume. Additionally, a NS was obtained in parallel with the condensate collection from each patient. All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated.", "All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated. After viral DNA and RNA extraction, EBC samples and nasal swabs were stored at -80°C. Three specimens were excluded from the study due to incorrect condensate collection.", "Three specimens were excluded from the study due to incorrect condensate collection. A short questionnaire was used to document the date of birth, the severity of respiratory complaints and to record the days of symptomatic illness from all volunteers. This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants.", "This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants. Viral DNA and RNA were isolated with the QIAamp MinElute Virus kit Qiagen, Westburg, The Netherlands according to the instruction manual. EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer.", "EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer. The breath condensates were screened for 11 respiratory RNA viruses CoV NL63, E229 and OC43, RV, HMPV, InfA&B and PIV1-4 using a OneStep RT-PCR Kit Qiagen, Westburg, The Netherlands in a 50 μl reaction containing 10 μl of the extracted RNA, 0.6 μM of forward and reverse primers Table 2 , 1.5 μl One Step Enzyme Mix, 10 μl 5 × One Step RT-PCR Buffer and 400 μM of each dNTP. For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl.", "For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl. The PCR primers used were located in conserved regions of the genomes of the respiratory pathogens Table 2 . The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C.", "The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C. The DNA amplification program was initiated with a denaturation step at 94°C for 3 min, followed by 45 cycles of 94°C for 30 s, 55°C for 30 s and a final extension step at 72°C for 1 min. The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide.", "The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide. PCR products were purified using the Invitek MSB Spin PCRapace Kit and cycle sequenced in forward and reverse direction using the ABI PRISM Big-Dye Termination Cycle Sequencing Ready Reaction kit Applied Biosystems, Foster City, CA, USA . Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA .", "Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA . Consensus sequences were obtained using the SeqMan II software DNASTAR, Madison, Wis. . For samples from HRSV was detected using a RT-PCR assay as previously described .", "For samples from HRSV was detected using a RT-PCR assay as previously described . In brief, a multiplex mix was prepared in a final volume of 25 μl using 5 μl extracted RNA, 12.5 μl of Eurogentec One-Step Reverse Transcriptase qPCR Master Mix containing ROX as a passive reference, 0.125 μl Euroscript + RT & RNase inhibitor Eurogentec, Seraing, Belgium 200 nM of HRSV-A and -B specific forward and reverse primers and 100 nM of HRSV-A and -B MGB probes. cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified.", "cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified. The viral load of RV positive samples were quantified by qRT-PCR as described in the manuscript published by Lu and coworkers . The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above.", "The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above. The primerset HRSV-AF F 669-695 ctgtgatagarttccaacaaaagaaca HRSV-AF F 718-745 agttacacctgcattaacactaaattcc HRSV-BN N 435-458 ggctccagaatataggcatgattc HRSV-BN N 480-508 tggttattacaagaagagcagctatacacagt MGB probes and probe, located in 5'UTR, were added to a final concentration of 1 μM and 0.1 μM, respectively. cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA .", "cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA . Quantification was performed with a spectrophotometer at 260 nm and converted to the molecule number . Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used.", "Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used. The RT-PCR assays were carried out on a ABI PRISM 7500 Sequence Detection System Applied Biosystems, Foster City, CA, USA . An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min.", "An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min. Finally, an amplification step of 45 cycli at 95°C for 15 sec and 1 min at 60°C was completed. 37.5% men, with a median age of 29 range 9 -46 years .", "37.5% men, with a median age of 29 range 9 -46 years . Age and gender was missing for 2 participants of the second group. In total, 52% of the participants were between 20-30 years old. Only 6% were younger than 20 years old and 3% were older than 70 years.", "Only 6% were younger than 20 years old and 3% were older than 70 years. In totality, 80 patients 78.4% were already feeling ill for 1 to 7 days at the day the sample was obtained. Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection.", "Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection. Data on the duration of symptoms was lacking for 6 patients. Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 .", "Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 . Forty-seven 46.1% volunteers complained about a constant runny or stuffy nose, 43 42.2% had frequent sneezing events and 38 37.3% participants had a serious sore throat Table 1 . In a first part of the study, we collected 70 EBCs.", "In a first part of the study, we collected 70 EBCs. Screening of the EBCs for 14 respiratory viruses Table 2 , showed 5 RV 7.1% positive samples Table 3 . In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner.", "In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner. Two of these EBCs were positive for one of the 14 investigated respiratory viruses, 1 for RV and 1 for InfB. To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison.", "To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison. In 15 out of 32 NS 46.8% , one or more viral pathogens were isolated. Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B.", "Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B. Quantification of the HRSV-B viral load demonstrated for samples 72 and 101 viral titers of 8.0 × 10 4 RNA copies/ml and 6.8 × 10 7 RNA copies/ml respectively. The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 .", "The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 . Presence of the same pathogen in both the EBC and the NS was confirmed for only 1 sample: sample 71, which tested positive for RV in both the EBC and the NS. For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection.", "For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection. For EBC samples that were collected in the fall and winter of 2009/2010, measurements with the ECoVent in Table 3 , sample 81 was positive for InfB when using the RTube™ in combination with the EcoVent. In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load.", "In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load. Then, an estimation of the RNA copies per litre exhaled air or per minute can be calculated. Quantification of the exhaled InfB would allow us to predict the generation rate for this virus.", "Quantification of the exhaled InfB would allow us to predict the generation rate for this virus. Due to insufficient sample volume, we could not determine the number of RNA copies in the sample. Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract.", "Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. The collection of EBC is easy to perform and can be conducted in a home environment. This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc.", "This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc. This aspect renders the method very attractive for routine laboratory diagnostics of viral infections. Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact .", "Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact . With the RTube™ collection device, aerosolized particles of the airway lining fluid are precipitated into a condensate when the breath is cooled which serves as an immediate starting point for molecular testing. Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses.", "Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses. Previous studies reported the inclusion of a limited subset of participants and investigated the presence of a limited number of viruses in the breath samples. The study performed by Fabian and colleagues, included 12 volunteers .", "The study performed by Fabian and colleagues, included 12 volunteers . Huynh and co-workers recruited 9 volunteers for exhaled breath sampling . In the study by Stelzer-Braid et al., 50 EBCs were analysed and St-George et al. report the participation of 12 adults .", "report the participation of 12 adults . These studies have focused on the detection of InfA and -B, PIV1-3, HRSV and HMPV, while we have screened the samples for a panel of 14 commonly circulating respiratory viruses. Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples.", "Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples. Since many of the volunteers had already been experiencing symptoms for 1 to 7 days, we initially presumed that they were already recovering from the infection and were no longer exhaling the virus. For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms.", "For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms. However, in a second part of our study we started collecting EBCs in parallel with nasal swabs from patients presenting themselves to their medical doctor, 1 to 3 days after onset of symptoms. Only for 1 condensate the same pathogen was detected in both the EBC and the NS.", "Only for 1 condensate the same pathogen was detected in both the EBC and the NS. The detection rate for respiratory viral pathogens in the NS was 46.8% which is much higher than the 7% detection rate in the EBCs. The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious.", "The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious. The discrepant detection rate between samples may also be explained by different severity of respiratory infection, since comparator samples were of different parts of the respiratory tract. Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection.", "Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection. However, the effect of nasal inhalation on EBC collection, guiding formed particles in the upper respiratory tract to the lower compartments, in stead of oral inhalation was not investigated. Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection.", "Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection. However, this was not different for 7 patients with positive NS. Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 .", "Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 . In the group of volunteers that provided an EBC negative or EBC and NS negative sample, the manifestation of symptoms were reported ranging from 1 day to more than two weeks. When reported symptoms were compared between EBC positive patients .", "When reported symptoms were compared between EBC positive patients . and NS positive patients . , 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group.", ", 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group. In all groups fever, headache, watering eyes, stuffed nose, frequent sneezing, sore throat and coughing were reported. Volunteers were not diagnosed with other pathogens before participation in the study.", "Volunteers were not diagnosed with other pathogens before participation in the study. Since we did not test these samples for other than viral pathogens, we can not exclude the possibility that some of the negative NS are positive for bacteria or other pathogens causing respiratory illness. Recently, one study reported a detection rate of 5% for influenza in EBC .", "Recently, one study reported a detection rate of 5% for influenza in EBC . This is in the same range of the detection rate that we report for respiratory viruses in general. Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included .", "Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included . Remarkably, the studies reporting this higher detection rate used collections masks, while the study using the RTube™ reported comparable findings. Face masks consist of electret which trap viruses based on permanently charged fibres .", "Face masks consist of electret which trap viruses based on permanently charged fibres . In addition, the Teflon filter has 2 μm pores which will retain all larger particles. Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials.", "Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials. The qRT-PCR developed by Lu and coworkers for the detection of RV, did not allow the assessment of the viral load present in the EBC samples . Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay.", "Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay. For diagnosis, more sensitive methods might be necessary to detect respiratory viruses present in EBC since it is unpredictable how diluted the viral particles in the specimen are. Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols .", "Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols . Also person-dependent factors, such as the number of particles produced, the exhaled volume and the age of the patient, have been suggested to play an important role for exhalation of viral particles. The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older .", "The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older . For hospitalized children a much higher rate of virus positive samples is reported . In our study, the majority of volunteers were between 20 and 30 years old.", "In our study, the majority of volunteers were between 20 and 30 years old. Only two children less than 10 years and 3 elderly people > 70 years were included. One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC.", "One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC. For influenza, an exhaled generation rate of <3.2 to 20 influenza RNA copies per minute was predicted by quantifying the virus aerosols that impacted on a removable Teflon filter of a collection mask . We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume.", "We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume. In this way, when the number of RNA copies in the EBC is quantified, the amount of viral particles that are exhaled per litre or per minute can be estimated. Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined.", "Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined. Although an inventive, new and promising method, EBC collected by the RTube™ does not appear to be appropriate for diagnosis of respiratory infections. Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses.", "Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses. This technique also confirms the observation that viruses are able to disseminate through normal breathing, particularly RV. In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns.", "In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns. In calves that were experimentally infected with bovine RSV, an increase in leukotriene B 4 , indicating oxidative stress, was observed. This increased level was also associated with the development of bronchial hyperresponsiveness .", "This increased level was also associated with the development of bronchial hyperresponsiveness . In humans, a transiently elevated H 2 O 2 level was observed during common cold infection. This marker returned to baseline values when volunteers recovered from infection.", "This marker returned to baseline values when volunteers recovered from infection. H 2 O 2 has also been recognized as an interesting marker in asthma, where it is associated with chronic lower airway inflammation . In InfA infected volunteers, an increased CO level was observed during upper respiratory infection.", "In InfA infected volunteers, an increased CO level was observed during upper respiratory infection. This observation might imply that CO is an indicator of airway inflammation or represents one of the host defence mechanisms against viral infection . Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection.", "Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection. This may contribute to the biomarker profiles established for diseases like asthma and COPD, for which viral infections are suggested to trigger or exacerbate symptoms ." ]

[ "BACKGROUND: Exhaled breath condensate EBC sampling has been considered an inventive and novel method for the isolation of respiratory viruses. METHODS: In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses.", "Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection.", "The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive.", "RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.", "CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections. Text: Human respiratory tract infections represent the most commonly encountered infections worldwide. In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection.", "In the majority of cases, the etiology of these infections remains undetermined due to rapid convalescence after infection. Respiratory tract infections in healthy adults can be caused by a variety of pathogens and the detection of these agents is currently based on their isolation from nasal swabs NS , bronchoalveolar lavages BAL , nasopharyngeal aspirates and sputum samples. The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient.", "The acquisition of these specimens by semi-invasive and invasive techniques is often unpleasant for the patient. Therefore, exhaled breath condensate EBC analysis has recently been explored as a new and non-invasive method to monitor lung inflammation and pulmonary disease such as chronic obstructive pulmonary disease COPD , asthma, cystic fibrosis, lung cancer etc. EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid .", "EBCs mainly consist of water vapour but a small fraction contains respiratory droplets derived from the airway lining fluid . This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid.", "At first, investigators suspected that turbulence of the inhaled air was responsible for the aerosolisation of the respiratory fluid. However, the effect of the turbulent airflow is limited to the upper airways since the turbulent airflow becomes laminar as it reaches the smaller bronchial airways and alveoli. Recently, the bronchiole fluid film burst model has been described .", "Recently, the bronchiole fluid film burst model has been described . This model suggests that aerosols are produced during inhalation by the bursting of fluid bubbles present in the bronchioles. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate.", "The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. Therefore we screened the EBC samples with virus specific PCR assays targeting 14 In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms defined in Table 1 , using a commercially available condenser RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA . The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes.", "The patient was instructed to breath orally at tidal volumes into a mouthpiece attached to a condenser for 10 minutes. No nose clips were used during collection and saliva contamination was avoided by the presence of a one-way valve and the T-shaped section of the mouthpiece. In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory.", "In a first part of the study that started during the winter and spring of 2008/2009, 70 EBC samples were collected from patients who voluntary presented themselves to our laboratory. The majority of these volunteers were students that responded to the information leaflet, distributed in the university buildings of the Catholic University of Leuven. The samples were collected with the aluminium cooler sleeve chilled at -80°C.", "The samples were collected with the aluminium cooler sleeve chilled at -80°C. In the fall and first half of the winter of 2009/2010, 32 condensates were collected from patients who presented themselves to their general practitioner. Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C.", "Due to practical circumstances, the condensates were collected with the cooler chilled at -20°C. For 13 out of 32 collections, the RTube™ was connected by a custom made connectingpiece to the ECoVent Jaeger, Germany . This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume.", "This device registers ventilatory parameters such as the exhaled volume, breathing frequency and tidal volume. Additionally, a NS was obtained in parallel with the condensate collection from each patient. All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated.", "All EBCs were immediately stored at -20°C. Nasal swabs NS were refrigerated. After viral DNA and RNA extraction, EBC samples and nasal swabs were stored at -80°C. Three specimens were excluded from the study due to incorrect condensate collection.", "Three specimens were excluded from the study due to incorrect condensate collection. A short questionnaire was used to document the date of birth, the severity of respiratory complaints and to record the days of symptomatic illness from all volunteers. This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants.", "This study was approved by the Medical Ethics Committee of the University Hospital of Leuven and informed consents were received from all participants. Viral DNA and RNA were isolated with the QIAamp MinElute Virus kit Qiagen, Westburg, The Netherlands according to the instruction manual. EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer.", "EBC extracts were eluted in 60 μl elution buffer and NS extracts in 110 μl elution buffer. The breath condensates were screened for 11 respiratory RNA viruses CoV NL63, E229 and OC43, RV, HMPV, InfA&B and PIV1-4 using a OneStep RT-PCR Kit Qiagen, Westburg, The Netherlands in a 50 μl reaction containing 10 μl of the extracted RNA, 0.6 μM of forward and reverse primers Table 2 , 1.5 μl One Step Enzyme Mix, 10 μl 5 × One Step RT-PCR Buffer and 400 μM of each dNTP. For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl.", "For adenovirus screening, a DNA PCR was carried out for which the amplification reaction mix contained 0.5 μM forward primer AdFW and reverse primer AdRV , 0.4 mM dNTPs, 10 μl Buffer C and 1 U Taq polymerase in a final volume of 50 μl. The PCR primers used were located in conserved regions of the genomes of the respiratory pathogens Table 2 . The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C.", "The reactions were carried out in a T3000 Thermocycler 48 Westburg, Leusden, The Netherlands with an initial reverse transcription step for RNA viruses at 50°C for 30 min, followed by PCR activation at 95°C for 30 s, 45 cycles of amplification followed by a final extension step for 10 min at 72°C. The DNA amplification program was initiated with a denaturation step at 94°C for 3 min, followed by 45 cycles of 94°C for 30 s, 55°C for 30 s and a final extension step at 72°C for 1 min. The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide.", "The amplicons were subjected to a 6% polyacrylamide gel and visualised under UV light by staining with ethidium bromide. PCR products were purified using the Invitek MSB Spin PCRapace Kit and cycle sequenced in forward and reverse direction using the ABI PRISM Big-Dye Termination Cycle Sequencing Ready Reaction kit Applied Biosystems, Foster City, CA, USA . Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA .", "Sequence analysis was performed with the ABI3130 Genetic Analyser Applied Biosystems, Foster City, CA, USA . Consensus sequences were obtained using the SeqMan II software DNASTAR, Madison, Wis. . For samples from HRSV was detected using a RT-PCR assay as previously described .", "For samples from HRSV was detected using a RT-PCR assay as previously described . In brief, a multiplex mix was prepared in a final volume of 25 μl using 5 μl extracted RNA, 12.5 μl of Eurogentec One-Step Reverse Transcriptase qPCR Master Mix containing ROX as a passive reference, 0.125 μl Euroscript + RT & RNase inhibitor Eurogentec, Seraing, Belgium 200 nM of HRSV-A and -B specific forward and reverse primers and 100 nM of HRSV-A and -B MGB probes. cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified.", "cRNA standards were constructed using the MEGAshortscript T7 kit Ambion, Austin, TX, USA and spectrophotometrically quantified. The viral load of RV positive samples were quantified by qRT-PCR as described in the manuscript published by Lu and coworkers . The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above.", "The Eurogentec One-Step Reverse Transcriptase qPCR kit was used for preparation of the master mix as described above. The primerset HRSV-AF F 669-695 ctgtgatagarttccaacaaaagaaca HRSV-AF F 718-745 agttacacctgcattaacactaaattcc HRSV-BN N 435-458 ggctccagaatataggcatgattc HRSV-BN N 480-508 tggttattacaagaagagcagctatacacagt MGB probes and probe, located in 5'UTR, were added to a final concentration of 1 μM and 0.1 μM, respectively. cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA .", "cRNA standards were constructed based on the PCR product of sample 1 using the MegaScript kit Ambion, Austin, TX, USA . Quantification was performed with a spectrophotometer at 260 nm and converted to the molecule number . Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used.", "Tenfold serial dilutions, allowing detection in a range of 8.6 × 10 6 to 8.6 × 10 2 RNA copies were used. The RT-PCR assays were carried out on a ABI PRISM 7500 Sequence Detection System Applied Biosystems, Foster City, CA, USA . An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min.", "An initial reverse transcription step was performed at 48°C for 30 min, followed by a denaturation step at 95°C for 10 min. Finally, an amplification step of 45 cycli at 95°C for 15 sec and 1 min at 60°C was completed. 37.5% men, with a median age of 29 range 9 -46 years .", "37.5% men, with a median age of 29 range 9 -46 years . Age and gender was missing for 2 participants of the second group. In total, 52% of the participants were between 20-30 years old. Only 6% were younger than 20 years old and 3% were older than 70 years.", "Only 6% were younger than 20 years old and 3% were older than 70 years. In totality, 80 patients 78.4% were already feeling ill for 1 to 7 days at the day the sample was obtained. Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection.", "Seven volunteers 6.8% were symptomatic for 8 to 14 days and 9 participants 8.8% were already ill for more than 14 days at the day of sample collection. Data on the duration of symptoms was lacking for 6 patients. Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 .", "Almost all volunteers experienced at least 2 symptoms except for two patients Table 1 . Forty-seven 46.1% volunteers complained about a constant runny or stuffy nose, 43 42.2% had frequent sneezing events and 38 37.3% participants had a serious sore throat Table 1 . In a first part of the study, we collected 70 EBCs.", "In a first part of the study, we collected 70 EBCs. Screening of the EBCs for 14 respiratory viruses Table 2 , showed 5 RV 7.1% positive samples Table 3 . In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner.", "In a second part, we collected 32 EBCs from patients that presented themselves to their general practitioner. Two of these EBCs were positive for one of the 14 investigated respiratory viruses, 1 for RV and 1 for InfB. To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison.", "To inspect the detection rate of respiratory viruses in the condensate, a NS was taken from this second group of volunteers for comparison. In 15 out of 32 NS 46.8% , one or more viral pathogens were isolated. Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B.", "Viral screening of the NS resulted in the detection of RV, InfA subtype H1N1 and HRSV-B. Quantification of the HRSV-B viral load demonstrated for samples 72 and 101 viral titers of 8.0 × 10 4 RNA copies/ml and 6.8 × 10 7 RNA copies/ml respectively. The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 .", "The RV RT-PCR assay did not allow the quantification of all samples that tested positive for RV by PCR Table 3 . Presence of the same pathogen in both the EBC and the NS was confirmed for only 1 sample: sample 71, which tested positive for RV in both the EBC and the NS. For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection.", "For sample 81, RV was detected in the NS and analysis of the EBC demonstrated an InfB infection. For EBC samples that were collected in the fall and winter of 2009/2010, measurements with the ECoVent in Table 3 , sample 81 was positive for InfB when using the RTube™ in combination with the EcoVent. In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load.", "In theory, the viral generation rate number of viral RNA copies exhaled per minute can be predicted by quantification of the exhaled viral load. Then, an estimation of the RNA copies per litre exhaled air or per minute can be calculated. Quantification of the exhaled InfB would allow us to predict the generation rate for this virus.", "Quantification of the exhaled InfB would allow us to predict the generation rate for this virus. Due to insufficient sample volume, we could not determine the number of RNA copies in the sample. Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract.", "Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. The collection of EBC is easy to perform and can be conducted in a home environment. This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc.", "This method is much more agreeable for the patient when compared to the unpleasant and invasive collection of nasal swabs, BAL, aspirates, etc. This aspect renders the method very attractive for routine laboratory diagnostics of viral infections. Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact .", "Most studies that perform breath analyses for viral detection use modified face masks, with a removable central region in electret or a removable Teflon filter on which exhaled particles impact . With the RTube™ collection device, aerosolized particles of the airway lining fluid are precipitated into a condensate when the breath is cooled which serves as an immediate starting point for molecular testing. Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses.", "Until now, this is the study with the largest subset of volunteers that investigated EBC as a specimen for the detection of respiratory viruses. Previous studies reported the inclusion of a limited subset of participants and investigated the presence of a limited number of viruses in the breath samples. The study performed by Fabian and colleagues, included 12 volunteers .", "The study performed by Fabian and colleagues, included 12 volunteers . Huynh and co-workers recruited 9 volunteers for exhaled breath sampling . In the study by Stelzer-Braid et al., 50 EBCs were analysed and St-George et al. report the participation of 12 adults .", "report the participation of 12 adults . These studies have focused on the detection of InfA and -B, PIV1-3, HRSV and HMPV, while we have screened the samples for a panel of 14 commonly circulating respiratory viruses. Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples.", "Based on the analysis of 99 EBCs 3 EBCs were excluded , our results support the exhalation of RV and InfB in 7% of our samples. Since many of the volunteers had already been experiencing symptoms for 1 to 7 days, we initially presumed that they were already recovering from the infection and were no longer exhaling the virus. For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms.", "For common cold infections it is suggested that a person may already be infectious for 1 or 2 days before experiencing any symptoms. However, in a second part of our study we started collecting EBCs in parallel with nasal swabs from patients presenting themselves to their medical doctor, 1 to 3 days after onset of symptoms. Only for 1 condensate the same pathogen was detected in both the EBC and the NS.", "Only for 1 condensate the same pathogen was detected in both the EBC and the NS. The detection rate for respiratory viral pathogens in the NS was 46.8% which is much higher than the 7% detection rate in the EBCs. The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious.", "The low detection of virus positive condensates can therefore not be attributed to the fact that volunteers were no longer infectious. The discrepant detection rate between samples may also be explained by different severity of respiratory infection, since comparator samples were of different parts of the respiratory tract. Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection.", "Patients that delivered a positive NS may have possibly suffered from an upper airway infection whereas EBC positive volunteers may have experienced a more advanced, lower respiratory tract infection. However, the effect of nasal inhalation on EBC collection, guiding formed particles in the upper respiratory tract to the lower compartments, in stead of oral inhalation was not investigated. Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection.", "Patients with positive EBC samples were experiencing symptoms for maximum two days at the time of collection. However, this was not different for 7 patients with positive NS. Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 .", "Six patients that provided positive NS were experiencing symptoms for a longer period at the time of collection Table 3 . In the group of volunteers that provided an EBC negative or EBC and NS negative sample, the manifestation of symptoms were reported ranging from 1 day to more than two weeks. When reported symptoms were compared between EBC positive patients .", "When reported symptoms were compared between EBC positive patients . and NS positive patients . , 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group.", ", 27% and 33% in the positive NS group experienced shivering and muscle pain whereas this symptom was not indicated by any patient of the EBC positive group. In all groups fever, headache, watering eyes, stuffed nose, frequent sneezing, sore throat and coughing were reported. Volunteers were not diagnosed with other pathogens before participation in the study.", "Volunteers were not diagnosed with other pathogens before participation in the study. Since we did not test these samples for other than viral pathogens, we can not exclude the possibility that some of the negative NS are positive for bacteria or other pathogens causing respiratory illness. Recently, one study reported a detection rate of 5% for influenza in EBC .", "Recently, one study reported a detection rate of 5% for influenza in EBC . This is in the same range of the detection rate that we report for respiratory viruses in general. Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included .", "Other studies with a limited number of patients, describe a markedly higher sensitivity of 33 to 36% but the higher percentage may be due to the low number of participants subjects were included . Remarkably, the studies reporting this higher detection rate used collections masks, while the study using the RTube™ reported comparable findings. Face masks consist of electret which trap viruses based on permanently charged fibres .", "Face masks consist of electret which trap viruses based on permanently charged fibres . In addition, the Teflon filter has 2 μm pores which will retain all larger particles. Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials.", "Possibly, the lower detection rate can partly be explained by the fact that the RTube™ is manufactured in polypropylene and does not possess a virus attracting and filtering feature like the aforementioned materials. The qRT-PCR developed by Lu and coworkers for the detection of RV, did not allow the assessment of the viral load present in the EBC samples . Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay.", "Also for 4 NS, the viral titer remained undetermined, probably due to the limited sensitivity of the assay. For diagnosis, more sensitive methods might be necessary to detect respiratory viruses present in EBC since it is unpredictable how diluted the viral particles in the specimen are. Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols .", "Recently, nested qRT-PCR assays have been developed to allow a more sensitive detection of viruses in aerosols . Also person-dependent factors, such as the number of particles produced, the exhaled volume and the age of the patient, have been suggested to play an important role for exhalation of viral particles. The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older .", "The participants that were recruited in the study of Fabian and coworkers were 12 years of age and older . For hospitalized children a much higher rate of virus positive samples is reported . In our study, the majority of volunteers were between 20 and 30 years old.", "In our study, the majority of volunteers were between 20 and 30 years old. Only two children less than 10 years and 3 elderly people > 70 years were included. One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC.", "One of the children tested positive for InfA in the NS, but the infection was not confirmed in the EBC. For influenza, an exhaled generation rate of <3.2 to 20 influenza RNA copies per minute was predicted by quantifying the virus aerosols that impacted on a removable Teflon filter of a collection mask . We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume.", "We used the RTube™ in combination with the ECoVent, that allowed the registration of additional ventilation parameters such as breathing frequency and exhaled volume. In this way, when the number of RNA copies in the EBC is quantified, the amount of viral particles that are exhaled per litre or per minute can be estimated. Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined.", "Unfortunately, we were not able to predict a virus generation rate for InfB since viral load remained undetermined. Although an inventive, new and promising method, EBC collected by the RTube™ does not appear to be appropriate for diagnosis of respiratory infections. Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses.", "Nonetheless, this method may provide an alternative for current sample procurement for epidemiological studies of circulating viruses. This technique also confirms the observation that viruses are able to disseminate through normal breathing, particularly RV. In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns.", "In addition, EBC collection from patients during respiratory infections may be further investigated for biomarker patterns. In calves that were experimentally infected with bovine RSV, an increase in leukotriene B 4 , indicating oxidative stress, was observed. This increased level was also associated with the development of bronchial hyperresponsiveness .", "This increased level was also associated with the development of bronchial hyperresponsiveness . In humans, a transiently elevated H 2 O 2 level was observed during common cold infection. This marker returned to baseline values when volunteers recovered from infection.", "This marker returned to baseline values when volunteers recovered from infection. H 2 O 2 has also been recognized as an interesting marker in asthma, where it is associated with chronic lower airway inflammation . In InfA infected volunteers, an increased CO level was observed during upper respiratory infection.", "In InfA infected volunteers, an increased CO level was observed during upper respiratory infection. This observation might imply that CO is an indicator of airway inflammation or represents one of the host defence mechanisms against viral infection . Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection.", "Therefore, a better identification of the biomarker signature in condensates of individuals experiencing a viral infection might imply interesting findings towards the identification of markers reflecting inflammation or antiviral protection. This may contribute to the biomarker profiles established for diseases like asthma and COPD, for which viral infections are suggested to trigger or exacerbate symptoms ." ]

[ "OBJECTIVE: To determine whether rapid polymerase chain reaction PCR testing for influenza and respiratory syncytial viruses RSV in emergency departments EDs is associated with better patient and laboratory outcomes than standard multiplex PCR testing. DESIGN, SETTING: A before‐and‐after study in four metropolitan EDs in New South Wales. PARTICIPANTS: 1491 consecutive patients tested by standard multiplex PCR during July–December 2016, and 2250 tested by rapid PCR during July–December 2017.", "PARTICIPANTS: 1491 consecutive patients tested by standard multiplex PCR during July–December 2016, and 2250 tested by rapid PCR during July–December 2017. MAIN OUTCOME MEASURES: Hospital admissions; ED length of stay LOS ; test turnaround time; patient receiving test result before leaving the ED; ordering of other laboratory tests. RESULTS: Compared with those tested by standard PCR, fewer patients tested by rapid PCR were admitted to hospital 73.3% v 77.7%; P < 0.001 and more received their test results before leaving the ED 67.4% v 1.3%; P < 0.001 ; the median test turnaround time was also shorter 2.4 h IQR, 1.6–3.9 h v 26.7 h IQR, 21.2–37.8 h .", "RESULTS: Compared with those tested by standard PCR, fewer patients tested by rapid PCR were admitted to hospital 73.3% v 77.7%; P < 0.001 and more received their test results before leaving the ED 67.4% v 1.3%; P < 0.001 ; the median test turnaround time was also shorter 2.4 h IQR, 1.6–3.9 h v 26.7 h IQR, 21.2–37.8 h . The proportion of patients admitted to hospital was also lower in the rapid PCR group for both children under 18 50.6% v 66.6%; P < 0.001 and patients over 60 years of age 84.3% v 91.8%; P < 0.001 . Significantly fewer blood culture, blood gas, sputum culture, and respiratory bacterial and viral serology tests were ordered for patients tested by rapid PCR.", "Significantly fewer blood culture, blood gas, sputum culture, and respiratory bacterial and viral serology tests were ordered for patients tested by rapid PCR. ED LOS was similar for the rapid 7.4 h; IQR, 5.0–12.9 h and standard PCR groups 6.5 h; IQR, 4.2–11.9 h; P = 0.27 . CONCLUSION: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system.", "CONCLUSION: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system. A formal cost–benefit analysis should be undertaken. Text: The health and economic burdens associated with acute respiratory infections by influenza and respiratory syncytial viruses RSV are significant in Australia and overseas.", "Text: The health and economic burdens associated with acute respiratory infections by influenza and respiratory syncytial viruses RSV are significant in Australia and overseas. 1-3 Polymerase chain reaction PCR testing is effective for confirming respiratory viral infections. 4 Multiplex PCR can detect numerous respiratory viruses, including influenza and parainfluenza viruses, RSV, adenovirus, rhinovirus, human metapneumovirus, enterovirus, bocavirus and coronavirus with very high sensitivity and specificity.", "4 Multiplex PCR can detect numerous respiratory viruses, including influenza and parainfluenza viruses, RSV, adenovirus, rhinovirus, human metapneumovirus, enterovirus, bocavirus and coronavirus with very high sensitivity and specificity. 5 Although the results of standard multiplex PCR are accurate and comprehensive, it has traditionally been performed in a central laboratory with a lengthy turnaround time, which may be inconvenient in settings where test results are urgently required, including emergency departments EDs . Rapid, easy-to-use PCR-based respiratory virus diagnostic tests have been introduced in recent years; 6,7 the GeneXpert system Cepheid , for instance, was introduced in New South Wales in July 2017.", "Rapid, easy-to-use PCR-based respiratory virus diagnostic tests have been introduced in recent years; 6,7 the GeneXpert system Cepheid , for instance, was introduced in New South Wales in July 2017. Rapid PCR tests were expected to facilitate timely and appropriate initiation of treatment, improve outbreak prevention and infection control measures, and expedite the assessment of patients in EDs. In this study, we analysed routinely collected data to determine whether rapid PCR testing for influenza and RSV infections in EDs is associated with improved patient and laboratory outcomes.", "In this study, we analysed routinely collected data to determine whether rapid PCR testing for influenza and RSV infections in EDs is associated with improved patient and laboratory outcomes. We compared data for patients tested for influenza A/B viruses and RSV immediately after rapid PCR diagnosis was introduced July-December 2017 with data for patients tested with a standard multiplex PCR system during July-December 2016. We undertook a before-and-after study in four metropolitan public hospital EDs in Sydney, NSW: three general hospitals EDs A, B and C; 76 228, 54 443 and 50 025 annual ED presentations respectively and one children's hospital ED D; 36 700 annual ED presentations; all data for January-December 2016 8 .", "We undertook a before-and-after study in four metropolitan public hospital EDs in Sydney, NSW: three general hospitals EDs A, B and C; 76 228, 54 443 and 50 025 annual ED presentations respectively and one children's hospital ED D; 36 700 annual ED presentations; all data for January-December 2016 8 . The four hospitals were served by a single pathology laboratory provider. We analysed data for all patients tested for influenza virus or RSV.", "We analysed data for all patients tested for influenza virus or RSV. During July-December 2016, patients were tested with the standard PCR system, a central laboratory-based multiplex PCR test for sixteen respiratory viruses including RSV and influenza viruses A and B , available as a referral test at the central laboratory in Hospital B. During July-December 2017, patients were tested with the rapid PCR system, a hospital laboratory-based test specific for RSV and influenza viruses A and B.", "During July-December 2017, patients were tested with the rapid PCR system, a hospital laboratory-based test specific for RSV and influenza viruses A and B. Hospitals A, B and D have onsite laboratories that perform rapid PCR testing; Hospital C sends samples to the nearby Hospital A. All tests were conducted in virology laboratories by trained staff, and test results were entered into laboratory information system datasets.", "All tests were conducted in virology laboratories by trained staff, and test results were entered into laboratory information system datasets. We obtained relevant patient characteristics and The proportion of patients admitted to hospital was also lower in the rapid PCR group for both children under 18 50.6% v 66.6%; P < 0.001 and patients over 60 years of age 84.3% v 91.8%; P < 0.001 . Significantly fewer blood culture, blood gas, sputum culture, and respiratory bacterial and viral serology tests were ordered for patients tested by rapid PCR.", "Significantly fewer blood culture, blood gas, sputum culture, and respiratory bacterial and viral serology tests were ordered for patients tested by rapid PCR. ED LOS was similar for the rapid 7.4 h; IQR, 5.0-12.9 h and standard PCR groups 6.5 h; IQR, 4.2-11.9 h; P = 0.27 . Conclusion: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system.", "Conclusion: Rapid PCR testing of ED patients for influenza virus and RSV was associated with better outcomes on a range of indicators, suggesting benefits for patients and the health care system. A formal cost-benefit analysis should be undertaken. The known: Rapid polymerase chain reaction PCR testing for influenza and respiratory syncytial viruses RSV was introduced in New South Wales in July 2017.", "The known: Rapid polymerase chain reaction PCR testing for influenza and respiratory syncytial viruses RSV was introduced in New South Wales in July 2017. Its impact on outcomes for emergency department ED patients has not been investigated. The new: Compared with standard PCR testing, rapid PCR was associated with significantly fewer hospital admissions, more rapid test turnaround, more patients receiving test results before leaving the ED, and reduced numbers of some other common microbiology tests.", "The new: Compared with standard PCR testing, rapid PCR was associated with significantly fewer hospital admissions, more rapid test turnaround, more patients receiving test results before leaving the ED, and reduced numbers of some other common microbiology tests. It did not significantly affect ED length of stay. The implications: Rapid PCR testing of ED patients for major respiratory viruses can benefit patients and reduce resource use.", "The implications: Rapid PCR testing of ED patients for major respiratory viruses can benefit patients and reduce resource use. MJA 210 . ▪ 15 April 2019 317 laboratory data by linking the ED and laboratory information system datasets. Detailed information about the datasets and the linkage process have been described previously.", "Detailed information about the datasets and the linkage process have been described previously. 9 The primary outcomes were admission to hospital, ED length of stay LOS , test turnaround time, and the patient receiving their test result before leaving the ED. ED LOS was defined as the time from arrival in the ED to discharge or admission to hospital.", "ED LOS was defined as the time from arrival in the ED to discharge or admission to hospital. Turnaround was defined as the time from when the sample was received by the laboratory to when the test result was available in hospital electronic records. As secondary outcomes, we compared ordering of typical biochemistry and haematology tests full blood count; electrolyte, urea, creatinine levels; liver function test; blood gas analysis; C-reactive protein level and microbiology tests blood culture; urine microscopy, culture and sensitivity analysis; sputum culture; respiratory bacteria and virus serology during the two study periods.", "As secondary outcomes, we compared ordering of typical biochemistry and haematology tests full blood count; electrolyte, urea, creatinine levels; liver function test; blood gas analysis; C-reactive protein level and microbiology tests blood culture; urine microscopy, culture and sensitivity analysis; sputum culture; respiratory bacteria and virus serology during the two study periods. Analyses were conducted in Stata 15 StataCorp . Descriptive statistics are reported medians with interquartile ranges IQRs , means with standard deviations SDs , numbers with proportions .", "Descriptive statistics are reported medians with interquartile ranges IQRs , means with standard deviations SDs , numbers with proportions . Baseline characteristics were compared in χ 2 tests categorical outcomes or Wilcoxon rank-sum tests continuous outcomes . Logistic regression analyses of binary outcomes eg, hospital admission: yes/no and quantile regression analyses of continuous outcomes eg, ED LOS were undertaken.", "Logistic regression analyses of binary outcomes eg, hospital admission: yes/no and quantile regression analyses of continuous outcomes eg, ED LOS were undertaken. All analyses were adjusted for baseline characteristics. Sensitivity analyses limited to data for children under 18 years of age or older patients over 60 years of age were conducted.", "Sensitivity analyses limited to data for children under 18 years of age or older patients over 60 years of age were conducted. P < 0.05 2-tailed was deemed statistically significant. Ethics approval for the investigation was granted by the Human Research Ethics Committee of the South Eastern Sydney Local Health District reference, HREC/16/POWH/412 .", "Ethics approval for the investigation was granted by the Human Research Ethics Committee of the South Eastern Sydney Local Health District reference, HREC/16/POWH/412 . We analysed data for 3741 patients presenting to the four EDs during two periods: 1491 consecutive patients during July-December 2016 standard PCR and 2250 during July-December 2017 rapid PCR . Baseline characteristics for the two groups were similar in terms of sex, triage category, and arrival day of the week, but differed significantly for age, arrival time, and mode of arrival Box 1 The overall numbers of tests per patient were similar in the standard PCR mean, 7.2 tests; SD, 3.8 and rapid PCR groups mean, 7.1 tests; SD, 3.4 .", "Baseline characteristics for the two groups were similar in terms of sex, triage category, and arrival day of the week, but differed significantly for age, arrival time, and mode of arrival Box 1 The overall numbers of tests per patient were similar in the standard PCR mean, 7.2 tests; SD, 3.8 and rapid PCR groups mean, 7.1 tests; SD, 3.4 . The mean number of microbiology tests per patient was significantly lower for the rapid PCR group 1.5 tests; SD, 1.8 than for the standard PCR group 2.0 tests; SD, 2.1; P < 0.001 after controlling for baseline characteristics . The 16 265 biochemistry/haematology and microbiology tests comprised 71.1% of the 22 876 other tests that is, not including PCR virus testing ordered for patients in the study.", "The 16 265 biochemistry/haematology and microbiology tests comprised 71.1% of the 22 876 other tests that is, not including PCR virus testing ordered for patients in the study. After adjusting for baseline characteristics, the proportions of patients for whom full blood count, electrolyte/urea/creatinine levels, liver function, or C-reactive protein were assessed were similar, as were the proportions for urine microscopy, culture and sensitivity tests. Significantly fewer blood culture, blood gas, sputum culture, and respiratory bacterial and viral serology tests were ordered for patients in the rapid PCR group Box 4 .", "Significantly fewer blood culture, blood gas, sputum culture, and respiratory bacterial and viral serology tests were ordered for patients in the rapid PCR group Box 4 . Information, figure 1 . ED LOS was similar for the standard PCR and rapid PCR groups in both age-based subgroups Supporting Information, figure 2A .", "ED LOS was similar for the standard PCR and rapid PCR groups in both age-based subgroups Supporting Information, figure 2A . The differences in test turnaround time identified in the main analysis were also evident for each age-based subgroup Supporting Information, figure 2B . In this before-and-after study, we found that rapid PCR testing of ED patients for major respiratory viruses was associated with significantly fewer admissions to hospital, more rapid delivery of test results, more patients receiving their test results before leaving the ED, and less frequent ordering of some common microbiology tests.", "In this before-and-after study, we found that rapid PCR testing of ED patients for major respiratory viruses was associated with significantly fewer admissions to hospital, more rapid delivery of test results, more patients receiving their test results before leaving the ED, and less frequent ordering of some common microbiology tests. Other studies have also reported that hospital admission numbers were significantly lower when rapid influenza virus testing was used in EDs. An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients.", "An analysis of outcomes for more than 300 adults at a tertiary care centre in New York found that early diagnosis of respiratory infections was associated with significantly fewer hospitalisations of influenza-positive patients. 7 In a small Irish study 73 patients , the hospital admission rate for obstetric patients declined from 88% to 45% after on-site rapid influenza PCR testing was introduced. 10 The differences in clinical setting and patient group may explain the smaller decline in our study from 78% to 67% .", "10 The differences in clinical setting and patient group may explain the smaller decline in our study from 78% to 67% . Non-PCR-based rapid diagnostic tests for respiratory viruses have also been associated with lower hospital admission rates. 11, 12 The main reason for fewer hospital admissions of patients tested by rapid PCR may be that the earlier availability of results enables clinicians to quickly diagnose or exclude respiratory infections and to make timely and informed decisions about whether to discharge the patient or admit them to hospital.", "11, 12 The main reason for fewer hospital admissions of patients tested by rapid PCR may be that the earlier availability of results enables clinicians to quickly diagnose or exclude respiratory infections and to make timely and informed decisions about whether to discharge the patient or admit them to hospital. When standard 2 Primary outcomes for 3741 patients at four metropolitan emergency departments EDs tested for influenza and respiratory syncytial viruses by standard or rapid polymerase chain reaction PCR After adjusting for baseline characteristics Box 1 : * P = 0.012; ** P < 0.001. ◆ MJA 210 .", "◆ MJA 210 . ▪ 15 April 2019 PCR was used, in contrast, our findings suggest that these decisions were made before the test results were available. The possible benefits of not admitting patients to hospital, beyond those for individual patient management, include better infection control and outbreak prevention, as well as reduced demands on hospital resources.", "The possible benefits of not admitting patients to hospital, beyond those for individual patient management, include better infection control and outbreak prevention, as well as reduced demands on hospital resources. 13, 14 The impact of rapid PCR testing on outbreak prevention and infection control measures should be evaluated. Rapid influenza virus testing may also have practical implications for hospital bed management.", "Rapid influenza virus testing may also have practical implications for hospital bed management. 10, 15 ED LOS was similar in our study before and after the introduction of rapid PCR methods. This finding was not unexpected, as test turnaround time is not the only rate-limiting factor for decision making in EDs.", "This finding was not unexpected, as test turnaround time is not the only rate-limiting factor for decision making in EDs. 16 Before rapid PCR methods were introduced, the long turnaround time of multiplex PCR did not necessarily extend a patient's stay in the ED, as they were usually admitted to hospital or discharged home before the results were available. Consequently, more rapid delivery of test results alone would not reduce ED LOS.", "Consequently, more rapid delivery of test results alone would not reduce ED LOS. Reports on the effect of rapid influenza virus testing and LOS have been conflicting. While evidence for an association between rapid testing and shorter overall inpatient LOS has been reported, 6,11 findings regarding ED LOS are inconsistent.", "While evidence for an association between rapid testing and shorter overall inpatient LOS has been reported, 6,11 findings regarding ED LOS are inconsistent. 7, 17, 18 For example, a Cochrane review based on three randomised controlled trials did not find a statistically significant association of rapid viral diagnosis with lower mean ED LOS. 18 In a study in children, ED LOS was actually 26 minutes longer with rapid PCR; inpatient LOS did not differ between the two groups, but was significantly shorter when the analysis was limited to patients with positive test results.", "18 In a study in children, ED LOS was actually 26 minutes longer with rapid PCR; inpatient LOS did not differ between the two groups, but was significantly shorter when the analysis was limited to patients with positive test results. 6 We found that ordering of some other microbiology tests, including blood culture, sputum culture, and respiratory bacterial and virus serology, was significantly less frequent for patients tested by rapid PCR. The effect of PCR-based rapid testing on the ordering of other laboratory tests has not previously been reported, although some studies of antigen-based pointof-care testing have examined this outcome.", "The effect of PCR-based rapid testing on the ordering of other laboratory tests has not previously been reported, although some studies of antigen-based pointof-care testing have examined this outcome. 12 Consistent with our finding, several investigators have reported fewer blood culture tests 19, 20 and basic biochemistry and haematology tests, including full blood count, 20,21 C-reactive protein testing, 21 and urinalysis, 20,21 when point-of-care testing was used. The higher rate of positive results for patients tested by rapid PCR than for those tested by standard PCR may reflect a higher prevalence of influenza during 2017 than in 2016.", "The higher rate of positive results for patients tested by rapid PCR than for those tested by standard PCR may reflect a higher prevalence of influenza during 2017 than in 2016. The rapid PCR system in our study accurately detects influenza viruses A/B and RSV but, unlike the standard multiplex PCR, cannot detect other clinically relevant respiratory viruses, such as rhinovirus, coronavirus, human metapneumovirus, parainfluenza virus, adenovirus, enterovirus, and bocavirus. If infection with other respiratory viruses is suspected, patients may therefore need further investigations.", "If infection with other respiratory viruses is suspected, patients may therefore need further investigations. Standard multiplex PCR can provide broader information, as it can detect multiple respiratory viruses in a single run, although the long turnaround time restricts its suitability for urgent clinical decision making. Improving the turnaround time of multiplex PCR analysis may achieve better outcomes.", "Improving the turnaround time of multiplex PCR analysis may achieve better outcomes. The strengths of our study include its relatively large sample size; further, unlike many similar investigations, ours was a multicentre study in four hospital EDs, enhancing the generalisability of our findings. However, our analyses were not adjusted for comorbid conditions, as this information was not available.", "However, our analyses were not adjusted for comorbid conditions, as this information was not available. Because our study was an uncontrolled before-and-after study, our results cannot be interpreted as indicating causal relationships. As with all non-randomised trials, we could not fully account for all potential confounding variables, nor for temporal trends and other unmeasured factors, such as changes in clinician testing practices or differences in the prevalence and severity of disease during the two study periods.", "As with all non-randomised trials, we could not fully account for all potential confounding variables, nor for temporal trends and other unmeasured factors, such as changes in clinician testing practices or differences in the prevalence and severity of disease during the two study periods. 22 For example, a shortage of inpatient beds caused by a high prevalence of influenza could influence decisions in a busy ED about admitting patients to hospital. However, we attempted to reduce seasonal effects by selecting similar time frames for the two study periods, to reduce selection bias by including all ED patients tested for influenza virus and RSV, and to control for differences in baseline patient characteristics by applying multivariate modelling.", "However, we attempted to reduce seasonal effects by selecting similar time frames for the two study periods, to reduce selection bias by including all ED patients tested for influenza virus and RSV, and to control for differences in baseline patient characteristics by applying multivariate modelling. As medications data were not available to us, we were unable to assess the impact of rapid PCR testing on antibiotic and antiviral drug use. Similarly, the cost-benefit balance of rapid testing was not evaluated because relevant data were not available.", "Similarly, the cost-benefit balance of rapid testing was not evaluated because relevant data were not available. The cost per patient of rapid PCR testing is generally higher than for central laboratory testing, but our findings suggest potential savings through lower numbers of hospital admissions and reduced resource use. This question could be evaluated in a further study.", "This question could be evaluated in a further study. Rapid PCR testing for influenza virus and RSV infections in patients attending EDs was associated with significant improvements in a range of patient and laboratory outcomes, suggesting potential benefits for both the patients and the health care system. A cost-benefit analysis could examine the impact of rapid PCR testing on bed management and antimicrobial drug prescribing." ]

[ "BACKGROUND/AIM: The role of humoral immunity in hepatitis C virus HCV infection is poorly understood. Nevertheless, there is increasing interest in characterizing the neutralizing antibodies in the serum of HCV-infected patients. Focus reduction assays have been widely used to evaluate neutralizing antibody responses against a range of non-cytopathic viruses.", "Focus reduction assays have been widely used to evaluate neutralizing antibody responses against a range of non-cytopathic viruses. Based on the recent development of a HCV cell culture system using the genotype 2 JFH-1-strain, we developed a focus reduction assay for HCV-neutralizing antibodies. METHODS: The focus reduction assay was based on a standard microneutralization assay in which immunostained foci on tissue culture plates are counted.", "METHODS: The focus reduction assay was based on a standard microneutralization assay in which immunostained foci on tissue culture plates are counted. The neutralizing anti-HCV antibodies titers of purified serum immunoglobulin samples from seventy-seven individuals were determined using a 50% focus reduction neutralization assay. Each titer was determined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%.", "Each titer was determined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%. IgG antibodies were first purified from each serum in order to avoid the facilitating effect of HDL on HCV entry. RESULTS: The assay's cut-off using an ELISA and RNA HCV-negative samples was found to be 1.25 log, corresponding to a dilution of 1:18.", "RESULTS: The assay's cut-off using an ELISA and RNA HCV-negative samples was found to be 1.25 log, corresponding to a dilution of 1:18. The assay was compared with a commercial HCV ELISA and exhibited specificity and sensitivity values of 100% and 96.5%, respectively, and good reproducibility with intra-assay and inter-assay coefficients of variation of 6.7% and 12.6%, respectively . The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples.", "The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples. The neutralizing antibodies titers were 2.13 log 1:134 for homologous samples from HCV genotype 2 infected patients harboring the same genotype as JFH-1 and 1.93 log 1:85 for heterologous samples from patients infected by genotypes other than type 2. These results confirm the presence of broadly cross-neutralizing antibodies already reported using the HCV pseudoparticles system.", "These results confirm the presence of broadly cross-neutralizing antibodies already reported using the HCV pseudoparticles system. CONCLUSION: This study presents a simple, specific and reproducible cell culture-based assay for determination of HCV-neutralizing antibodies in human sera. The assay should be an important tool for gauging the relationship between the neutralizing antibodies response and viral load kinetics in acutely or chronically infected patients and for investigating the possible eradication or prevention of HCV infection by neutralizing antibodies.", "The assay should be an important tool for gauging the relationship between the neutralizing antibodies response and viral load kinetics in acutely or chronically infected patients and for investigating the possible eradication or prevention of HCV infection by neutralizing antibodies. Text: Hepatitis C virus HCV, a member of the Flaviviridae family is an enveloped, positive-stranded RNA virus that preferentially replicates in hepatocytes. At least 170 million people worldwide are persistently infected with hepatitis C virus.", "At least 170 million people worldwide are persistently infected with hepatitis C virus. Chronic HCV infection is associated with a significant risk of progression to cirrhosis and hepatocellular carcinoma . Antiviral therapy with pegylated alpha-interferon and ribavirin the current best therapeutic regimen is only successful in about 50% of all treated patients.", "Antiviral therapy with pegylated alpha-interferon and ribavirin the current best therapeutic regimen is only successful in about 50% of all treated patients. Better knowledge of the viral and host factors that determine HCV clearance or persistence during the acute stage of infection is needed in order to improve antiviral therapy and to develop efficient vaccines. Studies focusing on innate and cellular immune responses have shown that a sufficiently large HCV inoculum is able to evade, subvert or circumvent the host's defences.", "Studies focusing on innate and cellular immune responses have shown that a sufficiently large HCV inoculum is able to evade, subvert or circumvent the host's defences. At present, the chimpanzee is the only reliable experimental animal model in which the initial post-HCV infection events and the efficacy of vaccine candidates can be evaluated . It has been shown that HCV-specific T-cell immunity is important in the control of HCV infection .", "It has been shown that HCV-specific T-cell immunity is important in the control of HCV infection . Several studies have indicated a role for humoral immunity in the acute stage of HCV infection but this aspect remains poorly characterized. The E1 and E2 glycoproteins are thought to be the viral attachment proteins and thus the main targets for HCV-neutralizing antibodies; identification of protective epitopes conserved across different strains of HCV is therefore a major challenge in vaccine design.", "The E1 and E2 glycoproteins are thought to be the viral attachment proteins and thus the main targets for HCV-neutralizing antibodies; identification of protective epitopes conserved across different strains of HCV is therefore a major challenge in vaccine design. A number of antibodies capable of blocking E2 binding to cells or cell receptors have been described, some of which neutralize HCV entry in animal or cellular models . Cell entry has been shown to involve several surface molecules notably including the tetraspanin CD81 and the SR-BI receptor , although further studies are needed to better understand how viral entry occurs and how it might be neutralized.", "Cell entry has been shown to involve several surface molecules notably including the tetraspanin CD81 and the SR-BI receptor , although further studies are needed to better understand how viral entry occurs and how it might be neutralized. Detection of neutralizing antibodies in human blood had been problematical until an efficient and reliable cell culture system for HCV became available. Hence, the development of an in vitro neutralization assay for HCV could be extremely valuable for characterizing the humoral immune response to HCV and for evaluating the potential of passive and active immunization against hepatitis C. Recent studies using an in vitro neutralization assay system based on infectious retroviral pseudoparticles HCVpp bearing HCV envelope glycoproteins have confirmed that HCV-infected patient sera can indeed neutralize infection .", "Hence, the development of an in vitro neutralization assay for HCV could be extremely valuable for characterizing the humoral immune response to HCV and for evaluating the potential of passive and active immunization against hepatitis C. Recent studies using an in vitro neutralization assay system based on infectious retroviral pseudoparticles HCVpp bearing HCV envelope glycoproteins have confirmed that HCV-infected patient sera can indeed neutralize infection . However, it has also been shown that the neutralizing activity of antibodies from HCV-infected patients is attenuated by a factor present in human serum, identified as the highdensity lipoprotein HDL fraction . HDL facilitation of HCVpp entry is a post-binding event , sug-gesting that HDLs favour internalization of virions and thus the latter's escape from neutralizing antibodies.", "HDL facilitation of HCVpp entry is a post-binding event , sug-gesting that HDLs favour internalization of virions and thus the latter's escape from neutralizing antibodies. Recently, an HCV cell culture model HCVcc has been developed , allowing the production of virus particles that can be efficiently propagated in cell culture. Some preliminary neutralization assays have been carried out by these authors.", "Some preliminary neutralization assays have been carried out by these authors. In this study, we describe how we set up a standardized focus reduction neutralization assay based on HCVcc. Focus reduction assays have been widely used to evaluate the neutralizing antibody responses to viruses that can form foci in infected cells.", "Focus reduction assays have been widely used to evaluate the neutralizing antibody responses to viruses that can form foci in infected cells. Following the recent development of the HCVcc model, the principle of the focus reduction assay has been applied to HCV-neutralizing antibodies detection. The JFH-1 HCV 2a viral strain was grown on a Huh-7 human hepatoma cell line.", "The JFH-1 HCV 2a viral strain was grown on a Huh-7 human hepatoma cell line. After three days of infection and cell permeabilization, detection of the HCV foci was carried out using an inactivated HCVpositive patient serum primary antibody and a peroxidase-coupled, Fc-specific anti-human IgG-antibody. The reaction was revealed with DAB peroxidase substrate.", "The reaction was revealed with DAB peroxidase substrate. The viral foci were thus stained brown, making them easy to count see Fig. 1a . It has been recently shown that the neutralizing activity of HCV antibodies is attenuated by a serum factor associated with the HDL fraction.", "It has been recently shown that the neutralizing activity of HCV antibodies is attenuated by a serum factor associated with the HDL fraction. Hence, HDLs were able to facilitate HCVpp and HCVcc entry via a mechanism which depended on the expression of the scavenger receptor BI SR-BI and its selective lipid-uptake function . In view of the role of HDL in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibody titer see Fig.", "In view of the role of HDL in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibody titer see Fig. 1b . The specificity of the HCV neutralization assay was assessed by testing 20 anti-HCV-ELISA-negative samples, including five positive for hepatitis B virus surface antibodies anti-HBs and five positive for heterophile antibodies.", "The specificity of the HCV neutralization assay was assessed by testing 20 anti-HCV-ELISA-negative samples, including five positive for hepatitis B virus surface antibodies anti-HBs and five positive for heterophile antibodies. All samples tested negative with two commercial anti-HCV antibody detection assays Axsym ® HCV Version 3.0, Abbott, Wiesbaden, Germany; Vitros ® Anti-HCV reagent pack, Ortho-Clinical Diagnostic, High Wycombe, United Kingdom and HCV-RNA-negative with a qualitative, commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France . These anti-HCV-negative samples were compared with 11 samples from patients chronically infected with HCV genotype 2.", "These anti-HCV-negative samples were compared with 11 samples from patients chronically infected with HCV genotype 2. The neutralization titers of anti-HCV-negative serum samples are shown in Fig. 2 ., with a mean value of 1.083 ± 0.083 corresponding to a dilution of 1:12 .", "2 ., with a mean value of 1.083 ± 0.083 corresponding to a dilution of 1:12 . The assay's cut-off determined as the mean value for negative samples plus two standard deviations corresponded to a dilution of 1:18. The assay exhibited specificity and sensibility values of 100% and 96.5%, respectively.", "The assay exhibited specificity and sensibility values of 100% and 96.5%, respectively. The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples data not shown . Conversely, the chronically HCV genotype 2-positive samples displayed strong reactions, with a mean value of 2.128 ± 0.365 corresponding to a dilution of 1:134 p < 0.001 .", "Conversely, the chronically HCV genotype 2-positive samples displayed strong reactions, with a mean value of 2.128 ± 0.365 corresponding to a dilution of 1:134 p < 0.001 . Inter-assay variability was determined by testing one HCV genotype 2 sample in 10 consecutive experiments n = 10 , whereas intra-assay variability was evaluated by testing the same sample 10 times n = 10 in the same experiment, whilst running the dilution series. The intra-assay and inter-assay coefficients of variation CV of the log neutralization titers were 6.7% and 12.6%, respectively.", "The intra-assay and inter-assay coefficients of variation CV of the log neutralization titers were 6.7% and 12.6%, respectively. Fifty-seven HCV-positive antibodies samples were evaluated using the HCV focus reduction neutralization assay. The genotypes were distributed as follows; for types 1a, 1b, 2, 3, 4 and 5, we studied 11, 11, 11, 12, 10 and 2 samples, respectively.", "The genotypes were distributed as follows; for types 1a, 1b, 2, 3, 4 and 5, we studied 11, 11, 11, 12, 10 and 2 samples, respectively. The mean values of the different genotypes is shown in Fig. 3 . and Table 1 .", "3 . and Table 1 . The mean log neutralization titers for genotypes 1a, 2 and 3 are very similar 2.046 ± 0.671 for genotype 1a, 2.128 ± 0.365 for genotype 2 and 2.148 ± 0.478 for genotype 3 . The mean average values are lower for genotype 1b 1.747 ± 0.462 and genotype 4 1.786 ± 0.236 .", "The mean average values are lower for genotype 1b 1.747 ± 0.462 and genotype 4 1.786 ± 0.236 . Strikingly, very high heterologous titers were observed for five patients -three infected with HCV genotype 1a and two infected with HCV genotype 3 see Fig. 3a .", "3a . There were too few genotype 5 samples to compare with the other genotypes but the corresponding results nevertheless indicate that the neutralization assay is suitable for this genotype. The two The distribution of the log neutralization titers across all the HCV ELISA and RNA-positive samples as a function of the HCV genotype is shown in Fig. 3b .", "3b . More than 60% of the neutralizing antibodies titers fell in the range from 1.7 to 2.69 log titers, corresponding to dilutions of 1:50 and 1:500, respectively. Overall, 3.5% of the samples displayed a titer greater than log 3.0 1:1000 and, conversely, 3.5% displayed a titer below the cut-off value, i.e.", "Overall, 3.5% of the samples displayed a titer greater than log 3.0 1:1000 and, conversely, 3.5% displayed a titer below the cut-off value, i.e. log 1.25 1:10 . Thus, of 57 HCV-infected patients, only two did not test positive for neutralizing antibodies in this assay the titers were 0.960 and 0.932, respectively .", "Thus, of 57 HCV-infected patients, only two did not test positive for neutralizing antibodies in this assay the titers were 0.960 and 0.932, respectively . The role of neutralizing antibodies during acute and chronic viral infection remains an important question and has generated controversial results. Initially, the presence of neutralizing antibodies was shown to control the HCV load and to contribute to viral eradication in patients capable of clearing the infection .", "Initially, the presence of neutralizing antibodies was shown to control the HCV load and to contribute to viral eradication in patients capable of clearing the infection . In other studies, the appearance of neutralizing antibodies was delayed and restricted to IgG1 antibodies in patients who develop a chronic infection . The chimpanzee model has been critical for the study of HCV transmission and host immune responses; however, neutralizing antibodies were not detected in some animals that resolved their infection -suggesting a minimal role in viral clearance, as also observed in human studies .", "The chimpanzee model has been critical for the study of HCV transmission and host immune responses; however, neutralizing antibodies were not detected in some animals that resolved their infection -suggesting a minimal role in viral clearance, as also observed in human studies . Experimentally infected chimpanzees and naturally infected humans can be re-infected with homologous and heterologous HCV strains, suggesting that the humoral immunity that develops after spontaneous resolution of acute hepatitis C is not sterilizing . During chronic infection in humans, the presence and/or production of neutralizing antibodies do not suffice for curing the infection but could regulate the spread of the virus.", "During chronic infection in humans, the presence and/or production of neutralizing antibodies do not suffice for curing the infection but could regulate the spread of the virus. Thus, it can be postulated that during chronic infection, viral mutants can continuously escape the renewed production of neutralizing antibodies. Retroviral pseudoparticles have been used to develop a very interesting tool for measuring neutralizing antibodies in vitro .", "Retroviral pseudoparticles have been used to develop a very interesting tool for measuring neutralizing antibodies in vitro . The assay has demonstrated the presence of HCV-neutralizing antibodies in human sera with relatively high titers >1:320 and broadly neutralizing activity against different HCV genotypes. However, this model does not represent genuine HCV virions; in particular, the budding of retroviral particles is thought to be very different and may involve a variety of cellular pathways.", "However, this model does not represent genuine HCV virions; in particular, the budding of retroviral particles is thought to be very different and may involve a variety of cellular pathways. Characterization of infectious retroviral pseudotype particles bearing HCV glycoproteins have been shown to be very heterogeneous, and so it is possible that these pseudoparticles may not be as relevant as the native HCV virions . The recent development of a cell culture model for HCV enables the production of native HCV virions that can be efficiently propagated in cell culture .", "The recent development of a cell culture model for HCV enables the production of native HCV virions that can be efficiently propagated in cell culture . This cell culture system has allowed us to develop a neutralization assay for evaluating the level and the proportion of HCVneutralizing antibodies in chronically infected HCV patients. We analysed a number of parameters such as practicability, reproducibility and specificity and tested the effect of a range of variables viral inoculum size, incubation time, fixation and permeabilization methods, blocking and revelation reagents on these parameters data not shown .", "We analysed a number of parameters such as practicability, reproducibility and specificity and tested the effect of a range of variables viral inoculum size, incubation time, fixation and permeabilization methods, blocking and revelation reagents on these parameters data not shown . Overall, the neutralization assay described in this study performs similarly to standardized neutralization assays for many other viruses . The assay relies on the ability of the specific JFH-1 genotype 2 viral strain to replicate and multiply on a Huh-7 human hepatoma cell line in a cell culture model, enabling the rapid detection of viral foci after 72 hours of infection.", "The assay relies on the ability of the specific JFH-1 genotype 2 viral strain to replicate and multiply on a Huh-7 human hepatoma cell line in a cell culture model, enabling the rapid detection of viral foci after 72 hours of infection. Moreover, no secondary foci were detectable at this time point. Fixation with paraformaldehyde and permeabilization with Triton X-100 were chosen in order to preserve antigenicity and prevent the cell monolayer from detaching during washes.", "Fixation with paraformaldehyde and permeabilization with Triton X-100 were chosen in order to preserve antigenicity and prevent the cell monolayer from detaching during washes. Development with DAB peroxide substrate made it easy to count specifically coloured viral foci. The viral inoculum size is an important parameter; it has to be low enough to enable good assay sensitivity but high enough to produce a statistically significant number of foci, i.e.", "The viral inoculum size is an important parameter; it has to be low enough to enable good assay sensitivity but high enough to produce a statistically significant number of foci, i.e. allowing the reduction in the number of foci and thus the effect of neutralization to be monitored. Thus, 100 FFUs were used as the inoculum in this neutralization assay.", "Thus, 100 FFUs were used as the inoculum in this neutralization assay. In order to test different human samples, we had to take into account the ability of HDL to facilitate HCVcc entry via a mechanism which depends on expression of the scavenger receptor BI . Given HDL's role in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibodies titer; this frees the assay of the risk of non-specific neutralization activity of the serum via the effects of HDL, the complement system and/or serum amyloid A protein SAA .", "Given HDL's role in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibodies titer; this frees the assay of the risk of non-specific neutralization activity of the serum via the effects of HDL, the complement system and/or serum amyloid A protein SAA . The HCV neutralization assay exhibited good reproducibility, for both duplicate assays and independent tests. As expected, the intra-assay coefficient of variation CV was lower than the interassay CV.", "As expected, the intra-assay coefficient of variation CV was lower than the interassay CV. The test also showed good specificity, since there was no interaction with anti-HIV, anti-HBV or heterophile antibodies. Very low titers were found with HCV ELISA and RNA-negative samples, and the assay's cut-off was determined as the mean titer for negative samples plus two standard deviations 1.25 log, corresponding to a dilution of 1:18 .", "Very low titers were found with HCV ELISA and RNA-negative samples, and the assay's cut-off was determined as the mean titer for negative samples plus two standard deviations 1.25 log, corresponding to a dilution of 1:18 . Given that only the JFH-1 strain of HCV genotype 2a was available for the assay, we evaluated the neutralization titer of sera from patients chronically infected with other HCV genotypes, i.e. 1, 2, 3, 4 and 5.", "1, 2, 3, 4 and 5. Most of these sera were detected as positive by the neutralization assay, except for two sera from HCV genotype 1-infected patients. These two samples presented a high specific antibody ratio according to the ELISA but only very low inhibition by neutralization assay far below the cut-off, in fact .", "These two samples presented a high specific antibody ratio according to the ELISA but only very low inhibition by neutralization assay far below the cut-off, in fact . We conclude that either the samples lacked neutralizing antibodies or that any such antibodies that were present did not cross-neutralize with HCV genotype 2a. The sensitivity was 100% -not only for genotype 2 the genotype of the strain used for the assay but also for other HCV genotypes except genotype 1 .", "The sensitivity was 100% -not only for genotype 2 the genotype of the strain used for the assay but also for other HCV genotypes except genotype 1 . HCV genotype 5 antibodies were also measured but there were too few samples for accurate testing. Moreover, the positive sera 96.5% had comparable and significantly high titers 1.99 ± 0.63 , whatever the genotype.", "Moreover, the positive sera 96.5% had comparable and significantly high titers 1.99 ± 0.63 , whatever the genotype. This finding suggests that most neutralizing antibodies are cross-reactive. Another possibility is that most of the patients had been previously infected by a genotype 2 strain.", "Another possibility is that most of the patients had been previously infected by a genotype 2 strain. However, this is unlikely because few genotype 2 strains are circulating in France . As expected for a neutralization test, the assay presented in the present study appeared to be very specific independently of the genotype and usable in most circumstances.", "As expected for a neutralization test, the assay presented in the present study appeared to be very specific independently of the genotype and usable in most circumstances. For most viral infections, neutralization assays such as that described in this study are used as reference assays. Thus, we are confident that as other HCVcc genotypes become available, these assays will replace the pseudoparticle assay in the near future because they are probably more relevant.", "Thus, we are confident that as other HCVcc genotypes become available, these assays will replace the pseudoparticle assay in the near future because they are probably more relevant. Our assay is somewhat time-consuming and could be simplified by using one dilution to count the foci; however, this type of \"short cut\" would make it difficult to extrapolate to the dilution neutralizing 50% of the inoculum. Another approach would consist in using recombinant HCV capable of expressing reporter genes such as luciferase in order to use a single dilution and obtain a quantitative result .", "Another approach would consist in using recombinant HCV capable of expressing reporter genes such as luciferase in order to use a single dilution and obtain a quantitative result . However, further neutralization studies using other genotypes are needed in order to complete our observations and to char- A simple, specific and reproducible cell culture-based neutralization assay was developed for the determination of neutralizing anti-HCV antibodies in human sera. This test should be an important tool for gauging the relationship between the neutralizing response and viral load kinetics in acutely and chronically infected patients.", "This test should be an important tool for gauging the relationship between the neutralizing response and viral load kinetics in acutely and chronically infected patients. The Huh-7 human hepatoma cells were grown in Dulbecco's minimum essential medium Invitrogen supplemented with 10% fetal bovine serum. All cell cultures were maintained in 5% CO 2 at 37°C.", "All cell cultures were maintained in 5% CO 2 at 37°C. The plasmid pJFH-1 containing the full-length cDNA of the JFH-1 isolate which belongs to subtype 2a GenBank accession no. AB047639 , was a gift from Dr Wakita Department of Microbiology, Tokyo Metropolitan Institute for Neuroscience, Tokyo, Japan and has been described previously .", "AB047639 , was a gift from Dr Wakita Department of Microbiology, Tokyo Metropolitan Institute for Neuroscience, Tokyo, Japan and has been described previously . To generate genomic HCV RNA, the plasmid pJFH-1 was linearized at the 3' end of the HCV cDNA and used as a template for in vitro transcription, as described previously . Viral stocks were obtained by harvesting cell culture supernatants and freezing them at -80°C.", "Viral stocks were obtained by harvesting cell culture supernatants and freezing them at -80°C. Virus titration was performed on Huh-7 cells with 6-well microtiter plates Corning, NY 72 hours after incubation, by immunostaining the cells with antibodies from a HCV-positive patient serum that had previously been inactivated at 56°C see the section on the virus neutralization assay . The viral titer was determined in triplicate from the mean number of foci and expressed as focus forming units/mL FFU/mL .", "The viral titer was determined in triplicate from the mean number of foci and expressed as focus forming units/mL FFU/mL . Seventy-seven human serum samples were tested. Collection of the sera was approved by the local Ethics Committee and informed consent had been obtained from the donors. Fifty-seven of these samples were obtained from chronically infected HCV patients.", "Fifty-seven of these samples were obtained from chronically infected HCV patients. The presence of HCV antibodies was determined and confirmed using two third-generation HCV EIA assays Axsym ® HCV Version 3.0, Abbott, Wiesbaden, Germany and Vitros ® Anti-HCV reagent pack, Ortho-Clinical Diagnostic, High Wycombe, United Kingdom . HCV RNA was determined with a qualitative commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France and HCV genotyping was performed by direct sequencing, as described elsewhere .", "HCV RNA was determined with a qualitative commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France and HCV genotyping was performed by direct sequencing, as described elsewhere . The genotypes were distributed as follows: 11, 11, 11, 12, 10 and 2 samples of types 1a, 1b, 2, 3, 4 and 5, respectively. A set of 20 anti-HCV-negative serum samples was used to evaluate the assay's specif-icity, including five serum samples with positive hepatitis B virus surface antibody anti-HBs status and five sera from Epstein-Barr virus-infected patients that had tested positive for heterophile antibodies.", "A set of 20 anti-HCV-negative serum samples was used to evaluate the assay's specif-icity, including five serum samples with positive hepatitis B virus surface antibody anti-HBs status and five sera from Epstein-Barr virus-infected patients that had tested positive for heterophile antibodies. All serum samples had been stored at -80°C upon collection and had not been thawed until the time of assay. Serum immunoglobulins G IgG fraction was purified using protein G-Sepharose GE Healthcare, Orsay, France The HCV focus reduction neutralization assay was performed in 96-well microtiter plates.", "Serum immunoglobulins G IgG fraction was purified using protein G-Sepharose GE Healthcare, Orsay, France The HCV focus reduction neutralization assay was performed in 96-well microtiter plates. Serial dilutions of purified IgG 10 μg ranging from 1:10 to 1:1,280 were established. Each dilution was tested twice.", "Each dilution was tested twice. 25 μL of each sample was mixed with 25 μL of virus 100 FFU in 96well microtiter plates and incubated for 1 hour at 37°C, 5% CO 2 . A volume of 100 μL of Huh-7 cell suspension 10,000 cells/well in culture medium was added and incubated for 5 hours at 37°C, 5% CO2.", "A volume of 100 μL of Huh-7 cell suspension 10,000 cells/well in culture medium was added and incubated for 5 hours at 37°C, 5% CO2. After 5 hours, the supernatants were removed and 100 μL of culture medium were added to the monolayers. After 72 hours, the cells were fixed with paraformaldehyde and permeabilized with 0.5% Triton X-100.", "After 72 hours, the cells were fixed with paraformaldehyde and permeabilized with 0.5% Triton X-100. Primary antibody a HCVpositive patient serum inactivated at 56°C was diluted to 1:500 prior to use and then incubated for 1 h at room temperature. A peroxidase-coupled, Fc-specific anti-human IgG antibody Sigma, Saint Quentin Fallavier, France diluted to 1:200 was dispensed onto the cell monolayer and incubated for 30 min at room temperature.", "A peroxidase-coupled, Fc-specific anti-human IgG antibody Sigma, Saint Quentin Fallavier, France diluted to 1:200 was dispensed onto the cell monolayer and incubated for 30 min at room temperature. The reaction was developed with DAB peroxidase substrate Sigma, Saint Quentin Fallavier, France and stopped after 10 min of incubation with distilled water. The number of HCV foci in each dilution was determined.", "The number of HCV foci in each dilution was determined. Controls were included in each assay non-neutralized virus, purified IgG from each patient at a 1:10 dilution . The dilution that neutralized 50% of the virus was calculated by curvilinear regression analysis using XLSTAT 2006 software Addinsoft SARL, Paris, France .", "The dilution that neutralized 50% of the virus was calculated by curvilinear regression analysis using XLSTAT 2006 software Addinsoft SARL, Paris, France . Each titer was deter-mined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%. Titers were expressed as logarithmic values and means ± standard deviation were calculated.", "Titers were expressed as logarithmic values and means ± standard deviation were calculated. Student's t-test was used to compare data between groups. p values below 0.05 were considered to be significant." ]

[ "BACKGROUND/AIM: The role of humoral immunity in hepatitis C virus HCV infection is poorly understood. Nevertheless, there is increasing interest in characterizing the neutralizing antibodies in the serum of HCV-infected patients. Focus reduction assays have been widely used to evaluate neutralizing antibody responses against a range of non-cytopathic viruses.", "Focus reduction assays have been widely used to evaluate neutralizing antibody responses against a range of non-cytopathic viruses. Based on the recent development of a HCV cell culture system using the genotype 2 JFH-1-strain, we developed a focus reduction assay for HCV-neutralizing antibodies. METHODS: The focus reduction assay was based on a standard microneutralization assay in which immunostained foci on tissue culture plates are counted.", "METHODS: The focus reduction assay was based on a standard microneutralization assay in which immunostained foci on tissue culture plates are counted. The neutralizing anti-HCV antibodies titers of purified serum immunoglobulin samples from seventy-seven individuals were determined using a 50% focus reduction neutralization assay. Each titer was determined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%.", "Each titer was determined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%. IgG antibodies were first purified from each serum in order to avoid the facilitating effect of HDL on HCV entry. RESULTS: The assay's cut-off using an ELISA and RNA HCV-negative samples was found to be 1.25 log, corresponding to a dilution of 1:18.", "RESULTS: The assay's cut-off using an ELISA and RNA HCV-negative samples was found to be 1.25 log, corresponding to a dilution of 1:18. The assay was compared with a commercial HCV ELISA and exhibited specificity and sensitivity values of 100% and 96.5%, respectively, and good reproducibility with intra-assay and inter-assay coefficients of variation of 6.7% and 12.6%, respectively . The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples.", "The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples. The neutralizing antibodies titers were 2.13 log 1:134 for homologous samples from HCV genotype 2 infected patients harboring the same genotype as JFH-1 and 1.93 log 1:85 for heterologous samples from patients infected by genotypes other than type 2. These results confirm the presence of broadly cross-neutralizing antibodies already reported using the HCV pseudoparticles system.", "These results confirm the presence of broadly cross-neutralizing antibodies already reported using the HCV pseudoparticles system. CONCLUSION: This study presents a simple, specific and reproducible cell culture-based assay for determination of HCV-neutralizing antibodies in human sera. The assay should be an important tool for gauging the relationship between the neutralizing antibodies response and viral load kinetics in acutely or chronically infected patients and for investigating the possible eradication or prevention of HCV infection by neutralizing antibodies.", "The assay should be an important tool for gauging the relationship between the neutralizing antibodies response and viral load kinetics in acutely or chronically infected patients and for investigating the possible eradication or prevention of HCV infection by neutralizing antibodies. Text: Hepatitis C virus HCV, a member of the Flaviviridae family is an enveloped, positive-stranded RNA virus that preferentially replicates in hepatocytes. At least 170 million people worldwide are persistently infected with hepatitis C virus.", "At least 170 million people worldwide are persistently infected with hepatitis C virus. Chronic HCV infection is associated with a significant risk of progression to cirrhosis and hepatocellular carcinoma . Antiviral therapy with pegylated alpha-interferon and ribavirin the current best therapeutic regimen is only successful in about 50% of all treated patients.", "Antiviral therapy with pegylated alpha-interferon and ribavirin the current best therapeutic regimen is only successful in about 50% of all treated patients. Better knowledge of the viral and host factors that determine HCV clearance or persistence during the acute stage of infection is needed in order to improve antiviral therapy and to develop efficient vaccines. Studies focusing on innate and cellular immune responses have shown that a sufficiently large HCV inoculum is able to evade, subvert or circumvent the host's defences.", "Studies focusing on innate and cellular immune responses have shown that a sufficiently large HCV inoculum is able to evade, subvert or circumvent the host's defences. At present, the chimpanzee is the only reliable experimental animal model in which the initial post-HCV infection events and the efficacy of vaccine candidates can be evaluated . It has been shown that HCV-specific T-cell immunity is important in the control of HCV infection .", "It has been shown that HCV-specific T-cell immunity is important in the control of HCV infection . Several studies have indicated a role for humoral immunity in the acute stage of HCV infection but this aspect remains poorly characterized. The E1 and E2 glycoproteins are thought to be the viral attachment proteins and thus the main targets for HCV-neutralizing antibodies; identification of protective epitopes conserved across different strains of HCV is therefore a major challenge in vaccine design.", "The E1 and E2 glycoproteins are thought to be the viral attachment proteins and thus the main targets for HCV-neutralizing antibodies; identification of protective epitopes conserved across different strains of HCV is therefore a major challenge in vaccine design. A number of antibodies capable of blocking E2 binding to cells or cell receptors have been described, some of which neutralize HCV entry in animal or cellular models . Cell entry has been shown to involve several surface molecules notably including the tetraspanin CD81 and the SR-BI receptor , although further studies are needed to better understand how viral entry occurs and how it might be neutralized.", "Cell entry has been shown to involve several surface molecules notably including the tetraspanin CD81 and the SR-BI receptor , although further studies are needed to better understand how viral entry occurs and how it might be neutralized. Detection of neutralizing antibodies in human blood had been problematical until an efficient and reliable cell culture system for HCV became available. Hence, the development of an in vitro neutralization assay for HCV could be extremely valuable for characterizing the humoral immune response to HCV and for evaluating the potential of passive and active immunization against hepatitis C. Recent studies using an in vitro neutralization assay system based on infectious retroviral pseudoparticles HCVpp bearing HCV envelope glycoproteins have confirmed that HCV-infected patient sera can indeed neutralize infection .", "Hence, the development of an in vitro neutralization assay for HCV could be extremely valuable for characterizing the humoral immune response to HCV and for evaluating the potential of passive and active immunization against hepatitis C. Recent studies using an in vitro neutralization assay system based on infectious retroviral pseudoparticles HCVpp bearing HCV envelope glycoproteins have confirmed that HCV-infected patient sera can indeed neutralize infection . However, it has also been shown that the neutralizing activity of antibodies from HCV-infected patients is attenuated by a factor present in human serum, identified as the highdensity lipoprotein HDL fraction . HDL facilitation of HCVpp entry is a post-binding event , sug-gesting that HDLs favour internalization of virions and thus the latter's escape from neutralizing antibodies.", "HDL facilitation of HCVpp entry is a post-binding event , sug-gesting that HDLs favour internalization of virions and thus the latter's escape from neutralizing antibodies. Recently, an HCV cell culture model HCVcc has been developed , allowing the production of virus particles that can be efficiently propagated in cell culture. Some preliminary neutralization assays have been carried out by these authors.", "Some preliminary neutralization assays have been carried out by these authors. In this study, we describe how we set up a standardized focus reduction neutralization assay based on HCVcc. Focus reduction assays have been widely used to evaluate the neutralizing antibody responses to viruses that can form foci in infected cells.", "Focus reduction assays have been widely used to evaluate the neutralizing antibody responses to viruses that can form foci in infected cells. Following the recent development of the HCVcc model, the principle of the focus reduction assay has been applied to HCV-neutralizing antibodies detection. The JFH-1 HCV 2a viral strain was grown on a Huh-7 human hepatoma cell line.", "The JFH-1 HCV 2a viral strain was grown on a Huh-7 human hepatoma cell line. After three days of infection and cell permeabilization, detection of the HCV foci was carried out using an inactivated HCVpositive patient serum primary antibody and a peroxidase-coupled, Fc-specific anti-human IgG-antibody. The reaction was revealed with DAB peroxidase substrate.", "The reaction was revealed with DAB peroxidase substrate. The viral foci were thus stained brown, making them easy to count see Fig. 1a . It has been recently shown that the neutralizing activity of HCV antibodies is attenuated by a serum factor associated with the HDL fraction.", "It has been recently shown that the neutralizing activity of HCV antibodies is attenuated by a serum factor associated with the HDL fraction. Hence, HDLs were able to facilitate HCVpp and HCVcc entry via a mechanism which depended on the expression of the scavenger receptor BI SR-BI and its selective lipid-uptake function . In view of the role of HDL in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibody titer see Fig.", "In view of the role of HDL in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibody titer see Fig. 1b . The specificity of the HCV neutralization assay was assessed by testing 20 anti-HCV-ELISA-negative samples, including five positive for hepatitis B virus surface antibodies anti-HBs and five positive for heterophile antibodies.", "The specificity of the HCV neutralization assay was assessed by testing 20 anti-HCV-ELISA-negative samples, including five positive for hepatitis B virus surface antibodies anti-HBs and five positive for heterophile antibodies. All samples tested negative with two commercial anti-HCV antibody detection assays Axsym ® HCV Version 3.0, Abbott, Wiesbaden, Germany; Vitros ® Anti-HCV reagent pack, Ortho-Clinical Diagnostic, High Wycombe, United Kingdom and HCV-RNA-negative with a qualitative, commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France . These anti-HCV-negative samples were compared with 11 samples from patients chronically infected with HCV genotype 2.", "These anti-HCV-negative samples were compared with 11 samples from patients chronically infected with HCV genotype 2. The neutralization titers of anti-HCV-negative serum samples are shown in Fig. 2 ., with a mean value of 1.083 ± 0.083 corresponding to a dilution of 1:12 .", "2 ., with a mean value of 1.083 ± 0.083 corresponding to a dilution of 1:12 . The assay's cut-off determined as the mean value for negative samples plus two standard deviations corresponded to a dilution of 1:18. The assay exhibited specificity and sensibility values of 100% and 96.5%, respectively.", "The assay exhibited specificity and sensibility values of 100% and 96.5%, respectively. The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples data not shown . Conversely, the chronically HCV genotype 2-positive samples displayed strong reactions, with a mean value of 2.128 ± 0.365 corresponding to a dilution of 1:134 p < 0.001 .", "Conversely, the chronically HCV genotype 2-positive samples displayed strong reactions, with a mean value of 2.128 ± 0.365 corresponding to a dilution of 1:134 p < 0.001 . Inter-assay variability was determined by testing one HCV genotype 2 sample in 10 consecutive experiments n = 10 , whereas intra-assay variability was evaluated by testing the same sample 10 times n = 10 in the same experiment, whilst running the dilution series. The intra-assay and inter-assay coefficients of variation CV of the log neutralization titers were 6.7% and 12.6%, respectively.", "The intra-assay and inter-assay coefficients of variation CV of the log neutralization titers were 6.7% and 12.6%, respectively. Fifty-seven HCV-positive antibodies samples were evaluated using the HCV focus reduction neutralization assay. The genotypes were distributed as follows; for types 1a, 1b, 2, 3, 4 and 5, we studied 11, 11, 11, 12, 10 and 2 samples, respectively.", "The genotypes were distributed as follows; for types 1a, 1b, 2, 3, 4 and 5, we studied 11, 11, 11, 12, 10 and 2 samples, respectively. The mean values of the different genotypes is shown in Fig. 3 . and Table 1 .", "3 . and Table 1 . The mean log neutralization titers for genotypes 1a, 2 and 3 are very similar 2.046 ± 0.671 for genotype 1a, 2.128 ± 0.365 for genotype 2 and 2.148 ± 0.478 for genotype 3 . The mean average values are lower for genotype 1b 1.747 ± 0.462 and genotype 4 1.786 ± 0.236 .", "The mean average values are lower for genotype 1b 1.747 ± 0.462 and genotype 4 1.786 ± 0.236 . Strikingly, very high heterologous titers were observed for five patients -three infected with HCV genotype 1a and two infected with HCV genotype 3 see Fig. 3a .", "3a . There were too few genotype 5 samples to compare with the other genotypes but the corresponding results nevertheless indicate that the neutralization assay is suitable for this genotype. The two The distribution of the log neutralization titers across all the HCV ELISA and RNA-positive samples as a function of the HCV genotype is shown in Fig. 3b .", "3b . More than 60% of the neutralizing antibodies titers fell in the range from 1.7 to 2.69 log titers, corresponding to dilutions of 1:50 and 1:500, respectively. Overall, 3.5% of the samples displayed a titer greater than log 3.0 1:1000 and, conversely, 3.5% displayed a titer below the cut-off value, i.e.", "Overall, 3.5% of the samples displayed a titer greater than log 3.0 1:1000 and, conversely, 3.5% displayed a titer below the cut-off value, i.e. log 1.25 1:10 . Thus, of 57 HCV-infected patients, only two did not test positive for neutralizing antibodies in this assay the titers were 0.960 and 0.932, respectively .", "Thus, of 57 HCV-infected patients, only two did not test positive for neutralizing antibodies in this assay the titers were 0.960 and 0.932, respectively . The role of neutralizing antibodies during acute and chronic viral infection remains an important question and has generated controversial results. Initially, the presence of neutralizing antibodies was shown to control the HCV load and to contribute to viral eradication in patients capable of clearing the infection .", "Initially, the presence of neutralizing antibodies was shown to control the HCV load and to contribute to viral eradication in patients capable of clearing the infection . In other studies, the appearance of neutralizing antibodies was delayed and restricted to IgG1 antibodies in patients who develop a chronic infection . The chimpanzee model has been critical for the study of HCV transmission and host immune responses; however, neutralizing antibodies were not detected in some animals that resolved their infection -suggesting a minimal role in viral clearance, as also observed in human studies .", "The chimpanzee model has been critical for the study of HCV transmission and host immune responses; however, neutralizing antibodies were not detected in some animals that resolved their infection -suggesting a minimal role in viral clearance, as also observed in human studies . Experimentally infected chimpanzees and naturally infected humans can be re-infected with homologous and heterologous HCV strains, suggesting that the humoral immunity that develops after spontaneous resolution of acute hepatitis C is not sterilizing . During chronic infection in humans, the presence and/or production of neutralizing antibodies do not suffice for curing the infection but could regulate the spread of the virus.", "During chronic infection in humans, the presence and/or production of neutralizing antibodies do not suffice for curing the infection but could regulate the spread of the virus. Thus, it can be postulated that during chronic infection, viral mutants can continuously escape the renewed production of neutralizing antibodies. Retroviral pseudoparticles have been used to develop a very interesting tool for measuring neutralizing antibodies in vitro .", "Retroviral pseudoparticles have been used to develop a very interesting tool for measuring neutralizing antibodies in vitro . The assay has demonstrated the presence of HCV-neutralizing antibodies in human sera with relatively high titers >1:320 and broadly neutralizing activity against different HCV genotypes. However, this model does not represent genuine HCV virions; in particular, the budding of retroviral particles is thought to be very different and may involve a variety of cellular pathways.", "However, this model does not represent genuine HCV virions; in particular, the budding of retroviral particles is thought to be very different and may involve a variety of cellular pathways. Characterization of infectious retroviral pseudotype particles bearing HCV glycoproteins have been shown to be very heterogeneous, and so it is possible that these pseudoparticles may not be as relevant as the native HCV virions . The recent development of a cell culture model for HCV enables the production of native HCV virions that can be efficiently propagated in cell culture .", "The recent development of a cell culture model for HCV enables the production of native HCV virions that can be efficiently propagated in cell culture . This cell culture system has allowed us to develop a neutralization assay for evaluating the level and the proportion of HCVneutralizing antibodies in chronically infected HCV patients. We analysed a number of parameters such as practicability, reproducibility and specificity and tested the effect of a range of variables viral inoculum size, incubation time, fixation and permeabilization methods, blocking and revelation reagents on these parameters data not shown .", "We analysed a number of parameters such as practicability, reproducibility and specificity and tested the effect of a range of variables viral inoculum size, incubation time, fixation and permeabilization methods, blocking and revelation reagents on these parameters data not shown . Overall, the neutralization assay described in this study performs similarly to standardized neutralization assays for many other viruses . The assay relies on the ability of the specific JFH-1 genotype 2 viral strain to replicate and multiply on a Huh-7 human hepatoma cell line in a cell culture model, enabling the rapid detection of viral foci after 72 hours of infection.", "The assay relies on the ability of the specific JFH-1 genotype 2 viral strain to replicate and multiply on a Huh-7 human hepatoma cell line in a cell culture model, enabling the rapid detection of viral foci after 72 hours of infection. Moreover, no secondary foci were detectable at this time point. Fixation with paraformaldehyde and permeabilization with Triton X-100 were chosen in order to preserve antigenicity and prevent the cell monolayer from detaching during washes.", "Fixation with paraformaldehyde and permeabilization with Triton X-100 were chosen in order to preserve antigenicity and prevent the cell monolayer from detaching during washes. Development with DAB peroxide substrate made it easy to count specifically coloured viral foci. The viral inoculum size is an important parameter; it has to be low enough to enable good assay sensitivity but high enough to produce a statistically significant number of foci, i.e.", "The viral inoculum size is an important parameter; it has to be low enough to enable good assay sensitivity but high enough to produce a statistically significant number of foci, i.e. allowing the reduction in the number of foci and thus the effect of neutralization to be monitored. Thus, 100 FFUs were used as the inoculum in this neutralization assay.", "Thus, 100 FFUs were used as the inoculum in this neutralization assay. In order to test different human samples, we had to take into account the ability of HDL to facilitate HCVcc entry via a mechanism which depends on expression of the scavenger receptor BI . Given HDL's role in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibodies titer; this frees the assay of the risk of non-specific neutralization activity of the serum via the effects of HDL, the complement system and/or serum amyloid A protein SAA .", "Given HDL's role in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibodies titer; this frees the assay of the risk of non-specific neutralization activity of the serum via the effects of HDL, the complement system and/or serum amyloid A protein SAA . The HCV neutralization assay exhibited good reproducibility, for both duplicate assays and independent tests. As expected, the intra-assay coefficient of variation CV was lower than the interassay CV.", "As expected, the intra-assay coefficient of variation CV was lower than the interassay CV. The test also showed good specificity, since there was no interaction with anti-HIV, anti-HBV or heterophile antibodies. Very low titers were found with HCV ELISA and RNA-negative samples, and the assay's cut-off was determined as the mean titer for negative samples plus two standard deviations 1.25 log, corresponding to a dilution of 1:18 .", "Very low titers were found with HCV ELISA and RNA-negative samples, and the assay's cut-off was determined as the mean titer for negative samples plus two standard deviations 1.25 log, corresponding to a dilution of 1:18 . Given that only the JFH-1 strain of HCV genotype 2a was available for the assay, we evaluated the neutralization titer of sera from patients chronically infected with other HCV genotypes, i.e. 1, 2, 3, 4 and 5.", "1, 2, 3, 4 and 5. Most of these sera were detected as positive by the neutralization assay, except for two sera from HCV genotype 1-infected patients. These two samples presented a high specific antibody ratio according to the ELISA but only very low inhibition by neutralization assay far below the cut-off, in fact .", "These two samples presented a high specific antibody ratio according to the ELISA but only very low inhibition by neutralization assay far below the cut-off, in fact . We conclude that either the samples lacked neutralizing antibodies or that any such antibodies that were present did not cross-neutralize with HCV genotype 2a. The sensitivity was 100% -not only for genotype 2 the genotype of the strain used for the assay but also for other HCV genotypes except genotype 1 .", "The sensitivity was 100% -not only for genotype 2 the genotype of the strain used for the assay but also for other HCV genotypes except genotype 1 . HCV genotype 5 antibodies were also measured but there were too few samples for accurate testing. Moreover, the positive sera 96.5% had comparable and significantly high titers 1.99 ± 0.63 , whatever the genotype.", "Moreover, the positive sera 96.5% had comparable and significantly high titers 1.99 ± 0.63 , whatever the genotype. This finding suggests that most neutralizing antibodies are cross-reactive. Another possibility is that most of the patients had been previously infected by a genotype 2 strain.", "Another possibility is that most of the patients had been previously infected by a genotype 2 strain. However, this is unlikely because few genotype 2 strains are circulating in France . As expected for a neutralization test, the assay presented in the present study appeared to be very specific independently of the genotype and usable in most circumstances.", "As expected for a neutralization test, the assay presented in the present study appeared to be very specific independently of the genotype and usable in most circumstances. For most viral infections, neutralization assays such as that described in this study are used as reference assays. Thus, we are confident that as other HCVcc genotypes become available, these assays will replace the pseudoparticle assay in the near future because they are probably more relevant.", "Thus, we are confident that as other HCVcc genotypes become available, these assays will replace the pseudoparticle assay in the near future because they are probably more relevant. Our assay is somewhat time-consuming and could be simplified by using one dilution to count the foci; however, this type of \"short cut\" would make it difficult to extrapolate to the dilution neutralizing 50% of the inoculum. Another approach would consist in using recombinant HCV capable of expressing reporter genes such as luciferase in order to use a single dilution and obtain a quantitative result .", "Another approach would consist in using recombinant HCV capable of expressing reporter genes such as luciferase in order to use a single dilution and obtain a quantitative result . However, further neutralization studies using other genotypes are needed in order to complete our observations and to char- A simple, specific and reproducible cell culture-based neutralization assay was developed for the determination of neutralizing anti-HCV antibodies in human sera. This test should be an important tool for gauging the relationship between the neutralizing response and viral load kinetics in acutely and chronically infected patients.", "This test should be an important tool for gauging the relationship between the neutralizing response and viral load kinetics in acutely and chronically infected patients. The Huh-7 human hepatoma cells were grown in Dulbecco's minimum essential medium Invitrogen supplemented with 10% fetal bovine serum. All cell cultures were maintained in 5% CO 2 at 37°C.", "All cell cultures were maintained in 5% CO 2 at 37°C. The plasmid pJFH-1 containing the full-length cDNA of the JFH-1 isolate which belongs to subtype 2a GenBank accession no. AB047639 , was a gift from Dr Wakita Department of Microbiology, Tokyo Metropolitan Institute for Neuroscience, Tokyo, Japan and has been described previously .", "AB047639 , was a gift from Dr Wakita Department of Microbiology, Tokyo Metropolitan Institute for Neuroscience, Tokyo, Japan and has been described previously . To generate genomic HCV RNA, the plasmid pJFH-1 was linearized at the 3' end of the HCV cDNA and used as a template for in vitro transcription, as described previously . Viral stocks were obtained by harvesting cell culture supernatants and freezing them at -80°C.", "Viral stocks were obtained by harvesting cell culture supernatants and freezing them at -80°C. Virus titration was performed on Huh-7 cells with 6-well microtiter plates Corning, NY 72 hours after incubation, by immunostaining the cells with antibodies from a HCV-positive patient serum that had previously been inactivated at 56°C see the section on the virus neutralization assay . The viral titer was determined in triplicate from the mean number of foci and expressed as focus forming units/mL FFU/mL .", "The viral titer was determined in triplicate from the mean number of foci and expressed as focus forming units/mL FFU/mL . Seventy-seven human serum samples were tested. Collection of the sera was approved by the local Ethics Committee and informed consent had been obtained from the donors. Fifty-seven of these samples were obtained from chronically infected HCV patients.", "Fifty-seven of these samples were obtained from chronically infected HCV patients. The presence of HCV antibodies was determined and confirmed using two third-generation HCV EIA assays Axsym ® HCV Version 3.0, Abbott, Wiesbaden, Germany and Vitros ® Anti-HCV reagent pack, Ortho-Clinical Diagnostic, High Wycombe, United Kingdom . HCV RNA was determined with a qualitative commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France and HCV genotyping was performed by direct sequencing, as described elsewhere .", "HCV RNA was determined with a qualitative commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France and HCV genotyping was performed by direct sequencing, as described elsewhere . The genotypes were distributed as follows: 11, 11, 11, 12, 10 and 2 samples of types 1a, 1b, 2, 3, 4 and 5, respectively. A set of 20 anti-HCV-negative serum samples was used to evaluate the assay's specif-icity, including five serum samples with positive hepatitis B virus surface antibody anti-HBs status and five sera from Epstein-Barr virus-infected patients that had tested positive for heterophile antibodies.", "A set of 20 anti-HCV-negative serum samples was used to evaluate the assay's specif-icity, including five serum samples with positive hepatitis B virus surface antibody anti-HBs status and five sera from Epstein-Barr virus-infected patients that had tested positive for heterophile antibodies. All serum samples had been stored at -80°C upon collection and had not been thawed until the time of assay. Serum immunoglobulins G IgG fraction was purified using protein G-Sepharose GE Healthcare, Orsay, France The HCV focus reduction neutralization assay was performed in 96-well microtiter plates.", "Serum immunoglobulins G IgG fraction was purified using protein G-Sepharose GE Healthcare, Orsay, France The HCV focus reduction neutralization assay was performed in 96-well microtiter plates. Serial dilutions of purified IgG 10 μg ranging from 1:10 to 1:1,280 were established. Each dilution was tested twice.", "Each dilution was tested twice. 25 μL of each sample was mixed with 25 μL of virus 100 FFU in 96well microtiter plates and incubated for 1 hour at 37°C, 5% CO 2 . A volume of 100 μL of Huh-7 cell suspension 10,000 cells/well in culture medium was added and incubated for 5 hours at 37°C, 5% CO2.", "A volume of 100 μL of Huh-7 cell suspension 10,000 cells/well in culture medium was added and incubated for 5 hours at 37°C, 5% CO2. After 5 hours, the supernatants were removed and 100 μL of culture medium were added to the monolayers. After 72 hours, the cells were fixed with paraformaldehyde and permeabilized with 0.5% Triton X-100.", "After 72 hours, the cells were fixed with paraformaldehyde and permeabilized with 0.5% Triton X-100. Primary antibody a HCVpositive patient serum inactivated at 56°C was diluted to 1:500 prior to use and then incubated for 1 h at room temperature. A peroxidase-coupled, Fc-specific anti-human IgG antibody Sigma, Saint Quentin Fallavier, France diluted to 1:200 was dispensed onto the cell monolayer and incubated for 30 min at room temperature.", "A peroxidase-coupled, Fc-specific anti-human IgG antibody Sigma, Saint Quentin Fallavier, France diluted to 1:200 was dispensed onto the cell monolayer and incubated for 30 min at room temperature. The reaction was developed with DAB peroxidase substrate Sigma, Saint Quentin Fallavier, France and stopped after 10 min of incubation with distilled water. The number of HCV foci in each dilution was determined.", "The number of HCV foci in each dilution was determined. Controls were included in each assay non-neutralized virus, purified IgG from each patient at a 1:10 dilution . The dilution that neutralized 50% of the virus was calculated by curvilinear regression analysis using XLSTAT 2006 software Addinsoft SARL, Paris, France .", "The dilution that neutralized 50% of the virus was calculated by curvilinear regression analysis using XLSTAT 2006 software Addinsoft SARL, Paris, France . Each titer was deter-mined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%. Titers were expressed as logarithmic values and means ± standard deviation were calculated.", "Titers were expressed as logarithmic values and means ± standard deviation were calculated. Student's t-test was used to compare data between groups. p values below 0.05 were considered to be significant." ]

[ "BACKGROUND/AIM: The role of humoral immunity in hepatitis C virus HCV infection is poorly understood. Nevertheless, there is increasing interest in characterizing the neutralizing antibodies in the serum of HCV-infected patients. Focus reduction assays have been widely used to evaluate neutralizing antibody responses against a range of non-cytopathic viruses.", "Focus reduction assays have been widely used to evaluate neutralizing antibody responses against a range of non-cytopathic viruses. Based on the recent development of a HCV cell culture system using the genotype 2 JFH-1-strain, we developed a focus reduction assay for HCV-neutralizing antibodies. METHODS: The focus reduction assay was based on a standard microneutralization assay in which immunostained foci on tissue culture plates are counted.", "METHODS: The focus reduction assay was based on a standard microneutralization assay in which immunostained foci on tissue culture plates are counted. The neutralizing anti-HCV antibodies titers of purified serum immunoglobulin samples from seventy-seven individuals were determined using a 50% focus reduction neutralization assay. Each titer was determined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%.", "Each titer was determined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%. IgG antibodies were first purified from each serum in order to avoid the facilitating effect of HDL on HCV entry. RESULTS: The assay's cut-off using an ELISA and RNA HCV-negative samples was found to be 1.25 log, corresponding to a dilution of 1:18.", "RESULTS: The assay's cut-off using an ELISA and RNA HCV-negative samples was found to be 1.25 log, corresponding to a dilution of 1:18. The assay was compared with a commercial HCV ELISA and exhibited specificity and sensitivity values of 100% and 96.5%, respectively, and good reproducibility with intra-assay and inter-assay coefficients of variation of 6.7% and 12.6%, respectively . The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples.", "The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples. The neutralizing antibodies titers were 2.13 log 1:134 for homologous samples from HCV genotype 2 infected patients harboring the same genotype as JFH-1 and 1.93 log 1:85 for heterologous samples from patients infected by genotypes other than type 2. These results confirm the presence of broadly cross-neutralizing antibodies already reported using the HCV pseudoparticles system.", "These results confirm the presence of broadly cross-neutralizing antibodies already reported using the HCV pseudoparticles system. CONCLUSION: This study presents a simple, specific and reproducible cell culture-based assay for determination of HCV-neutralizing antibodies in human sera. The assay should be an important tool for gauging the relationship between the neutralizing antibodies response and viral load kinetics in acutely or chronically infected patients and for investigating the possible eradication or prevention of HCV infection by neutralizing antibodies.", "The assay should be an important tool for gauging the relationship between the neutralizing antibodies response and viral load kinetics in acutely or chronically infected patients and for investigating the possible eradication or prevention of HCV infection by neutralizing antibodies. Text: Hepatitis C virus HCV, a member of the Flaviviridae family is an enveloped, positive-stranded RNA virus that preferentially replicates in hepatocytes. At least 170 million people worldwide are persistently infected with hepatitis C virus.", "At least 170 million people worldwide are persistently infected with hepatitis C virus. Chronic HCV infection is associated with a significant risk of progression to cirrhosis and hepatocellular carcinoma . Antiviral therapy with pegylated alpha-interferon and ribavirin the current best therapeutic regimen is only successful in about 50% of all treated patients.", "Antiviral therapy with pegylated alpha-interferon and ribavirin the current best therapeutic regimen is only successful in about 50% of all treated patients. Better knowledge of the viral and host factors that determine HCV clearance or persistence during the acute stage of infection is needed in order to improve antiviral therapy and to develop efficient vaccines. Studies focusing on innate and cellular immune responses have shown that a sufficiently large HCV inoculum is able to evade, subvert or circumvent the host's defences.", "Studies focusing on innate and cellular immune responses have shown that a sufficiently large HCV inoculum is able to evade, subvert or circumvent the host's defences. At present, the chimpanzee is the only reliable experimental animal model in which the initial post-HCV infection events and the efficacy of vaccine candidates can be evaluated . It has been shown that HCV-specific T-cell immunity is important in the control of HCV infection .", "It has been shown that HCV-specific T-cell immunity is important in the control of HCV infection . Several studies have indicated a role for humoral immunity in the acute stage of HCV infection but this aspect remains poorly characterized. The E1 and E2 glycoproteins are thought to be the viral attachment proteins and thus the main targets for HCV-neutralizing antibodies; identification of protective epitopes conserved across different strains of HCV is therefore a major challenge in vaccine design.", "The E1 and E2 glycoproteins are thought to be the viral attachment proteins and thus the main targets for HCV-neutralizing antibodies; identification of protective epitopes conserved across different strains of HCV is therefore a major challenge in vaccine design. A number of antibodies capable of blocking E2 binding to cells or cell receptors have been described, some of which neutralize HCV entry in animal or cellular models . Cell entry has been shown to involve several surface molecules notably including the tetraspanin CD81 and the SR-BI receptor , although further studies are needed to better understand how viral entry occurs and how it might be neutralized.", "Cell entry has been shown to involve several surface molecules notably including the tetraspanin CD81 and the SR-BI receptor , although further studies are needed to better understand how viral entry occurs and how it might be neutralized. Detection of neutralizing antibodies in human blood had been problematical until an efficient and reliable cell culture system for HCV became available. Hence, the development of an in vitro neutralization assay for HCV could be extremely valuable for characterizing the humoral immune response to HCV and for evaluating the potential of passive and active immunization against hepatitis C. Recent studies using an in vitro neutralization assay system based on infectious retroviral pseudoparticles HCVpp bearing HCV envelope glycoproteins have confirmed that HCV-infected patient sera can indeed neutralize infection .", "Hence, the development of an in vitro neutralization assay for HCV could be extremely valuable for characterizing the humoral immune response to HCV and for evaluating the potential of passive and active immunization against hepatitis C. Recent studies using an in vitro neutralization assay system based on infectious retroviral pseudoparticles HCVpp bearing HCV envelope glycoproteins have confirmed that HCV-infected patient sera can indeed neutralize infection . However, it has also been shown that the neutralizing activity of antibodies from HCV-infected patients is attenuated by a factor present in human serum, identified as the highdensity lipoprotein HDL fraction . HDL facilitation of HCVpp entry is a post-binding event , sug-gesting that HDLs favour internalization of virions and thus the latter's escape from neutralizing antibodies.", "HDL facilitation of HCVpp entry is a post-binding event , sug-gesting that HDLs favour internalization of virions and thus the latter's escape from neutralizing antibodies. Recently, an HCV cell culture model HCVcc has been developed , allowing the production of virus particles that can be efficiently propagated in cell culture. Some preliminary neutralization assays have been carried out by these authors.", "Some preliminary neutralization assays have been carried out by these authors. In this study, we describe how we set up a standardized focus reduction neutralization assay based on HCVcc. Focus reduction assays have been widely used to evaluate the neutralizing antibody responses to viruses that can form foci in infected cells.", "Focus reduction assays have been widely used to evaluate the neutralizing antibody responses to viruses that can form foci in infected cells. Following the recent development of the HCVcc model, the principle of the focus reduction assay has been applied to HCV-neutralizing antibodies detection. The JFH-1 HCV 2a viral strain was grown on a Huh-7 human hepatoma cell line.", "The JFH-1 HCV 2a viral strain was grown on a Huh-7 human hepatoma cell line. After three days of infection and cell permeabilization, detection of the HCV foci was carried out using an inactivated HCVpositive patient serum primary antibody and a peroxidase-coupled, Fc-specific anti-human IgG-antibody. The reaction was revealed with DAB peroxidase substrate.", "The reaction was revealed with DAB peroxidase substrate. The viral foci were thus stained brown, making them easy to count see Fig. 1a . It has been recently shown that the neutralizing activity of HCV antibodies is attenuated by a serum factor associated with the HDL fraction.", "It has been recently shown that the neutralizing activity of HCV antibodies is attenuated by a serum factor associated with the HDL fraction. Hence, HDLs were able to facilitate HCVpp and HCVcc entry via a mechanism which depended on the expression of the scavenger receptor BI SR-BI and its selective lipid-uptake function . In view of the role of HDL in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibody titer see Fig.", "In view of the role of HDL in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibody titer see Fig. 1b . The specificity of the HCV neutralization assay was assessed by testing 20 anti-HCV-ELISA-negative samples, including five positive for hepatitis B virus surface antibodies anti-HBs and five positive for heterophile antibodies.", "The specificity of the HCV neutralization assay was assessed by testing 20 anti-HCV-ELISA-negative samples, including five positive for hepatitis B virus surface antibodies anti-HBs and five positive for heterophile antibodies. All samples tested negative with two commercial anti-HCV antibody detection assays Axsym ® HCV Version 3.0, Abbott, Wiesbaden, Germany; Vitros ® Anti-HCV reagent pack, Ortho-Clinical Diagnostic, High Wycombe, United Kingdom and HCV-RNA-negative with a qualitative, commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France . These anti-HCV-negative samples were compared with 11 samples from patients chronically infected with HCV genotype 2.", "These anti-HCV-negative samples were compared with 11 samples from patients chronically infected with HCV genotype 2. The neutralization titers of anti-HCV-negative serum samples are shown in Fig. 2 ., with a mean value of 1.083 ± 0.083 corresponding to a dilution of 1:12 .", "2 ., with a mean value of 1.083 ± 0.083 corresponding to a dilution of 1:12 . The assay's cut-off determined as the mean value for negative samples plus two standard deviations corresponded to a dilution of 1:18. The assay exhibited specificity and sensibility values of 100% and 96.5%, respectively.", "The assay exhibited specificity and sensibility values of 100% and 96.5%, respectively. The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples data not shown . Conversely, the chronically HCV genotype 2-positive samples displayed strong reactions, with a mean value of 2.128 ± 0.365 corresponding to a dilution of 1:134 p < 0.001 .", "Conversely, the chronically HCV genotype 2-positive samples displayed strong reactions, with a mean value of 2.128 ± 0.365 corresponding to a dilution of 1:134 p < 0.001 . Inter-assay variability was determined by testing one HCV genotype 2 sample in 10 consecutive experiments n = 10 , whereas intra-assay variability was evaluated by testing the same sample 10 times n = 10 in the same experiment, whilst running the dilution series. The intra-assay and inter-assay coefficients of variation CV of the log neutralization titers were 6.7% and 12.6%, respectively.", "The intra-assay and inter-assay coefficients of variation CV of the log neutralization titers were 6.7% and 12.6%, respectively. Fifty-seven HCV-positive antibodies samples were evaluated using the HCV focus reduction neutralization assay. The genotypes were distributed as follows; for types 1a, 1b, 2, 3, 4 and 5, we studied 11, 11, 11, 12, 10 and 2 samples, respectively.", "The genotypes were distributed as follows; for types 1a, 1b, 2, 3, 4 and 5, we studied 11, 11, 11, 12, 10 and 2 samples, respectively. The mean values of the different genotypes is shown in Fig. 3 . and Table 1 .", "3 . and Table 1 . The mean log neutralization titers for genotypes 1a, 2 and 3 are very similar 2.046 ± 0.671 for genotype 1a, 2.128 ± 0.365 for genotype 2 and 2.148 ± 0.478 for genotype 3 . The mean average values are lower for genotype 1b 1.747 ± 0.462 and genotype 4 1.786 ± 0.236 .", "The mean average values are lower for genotype 1b 1.747 ± 0.462 and genotype 4 1.786 ± 0.236 . Strikingly, very high heterologous titers were observed for five patients -three infected with HCV genotype 1a and two infected with HCV genotype 3 see Fig. 3a .", "3a . There were too few genotype 5 samples to compare with the other genotypes but the corresponding results nevertheless indicate that the neutralization assay is suitable for this genotype. The two The distribution of the log neutralization titers across all the HCV ELISA and RNA-positive samples as a function of the HCV genotype is shown in Fig. 3b .", "3b . More than 60% of the neutralizing antibodies titers fell in the range from 1.7 to 2.69 log titers, corresponding to dilutions of 1:50 and 1:500, respectively. Overall, 3.5% of the samples displayed a titer greater than log 3.0 1:1000 and, conversely, 3.5% displayed a titer below the cut-off value, i.e.", "Overall, 3.5% of the samples displayed a titer greater than log 3.0 1:1000 and, conversely, 3.5% displayed a titer below the cut-off value, i.e. log 1.25 1:10 . Thus, of 57 HCV-infected patients, only two did not test positive for neutralizing antibodies in this assay the titers were 0.960 and 0.932, respectively .", "Thus, of 57 HCV-infected patients, only two did not test positive for neutralizing antibodies in this assay the titers were 0.960 and 0.932, respectively . The role of neutralizing antibodies during acute and chronic viral infection remains an important question and has generated controversial results. Initially, the presence of neutralizing antibodies was shown to control the HCV load and to contribute to viral eradication in patients capable of clearing the infection .", "Initially, the presence of neutralizing antibodies was shown to control the HCV load and to contribute to viral eradication in patients capable of clearing the infection . In other studies, the appearance of neutralizing antibodies was delayed and restricted to IgG1 antibodies in patients who develop a chronic infection . The chimpanzee model has been critical for the study of HCV transmission and host immune responses; however, neutralizing antibodies were not detected in some animals that resolved their infection -suggesting a minimal role in viral clearance, as also observed in human studies .", "The chimpanzee model has been critical for the study of HCV transmission and host immune responses; however, neutralizing antibodies were not detected in some animals that resolved their infection -suggesting a minimal role in viral clearance, as also observed in human studies . Experimentally infected chimpanzees and naturally infected humans can be re-infected with homologous and heterologous HCV strains, suggesting that the humoral immunity that develops after spontaneous resolution of acute hepatitis C is not sterilizing . During chronic infection in humans, the presence and/or production of neutralizing antibodies do not suffice for curing the infection but could regulate the spread of the virus.", "During chronic infection in humans, the presence and/or production of neutralizing antibodies do not suffice for curing the infection but could regulate the spread of the virus. Thus, it can be postulated that during chronic infection, viral mutants can continuously escape the renewed production of neutralizing antibodies. Retroviral pseudoparticles have been used to develop a very interesting tool for measuring neutralizing antibodies in vitro .", "Retroviral pseudoparticles have been used to develop a very interesting tool for measuring neutralizing antibodies in vitro . The assay has demonstrated the presence of HCV-neutralizing antibodies in human sera with relatively high titers >1:320 and broadly neutralizing activity against different HCV genotypes. However, this model does not represent genuine HCV virions; in particular, the budding of retroviral particles is thought to be very different and may involve a variety of cellular pathways.", "However, this model does not represent genuine HCV virions; in particular, the budding of retroviral particles is thought to be very different and may involve a variety of cellular pathways. Characterization of infectious retroviral pseudotype particles bearing HCV glycoproteins have been shown to be very heterogeneous, and so it is possible that these pseudoparticles may not be as relevant as the native HCV virions . The recent development of a cell culture model for HCV enables the production of native HCV virions that can be efficiently propagated in cell culture .", "The recent development of a cell culture model for HCV enables the production of native HCV virions that can be efficiently propagated in cell culture . This cell culture system has allowed us to develop a neutralization assay for evaluating the level and the proportion of HCVneutralizing antibodies in chronically infected HCV patients. We analysed a number of parameters such as practicability, reproducibility and specificity and tested the effect of a range of variables viral inoculum size, incubation time, fixation and permeabilization methods, blocking and revelation reagents on these parameters data not shown .", "We analysed a number of parameters such as practicability, reproducibility and specificity and tested the effect of a range of variables viral inoculum size, incubation time, fixation and permeabilization methods, blocking and revelation reagents on these parameters data not shown . Overall, the neutralization assay described in this study performs similarly to standardized neutralization assays for many other viruses . The assay relies on the ability of the specific JFH-1 genotype 2 viral strain to replicate and multiply on a Huh-7 human hepatoma cell line in a cell culture model, enabling the rapid detection of viral foci after 72 hours of infection.", "The assay relies on the ability of the specific JFH-1 genotype 2 viral strain to replicate and multiply on a Huh-7 human hepatoma cell line in a cell culture model, enabling the rapid detection of viral foci after 72 hours of infection. Moreover, no secondary foci were detectable at this time point. Fixation with paraformaldehyde and permeabilization with Triton X-100 were chosen in order to preserve antigenicity and prevent the cell monolayer from detaching during washes.", "Fixation with paraformaldehyde and permeabilization with Triton X-100 were chosen in order to preserve antigenicity and prevent the cell monolayer from detaching during washes. Development with DAB peroxide substrate made it easy to count specifically coloured viral foci. The viral inoculum size is an important parameter; it has to be low enough to enable good assay sensitivity but high enough to produce a statistically significant number of foci, i.e.", "The viral inoculum size is an important parameter; it has to be low enough to enable good assay sensitivity but high enough to produce a statistically significant number of foci, i.e. allowing the reduction in the number of foci and thus the effect of neutralization to be monitored. Thus, 100 FFUs were used as the inoculum in this neutralization assay.", "Thus, 100 FFUs were used as the inoculum in this neutralization assay. In order to test different human samples, we had to take into account the ability of HDL to facilitate HCVcc entry via a mechanism which depends on expression of the scavenger receptor BI . Given HDL's role in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibodies titer; this frees the assay of the risk of non-specific neutralization activity of the serum via the effects of HDL, the complement system and/or serum amyloid A protein SAA .", "Given HDL's role in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibodies titer; this frees the assay of the risk of non-specific neutralization activity of the serum via the effects of HDL, the complement system and/or serum amyloid A protein SAA . The HCV neutralization assay exhibited good reproducibility, for both duplicate assays and independent tests. As expected, the intra-assay coefficient of variation CV was lower than the interassay CV.", "As expected, the intra-assay coefficient of variation CV was lower than the interassay CV. The test also showed good specificity, since there was no interaction with anti-HIV, anti-HBV or heterophile antibodies. Very low titers were found with HCV ELISA and RNA-negative samples, and the assay's cut-off was determined as the mean titer for negative samples plus two standard deviations 1.25 log, corresponding to a dilution of 1:18 .", "Very low titers were found with HCV ELISA and RNA-negative samples, and the assay's cut-off was determined as the mean titer for negative samples plus two standard deviations 1.25 log, corresponding to a dilution of 1:18 . Given that only the JFH-1 strain of HCV genotype 2a was available for the assay, we evaluated the neutralization titer of sera from patients chronically infected with other HCV genotypes, i.e. 1, 2, 3, 4 and 5.", "1, 2, 3, 4 and 5. Most of these sera were detected as positive by the neutralization assay, except for two sera from HCV genotype 1-infected patients. These two samples presented a high specific antibody ratio according to the ELISA but only very low inhibition by neutralization assay far below the cut-off, in fact .", "These two samples presented a high specific antibody ratio according to the ELISA but only very low inhibition by neutralization assay far below the cut-off, in fact . We conclude that either the samples lacked neutralizing antibodies or that any such antibodies that were present did not cross-neutralize with HCV genotype 2a. The sensitivity was 100% -not only for genotype 2 the genotype of the strain used for the assay but also for other HCV genotypes except genotype 1 .", "The sensitivity was 100% -not only for genotype 2 the genotype of the strain used for the assay but also for other HCV genotypes except genotype 1 . HCV genotype 5 antibodies were also measured but there were too few samples for accurate testing. Moreover, the positive sera 96.5% had comparable and significantly high titers 1.99 ± 0.63 , whatever the genotype.", "Moreover, the positive sera 96.5% had comparable and significantly high titers 1.99 ± 0.63 , whatever the genotype. This finding suggests that most neutralizing antibodies are cross-reactive. Another possibility is that most of the patients had been previously infected by a genotype 2 strain.", "Another possibility is that most of the patients had been previously infected by a genotype 2 strain. However, this is unlikely because few genotype 2 strains are circulating in France . As expected for a neutralization test, the assay presented in the present study appeared to be very specific independently of the genotype and usable in most circumstances.", "As expected for a neutralization test, the assay presented in the present study appeared to be very specific independently of the genotype and usable in most circumstances. For most viral infections, neutralization assays such as that described in this study are used as reference assays. Thus, we are confident that as other HCVcc genotypes become available, these assays will replace the pseudoparticle assay in the near future because they are probably more relevant.", "Thus, we are confident that as other HCVcc genotypes become available, these assays will replace the pseudoparticle assay in the near future because they are probably more relevant. Our assay is somewhat time-consuming and could be simplified by using one dilution to count the foci; however, this type of \"short cut\" would make it difficult to extrapolate to the dilution neutralizing 50% of the inoculum. Another approach would consist in using recombinant HCV capable of expressing reporter genes such as luciferase in order to use a single dilution and obtain a quantitative result .", "Another approach would consist in using recombinant HCV capable of expressing reporter genes such as luciferase in order to use a single dilution and obtain a quantitative result . However, further neutralization studies using other genotypes are needed in order to complete our observations and to char- A simple, specific and reproducible cell culture-based neutralization assay was developed for the determination of neutralizing anti-HCV antibodies in human sera. This test should be an important tool for gauging the relationship between the neutralizing response and viral load kinetics in acutely and chronically infected patients.", "This test should be an important tool for gauging the relationship between the neutralizing response and viral load kinetics in acutely and chronically infected patients. The Huh-7 human hepatoma cells were grown in Dulbecco's minimum essential medium Invitrogen supplemented with 10% fetal bovine serum. All cell cultures were maintained in 5% CO 2 at 37°C.", "All cell cultures were maintained in 5% CO 2 at 37°C. The plasmid pJFH-1 containing the full-length cDNA of the JFH-1 isolate which belongs to subtype 2a GenBank accession no. AB047639 , was a gift from Dr Wakita Department of Microbiology, Tokyo Metropolitan Institute for Neuroscience, Tokyo, Japan and has been described previously .", "AB047639 , was a gift from Dr Wakita Department of Microbiology, Tokyo Metropolitan Institute for Neuroscience, Tokyo, Japan and has been described previously . To generate genomic HCV RNA, the plasmid pJFH-1 was linearized at the 3' end of the HCV cDNA and used as a template for in vitro transcription, as described previously . Viral stocks were obtained by harvesting cell culture supernatants and freezing them at -80°C.", "Viral stocks were obtained by harvesting cell culture supernatants and freezing them at -80°C. Virus titration was performed on Huh-7 cells with 6-well microtiter plates Corning, NY 72 hours after incubation, by immunostaining the cells with antibodies from a HCV-positive patient serum that had previously been inactivated at 56°C see the section on the virus neutralization assay . The viral titer was determined in triplicate from the mean number of foci and expressed as focus forming units/mL FFU/mL .", "The viral titer was determined in triplicate from the mean number of foci and expressed as focus forming units/mL FFU/mL . Seventy-seven human serum samples were tested. Collection of the sera was approved by the local Ethics Committee and informed consent had been obtained from the donors. Fifty-seven of these samples were obtained from chronically infected HCV patients.", "Fifty-seven of these samples were obtained from chronically infected HCV patients. The presence of HCV antibodies was determined and confirmed using two third-generation HCV EIA assays Axsym ® HCV Version 3.0, Abbott, Wiesbaden, Germany and Vitros ® Anti-HCV reagent pack, Ortho-Clinical Diagnostic, High Wycombe, United Kingdom . HCV RNA was determined with a qualitative commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France and HCV genotyping was performed by direct sequencing, as described elsewhere .", "HCV RNA was determined with a qualitative commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France and HCV genotyping was performed by direct sequencing, as described elsewhere . The genotypes were distributed as follows: 11, 11, 11, 12, 10 and 2 samples of types 1a, 1b, 2, 3, 4 and 5, respectively. A set of 20 anti-HCV-negative serum samples was used to evaluate the assay's specif-icity, including five serum samples with positive hepatitis B virus surface antibody anti-HBs status and five sera from Epstein-Barr virus-infected patients that had tested positive for heterophile antibodies.", "A set of 20 anti-HCV-negative serum samples was used to evaluate the assay's specif-icity, including five serum samples with positive hepatitis B virus surface antibody anti-HBs status and five sera from Epstein-Barr virus-infected patients that had tested positive for heterophile antibodies. All serum samples had been stored at -80°C upon collection and had not been thawed until the time of assay. Serum immunoglobulins G IgG fraction was purified using protein G-Sepharose GE Healthcare, Orsay, France The HCV focus reduction neutralization assay was performed in 96-well microtiter plates.", "Serum immunoglobulins G IgG fraction was purified using protein G-Sepharose GE Healthcare, Orsay, France The HCV focus reduction neutralization assay was performed in 96-well microtiter plates. Serial dilutions of purified IgG 10 μg ranging from 1:10 to 1:1,280 were established. Each dilution was tested twice.", "Each dilution was tested twice. 25 μL of each sample was mixed with 25 μL of virus 100 FFU in 96well microtiter plates and incubated for 1 hour at 37°C, 5% CO 2 . A volume of 100 μL of Huh-7 cell suspension 10,000 cells/well in culture medium was added and incubated for 5 hours at 37°C, 5% CO2.", "A volume of 100 μL of Huh-7 cell suspension 10,000 cells/well in culture medium was added and incubated for 5 hours at 37°C, 5% CO2. After 5 hours, the supernatants were removed and 100 μL of culture medium were added to the monolayers. After 72 hours, the cells were fixed with paraformaldehyde and permeabilized with 0.5% Triton X-100.", "After 72 hours, the cells were fixed with paraformaldehyde and permeabilized with 0.5% Triton X-100. Primary antibody a HCVpositive patient serum inactivated at 56°C was diluted to 1:500 prior to use and then incubated for 1 h at room temperature. A peroxidase-coupled, Fc-specific anti-human IgG antibody Sigma, Saint Quentin Fallavier, France diluted to 1:200 was dispensed onto the cell monolayer and incubated for 30 min at room temperature.", "A peroxidase-coupled, Fc-specific anti-human IgG antibody Sigma, Saint Quentin Fallavier, France diluted to 1:200 was dispensed onto the cell monolayer and incubated for 30 min at room temperature. The reaction was developed with DAB peroxidase substrate Sigma, Saint Quentin Fallavier, France and stopped after 10 min of incubation with distilled water. The number of HCV foci in each dilution was determined.", "The number of HCV foci in each dilution was determined. Controls were included in each assay non-neutralized virus, purified IgG from each patient at a 1:10 dilution . The dilution that neutralized 50% of the virus was calculated by curvilinear regression analysis using XLSTAT 2006 software Addinsoft SARL, Paris, France .", "The dilution that neutralized 50% of the virus was calculated by curvilinear regression analysis using XLSTAT 2006 software Addinsoft SARL, Paris, France . Each titer was deter-mined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%. Titers were expressed as logarithmic values and means ± standard deviation were calculated.", "Titers were expressed as logarithmic values and means ± standard deviation were calculated. Student's t-test was used to compare data between groups. p values below 0.05 were considered to be significant." ]

[ "BACKGROUND/AIM: The role of humoral immunity in hepatitis C virus HCV infection is poorly understood. Nevertheless, there is increasing interest in characterizing the neutralizing antibodies in the serum of HCV-infected patients. Focus reduction assays have been widely used to evaluate neutralizing antibody responses against a range of non-cytopathic viruses.", "Focus reduction assays have been widely used to evaluate neutralizing antibody responses against a range of non-cytopathic viruses. Based on the recent development of a HCV cell culture system using the genotype 2 JFH-1-strain, we developed a focus reduction assay for HCV-neutralizing antibodies. METHODS: The focus reduction assay was based on a standard microneutralization assay in which immunostained foci on tissue culture plates are counted.", "METHODS: The focus reduction assay was based on a standard microneutralization assay in which immunostained foci on tissue culture plates are counted. The neutralizing anti-HCV antibodies titers of purified serum immunoglobulin samples from seventy-seven individuals were determined using a 50% focus reduction neutralization assay. Each titer was determined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%.", "Each titer was determined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%. IgG antibodies were first purified from each serum in order to avoid the facilitating effect of HDL on HCV entry. RESULTS: The assay's cut-off using an ELISA and RNA HCV-negative samples was found to be 1.25 log, corresponding to a dilution of 1:18.", "RESULTS: The assay's cut-off using an ELISA and RNA HCV-negative samples was found to be 1.25 log, corresponding to a dilution of 1:18. The assay was compared with a commercial HCV ELISA and exhibited specificity and sensitivity values of 100% and 96.5%, respectively, and good reproducibility with intra-assay and inter-assay coefficients of variation of 6.7% and 12.6%, respectively . The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples.", "The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples. The neutralizing antibodies titers were 2.13 log 1:134 for homologous samples from HCV genotype 2 infected patients harboring the same genotype as JFH-1 and 1.93 log 1:85 for heterologous samples from patients infected by genotypes other than type 2. These results confirm the presence of broadly cross-neutralizing antibodies already reported using the HCV pseudoparticles system.", "These results confirm the presence of broadly cross-neutralizing antibodies already reported using the HCV pseudoparticles system. CONCLUSION: This study presents a simple, specific and reproducible cell culture-based assay for determination of HCV-neutralizing antibodies in human sera. The assay should be an important tool for gauging the relationship between the neutralizing antibodies response and viral load kinetics in acutely or chronically infected patients and for investigating the possible eradication or prevention of HCV infection by neutralizing antibodies.", "The assay should be an important tool for gauging the relationship between the neutralizing antibodies response and viral load kinetics in acutely or chronically infected patients and for investigating the possible eradication or prevention of HCV infection by neutralizing antibodies. Text: Hepatitis C virus HCV, a member of the Flaviviridae family is an enveloped, positive-stranded RNA virus that preferentially replicates in hepatocytes. At least 170 million people worldwide are persistently infected with hepatitis C virus.", "At least 170 million people worldwide are persistently infected with hepatitis C virus. Chronic HCV infection is associated with a significant risk of progression to cirrhosis and hepatocellular carcinoma . Antiviral therapy with pegylated alpha-interferon and ribavirin the current best therapeutic regimen is only successful in about 50% of all treated patients.", "Antiviral therapy with pegylated alpha-interferon and ribavirin the current best therapeutic regimen is only successful in about 50% of all treated patients. Better knowledge of the viral and host factors that determine HCV clearance or persistence during the acute stage of infection is needed in order to improve antiviral therapy and to develop efficient vaccines. Studies focusing on innate and cellular immune responses have shown that a sufficiently large HCV inoculum is able to evade, subvert or circumvent the host's defences.", "Studies focusing on innate and cellular immune responses have shown that a sufficiently large HCV inoculum is able to evade, subvert or circumvent the host's defences. At present, the chimpanzee is the only reliable experimental animal model in which the initial post-HCV infection events and the efficacy of vaccine candidates can be evaluated . It has been shown that HCV-specific T-cell immunity is important in the control of HCV infection .", "It has been shown that HCV-specific T-cell immunity is important in the control of HCV infection . Several studies have indicated a role for humoral immunity in the acute stage of HCV infection but this aspect remains poorly characterized. The E1 and E2 glycoproteins are thought to be the viral attachment proteins and thus the main targets for HCV-neutralizing antibodies; identification of protective epitopes conserved across different strains of HCV is therefore a major challenge in vaccine design.", "The E1 and E2 glycoproteins are thought to be the viral attachment proteins and thus the main targets for HCV-neutralizing antibodies; identification of protective epitopes conserved across different strains of HCV is therefore a major challenge in vaccine design. A number of antibodies capable of blocking E2 binding to cells or cell receptors have been described, some of which neutralize HCV entry in animal or cellular models . Cell entry has been shown to involve several surface molecules notably including the tetraspanin CD81 and the SR-BI receptor , although further studies are needed to better understand how viral entry occurs and how it might be neutralized.", "Cell entry has been shown to involve several surface molecules notably including the tetraspanin CD81 and the SR-BI receptor , although further studies are needed to better understand how viral entry occurs and how it might be neutralized. Detection of neutralizing antibodies in human blood had been problematical until an efficient and reliable cell culture system for HCV became available. Hence, the development of an in vitro neutralization assay for HCV could be extremely valuable for characterizing the humoral immune response to HCV and for evaluating the potential of passive and active immunization against hepatitis C. Recent studies using an in vitro neutralization assay system based on infectious retroviral pseudoparticles HCVpp bearing HCV envelope glycoproteins have confirmed that HCV-infected patient sera can indeed neutralize infection .", "Hence, the development of an in vitro neutralization assay for HCV could be extremely valuable for characterizing the humoral immune response to HCV and for evaluating the potential of passive and active immunization against hepatitis C. Recent studies using an in vitro neutralization assay system based on infectious retroviral pseudoparticles HCVpp bearing HCV envelope glycoproteins have confirmed that HCV-infected patient sera can indeed neutralize infection . However, it has also been shown that the neutralizing activity of antibodies from HCV-infected patients is attenuated by a factor present in human serum, identified as the highdensity lipoprotein HDL fraction . HDL facilitation of HCVpp entry is a post-binding event , sug-gesting that HDLs favour internalization of virions and thus the latter's escape from neutralizing antibodies.", "HDL facilitation of HCVpp entry is a post-binding event , sug-gesting that HDLs favour internalization of virions and thus the latter's escape from neutralizing antibodies. Recently, an HCV cell culture model HCVcc has been developed , allowing the production of virus particles that can be efficiently propagated in cell culture. Some preliminary neutralization assays have been carried out by these authors.", "Some preliminary neutralization assays have been carried out by these authors. In this study, we describe how we set up a standardized focus reduction neutralization assay based on HCVcc. Focus reduction assays have been widely used to evaluate the neutralizing antibody responses to viruses that can form foci in infected cells.", "Focus reduction assays have been widely used to evaluate the neutralizing antibody responses to viruses that can form foci in infected cells. Following the recent development of the HCVcc model, the principle of the focus reduction assay has been applied to HCV-neutralizing antibodies detection. The JFH-1 HCV 2a viral strain was grown on a Huh-7 human hepatoma cell line.", "The JFH-1 HCV 2a viral strain was grown on a Huh-7 human hepatoma cell line. After three days of infection and cell permeabilization, detection of the HCV foci was carried out using an inactivated HCVpositive patient serum primary antibody and a peroxidase-coupled, Fc-specific anti-human IgG-antibody. The reaction was revealed with DAB peroxidase substrate.", "The reaction was revealed with DAB peroxidase substrate. The viral foci were thus stained brown, making them easy to count see Fig. 1a . It has been recently shown that the neutralizing activity of HCV antibodies is attenuated by a serum factor associated with the HDL fraction.", "It has been recently shown that the neutralizing activity of HCV antibodies is attenuated by a serum factor associated with the HDL fraction. Hence, HDLs were able to facilitate HCVpp and HCVcc entry via a mechanism which depended on the expression of the scavenger receptor BI SR-BI and its selective lipid-uptake function . In view of the role of HDL in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibody titer see Fig.", "In view of the role of HDL in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibody titer see Fig. 1b . The specificity of the HCV neutralization assay was assessed by testing 20 anti-HCV-ELISA-negative samples, including five positive for hepatitis B virus surface antibodies anti-HBs and five positive for heterophile antibodies.", "The specificity of the HCV neutralization assay was assessed by testing 20 anti-HCV-ELISA-negative samples, including five positive for hepatitis B virus surface antibodies anti-HBs and five positive for heterophile antibodies. All samples tested negative with two commercial anti-HCV antibody detection assays Axsym ® HCV Version 3.0, Abbott, Wiesbaden, Germany; Vitros ® Anti-HCV reagent pack, Ortho-Clinical Diagnostic, High Wycombe, United Kingdom and HCV-RNA-negative with a qualitative, commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France . These anti-HCV-negative samples were compared with 11 samples from patients chronically infected with HCV genotype 2.", "These anti-HCV-negative samples were compared with 11 samples from patients chronically infected with HCV genotype 2. The neutralization titers of anti-HCV-negative serum samples are shown in Fig. 2 ., with a mean value of 1.083 ± 0.083 corresponding to a dilution of 1:12 .", "2 ., with a mean value of 1.083 ± 0.083 corresponding to a dilution of 1:12 . The assay's cut-off determined as the mean value for negative samples plus two standard deviations corresponded to a dilution of 1:18. The assay exhibited specificity and sensibility values of 100% and 96.5%, respectively.", "The assay exhibited specificity and sensibility values of 100% and 96.5%, respectively. The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples data not shown . Conversely, the chronically HCV genotype 2-positive samples displayed strong reactions, with a mean value of 2.128 ± 0.365 corresponding to a dilution of 1:134 p < 0.001 .", "Conversely, the chronically HCV genotype 2-positive samples displayed strong reactions, with a mean value of 2.128 ± 0.365 corresponding to a dilution of 1:134 p < 0.001 . Inter-assay variability was determined by testing one HCV genotype 2 sample in 10 consecutive experiments n = 10 , whereas intra-assay variability was evaluated by testing the same sample 10 times n = 10 in the same experiment, whilst running the dilution series. The intra-assay and inter-assay coefficients of variation CV of the log neutralization titers were 6.7% and 12.6%, respectively.", "The intra-assay and inter-assay coefficients of variation CV of the log neutralization titers were 6.7% and 12.6%, respectively. Fifty-seven HCV-positive antibodies samples were evaluated using the HCV focus reduction neutralization assay. The genotypes were distributed as follows; for types 1a, 1b, 2, 3, 4 and 5, we studied 11, 11, 11, 12, 10 and 2 samples, respectively.", "The genotypes were distributed as follows; for types 1a, 1b, 2, 3, 4 and 5, we studied 11, 11, 11, 12, 10 and 2 samples, respectively. The mean values of the different genotypes is shown in Fig. 3 . and Table 1 .", "3 . and Table 1 . The mean log neutralization titers for genotypes 1a, 2 and 3 are very similar 2.046 ± 0.671 for genotype 1a, 2.128 ± 0.365 for genotype 2 and 2.148 ± 0.478 for genotype 3 . The mean average values are lower for genotype 1b 1.747 ± 0.462 and genotype 4 1.786 ± 0.236 .", "The mean average values are lower for genotype 1b 1.747 ± 0.462 and genotype 4 1.786 ± 0.236 . Strikingly, very high heterologous titers were observed for five patients -three infected with HCV genotype 1a and two infected with HCV genotype 3 see Fig. 3a .", "3a . There were too few genotype 5 samples to compare with the other genotypes but the corresponding results nevertheless indicate that the neutralization assay is suitable for this genotype. The two The distribution of the log neutralization titers across all the HCV ELISA and RNA-positive samples as a function of the HCV genotype is shown in Fig. 3b .", "3b . More than 60% of the neutralizing antibodies titers fell in the range from 1.7 to 2.69 log titers, corresponding to dilutions of 1:50 and 1:500, respectively. Overall, 3.5% of the samples displayed a titer greater than log 3.0 1:1000 and, conversely, 3.5% displayed a titer below the cut-off value, i.e.", "Overall, 3.5% of the samples displayed a titer greater than log 3.0 1:1000 and, conversely, 3.5% displayed a titer below the cut-off value, i.e. log 1.25 1:10 . Thus, of 57 HCV-infected patients, only two did not test positive for neutralizing antibodies in this assay the titers were 0.960 and 0.932, respectively .", "Thus, of 57 HCV-infected patients, only two did not test positive for neutralizing antibodies in this assay the titers were 0.960 and 0.932, respectively . The role of neutralizing antibodies during acute and chronic viral infection remains an important question and has generated controversial results. Initially, the presence of neutralizing antibodies was shown to control the HCV load and to contribute to viral eradication in patients capable of clearing the infection .", "Initially, the presence of neutralizing antibodies was shown to control the HCV load and to contribute to viral eradication in patients capable of clearing the infection . In other studies, the appearance of neutralizing antibodies was delayed and restricted to IgG1 antibodies in patients who develop a chronic infection . The chimpanzee model has been critical for the study of HCV transmission and host immune responses; however, neutralizing antibodies were not detected in some animals that resolved their infection -suggesting a minimal role in viral clearance, as also observed in human studies .", "The chimpanzee model has been critical for the study of HCV transmission and host immune responses; however, neutralizing antibodies were not detected in some animals that resolved their infection -suggesting a minimal role in viral clearance, as also observed in human studies . Experimentally infected chimpanzees and naturally infected humans can be re-infected with homologous and heterologous HCV strains, suggesting that the humoral immunity that develops after spontaneous resolution of acute hepatitis C is not sterilizing . During chronic infection in humans, the presence and/or production of neutralizing antibodies do not suffice for curing the infection but could regulate the spread of the virus.", "During chronic infection in humans, the presence and/or production of neutralizing antibodies do not suffice for curing the infection but could regulate the spread of the virus. Thus, it can be postulated that during chronic infection, viral mutants can continuously escape the renewed production of neutralizing antibodies. Retroviral pseudoparticles have been used to develop a very interesting tool for measuring neutralizing antibodies in vitro .", "Retroviral pseudoparticles have been used to develop a very interesting tool for measuring neutralizing antibodies in vitro . The assay has demonstrated the presence of HCV-neutralizing antibodies in human sera with relatively high titers >1:320 and broadly neutralizing activity against different HCV genotypes. However, this model does not represent genuine HCV virions; in particular, the budding of retroviral particles is thought to be very different and may involve a variety of cellular pathways.", "However, this model does not represent genuine HCV virions; in particular, the budding of retroviral particles is thought to be very different and may involve a variety of cellular pathways. Characterization of infectious retroviral pseudotype particles bearing HCV glycoproteins have been shown to be very heterogeneous, and so it is possible that these pseudoparticles may not be as relevant as the native HCV virions . The recent development of a cell culture model for HCV enables the production of native HCV virions that can be efficiently propagated in cell culture .", "The recent development of a cell culture model for HCV enables the production of native HCV virions that can be efficiently propagated in cell culture . This cell culture system has allowed us to develop a neutralization assay for evaluating the level and the proportion of HCVneutralizing antibodies in chronically infected HCV patients. We analysed a number of parameters such as practicability, reproducibility and specificity and tested the effect of a range of variables viral inoculum size, incubation time, fixation and permeabilization methods, blocking and revelation reagents on these parameters data not shown .", "We analysed a number of parameters such as practicability, reproducibility and specificity and tested the effect of a range of variables viral inoculum size, incubation time, fixation and permeabilization methods, blocking and revelation reagents on these parameters data not shown . Overall, the neutralization assay described in this study performs similarly to standardized neutralization assays for many other viruses . The assay relies on the ability of the specific JFH-1 genotype 2 viral strain to replicate and multiply on a Huh-7 human hepatoma cell line in a cell culture model, enabling the rapid detection of viral foci after 72 hours of infection.", "The assay relies on the ability of the specific JFH-1 genotype 2 viral strain to replicate and multiply on a Huh-7 human hepatoma cell line in a cell culture model, enabling the rapid detection of viral foci after 72 hours of infection. Moreover, no secondary foci were detectable at this time point. Fixation with paraformaldehyde and permeabilization with Triton X-100 were chosen in order to preserve antigenicity and prevent the cell monolayer from detaching during washes.", "Fixation with paraformaldehyde and permeabilization with Triton X-100 were chosen in order to preserve antigenicity and prevent the cell monolayer from detaching during washes. Development with DAB peroxide substrate made it easy to count specifically coloured viral foci. The viral inoculum size is an important parameter; it has to be low enough to enable good assay sensitivity but high enough to produce a statistically significant number of foci, i.e.", "The viral inoculum size is an important parameter; it has to be low enough to enable good assay sensitivity but high enough to produce a statistically significant number of foci, i.e. allowing the reduction in the number of foci and thus the effect of neutralization to be monitored. Thus, 100 FFUs were used as the inoculum in this neutralization assay.", "Thus, 100 FFUs were used as the inoculum in this neutralization assay. In order to test different human samples, we had to take into account the ability of HDL to facilitate HCVcc entry via a mechanism which depends on expression of the scavenger receptor BI . Given HDL's role in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibodies titer; this frees the assay of the risk of non-specific neutralization activity of the serum via the effects of HDL, the complement system and/or serum amyloid A protein SAA .", "Given HDL's role in HCV entry, immunoglobulins were purified from each serum sample prior to determination of the neutralizing antibodies titer; this frees the assay of the risk of non-specific neutralization activity of the serum via the effects of HDL, the complement system and/or serum amyloid A protein SAA . The HCV neutralization assay exhibited good reproducibility, for both duplicate assays and independent tests. As expected, the intra-assay coefficient of variation CV was lower than the interassay CV.", "As expected, the intra-assay coefficient of variation CV was lower than the interassay CV. The test also showed good specificity, since there was no interaction with anti-HIV, anti-HBV or heterophile antibodies. Very low titers were found with HCV ELISA and RNA-negative samples, and the assay's cut-off was determined as the mean titer for negative samples plus two standard deviations 1.25 log, corresponding to a dilution of 1:18 .", "Very low titers were found with HCV ELISA and RNA-negative samples, and the assay's cut-off was determined as the mean titer for negative samples plus two standard deviations 1.25 log, corresponding to a dilution of 1:18 . Given that only the JFH-1 strain of HCV genotype 2a was available for the assay, we evaluated the neutralization titer of sera from patients chronically infected with other HCV genotypes, i.e. 1, 2, 3, 4 and 5.", "1, 2, 3, 4 and 5. Most of these sera were detected as positive by the neutralization assay, except for two sera from HCV genotype 1-infected patients. These two samples presented a high specific antibody ratio according to the ELISA but only very low inhibition by neutralization assay far below the cut-off, in fact .", "These two samples presented a high specific antibody ratio according to the ELISA but only very low inhibition by neutralization assay far below the cut-off, in fact . We conclude that either the samples lacked neutralizing antibodies or that any such antibodies that were present did not cross-neutralize with HCV genotype 2a. The sensitivity was 100% -not only for genotype 2 the genotype of the strain used for the assay but also for other HCV genotypes except genotype 1 .", "The sensitivity was 100% -not only for genotype 2 the genotype of the strain used for the assay but also for other HCV genotypes except genotype 1 . HCV genotype 5 antibodies were also measured but there were too few samples for accurate testing. Moreover, the positive sera 96.5% had comparable and significantly high titers 1.99 ± 0.63 , whatever the genotype.", "Moreover, the positive sera 96.5% had comparable and significantly high titers 1.99 ± 0.63 , whatever the genotype. This finding suggests that most neutralizing antibodies are cross-reactive. Another possibility is that most of the patients had been previously infected by a genotype 2 strain.", "Another possibility is that most of the patients had been previously infected by a genotype 2 strain. However, this is unlikely because few genotype 2 strains are circulating in France . As expected for a neutralization test, the assay presented in the present study appeared to be very specific independently of the genotype and usable in most circumstances.", "As expected for a neutralization test, the assay presented in the present study appeared to be very specific independently of the genotype and usable in most circumstances. For most viral infections, neutralization assays such as that described in this study are used as reference assays. Thus, we are confident that as other HCVcc genotypes become available, these assays will replace the pseudoparticle assay in the near future because they are probably more relevant.", "Thus, we are confident that as other HCVcc genotypes become available, these assays will replace the pseudoparticle assay in the near future because they are probably more relevant. Our assay is somewhat time-consuming and could be simplified by using one dilution to count the foci; however, this type of \"short cut\" would make it difficult to extrapolate to the dilution neutralizing 50% of the inoculum. Another approach would consist in using recombinant HCV capable of expressing reporter genes such as luciferase in order to use a single dilution and obtain a quantitative result .", "Another approach would consist in using recombinant HCV capable of expressing reporter genes such as luciferase in order to use a single dilution and obtain a quantitative result . However, further neutralization studies using other genotypes are needed in order to complete our observations and to char- A simple, specific and reproducible cell culture-based neutralization assay was developed for the determination of neutralizing anti-HCV antibodies in human sera. This test should be an important tool for gauging the relationship between the neutralizing response and viral load kinetics in acutely and chronically infected patients.", "This test should be an important tool for gauging the relationship between the neutralizing response and viral load kinetics in acutely and chronically infected patients. The Huh-7 human hepatoma cells were grown in Dulbecco's minimum essential medium Invitrogen supplemented with 10% fetal bovine serum. All cell cultures were maintained in 5% CO 2 at 37°C.", "All cell cultures were maintained in 5% CO 2 at 37°C. The plasmid pJFH-1 containing the full-length cDNA of the JFH-1 isolate which belongs to subtype 2a GenBank accession no. AB047639 , was a gift from Dr Wakita Department of Microbiology, Tokyo Metropolitan Institute for Neuroscience, Tokyo, Japan and has been described previously .", "AB047639 , was a gift from Dr Wakita Department of Microbiology, Tokyo Metropolitan Institute for Neuroscience, Tokyo, Japan and has been described previously . To generate genomic HCV RNA, the plasmid pJFH-1 was linearized at the 3' end of the HCV cDNA and used as a template for in vitro transcription, as described previously . Viral stocks were obtained by harvesting cell culture supernatants and freezing them at -80°C.", "Viral stocks were obtained by harvesting cell culture supernatants and freezing them at -80°C. Virus titration was performed on Huh-7 cells with 6-well microtiter plates Corning, NY 72 hours after incubation, by immunostaining the cells with antibodies from a HCV-positive patient serum that had previously been inactivated at 56°C see the section on the virus neutralization assay . The viral titer was determined in triplicate from the mean number of foci and expressed as focus forming units/mL FFU/mL .", "The viral titer was determined in triplicate from the mean number of foci and expressed as focus forming units/mL FFU/mL . Seventy-seven human serum samples were tested. Collection of the sera was approved by the local Ethics Committee and informed consent had been obtained from the donors. Fifty-seven of these samples were obtained from chronically infected HCV patients.", "Fifty-seven of these samples were obtained from chronically infected HCV patients. The presence of HCV antibodies was determined and confirmed using two third-generation HCV EIA assays Axsym ® HCV Version 3.0, Abbott, Wiesbaden, Germany and Vitros ® Anti-HCV reagent pack, Ortho-Clinical Diagnostic, High Wycombe, United Kingdom . HCV RNA was determined with a qualitative commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France and HCV genotyping was performed by direct sequencing, as described elsewhere .", "HCV RNA was determined with a qualitative commercial assay Cobas Amplicor HCV test Version 2.0, Roche Diagnostics, Meylan, France and HCV genotyping was performed by direct sequencing, as described elsewhere . The genotypes were distributed as follows: 11, 11, 11, 12, 10 and 2 samples of types 1a, 1b, 2, 3, 4 and 5, respectively. A set of 20 anti-HCV-negative serum samples was used to evaluate the assay's specif-icity, including five serum samples with positive hepatitis B virus surface antibody anti-HBs status and five sera from Epstein-Barr virus-infected patients that had tested positive for heterophile antibodies.", "A set of 20 anti-HCV-negative serum samples was used to evaluate the assay's specif-icity, including five serum samples with positive hepatitis B virus surface antibody anti-HBs status and five sera from Epstein-Barr virus-infected patients that had tested positive for heterophile antibodies. All serum samples had been stored at -80°C upon collection and had not been thawed until the time of assay. Serum immunoglobulins G IgG fraction was purified using protein G-Sepharose GE Healthcare, Orsay, France The HCV focus reduction neutralization assay was performed in 96-well microtiter plates.", "Serum immunoglobulins G IgG fraction was purified using protein G-Sepharose GE Healthcare, Orsay, France The HCV focus reduction neutralization assay was performed in 96-well microtiter plates. Serial dilutions of purified IgG 10 μg ranging from 1:10 to 1:1,280 were established. Each dilution was tested twice.", "Each dilution was tested twice. 25 μL of each sample was mixed with 25 μL of virus 100 FFU in 96well microtiter plates and incubated for 1 hour at 37°C, 5% CO 2 . A volume of 100 μL of Huh-7 cell suspension 10,000 cells/well in culture medium was added and incubated for 5 hours at 37°C, 5% CO2.", "A volume of 100 μL of Huh-7 cell suspension 10,000 cells/well in culture medium was added and incubated for 5 hours at 37°C, 5% CO2. After 5 hours, the supernatants were removed and 100 μL of culture medium were added to the monolayers. After 72 hours, the cells were fixed with paraformaldehyde and permeabilized with 0.5% Triton X-100.", "After 72 hours, the cells were fixed with paraformaldehyde and permeabilized with 0.5% Triton X-100. Primary antibody a HCVpositive patient serum inactivated at 56°C was diluted to 1:500 prior to use and then incubated for 1 h at room temperature. A peroxidase-coupled, Fc-specific anti-human IgG antibody Sigma, Saint Quentin Fallavier, France diluted to 1:200 was dispensed onto the cell monolayer and incubated for 30 min at room temperature.", "A peroxidase-coupled, Fc-specific anti-human IgG antibody Sigma, Saint Quentin Fallavier, France diluted to 1:200 was dispensed onto the cell monolayer and incubated for 30 min at room temperature. The reaction was developed with DAB peroxidase substrate Sigma, Saint Quentin Fallavier, France and stopped after 10 min of incubation with distilled water. The number of HCV foci in each dilution was determined.", "The number of HCV foci in each dilution was determined. Controls were included in each assay non-neutralized virus, purified IgG from each patient at a 1:10 dilution . The dilution that neutralized 50% of the virus was calculated by curvilinear regression analysis using XLSTAT 2006 software Addinsoft SARL, Paris, France .", "The dilution that neutralized 50% of the virus was calculated by curvilinear regression analysis using XLSTAT 2006 software Addinsoft SARL, Paris, France . Each titer was deter-mined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%. Titers were expressed as logarithmic values and means ± standard deviation were calculated.", "Titers were expressed as logarithmic values and means ± standard deviation were calculated. Student's t-test was used to compare data between groups. p values below 0.05 were considered to be significant." ]

[ "BACKGROUND: Volume-infection relationships have been examined for high-risk surgical procedures, but the conclusions remain controversial. The inconsistency might be due to inaccurate identification of cases of infection and different methods of categorizing service volumes. This study takes coronary artery bypass graft CABG surgical site infections SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, when different SSIs case identification, definitions and categorization methods of operation volumes were implemented.", "This study takes coronary artery bypass graft CABG surgical site infections SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, when different SSIs case identification, definitions and categorization methods of operation volumes were implemented. METHODS: A population-based cross-sectional multilevel study was conducted. A total of 7,007 patients who received CABG surgery between 2006 and 2008 from19 medical centers in Taiwan were recruited.", "A total of 7,007 patients who received CABG surgery between 2006 and 2008 from19 medical centers in Taiwan were recruited. SSIs associated with CABG surgery were identified using International Classification of Diseases, 9th Revision, Clinical Modification ICD-9 CM codes and a Classification and Regression Trees CART model. Two definitions of surgeon and hospital operation volumes were used: .", "Two definitions of surgeon and hospital operation volumes were used: . the cumulative CABG operation volumes within the study period; and . the cumulative CABG operation volumes in the previous one year before each CABG surgery. Operation volumes were further treated in three different ways: . a continuous variable; .", "Operation volumes were further treated in three different ways: . a continuous variable; . a categorical variable based on the quartile; and . a data-driven categorical variable based on k-means clustering algorithm. Furthermore, subgroup analysis for comorbidities was also conducted.", "Furthermore, subgroup analysis for comorbidities was also conducted. RESULTS: This study showed that hospital volumes were not significantly associated with SSIs, no matter which definitions or categorization methods of operation volume, or SSIs case identification approaches were used. On the contrary, the relationships between surgeon’s volumes varied.", "On the contrary, the relationships between surgeon’s volumes varied. Most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons. CONCLUSION: Surgeon volumes were more important than hospital volumes in exploring the relationship between CABG operation volumes and SSIs in Taiwan. However, the relationships were not robust.", "However, the relationships were not robust. Definitions and categorization methods of operation volume and correct identification of SSIs are important issues for future research. Text: data, which should use hierarchical models, may result in biased estimation of the variation and also lead to incorrect conclusions.", "Text: data, which should use hierarchical models, may result in biased estimation of the variation and also lead to incorrect conclusions. SSIs following coronary artery bypass graft CABG procedures place a heavy burden on patients and healthcare systems. The total length of stay and expenditure for patients with SSIs after CABG surgery is significantly longer and higher than those without SSIs.", "The total length of stay and expenditure for patients with SSIs after CABG surgery is significantly longer and higher than those without SSIs. In 2008, the Centers for Medicare & Medicaid of the United States of America implemented the \"Never Event\" policy, where hospitals would no longer receive higher payments for the additional costs associated with treating patients for certain healthcare-acquired infections, including those related to CABG. In view of the accuracy of SSIs identification and the heterogeneity of definition and categorization methods, no existing studies have used different infection case identification nor definitions and categorization methods of operation volume simultaneously to explore the relationship between operation volumes and infection.", "In view of the accuracy of SSIs identification and the heterogeneity of definition and categorization methods, no existing studies have used different infection case identification nor definitions and categorization methods of operation volume simultaneously to explore the relationship between operation volumes and infection. The current study takes CABG SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, given different SSI cases identification, operation volume definitions and categorization methods. This retrospective and cross-sectional study adopted a multilevel design to examine the relationships between provider volumes and SSIs after adjusting for patient-, surgeon-, and hospital-level covariates.", "This retrospective and cross-sectional study adopted a multilevel design to examine the relationships between provider volumes and SSIs after adjusting for patient-, surgeon-, and hospital-level covariates. We used data from the Taiwan National Health Insurance Research Database NHIRD from 2005 and 2008. The NHIRD, published by the Taiwan National Health Research Institute, includes all the original claims data and registration files for beneficiaries enrolled under the National Health Insurance NHI program.", "The NHIRD, published by the Taiwan National Health Research Institute, includes all the original claims data and registration files for beneficiaries enrolled under the National Health Insurance NHI program. The database covers the 23 million Taiwanese enrollees approximately 98% of the population in the NHI program. It is a de-identified secondary database containing patient-level demographic and administrative information; however, treatment items are aggregated and without time-related and clinical information.", "It is a de-identified secondary database containing patient-level demographic and administrative information; however, treatment items are aggregated and without time-related and clinical information. The data is released for research purposes. The protocol for the study was approved by the Institutional Review Board of the National Taiwan University Hospital protocol #201001027R .", "The protocol for the study was approved by the Institutional Review Board of the National Taiwan University Hospital protocol #201001027R . The dataset we used in this study was secondary data; all information was de-identified by data owners. In this study, we adopted the ICD-9-CM SSI codes hereafter referred to as the ICD-9-CM based model and the Classification and Regression Trees CART model, which was developed in our previous work to identify SSI cases.", "In this study, we adopted the ICD-9-CM SSI codes hereafter referred to as the ICD-9-CM based model and the Classification and Regression Trees CART model, which was developed in our previous work to identify SSI cases. As we mentioned above, the ICD-9-CM SSI codes were the most popular tool to identify the SSI cases in claims data. In the ICD-9-CM based model, SSI cases were divided into two categories: index hospitalization events and post-discharge events i.e., SSIs that occurred within 1 year after discharge and required readmission to a hospital and/ or the use of ambulatory services .", "In the ICD-9-CM based model, SSI cases were divided into two categories: index hospitalization events and post-discharge events i.e., SSIs that occurred within 1 year after discharge and required readmission to a hospital and/ or the use of ambulatory services . Following Wu et al , this study adopted the secondary ICD-9-CM diagnosis codes for index hospitalization events ICD-9-CM code: 996.03, 996.61, 996.72, and 998.5 , and the primary and secondary diagnosis codes for post-discharge events ICD-9-CM code: 038.0-038. 4 as the criteria for SSI identification, in order to avoid cases in which infection existed prior to hospitalization.", "4 as the criteria for SSI identification, in order to avoid cases in which infection existed prior to hospitalization. If a case had an index hospitalization event or a post-discharge event, then he/ she will be identified as SSIs by the ICD-9-CM based model. In the CART model, we adopted the type of antibiotics, dose of cefazolin, length of stay, and number of vessels obstructed as a proxy indicator of duration of operation as the parameters to identify the SSIs, according to our previous findings.", "In the CART model, we adopted the type of antibiotics, dose of cefazolin, length of stay, and number of vessels obstructed as a proxy indicator of duration of operation as the parameters to identify the SSIs, according to our previous findings. In our previous work, we used the 2005-2008 National Health Insurance claims data and healthcare-associated infection surveillance data from two medical centers for model development and model verification. Infection cases based on surveillance were identified by infection control personnel if the patient met the Taiwan CDC's criteria, which are the same as those adopted in the U.S. CDC.", "Infection cases based on surveillance were identified by infection control personnel if the patient met the Taiwan CDC's criteria, which are the same as those adopted in the U.S. CDC. They manually review medical records of all patients at risk for the specified healthcare-associated infection. The classification algorithms, the multivariable regression model, and the data mining model were adopted to develop alternative models based on surrogate indicators to identify cases of CABG SSIs and to compare the performance among these models and the ICD-9-CMbased model.", "The classification algorithms, the multivariable regression model, and the data mining model were adopted to develop alternative models based on surrogate indicators to identify cases of CABG SSIs and to compare the performance among these models and the ICD-9-CMbased model. For the classification algorithms, researchers build up several criteria, and if a case satisfies or exceeds a specific number of criteria, then it will be identified as a case of infection. For the multivariable regression model, researchers usually calculated a risk score by the logistic regression model, and the optimal cutoff point was determined according to the resulting receiver operating characteristic curve.", "For the multivariable regression model, researchers usually calculated a risk score by the logistic regression model, and the optimal cutoff point was determined according to the resulting receiver operating characteristic curve. Concerning the data mining approach, which is widely used for predicting and classifying objects, the characteristics are: automatic discovery of patterns, prediction of likely outcomes, creation of actionable information, and focus on large data sets and databases. The classification and regression tree CART model, which is the most popular approach as applied in our work, and the growing, stopping, and pruning of the tree were determined by Gini improvement measures.", "The classification and regression tree CART model, which is the most popular approach as applied in our work, and the growing, stopping, and pruning of the tree were determined by Gini improvement measures. After referring to the literature and conferring with infectious disease specialists, we adopted the following seven parameters: type of antibiotic, doses of antibiotic, doses of cefazolin, use of second-line antibiotics, length of stay, and number of vessels obstructed. Additionally, cross-validation was also employed, where data from one medical center was used for model development, and another one was used for model validation.", "Additionally, cross-validation was also employed, where data from one medical center was used for model development, and another one was used for model validation. The results of our previous work revealed that the CART model offered better performance than that of the other identification models or the ICD-9-CM based model, especially in the positive predictive value >70% , which was only found to be 20% in the ICD-9-CM based model. Table 1 The findings also implied that the CART was a decidedly better tool for identifying cases of SSI in the Taiwan National Health Insurance database.", "Table 1 The findings also implied that the CART was a decidedly better tool for identifying cases of SSI in the Taiwan National Health Insurance database. Therefore, this study also adopted the CART model for identifying CABG SSIs. To ensure homogeneity, current study analyzed 7,007 patients from 19 medical centers in Taiwan who underwent CABG surgery ICD-9-CM procedure codes 36.1x-36.2x between 2006 and 2008.", "To ensure homogeneity, current study analyzed 7,007 patients from 19 medical centers in Taiwan who underwent CABG surgery ICD-9-CM procedure codes 36.1x-36.2x between 2006 and 2008. CABG patients under the age of 18 years or over 85 years were excluded in this study. A total of 302 cases were identified as SSIs by ICD-9-CM based model, and a total of 107 cases were identified as SSIs by CART model.", "A total of 302 cases were identified as SSIs by ICD-9-CM based model, and a total of 107 cases were identified as SSIs by CART model. In this study, we used the following two definitions to define operation volumes: . the cumulative operation volumes by each surgeon and hospital within the study period, which was the most common definition in the literature; and .", "the cumulative operation volumes by each surgeon and hospital within the study period, which was the most common definition in the literature; and . following Yasunaga et al. 's study, cumulative operation volumes by each surgeon and hospital in the previous one year for each surgery.", "'s study, cumulative operation volumes by each surgeon and hospital in the previous one year for each surgery. However, our data was skewed, which did not follow a normal distribution. Therefore, we conducted the log transformations on operation volumes. The current work treated operation volumes in three different ways: . a continuous variable; .", "a continuous variable; . a categorical variable based on the first and the third quartile as cutoff points the most common method to categorize service/ operation volumes ; and . a data-driven categorical variable based on k-means clustering algorithm.", "a data-driven categorical variable based on k-means clustering algorithm. This study categorized surgeon and hospital volumes into low, medium, and high volume groups by quartile method and kmeans clustering algorithm. In the quartile method, the cut-off value transformed by logarithm of the first quartile <25% for hospital volumes was 5.65, and the third quartile >75% was 6.43.", "In the quartile method, the cut-off value transformed by logarithm of the first quartile <25% for hospital volumes was 5.65, and the third quartile >75% was 6.43. In terms of surgeon volumes, the first quartile was 4.38, and the third was 5.35, when we used the cumulative operation volumes within the study period as the definition. While the definition changed, first quartile <25% for hospital volumes was 4.66, and the third quartile >75% was 5.31.", "While the definition changed, first quartile <25% for hospital volumes was 4.66, and the third quartile >75% was 5.31. In terms of surgeon volumes, the first quartile was 3.40, and the third was 4.32. K-means clustering is an unsupervised machine-learning algorithm introduced by MacQueen in 1960s.", "K-means clustering is an unsupervised machine-learning algorithm introduced by MacQueen in 1960s. This method is not only a simple and very reliable method in categorization/ classification, but is also recognized as one of the top 10 algorithms in data mining. This method has often been applied in many fields.", "This method has often been applied in many fields. Yu and his colleagues even applied it to define the quality of CABG care, and to explore the relationship among patient's income status, the level of quality of care, and inpatient mortality. The main idea of this method is to partition observed data points into k non-overlapping clusters by minimizing the within-group sum of squares.", "The main idea of this method is to partition observed data points into k non-overlapping clusters by minimizing the within-group sum of squares. Each point is assigned to the mean of its cluster using the Euclidian distance. Firstly, k cluster centers were randomly generated.", "Firstly, k cluster centers were randomly generated. Previous studies usually divided surgeons and hospitals into low-, medium-, and high-volume groups; therefore, we also predetermined the surgeon and hospital service volumes into 3 groups k = 3 . Then, participants were assigned to the cluster with the shortest distance to these cluster centers.", "Then, participants were assigned to the cluster with the shortest distance to these cluster centers. Finally, the cluster centers were recomputed using the new cluster assignment and these steps would be iterated until convergence was achieved. The cut-off values of hospital volumes were 5.21 and 5.69, and for surgeon's volumes were 2.40 and 4.38 respectively, when cumulative operation volumes within the study period was used as the definition.", "The cut-off values of hospital volumes were 5.21 and 5.69, and for surgeon's volumes were 2.40 and 4.38 respectively, when cumulative operation volumes within the study period was used as the definition. Likewise, when cumulative operation volumes before each surgery was used as definition, the cut-off values were 4.11 and 4.89 for hospital volumes, and 2.64 and 3.91 for surgeon's volumes. All cutoff values were transformed by logarithm.", "All cutoff values were transformed by logarithm. The results of k-means clustering are demonstrated in Figs 1-4. As the results show, the operation volumes were divided into three groups separately. In addition to surgeon and hospital volumes and SSI, we collected patient-, surgeon-, and hospital-level data.", "In addition to surgeon and hospital volumes and SSI, we collected patient-, surgeon-, and hospital-level data. Firstly, patient-level variables included age, gender, length of ICU stay, number of vessels obstructed that were involved in the surgical operation, and the presence of important underlying diseases e.g. diabetes mellitus, chronic obstructive pulmonary disease COPD , heart failure, renal failure and renal insufficiency, which were associated with SSI .", "diabetes mellitus, chronic obstructive pulmonary disease COPD , heart failure, renal failure and renal insufficiency, which were associated with SSI . Secondly, the surgeon-level variables included age and gender. Thirdly, the hospital-level variables included hospital ownership and geographic location.", "Thirdly, the hospital-level variables included hospital ownership and geographic location. All statistical analyses of volume-infection relationship were performed using SAS version 9.2, SAS Institution Inc., Cary, NC, USA . In statistical testing, a two-sided p value 0.05 was considered statistically significant.", "In statistical testing, a two-sided p value 0.05 was considered statistically significant. The distributional properties of continuous variables were expressed by mean ± standard deviation SD , whereas categorical variables were presented by frequency and percentage. In univariate analysis, the potential three-level predictors of SSI were examined using chi-square test or two-sample t-test as appropriate.", "In univariate analysis, the potential three-level predictors of SSI were examined using chi-square test or two-sample t-test as appropriate. Next, to account for the correlations within surgeon level-2 and hospital level-3 , multivariate analysis was conducted by fitting mixed-effects logistic regression models to each patient's data for estimating the effects of three-level predictors on the probability of post-operational SSI. Furthermore, subgroup analysis for comorbidities was also conducted.", "Furthermore, subgroup analysis for comorbidities was also conducted. Table 2 shows that there were 7,007 patients with CABG performed by 199 surgeons in 19 hospitals during 2006-2008 in Taiwan. The majority of patients were male 77.5% , and the mean age of patients was 65.3 years.", "The majority of patients were male 77.5% , and the mean age of patients was 65.3 years. The average ICU stay was 6.05 days, the mean level of number of vessels obstructed was around 1.6, while 51.8% of patients had diabetes mellitus, 33.3% had heart failure, 14.1% had renal failure and renal insufficiency, and 22.0% had COPD. Three hundred and two patients 4.31% were identified as having the ICD-9-CM SSI codes.", "Three hundred and two patients 4.31% were identified as having the ICD-9-CM SSI codes. However, identification by the CART model only revealed 107 infection cases, and 94 cases were identified in both models. Most cases received CABG surgery by male surgeons, with a mean age of 45.0 years, and the surgeon's average operation volumes within the study period was 151.64, while the average operation volumes before surgery was 52.18.", "Most cases received CABG surgery by male surgeons, with a mean age of 45.0 years, and the surgeon's average operation volumes within the study period was 151.64, while the average operation volumes before surgery was 52.18. More than half of the cases were performed with CABG in not-for-profit hospitals, and the hospitals' average operation volumes within the study period was 473.60, while the average operation volumes before each surgery was 158.79. Moreover, most of patients received their surgeries by high-volume surgeons and hospitals, when k-means algorithm was used for categorization, regardless of which definition of operation volumes were used.", "Moreover, most of patients received their surgeries by high-volume surgeons and hospitals, when k-means algorithm was used for categorization, regardless of which definition of operation volumes were used. Table 3 shows the results of multilevel mixed-effect models, with the SSIs being identified by ICD-9-CM codes, and the operation volumes defined as the cumulative volumes within the study period. The results of Model 1 continuous reveal that the surgeon's volumes were negatively associated with SSIs, while hospital's volumes were not associated with surgical site infection SSIs.", "The results of Model 1 continuous reveal that the surgeon's volumes were negatively associated with SSIs, while hospital's volumes were not associated with surgical site infection SSIs. Model 2 quartile suggests that low-volume surgeons had higher SSI risk OR = 2.220, p-value = 0.022 than high-volume surgeons. There were also no associations between hospital's operation volumes and SSIs.", "There were also no associations between hospital's operation volumes and SSIs. Model 3 k-means shows that the association did not exist between hospital's/ surgeon's volumes and SSIs. Table 4 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volumes within the study period.", "Table 4 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volumes within the study period. Model 1 again indicated a negative association between surgeon's volumes and SSIs, and hospital's volumes were not found to be associated with SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results revealed low-volume surgeons had higher risk OR = 1.691, p = 0.002 than high-volume surgeons. Table 5 displays the results of multilevel mixed-effect models, in which the SSIs were identified by ICD-9-CM codes, but the operation volumes were defined as the cumulative volume in the previous one year for each surgery.", "Table 5 displays the results of multilevel mixed-effect models, in which the SSIs were identified by ICD-9-CM codes, but the operation volumes were defined as the cumulative volume in the previous one year for each surgery. Model 1 also indicated a negative association between surgeon's volumes and SSIs, and hospital's volumes were not found to be associated with SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results also revealed low-volume surgeons had higher risk OR = 1.642, p = 0.040 than high-volume surgeons. Table 6 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volume in previous one year for each surgery.", "Table 6 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volume in previous one year for each surgery. In Model 1, different to the above findings, there was no association between hospital's/ surgeon's volumes and SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results also revealed low-volume surgeons had higher risk OR = 1.163, p = 0.020 than high-volume surgeons. We further examined the associations of surgeon and hospital volumes with SSIs in stratification analyses by underlying diseases.", "We further examined the associations of surgeon and hospital volumes with SSIs in stratification analyses by underlying diseases. When the operation volumes were defined as the cumulative operation volume within the study period, no relationships existed between hospital/ surgeon operation volumes and SSIs. Table 7 However, when the operation volumes were defined as the cumulative operation volumes in the previous one year for each surgery, the results suggested that there was a negative association between surgeon volumes and SSIs in the diabetes group, except that the volumes were treated as continuous variable and the infection cases were identified by ICD-9 codes.", "Table 7 However, when the operation volumes were defined as the cumulative operation volumes in the previous one year for each surgery, the results suggested that there was a negative association between surgeon volumes and SSIs in the diabetes group, except that the volumes were treated as continuous variable and the infection cases were identified by ICD-9 codes. In terms of hospital operation volumes, the association did not exist. Table 8 No studies have evaluated how different service/ operation volumes definitions and categorization methods affect volume-infection relationships.", "Table 8 No studies have evaluated how different service/ operation volumes definitions and categorization methods affect volume-infection relationships. Moreover, several studies have pointed out the inappropriateness of identifying infection cases using the ICD-9-CM codes in claims data. Given these reasons, this study adopted two approaches to identifying SSIs, two definitions of operation volumes, and three methods for categorizing operation volumes to examine the relationships between operation volumes and SSIs.", "Given these reasons, this study adopted two approaches to identifying SSIs, two definitions of operation volumes, and three methods for categorizing operation volumes to examine the relationships between operation volumes and SSIs. Our findings showed that the relationships between hospital volumes and SSIs did not exist, no matter which definitions, categorization mehods, or SSIs case identification approaches were used. On the contrary, the relationships between surgeon volumes and SSIs were not robust in our data.", "On the contrary, the relationships between surgeon volumes and SSIs were not robust in our data. It might be affected by different definitions and categorization methods of operation volumes, and also by different SSI cases identification approaches. In summary, most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons, and they also showed the risks were similar between medium-volume and high-volume surgeons.", "In summary, most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons, and they also showed the risks were similar between medium-volume and high-volume surgeons. However, why did surgeon volume relate to SSIs, but hospital volume did not? Except for those issues we were concerned about in this study, there are some disagreements in the literature.", "Except for those issues we were concerned about in this study, there are some disagreements in the literature. Such as \"Does provider volume really represent quality of care?\" Or \"Is provider volume the only one predictor for outcome of care?\"", "Or \"Is provider volume the only one predictor for outcome of care?\" These issues are worthy of further discussion, but are out of the scope of this study. Service/ operation volumes are treated as a proxy indicator for experiences; previous studies used it to examine whether practice makes perfect or not.", "Service/ operation volumes are treated as a proxy indicator for experiences; previous studies used it to examine whether practice makes perfect or not. But, except for provider's experiences, SSIs are also impacted by many factors, such as environmental and clinical factors. Wu et al once used Taiwan 2001 NHI claims data to explore the relationship between provider CABG operation volumes and SSIs.", "Wu et al once used Taiwan 2001 NHI claims data to explore the relationship between provider CABG operation volumes and SSIs. They found that hospital volumes had a greater effect than surgeon volumes and claimed that this may imply that hospital teamwork is more important than individual surgeon. However, our findings demonstrated that there was no relationship between hospital volumes and SSIs.", "However, our findings demonstrated that there was no relationship between hospital volumes and SSIs. Wu et al. adopted the cumulative operation volumes within the study period as the definition, and identified SSIs by ICD-9-CM codes.", "adopted the cumulative operation volumes within the study period as the definition, and identified SSIs by ICD-9-CM codes. Except, there were two differences between our work and Wu et al., which were the length and year of the data; our data was longer and more updated than theirs. Moreover, it is worth noting that there was an outbreak of severe acute respiratory syndrome SARS in Taiwan in 2003, after which the hospital infection control system in Taiwan was reviewed and re-designed.", "Moreover, it is worth noting that there was an outbreak of severe acute respiratory syndrome SARS in Taiwan in 2003, after which the hospital infection control system in Taiwan was reviewed and re-designed. Wu et al data was before SARS, so these efforts may also have improved the level of SSIs control in hospitals, leading to different findings in this study. In addition, although most models revealed that there were negative relationships between surgeon's volumes and surgical site infection, the relationships were not robust.", "In addition, although most models revealed that there were negative relationships between surgeon's volumes and surgical site infection, the relationships were not robust. The results varied between different definitions and categorization method of operation volumes, and between SSIs identification approaches. Researchers need to consider how to identify SSIs correctly, how to choose optimal cut-off values, and how to decide on which definition is appropriate.", "Researchers need to consider how to identify SSIs correctly, how to choose optimal cut-off values, and how to decide on which definition is appropriate. Finally, the results of stratification analyses showed that low-volume surgeon had higher risk than high-volume surgeon in the diabetes mellitus group, when the cumulative operation in the previous one year before surgery was used as definition. A large number of studies have indicated diabetes mellitus is associated with a higher risk of SSIs, and the findings of this study suggest that CABG patients with diabetes mellitus should be cared for by experienced surgeons.", "A large number of studies have indicated diabetes mellitus is associated with a higher risk of SSIs, and the findings of this study suggest that CABG patients with diabetes mellitus should be cared for by experienced surgeons. A multilevel analysis was applied to manage the nested factors, and two definitions of operation volume along with three different operation volume categorization methods were adopted to examine the relationship between volume and SSIs under two kinds of SSIs identification approaches. Nevertheless, the study suffered from several major limitations.", "Nevertheless, the study suffered from several major limitations. First, the accuracy of SSIs identification was still an issue. Although the performance of the CART model to identify CABG SSIs was better than ICD-9-CM codes in Taiwan NHI claims data, it did not reach the perfect scenario.", "Although the performance of the CART model to identify CABG SSIs was better than ICD-9-CM codes in Taiwan NHI claims data, it did not reach the perfect scenario. The accuracy of SSIs identification was still a challenge in our work. The second limitation relates to unmeasured variables, such as length of stay before operation, infection condition, hair removal, clinical information e.g.", "The second limitation relates to unmeasured variables, such as length of stay before operation, infection condition, hair removal, clinical information e.g. blood glucose level, causative microorganism , time-related information e.g. the duration of operation , the environment, surgical skills, use of post-operative drains, number of operations involved, and surgical site and wound care, etc.", "the duration of operation , the environment, surgical skills, use of post-operative drains, number of operations involved, and surgical site and wound care, etc. Furthermore, information about type elective or urgent and incision site for surgery was not available in the Taiwan NHI claims data. In conclusion, the findings of this study suggest that different definitions and categorization methods of operation volumes, and different SSIs identification approaches might lead to different findings, although surgeon volumes were more important than hospital volumes in exploring the relationships between CABG operation volumes and SSIs in Taiwan, but they were still not robust.", "In conclusion, the findings of this study suggest that different definitions and categorization methods of operation volumes, and different SSIs identification approaches might lead to different findings, although surgeon volumes were more important than hospital volumes in exploring the relationships between CABG operation volumes and SSIs in Taiwan, but they were still not robust. Definitions and categorization methods of operation volumes, and correct identification of SSIs are important issues for future research." ]

[ "BACKGROUND: Volume-infection relationships have been examined for high-risk surgical procedures, but the conclusions remain controversial. The inconsistency might be due to inaccurate identification of cases of infection and different methods of categorizing service volumes. This study takes coronary artery bypass graft CABG surgical site infections SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, when different SSIs case identification, definitions and categorization methods of operation volumes were implemented.", "This study takes coronary artery bypass graft CABG surgical site infections SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, when different SSIs case identification, definitions and categorization methods of operation volumes were implemented. METHODS: A population-based cross-sectional multilevel study was conducted. A total of 7,007 patients who received CABG surgery between 2006 and 2008 from19 medical centers in Taiwan were recruited.", "A total of 7,007 patients who received CABG surgery between 2006 and 2008 from19 medical centers in Taiwan were recruited. SSIs associated with CABG surgery were identified using International Classification of Diseases, 9th Revision, Clinical Modification ICD-9 CM codes and a Classification and Regression Trees CART model. Two definitions of surgeon and hospital operation volumes were used: .", "Two definitions of surgeon and hospital operation volumes were used: . the cumulative CABG operation volumes within the study period; and . the cumulative CABG operation volumes in the previous one year before each CABG surgery. Operation volumes were further treated in three different ways: . a continuous variable; .", "Operation volumes were further treated in three different ways: . a continuous variable; . a categorical variable based on the quartile; and . a data-driven categorical variable based on k-means clustering algorithm. Furthermore, subgroup analysis for comorbidities was also conducted.", "Furthermore, subgroup analysis for comorbidities was also conducted. RESULTS: This study showed that hospital volumes were not significantly associated with SSIs, no matter which definitions or categorization methods of operation volume, or SSIs case identification approaches were used. On the contrary, the relationships between surgeon’s volumes varied.", "On the contrary, the relationships between surgeon’s volumes varied. Most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons. CONCLUSION: Surgeon volumes were more important than hospital volumes in exploring the relationship between CABG operation volumes and SSIs in Taiwan. However, the relationships were not robust.", "However, the relationships were not robust. Definitions and categorization methods of operation volume and correct identification of SSIs are important issues for future research. Text: data, which should use hierarchical models, may result in biased estimation of the variation and also lead to incorrect conclusions.", "Text: data, which should use hierarchical models, may result in biased estimation of the variation and also lead to incorrect conclusions. SSIs following coronary artery bypass graft CABG procedures place a heavy burden on patients and healthcare systems. The total length of stay and expenditure for patients with SSIs after CABG surgery is significantly longer and higher than those without SSIs.", "The total length of stay and expenditure for patients with SSIs after CABG surgery is significantly longer and higher than those without SSIs. In 2008, the Centers for Medicare & Medicaid of the United States of America implemented the \"Never Event\" policy, where hospitals would no longer receive higher payments for the additional costs associated with treating patients for certain healthcare-acquired infections, including those related to CABG. In view of the accuracy of SSIs identification and the heterogeneity of definition and categorization methods, no existing studies have used different infection case identification nor definitions and categorization methods of operation volume simultaneously to explore the relationship between operation volumes and infection.", "In view of the accuracy of SSIs identification and the heterogeneity of definition and categorization methods, no existing studies have used different infection case identification nor definitions and categorization methods of operation volume simultaneously to explore the relationship between operation volumes and infection. The current study takes CABG SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, given different SSI cases identification, operation volume definitions and categorization methods. This retrospective and cross-sectional study adopted a multilevel design to examine the relationships between provider volumes and SSIs after adjusting for patient-, surgeon-, and hospital-level covariates.", "This retrospective and cross-sectional study adopted a multilevel design to examine the relationships between provider volumes and SSIs after adjusting for patient-, surgeon-, and hospital-level covariates. We used data from the Taiwan National Health Insurance Research Database NHIRD from 2005 and 2008. The NHIRD, published by the Taiwan National Health Research Institute, includes all the original claims data and registration files for beneficiaries enrolled under the National Health Insurance NHI program.", "The NHIRD, published by the Taiwan National Health Research Institute, includes all the original claims data and registration files for beneficiaries enrolled under the National Health Insurance NHI program. The database covers the 23 million Taiwanese enrollees approximately 98% of the population in the NHI program. It is a de-identified secondary database containing patient-level demographic and administrative information; however, treatment items are aggregated and without time-related and clinical information.", "It is a de-identified secondary database containing patient-level demographic and administrative information; however, treatment items are aggregated and without time-related and clinical information. The data is released for research purposes. The protocol for the study was approved by the Institutional Review Board of the National Taiwan University Hospital protocol #201001027R .", "The protocol for the study was approved by the Institutional Review Board of the National Taiwan University Hospital protocol #201001027R . The dataset we used in this study was secondary data; all information was de-identified by data owners. In this study, we adopted the ICD-9-CM SSI codes hereafter referred to as the ICD-9-CM based model and the Classification and Regression Trees CART model, which was developed in our previous work to identify SSI cases.", "In this study, we adopted the ICD-9-CM SSI codes hereafter referred to as the ICD-9-CM based model and the Classification and Regression Trees CART model, which was developed in our previous work to identify SSI cases. As we mentioned above, the ICD-9-CM SSI codes were the most popular tool to identify the SSI cases in claims data. In the ICD-9-CM based model, SSI cases were divided into two categories: index hospitalization events and post-discharge events i.e., SSIs that occurred within 1 year after discharge and required readmission to a hospital and/ or the use of ambulatory services .", "In the ICD-9-CM based model, SSI cases were divided into two categories: index hospitalization events and post-discharge events i.e., SSIs that occurred within 1 year after discharge and required readmission to a hospital and/ or the use of ambulatory services . Following Wu et al , this study adopted the secondary ICD-9-CM diagnosis codes for index hospitalization events ICD-9-CM code: 996.03, 996.61, 996.72, and 998.5 , and the primary and secondary diagnosis codes for post-discharge events ICD-9-CM code: 038.0-038. 4 as the criteria for SSI identification, in order to avoid cases in which infection existed prior to hospitalization.", "4 as the criteria for SSI identification, in order to avoid cases in which infection existed prior to hospitalization. If a case had an index hospitalization event or a post-discharge event, then he/ she will be identified as SSIs by the ICD-9-CM based model. In the CART model, we adopted the type of antibiotics, dose of cefazolin, length of stay, and number of vessels obstructed as a proxy indicator of duration of operation as the parameters to identify the SSIs, according to our previous findings.", "In the CART model, we adopted the type of antibiotics, dose of cefazolin, length of stay, and number of vessels obstructed as a proxy indicator of duration of operation as the parameters to identify the SSIs, according to our previous findings. In our previous work, we used the 2005-2008 National Health Insurance claims data and healthcare-associated infection surveillance data from two medical centers for model development and model verification. Infection cases based on surveillance were identified by infection control personnel if the patient met the Taiwan CDC's criteria, which are the same as those adopted in the U.S. CDC.", "Infection cases based on surveillance were identified by infection control personnel if the patient met the Taiwan CDC's criteria, which are the same as those adopted in the U.S. CDC. They manually review medical records of all patients at risk for the specified healthcare-associated infection. The classification algorithms, the multivariable regression model, and the data mining model were adopted to develop alternative models based on surrogate indicators to identify cases of CABG SSIs and to compare the performance among these models and the ICD-9-CMbased model.", "The classification algorithms, the multivariable regression model, and the data mining model were adopted to develop alternative models based on surrogate indicators to identify cases of CABG SSIs and to compare the performance among these models and the ICD-9-CMbased model. For the classification algorithms, researchers build up several criteria, and if a case satisfies or exceeds a specific number of criteria, then it will be identified as a case of infection. For the multivariable regression model, researchers usually calculated a risk score by the logistic regression model, and the optimal cutoff point was determined according to the resulting receiver operating characteristic curve.", "For the multivariable regression model, researchers usually calculated a risk score by the logistic regression model, and the optimal cutoff point was determined according to the resulting receiver operating characteristic curve. Concerning the data mining approach, which is widely used for predicting and classifying objects, the characteristics are: automatic discovery of patterns, prediction of likely outcomes, creation of actionable information, and focus on large data sets and databases. The classification and regression tree CART model, which is the most popular approach as applied in our work, and the growing, stopping, and pruning of the tree were determined by Gini improvement measures.", "The classification and regression tree CART model, which is the most popular approach as applied in our work, and the growing, stopping, and pruning of the tree were determined by Gini improvement measures. After referring to the literature and conferring with infectious disease specialists, we adopted the following seven parameters: type of antibiotic, doses of antibiotic, doses of cefazolin, use of second-line antibiotics, length of stay, and number of vessels obstructed. Additionally, cross-validation was also employed, where data from one medical center was used for model development, and another one was used for model validation.", "Additionally, cross-validation was also employed, where data from one medical center was used for model development, and another one was used for model validation. The results of our previous work revealed that the CART model offered better performance than that of the other identification models or the ICD-9-CM based model, especially in the positive predictive value >70% , which was only found to be 20% in the ICD-9-CM based model. Table 1 The findings also implied that the CART was a decidedly better tool for identifying cases of SSI in the Taiwan National Health Insurance database.", "Table 1 The findings also implied that the CART was a decidedly better tool for identifying cases of SSI in the Taiwan National Health Insurance database. Therefore, this study also adopted the CART model for identifying CABG SSIs. To ensure homogeneity, current study analyzed 7,007 patients from 19 medical centers in Taiwan who underwent CABG surgery ICD-9-CM procedure codes 36.1x-36.2x between 2006 and 2008.", "To ensure homogeneity, current study analyzed 7,007 patients from 19 medical centers in Taiwan who underwent CABG surgery ICD-9-CM procedure codes 36.1x-36.2x between 2006 and 2008. CABG patients under the age of 18 years or over 85 years were excluded in this study. A total of 302 cases were identified as SSIs by ICD-9-CM based model, and a total of 107 cases were identified as SSIs by CART model.", "A total of 302 cases were identified as SSIs by ICD-9-CM based model, and a total of 107 cases were identified as SSIs by CART model. In this study, we used the following two definitions to define operation volumes: . the cumulative operation volumes by each surgeon and hospital within the study period, which was the most common definition in the literature; and .", "the cumulative operation volumes by each surgeon and hospital within the study period, which was the most common definition in the literature; and . following Yasunaga et al. 's study, cumulative operation volumes by each surgeon and hospital in the previous one year for each surgery.", "'s study, cumulative operation volumes by each surgeon and hospital in the previous one year for each surgery. However, our data was skewed, which did not follow a normal distribution. Therefore, we conducted the log transformations on operation volumes. The current work treated operation volumes in three different ways: . a continuous variable; .", "a continuous variable; . a categorical variable based on the first and the third quartile as cutoff points the most common method to categorize service/ operation volumes ; and . a data-driven categorical variable based on k-means clustering algorithm.", "a data-driven categorical variable based on k-means clustering algorithm. This study categorized surgeon and hospital volumes into low, medium, and high volume groups by quartile method and kmeans clustering algorithm. In the quartile method, the cut-off value transformed by logarithm of the first quartile <25% for hospital volumes was 5.65, and the third quartile >75% was 6.43.", "In the quartile method, the cut-off value transformed by logarithm of the first quartile <25% for hospital volumes was 5.65, and the third quartile >75% was 6.43. In terms of surgeon volumes, the first quartile was 4.38, and the third was 5.35, when we used the cumulative operation volumes within the study period as the definition. While the definition changed, first quartile <25% for hospital volumes was 4.66, and the third quartile >75% was 5.31.", "While the definition changed, first quartile <25% for hospital volumes was 4.66, and the third quartile >75% was 5.31. In terms of surgeon volumes, the first quartile was 3.40, and the third was 4.32. K-means clustering is an unsupervised machine-learning algorithm introduced by MacQueen in 1960s.", "K-means clustering is an unsupervised machine-learning algorithm introduced by MacQueen in 1960s. This method is not only a simple and very reliable method in categorization/ classification, but is also recognized as one of the top 10 algorithms in data mining. This method has often been applied in many fields.", "This method has often been applied in many fields. Yu and his colleagues even applied it to define the quality of CABG care, and to explore the relationship among patient's income status, the level of quality of care, and inpatient mortality. The main idea of this method is to partition observed data points into k non-overlapping clusters by minimizing the within-group sum of squares.", "The main idea of this method is to partition observed data points into k non-overlapping clusters by minimizing the within-group sum of squares. Each point is assigned to the mean of its cluster using the Euclidian distance. Firstly, k cluster centers were randomly generated.", "Firstly, k cluster centers were randomly generated. Previous studies usually divided surgeons and hospitals into low-, medium-, and high-volume groups; therefore, we also predetermined the surgeon and hospital service volumes into 3 groups k = 3 . Then, participants were assigned to the cluster with the shortest distance to these cluster centers.", "Then, participants were assigned to the cluster with the shortest distance to these cluster centers. Finally, the cluster centers were recomputed using the new cluster assignment and these steps would be iterated until convergence was achieved. The cut-off values of hospital volumes were 5.21 and 5.69, and for surgeon's volumes were 2.40 and 4.38 respectively, when cumulative operation volumes within the study period was used as the definition.", "The cut-off values of hospital volumes were 5.21 and 5.69, and for surgeon's volumes were 2.40 and 4.38 respectively, when cumulative operation volumes within the study period was used as the definition. Likewise, when cumulative operation volumes before each surgery was used as definition, the cut-off values were 4.11 and 4.89 for hospital volumes, and 2.64 and 3.91 for surgeon's volumes. All cutoff values were transformed by logarithm.", "All cutoff values were transformed by logarithm. The results of k-means clustering are demonstrated in Figs 1-4. As the results show, the operation volumes were divided into three groups separately. In addition to surgeon and hospital volumes and SSI, we collected patient-, surgeon-, and hospital-level data.", "In addition to surgeon and hospital volumes and SSI, we collected patient-, surgeon-, and hospital-level data. Firstly, patient-level variables included age, gender, length of ICU stay, number of vessels obstructed that were involved in the surgical operation, and the presence of important underlying diseases e.g. diabetes mellitus, chronic obstructive pulmonary disease COPD , heart failure, renal failure and renal insufficiency, which were associated with SSI .", "diabetes mellitus, chronic obstructive pulmonary disease COPD , heart failure, renal failure and renal insufficiency, which were associated with SSI . Secondly, the surgeon-level variables included age and gender. Thirdly, the hospital-level variables included hospital ownership and geographic location.", "Thirdly, the hospital-level variables included hospital ownership and geographic location. All statistical analyses of volume-infection relationship were performed using SAS version 9.2, SAS Institution Inc., Cary, NC, USA . In statistical testing, a two-sided p value 0.05 was considered statistically significant.", "In statistical testing, a two-sided p value 0.05 was considered statistically significant. The distributional properties of continuous variables were expressed by mean ± standard deviation SD , whereas categorical variables were presented by frequency and percentage. In univariate analysis, the potential three-level predictors of SSI were examined using chi-square test or two-sample t-test as appropriate.", "In univariate analysis, the potential three-level predictors of SSI were examined using chi-square test or two-sample t-test as appropriate. Next, to account for the correlations within surgeon level-2 and hospital level-3 , multivariate analysis was conducted by fitting mixed-effects logistic regression models to each patient's data for estimating the effects of three-level predictors on the probability of post-operational SSI. Furthermore, subgroup analysis for comorbidities was also conducted.", "Furthermore, subgroup analysis for comorbidities was also conducted. Table 2 shows that there were 7,007 patients with CABG performed by 199 surgeons in 19 hospitals during 2006-2008 in Taiwan. The majority of patients were male 77.5% , and the mean age of patients was 65.3 years.", "The majority of patients were male 77.5% , and the mean age of patients was 65.3 years. The average ICU stay was 6.05 days, the mean level of number of vessels obstructed was around 1.6, while 51.8% of patients had diabetes mellitus, 33.3% had heart failure, 14.1% had renal failure and renal insufficiency, and 22.0% had COPD. Three hundred and two patients 4.31% were identified as having the ICD-9-CM SSI codes.", "Three hundred and two patients 4.31% were identified as having the ICD-9-CM SSI codes. However, identification by the CART model only revealed 107 infection cases, and 94 cases were identified in both models. Most cases received CABG surgery by male surgeons, with a mean age of 45.0 years, and the surgeon's average operation volumes within the study period was 151.64, while the average operation volumes before surgery was 52.18.", "Most cases received CABG surgery by male surgeons, with a mean age of 45.0 years, and the surgeon's average operation volumes within the study period was 151.64, while the average operation volumes before surgery was 52.18. More than half of the cases were performed with CABG in not-for-profit hospitals, and the hospitals' average operation volumes within the study period was 473.60, while the average operation volumes before each surgery was 158.79. Moreover, most of patients received their surgeries by high-volume surgeons and hospitals, when k-means algorithm was used for categorization, regardless of which definition of operation volumes were used.", "Moreover, most of patients received their surgeries by high-volume surgeons and hospitals, when k-means algorithm was used for categorization, regardless of which definition of operation volumes were used. Table 3 shows the results of multilevel mixed-effect models, with the SSIs being identified by ICD-9-CM codes, and the operation volumes defined as the cumulative volumes within the study period. The results of Model 1 continuous reveal that the surgeon's volumes were negatively associated with SSIs, while hospital's volumes were not associated with surgical site infection SSIs.", "The results of Model 1 continuous reveal that the surgeon's volumes were negatively associated with SSIs, while hospital's volumes were not associated with surgical site infection SSIs. Model 2 quartile suggests that low-volume surgeons had higher SSI risk OR = 2.220, p-value = 0.022 than high-volume surgeons. There were also no associations between hospital's operation volumes and SSIs.", "There were also no associations between hospital's operation volumes and SSIs. Model 3 k-means shows that the association did not exist between hospital's/ surgeon's volumes and SSIs. Table 4 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volumes within the study period.", "Table 4 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volumes within the study period. Model 1 again indicated a negative association between surgeon's volumes and SSIs, and hospital's volumes were not found to be associated with SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results revealed low-volume surgeons had higher risk OR = 1.691, p = 0.002 than high-volume surgeons. Table 5 displays the results of multilevel mixed-effect models, in which the SSIs were identified by ICD-9-CM codes, but the operation volumes were defined as the cumulative volume in the previous one year for each surgery.", "Table 5 displays the results of multilevel mixed-effect models, in which the SSIs were identified by ICD-9-CM codes, but the operation volumes were defined as the cumulative volume in the previous one year for each surgery. Model 1 also indicated a negative association between surgeon's volumes and SSIs, and hospital's volumes were not found to be associated with SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results also revealed low-volume surgeons had higher risk OR = 1.642, p = 0.040 than high-volume surgeons. Table 6 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volume in previous one year for each surgery.", "Table 6 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volume in previous one year for each surgery. In Model 1, different to the above findings, there was no association between hospital's/ surgeon's volumes and SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results also revealed low-volume surgeons had higher risk OR = 1.163, p = 0.020 than high-volume surgeons. We further examined the associations of surgeon and hospital volumes with SSIs in stratification analyses by underlying diseases.", "We further examined the associations of surgeon and hospital volumes with SSIs in stratification analyses by underlying diseases. When the operation volumes were defined as the cumulative operation volume within the study period, no relationships existed between hospital/ surgeon operation volumes and SSIs. Table 7 However, when the operation volumes were defined as the cumulative operation volumes in the previous one year for each surgery, the results suggested that there was a negative association between surgeon volumes and SSIs in the diabetes group, except that the volumes were treated as continuous variable and the infection cases were identified by ICD-9 codes.", "Table 7 However, when the operation volumes were defined as the cumulative operation volumes in the previous one year for each surgery, the results suggested that there was a negative association between surgeon volumes and SSIs in the diabetes group, except that the volumes were treated as continuous variable and the infection cases were identified by ICD-9 codes. In terms of hospital operation volumes, the association did not exist. Table 8 No studies have evaluated how different service/ operation volumes definitions and categorization methods affect volume-infection relationships.", "Table 8 No studies have evaluated how different service/ operation volumes definitions and categorization methods affect volume-infection relationships. Moreover, several studies have pointed out the inappropriateness of identifying infection cases using the ICD-9-CM codes in claims data. Given these reasons, this study adopted two approaches to identifying SSIs, two definitions of operation volumes, and three methods for categorizing operation volumes to examine the relationships between operation volumes and SSIs.", "Given these reasons, this study adopted two approaches to identifying SSIs, two definitions of operation volumes, and three methods for categorizing operation volumes to examine the relationships between operation volumes and SSIs. Our findings showed that the relationships between hospital volumes and SSIs did not exist, no matter which definitions, categorization mehods, or SSIs case identification approaches were used. On the contrary, the relationships between surgeon volumes and SSIs were not robust in our data.", "On the contrary, the relationships between surgeon volumes and SSIs were not robust in our data. It might be affected by different definitions and categorization methods of operation volumes, and also by different SSI cases identification approaches. In summary, most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons, and they also showed the risks were similar between medium-volume and high-volume surgeons.", "In summary, most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons, and they also showed the risks were similar between medium-volume and high-volume surgeons. However, why did surgeon volume relate to SSIs, but hospital volume did not? Except for those issues we were concerned about in this study, there are some disagreements in the literature.", "Except for those issues we were concerned about in this study, there are some disagreements in the literature. Such as \"Does provider volume really represent quality of care?\" Or \"Is provider volume the only one predictor for outcome of care?\"", "Or \"Is provider volume the only one predictor for outcome of care?\" These issues are worthy of further discussion, but are out of the scope of this study. Service/ operation volumes are treated as a proxy indicator for experiences; previous studies used it to examine whether practice makes perfect or not.", "Service/ operation volumes are treated as a proxy indicator for experiences; previous studies used it to examine whether practice makes perfect or not. But, except for provider's experiences, SSIs are also impacted by many factors, such as environmental and clinical factors. Wu et al once used Taiwan 2001 NHI claims data to explore the relationship between provider CABG operation volumes and SSIs.", "Wu et al once used Taiwan 2001 NHI claims data to explore the relationship between provider CABG operation volumes and SSIs. They found that hospital volumes had a greater effect than surgeon volumes and claimed that this may imply that hospital teamwork is more important than individual surgeon. However, our findings demonstrated that there was no relationship between hospital volumes and SSIs.", "However, our findings demonstrated that there was no relationship between hospital volumes and SSIs. Wu et al. adopted the cumulative operation volumes within the study period as the definition, and identified SSIs by ICD-9-CM codes.", "adopted the cumulative operation volumes within the study period as the definition, and identified SSIs by ICD-9-CM codes. Except, there were two differences between our work and Wu et al., which were the length and year of the data; our data was longer and more updated than theirs. Moreover, it is worth noting that there was an outbreak of severe acute respiratory syndrome SARS in Taiwan in 2003, after which the hospital infection control system in Taiwan was reviewed and re-designed.", "Moreover, it is worth noting that there was an outbreak of severe acute respiratory syndrome SARS in Taiwan in 2003, after which the hospital infection control system in Taiwan was reviewed and re-designed. Wu et al data was before SARS, so these efforts may also have improved the level of SSIs control in hospitals, leading to different findings in this study. In addition, although most models revealed that there were negative relationships between surgeon's volumes and surgical site infection, the relationships were not robust.", "In addition, although most models revealed that there were negative relationships between surgeon's volumes and surgical site infection, the relationships were not robust. The results varied between different definitions and categorization method of operation volumes, and between SSIs identification approaches. Researchers need to consider how to identify SSIs correctly, how to choose optimal cut-off values, and how to decide on which definition is appropriate.", "Researchers need to consider how to identify SSIs correctly, how to choose optimal cut-off values, and how to decide on which definition is appropriate. Finally, the results of stratification analyses showed that low-volume surgeon had higher risk than high-volume surgeon in the diabetes mellitus group, when the cumulative operation in the previous one year before surgery was used as definition. A large number of studies have indicated diabetes mellitus is associated with a higher risk of SSIs, and the findings of this study suggest that CABG patients with diabetes mellitus should be cared for by experienced surgeons.", "A large number of studies have indicated diabetes mellitus is associated with a higher risk of SSIs, and the findings of this study suggest that CABG patients with diabetes mellitus should be cared for by experienced surgeons. A multilevel analysis was applied to manage the nested factors, and two definitions of operation volume along with three different operation volume categorization methods were adopted to examine the relationship between volume and SSIs under two kinds of SSIs identification approaches. Nevertheless, the study suffered from several major limitations.", "Nevertheless, the study suffered from several major limitations. First, the accuracy of SSIs identification was still an issue. Although the performance of the CART model to identify CABG SSIs was better than ICD-9-CM codes in Taiwan NHI claims data, it did not reach the perfect scenario.", "Although the performance of the CART model to identify CABG SSIs was better than ICD-9-CM codes in Taiwan NHI claims data, it did not reach the perfect scenario. The accuracy of SSIs identification was still a challenge in our work. The second limitation relates to unmeasured variables, such as length of stay before operation, infection condition, hair removal, clinical information e.g.", "The second limitation relates to unmeasured variables, such as length of stay before operation, infection condition, hair removal, clinical information e.g. blood glucose level, causative microorganism , time-related information e.g. the duration of operation , the environment, surgical skills, use of post-operative drains, number of operations involved, and surgical site and wound care, etc.", "the duration of operation , the environment, surgical skills, use of post-operative drains, number of operations involved, and surgical site and wound care, etc. Furthermore, information about type elective or urgent and incision site for surgery was not available in the Taiwan NHI claims data. In conclusion, the findings of this study suggest that different definitions and categorization methods of operation volumes, and different SSIs identification approaches might lead to different findings, although surgeon volumes were more important than hospital volumes in exploring the relationships between CABG operation volumes and SSIs in Taiwan, but they were still not robust.", "In conclusion, the findings of this study suggest that different definitions and categorization methods of operation volumes, and different SSIs identification approaches might lead to different findings, although surgeon volumes were more important than hospital volumes in exploring the relationships between CABG operation volumes and SSIs in Taiwan, but they were still not robust. Definitions and categorization methods of operation volumes, and correct identification of SSIs are important issues for future research." ]

[ "BACKGROUND: Volume-infection relationships have been examined for high-risk surgical procedures, but the conclusions remain controversial. The inconsistency might be due to inaccurate identification of cases of infection and different methods of categorizing service volumes. This study takes coronary artery bypass graft CABG surgical site infections SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, when different SSIs case identification, definitions and categorization methods of operation volumes were implemented.", "This study takes coronary artery bypass graft CABG surgical site infections SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, when different SSIs case identification, definitions and categorization methods of operation volumes were implemented. METHODS: A population-based cross-sectional multilevel study was conducted. A total of 7,007 patients who received CABG surgery between 2006 and 2008 from19 medical centers in Taiwan were recruited.", "A total of 7,007 patients who received CABG surgery between 2006 and 2008 from19 medical centers in Taiwan were recruited. SSIs associated with CABG surgery were identified using International Classification of Diseases, 9th Revision, Clinical Modification ICD-9 CM codes and a Classification and Regression Trees CART model. Two definitions of surgeon and hospital operation volumes were used: .", "Two definitions of surgeon and hospital operation volumes were used: . the cumulative CABG operation volumes within the study period; and . the cumulative CABG operation volumes in the previous one year before each CABG surgery. Operation volumes were further treated in three different ways: . a continuous variable; .", "Operation volumes were further treated in three different ways: . a continuous variable; . a categorical variable based on the quartile; and . a data-driven categorical variable based on k-means clustering algorithm. Furthermore, subgroup analysis for comorbidities was also conducted.", "Furthermore, subgroup analysis for comorbidities was also conducted. RESULTS: This study showed that hospital volumes were not significantly associated with SSIs, no matter which definitions or categorization methods of operation volume, or SSIs case identification approaches were used. On the contrary, the relationships between surgeon’s volumes varied.", "On the contrary, the relationships between surgeon’s volumes varied. Most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons. CONCLUSION: Surgeon volumes were more important than hospital volumes in exploring the relationship between CABG operation volumes and SSIs in Taiwan. However, the relationships were not robust.", "However, the relationships were not robust. Definitions and categorization methods of operation volume and correct identification of SSIs are important issues for future research. Text: data, which should use hierarchical models, may result in biased estimation of the variation and also lead to incorrect conclusions.", "Text: data, which should use hierarchical models, may result in biased estimation of the variation and also lead to incorrect conclusions. SSIs following coronary artery bypass graft CABG procedures place a heavy burden on patients and healthcare systems. The total length of stay and expenditure for patients with SSIs after CABG surgery is significantly longer and higher than those without SSIs.", "The total length of stay and expenditure for patients with SSIs after CABG surgery is significantly longer and higher than those without SSIs. In 2008, the Centers for Medicare & Medicaid of the United States of America implemented the \"Never Event\" policy, where hospitals would no longer receive higher payments for the additional costs associated with treating patients for certain healthcare-acquired infections, including those related to CABG. In view of the accuracy of SSIs identification and the heterogeneity of definition and categorization methods, no existing studies have used different infection case identification nor definitions and categorization methods of operation volume simultaneously to explore the relationship between operation volumes and infection.", "In view of the accuracy of SSIs identification and the heterogeneity of definition and categorization methods, no existing studies have used different infection case identification nor definitions and categorization methods of operation volume simultaneously to explore the relationship between operation volumes and infection. The current study takes CABG SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, given different SSI cases identification, operation volume definitions and categorization methods. This retrospective and cross-sectional study adopted a multilevel design to examine the relationships between provider volumes and SSIs after adjusting for patient-, surgeon-, and hospital-level covariates.", "This retrospective and cross-sectional study adopted a multilevel design to examine the relationships between provider volumes and SSIs after adjusting for patient-, surgeon-, and hospital-level covariates. We used data from the Taiwan National Health Insurance Research Database NHIRD from 2005 and 2008. The NHIRD, published by the Taiwan National Health Research Institute, includes all the original claims data and registration files for beneficiaries enrolled under the National Health Insurance NHI program.", "The NHIRD, published by the Taiwan National Health Research Institute, includes all the original claims data and registration files for beneficiaries enrolled under the National Health Insurance NHI program. The database covers the 23 million Taiwanese enrollees approximately 98% of the population in the NHI program. It is a de-identified secondary database containing patient-level demographic and administrative information; however, treatment items are aggregated and without time-related and clinical information.", "It is a de-identified secondary database containing patient-level demographic and administrative information; however, treatment items are aggregated and without time-related and clinical information. The data is released for research purposes. The protocol for the study was approved by the Institutional Review Board of the National Taiwan University Hospital protocol #201001027R .", "The protocol for the study was approved by the Institutional Review Board of the National Taiwan University Hospital protocol #201001027R . The dataset we used in this study was secondary data; all information was de-identified by data owners. In this study, we adopted the ICD-9-CM SSI codes hereafter referred to as the ICD-9-CM based model and the Classification and Regression Trees CART model, which was developed in our previous work to identify SSI cases.", "In this study, we adopted the ICD-9-CM SSI codes hereafter referred to as the ICD-9-CM based model and the Classification and Regression Trees CART model, which was developed in our previous work to identify SSI cases. As we mentioned above, the ICD-9-CM SSI codes were the most popular tool to identify the SSI cases in claims data. In the ICD-9-CM based model, SSI cases were divided into two categories: index hospitalization events and post-discharge events i.e., SSIs that occurred within 1 year after discharge and required readmission to a hospital and/ or the use of ambulatory services .", "In the ICD-9-CM based model, SSI cases were divided into two categories: index hospitalization events and post-discharge events i.e., SSIs that occurred within 1 year after discharge and required readmission to a hospital and/ or the use of ambulatory services . Following Wu et al , this study adopted the secondary ICD-9-CM diagnosis codes for index hospitalization events ICD-9-CM code: 996.03, 996.61, 996.72, and 998.5 , and the primary and secondary diagnosis codes for post-discharge events ICD-9-CM code: 038.0-038. 4 as the criteria for SSI identification, in order to avoid cases in which infection existed prior to hospitalization.", "4 as the criteria for SSI identification, in order to avoid cases in which infection existed prior to hospitalization. If a case had an index hospitalization event or a post-discharge event, then he/ she will be identified as SSIs by the ICD-9-CM based model. In the CART model, we adopted the type of antibiotics, dose of cefazolin, length of stay, and number of vessels obstructed as a proxy indicator of duration of operation as the parameters to identify the SSIs, according to our previous findings.", "In the CART model, we adopted the type of antibiotics, dose of cefazolin, length of stay, and number of vessels obstructed as a proxy indicator of duration of operation as the parameters to identify the SSIs, according to our previous findings. In our previous work, we used the 2005-2008 National Health Insurance claims data and healthcare-associated infection surveillance data from two medical centers for model development and model verification. Infection cases based on surveillance were identified by infection control personnel if the patient met the Taiwan CDC's criteria, which are the same as those adopted in the U.S. CDC.", "Infection cases based on surveillance were identified by infection control personnel if the patient met the Taiwan CDC's criteria, which are the same as those adopted in the U.S. CDC. They manually review medical records of all patients at risk for the specified healthcare-associated infection. The classification algorithms, the multivariable regression model, and the data mining model were adopted to develop alternative models based on surrogate indicators to identify cases of CABG SSIs and to compare the performance among these models and the ICD-9-CMbased model.", "The classification algorithms, the multivariable regression model, and the data mining model were adopted to develop alternative models based on surrogate indicators to identify cases of CABG SSIs and to compare the performance among these models and the ICD-9-CMbased model. For the classification algorithms, researchers build up several criteria, and if a case satisfies or exceeds a specific number of criteria, then it will be identified as a case of infection. For the multivariable regression model, researchers usually calculated a risk score by the logistic regression model, and the optimal cutoff point was determined according to the resulting receiver operating characteristic curve.", "For the multivariable regression model, researchers usually calculated a risk score by the logistic regression model, and the optimal cutoff point was determined according to the resulting receiver operating characteristic curve. Concerning the data mining approach, which is widely used for predicting and classifying objects, the characteristics are: automatic discovery of patterns, prediction of likely outcomes, creation of actionable information, and focus on large data sets and databases. The classification and regression tree CART model, which is the most popular approach as applied in our work, and the growing, stopping, and pruning of the tree were determined by Gini improvement measures.", "The classification and regression tree CART model, which is the most popular approach as applied in our work, and the growing, stopping, and pruning of the tree were determined by Gini improvement measures. After referring to the literature and conferring with infectious disease specialists, we adopted the following seven parameters: type of antibiotic, doses of antibiotic, doses of cefazolin, use of second-line antibiotics, length of stay, and number of vessels obstructed. Additionally, cross-validation was also employed, where data from one medical center was used for model development, and another one was used for model validation.", "Additionally, cross-validation was also employed, where data from one medical center was used for model development, and another one was used for model validation. The results of our previous work revealed that the CART model offered better performance than that of the other identification models or the ICD-9-CM based model, especially in the positive predictive value >70% , which was only found to be 20% in the ICD-9-CM based model. Table 1 The findings also implied that the CART was a decidedly better tool for identifying cases of SSI in the Taiwan National Health Insurance database.", "Table 1 The findings also implied that the CART was a decidedly better tool for identifying cases of SSI in the Taiwan National Health Insurance database. Therefore, this study also adopted the CART model for identifying CABG SSIs. To ensure homogeneity, current study analyzed 7,007 patients from 19 medical centers in Taiwan who underwent CABG surgery ICD-9-CM procedure codes 36.1x-36.2x between 2006 and 2008.", "To ensure homogeneity, current study analyzed 7,007 patients from 19 medical centers in Taiwan who underwent CABG surgery ICD-9-CM procedure codes 36.1x-36.2x between 2006 and 2008. CABG patients under the age of 18 years or over 85 years were excluded in this study. A total of 302 cases were identified as SSIs by ICD-9-CM based model, and a total of 107 cases were identified as SSIs by CART model.", "A total of 302 cases were identified as SSIs by ICD-9-CM based model, and a total of 107 cases were identified as SSIs by CART model. In this study, we used the following two definitions to define operation volumes: . the cumulative operation volumes by each surgeon and hospital within the study period, which was the most common definition in the literature; and .", "the cumulative operation volumes by each surgeon and hospital within the study period, which was the most common definition in the literature; and . following Yasunaga et al. 's study, cumulative operation volumes by each surgeon and hospital in the previous one year for each surgery.", "'s study, cumulative operation volumes by each surgeon and hospital in the previous one year for each surgery. However, our data was skewed, which did not follow a normal distribution. Therefore, we conducted the log transformations on operation volumes. The current work treated operation volumes in three different ways: . a continuous variable; .", "a continuous variable; . a categorical variable based on the first and the third quartile as cutoff points the most common method to categorize service/ operation volumes ; and . a data-driven categorical variable based on k-means clustering algorithm.", "a data-driven categorical variable based on k-means clustering algorithm. This study categorized surgeon and hospital volumes into low, medium, and high volume groups by quartile method and kmeans clustering algorithm. In the quartile method, the cut-off value transformed by logarithm of the first quartile <25% for hospital volumes was 5.65, and the third quartile >75% was 6.43.", "In the quartile method, the cut-off value transformed by logarithm of the first quartile <25% for hospital volumes was 5.65, and the third quartile >75% was 6.43. In terms of surgeon volumes, the first quartile was 4.38, and the third was 5.35, when we used the cumulative operation volumes within the study period as the definition. While the definition changed, first quartile <25% for hospital volumes was 4.66, and the third quartile >75% was 5.31.", "While the definition changed, first quartile <25% for hospital volumes was 4.66, and the third quartile >75% was 5.31. In terms of surgeon volumes, the first quartile was 3.40, and the third was 4.32. K-means clustering is an unsupervised machine-learning algorithm introduced by MacQueen in 1960s.", "K-means clustering is an unsupervised machine-learning algorithm introduced by MacQueen in 1960s. This method is not only a simple and very reliable method in categorization/ classification, but is also recognized as one of the top 10 algorithms in data mining. This method has often been applied in many fields.", "This method has often been applied in many fields. Yu and his colleagues even applied it to define the quality of CABG care, and to explore the relationship among patient's income status, the level of quality of care, and inpatient mortality. The main idea of this method is to partition observed data points into k non-overlapping clusters by minimizing the within-group sum of squares.", "The main idea of this method is to partition observed data points into k non-overlapping clusters by minimizing the within-group sum of squares. Each point is assigned to the mean of its cluster using the Euclidian distance. Firstly, k cluster centers were randomly generated.", "Firstly, k cluster centers were randomly generated. Previous studies usually divided surgeons and hospitals into low-, medium-, and high-volume groups; therefore, we also predetermined the surgeon and hospital service volumes into 3 groups k = 3 . Then, participants were assigned to the cluster with the shortest distance to these cluster centers.", "Then, participants were assigned to the cluster with the shortest distance to these cluster centers. Finally, the cluster centers were recomputed using the new cluster assignment and these steps would be iterated until convergence was achieved. The cut-off values of hospital volumes were 5.21 and 5.69, and for surgeon's volumes were 2.40 and 4.38 respectively, when cumulative operation volumes within the study period was used as the definition.", "The cut-off values of hospital volumes were 5.21 and 5.69, and for surgeon's volumes were 2.40 and 4.38 respectively, when cumulative operation volumes within the study period was used as the definition. Likewise, when cumulative operation volumes before each surgery was used as definition, the cut-off values were 4.11 and 4.89 for hospital volumes, and 2.64 and 3.91 for surgeon's volumes. All cutoff values were transformed by logarithm.", "All cutoff values were transformed by logarithm. The results of k-means clustering are demonstrated in Figs 1-4. As the results show, the operation volumes were divided into three groups separately. In addition to surgeon and hospital volumes and SSI, we collected patient-, surgeon-, and hospital-level data.", "In addition to surgeon and hospital volumes and SSI, we collected patient-, surgeon-, and hospital-level data. Firstly, patient-level variables included age, gender, length of ICU stay, number of vessels obstructed that were involved in the surgical operation, and the presence of important underlying diseases e.g. diabetes mellitus, chronic obstructive pulmonary disease COPD , heart failure, renal failure and renal insufficiency, which were associated with SSI .", "diabetes mellitus, chronic obstructive pulmonary disease COPD , heart failure, renal failure and renal insufficiency, which were associated with SSI . Secondly, the surgeon-level variables included age and gender. Thirdly, the hospital-level variables included hospital ownership and geographic location.", "Thirdly, the hospital-level variables included hospital ownership and geographic location. All statistical analyses of volume-infection relationship were performed using SAS version 9.2, SAS Institution Inc., Cary, NC, USA . In statistical testing, a two-sided p value 0.05 was considered statistically significant.", "In statistical testing, a two-sided p value 0.05 was considered statistically significant. The distributional properties of continuous variables were expressed by mean ± standard deviation SD , whereas categorical variables were presented by frequency and percentage. In univariate analysis, the potential three-level predictors of SSI were examined using chi-square test or two-sample t-test as appropriate.", "In univariate analysis, the potential three-level predictors of SSI were examined using chi-square test or two-sample t-test as appropriate. Next, to account for the correlations within surgeon level-2 and hospital level-3 , multivariate analysis was conducted by fitting mixed-effects logistic regression models to each patient's data for estimating the effects of three-level predictors on the probability of post-operational SSI. Furthermore, subgroup analysis for comorbidities was also conducted.", "Furthermore, subgroup analysis for comorbidities was also conducted. Table 2 shows that there were 7,007 patients with CABG performed by 199 surgeons in 19 hospitals during 2006-2008 in Taiwan. The majority of patients were male 77.5% , and the mean age of patients was 65.3 years.", "The majority of patients were male 77.5% , and the mean age of patients was 65.3 years. The average ICU stay was 6.05 days, the mean level of number of vessels obstructed was around 1.6, while 51.8% of patients had diabetes mellitus, 33.3% had heart failure, 14.1% had renal failure and renal insufficiency, and 22.0% had COPD. Three hundred and two patients 4.31% were identified as having the ICD-9-CM SSI codes.", "Three hundred and two patients 4.31% were identified as having the ICD-9-CM SSI codes. However, identification by the CART model only revealed 107 infection cases, and 94 cases were identified in both models. Most cases received CABG surgery by male surgeons, with a mean age of 45.0 years, and the surgeon's average operation volumes within the study period was 151.64, while the average operation volumes before surgery was 52.18.", "Most cases received CABG surgery by male surgeons, with a mean age of 45.0 years, and the surgeon's average operation volumes within the study period was 151.64, while the average operation volumes before surgery was 52.18. More than half of the cases were performed with CABG in not-for-profit hospitals, and the hospitals' average operation volumes within the study period was 473.60, while the average operation volumes before each surgery was 158.79. Moreover, most of patients received their surgeries by high-volume surgeons and hospitals, when k-means algorithm was used for categorization, regardless of which definition of operation volumes were used.", "Moreover, most of patients received their surgeries by high-volume surgeons and hospitals, when k-means algorithm was used for categorization, regardless of which definition of operation volumes were used. Table 3 shows the results of multilevel mixed-effect models, with the SSIs being identified by ICD-9-CM codes, and the operation volumes defined as the cumulative volumes within the study period. The results of Model 1 continuous reveal that the surgeon's volumes were negatively associated with SSIs, while hospital's volumes were not associated with surgical site infection SSIs.", "The results of Model 1 continuous reveal that the surgeon's volumes were negatively associated with SSIs, while hospital's volumes were not associated with surgical site infection SSIs. Model 2 quartile suggests that low-volume surgeons had higher SSI risk OR = 2.220, p-value = 0.022 than high-volume surgeons. There were also no associations between hospital's operation volumes and SSIs.", "There were also no associations between hospital's operation volumes and SSIs. Model 3 k-means shows that the association did not exist between hospital's/ surgeon's volumes and SSIs. Table 4 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volumes within the study period.", "Table 4 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volumes within the study period. Model 1 again indicated a negative association between surgeon's volumes and SSIs, and hospital's volumes were not found to be associated with SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results revealed low-volume surgeons had higher risk OR = 1.691, p = 0.002 than high-volume surgeons. Table 5 displays the results of multilevel mixed-effect models, in which the SSIs were identified by ICD-9-CM codes, but the operation volumes were defined as the cumulative volume in the previous one year for each surgery.", "Table 5 displays the results of multilevel mixed-effect models, in which the SSIs were identified by ICD-9-CM codes, but the operation volumes were defined as the cumulative volume in the previous one year for each surgery. Model 1 also indicated a negative association between surgeon's volumes and SSIs, and hospital's volumes were not found to be associated with SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results also revealed low-volume surgeons had higher risk OR = 1.642, p = 0.040 than high-volume surgeons. Table 6 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volume in previous one year for each surgery.", "Table 6 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volume in previous one year for each surgery. In Model 1, different to the above findings, there was no association between hospital's/ surgeon's volumes and SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results also revealed low-volume surgeons had higher risk OR = 1.163, p = 0.020 than high-volume surgeons. We further examined the associations of surgeon and hospital volumes with SSIs in stratification analyses by underlying diseases.", "We further examined the associations of surgeon and hospital volumes with SSIs in stratification analyses by underlying diseases. When the operation volumes were defined as the cumulative operation volume within the study period, no relationships existed between hospital/ surgeon operation volumes and SSIs. Table 7 However, when the operation volumes were defined as the cumulative operation volumes in the previous one year for each surgery, the results suggested that there was a negative association between surgeon volumes and SSIs in the diabetes group, except that the volumes were treated as continuous variable and the infection cases were identified by ICD-9 codes.", "Table 7 However, when the operation volumes were defined as the cumulative operation volumes in the previous one year for each surgery, the results suggested that there was a negative association between surgeon volumes and SSIs in the diabetes group, except that the volumes were treated as continuous variable and the infection cases were identified by ICD-9 codes. In terms of hospital operation volumes, the association did not exist. Table 8 No studies have evaluated how different service/ operation volumes definitions and categorization methods affect volume-infection relationships.", "Table 8 No studies have evaluated how different service/ operation volumes definitions and categorization methods affect volume-infection relationships. Moreover, several studies have pointed out the inappropriateness of identifying infection cases using the ICD-9-CM codes in claims data. Given these reasons, this study adopted two approaches to identifying SSIs, two definitions of operation volumes, and three methods for categorizing operation volumes to examine the relationships between operation volumes and SSIs.", "Given these reasons, this study adopted two approaches to identifying SSIs, two definitions of operation volumes, and three methods for categorizing operation volumes to examine the relationships between operation volumes and SSIs. Our findings showed that the relationships between hospital volumes and SSIs did not exist, no matter which definitions, categorization mehods, or SSIs case identification approaches were used. On the contrary, the relationships between surgeon volumes and SSIs were not robust in our data.", "On the contrary, the relationships between surgeon volumes and SSIs were not robust in our data. It might be affected by different definitions and categorization methods of operation volumes, and also by different SSI cases identification approaches. In summary, most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons, and they also showed the risks were similar between medium-volume and high-volume surgeons.", "In summary, most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons, and they also showed the risks were similar between medium-volume and high-volume surgeons. However, why did surgeon volume relate to SSIs, but hospital volume did not? Except for those issues we were concerned about in this study, there are some disagreements in the literature.", "Except for those issues we were concerned about in this study, there are some disagreements in the literature. Such as \"Does provider volume really represent quality of care?\" Or \"Is provider volume the only one predictor for outcome of care?\"", "Or \"Is provider volume the only one predictor for outcome of care?\" These issues are worthy of further discussion, but are out of the scope of this study. Service/ operation volumes are treated as a proxy indicator for experiences; previous studies used it to examine whether practice makes perfect or not.", "Service/ operation volumes are treated as a proxy indicator for experiences; previous studies used it to examine whether practice makes perfect or not. But, except for provider's experiences, SSIs are also impacted by many factors, such as environmental and clinical factors. Wu et al once used Taiwan 2001 NHI claims data to explore the relationship between provider CABG operation volumes and SSIs.", "Wu et al once used Taiwan 2001 NHI claims data to explore the relationship between provider CABG operation volumes and SSIs. They found that hospital volumes had a greater effect than surgeon volumes and claimed that this may imply that hospital teamwork is more important than individual surgeon. However, our findings demonstrated that there was no relationship between hospital volumes and SSIs.", "However, our findings demonstrated that there was no relationship between hospital volumes and SSIs. Wu et al. adopted the cumulative operation volumes within the study period as the definition, and identified SSIs by ICD-9-CM codes.", "adopted the cumulative operation volumes within the study period as the definition, and identified SSIs by ICD-9-CM codes. Except, there were two differences between our work and Wu et al., which were the length and year of the data; our data was longer and more updated than theirs. Moreover, it is worth noting that there was an outbreak of severe acute respiratory syndrome SARS in Taiwan in 2003, after which the hospital infection control system in Taiwan was reviewed and re-designed.", "Moreover, it is worth noting that there was an outbreak of severe acute respiratory syndrome SARS in Taiwan in 2003, after which the hospital infection control system in Taiwan was reviewed and re-designed. Wu et al data was before SARS, so these efforts may also have improved the level of SSIs control in hospitals, leading to different findings in this study. In addition, although most models revealed that there were negative relationships between surgeon's volumes and surgical site infection, the relationships were not robust.", "In addition, although most models revealed that there were negative relationships between surgeon's volumes and surgical site infection, the relationships were not robust. The results varied between different definitions and categorization method of operation volumes, and between SSIs identification approaches. Researchers need to consider how to identify SSIs correctly, how to choose optimal cut-off values, and how to decide on which definition is appropriate.", "Researchers need to consider how to identify SSIs correctly, how to choose optimal cut-off values, and how to decide on which definition is appropriate. Finally, the results of stratification analyses showed that low-volume surgeon had higher risk than high-volume surgeon in the diabetes mellitus group, when the cumulative operation in the previous one year before surgery was used as definition. A large number of studies have indicated diabetes mellitus is associated with a higher risk of SSIs, and the findings of this study suggest that CABG patients with diabetes mellitus should be cared for by experienced surgeons.", "A large number of studies have indicated diabetes mellitus is associated with a higher risk of SSIs, and the findings of this study suggest that CABG patients with diabetes mellitus should be cared for by experienced surgeons. A multilevel analysis was applied to manage the nested factors, and two definitions of operation volume along with three different operation volume categorization methods were adopted to examine the relationship between volume and SSIs under two kinds of SSIs identification approaches. Nevertheless, the study suffered from several major limitations.", "Nevertheless, the study suffered from several major limitations. First, the accuracy of SSIs identification was still an issue. Although the performance of the CART model to identify CABG SSIs was better than ICD-9-CM codes in Taiwan NHI claims data, it did not reach the perfect scenario.", "Although the performance of the CART model to identify CABG SSIs was better than ICD-9-CM codes in Taiwan NHI claims data, it did not reach the perfect scenario. The accuracy of SSIs identification was still a challenge in our work. The second limitation relates to unmeasured variables, such as length of stay before operation, infection condition, hair removal, clinical information e.g.", "The second limitation relates to unmeasured variables, such as length of stay before operation, infection condition, hair removal, clinical information e.g. blood glucose level, causative microorganism , time-related information e.g. the duration of operation , the environment, surgical skills, use of post-operative drains, number of operations involved, and surgical site and wound care, etc.", "the duration of operation , the environment, surgical skills, use of post-operative drains, number of operations involved, and surgical site and wound care, etc. Furthermore, information about type elective or urgent and incision site for surgery was not available in the Taiwan NHI claims data. In conclusion, the findings of this study suggest that different definitions and categorization methods of operation volumes, and different SSIs identification approaches might lead to different findings, although surgeon volumes were more important than hospital volumes in exploring the relationships between CABG operation volumes and SSIs in Taiwan, but they were still not robust.", "In conclusion, the findings of this study suggest that different definitions and categorization methods of operation volumes, and different SSIs identification approaches might lead to different findings, although surgeon volumes were more important than hospital volumes in exploring the relationships between CABG operation volumes and SSIs in Taiwan, but they were still not robust. Definitions and categorization methods of operation volumes, and correct identification of SSIs are important issues for future research." ]

[ "BACKGROUND: Volume-infection relationships have been examined for high-risk surgical procedures, but the conclusions remain controversial. The inconsistency might be due to inaccurate identification of cases of infection and different methods of categorizing service volumes. This study takes coronary artery bypass graft CABG surgical site infections SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, when different SSIs case identification, definitions and categorization methods of operation volumes were implemented.", "This study takes coronary artery bypass graft CABG surgical site infections SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, when different SSIs case identification, definitions and categorization methods of operation volumes were implemented. METHODS: A population-based cross-sectional multilevel study was conducted. A total of 7,007 patients who received CABG surgery between 2006 and 2008 from19 medical centers in Taiwan were recruited.", "A total of 7,007 patients who received CABG surgery between 2006 and 2008 from19 medical centers in Taiwan were recruited. SSIs associated with CABG surgery were identified using International Classification of Diseases, 9th Revision, Clinical Modification ICD-9 CM codes and a Classification and Regression Trees CART model. Two definitions of surgeon and hospital operation volumes were used: .", "Two definitions of surgeon and hospital operation volumes were used: . the cumulative CABG operation volumes within the study period; and . the cumulative CABG operation volumes in the previous one year before each CABG surgery. Operation volumes were further treated in three different ways: . a continuous variable; .", "Operation volumes were further treated in three different ways: . a continuous variable; . a categorical variable based on the quartile; and . a data-driven categorical variable based on k-means clustering algorithm. Furthermore, subgroup analysis for comorbidities was also conducted.", "Furthermore, subgroup analysis for comorbidities was also conducted. RESULTS: This study showed that hospital volumes were not significantly associated with SSIs, no matter which definitions or categorization methods of operation volume, or SSIs case identification approaches were used. On the contrary, the relationships between surgeon’s volumes varied.", "On the contrary, the relationships between surgeon’s volumes varied. Most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons. CONCLUSION: Surgeon volumes were more important than hospital volumes in exploring the relationship between CABG operation volumes and SSIs in Taiwan. However, the relationships were not robust.", "However, the relationships were not robust. Definitions and categorization methods of operation volume and correct identification of SSIs are important issues for future research. Text: data, which should use hierarchical models, may result in biased estimation of the variation and also lead to incorrect conclusions.", "Text: data, which should use hierarchical models, may result in biased estimation of the variation and also lead to incorrect conclusions. SSIs following coronary artery bypass graft CABG procedures place a heavy burden on patients and healthcare systems. The total length of stay and expenditure for patients with SSIs after CABG surgery is significantly longer and higher than those without SSIs.", "The total length of stay and expenditure for patients with SSIs after CABG surgery is significantly longer and higher than those without SSIs. In 2008, the Centers for Medicare & Medicaid of the United States of America implemented the \"Never Event\" policy, where hospitals would no longer receive higher payments for the additional costs associated with treating patients for certain healthcare-acquired infections, including those related to CABG. In view of the accuracy of SSIs identification and the heterogeneity of definition and categorization methods, no existing studies have used different infection case identification nor definitions and categorization methods of operation volume simultaneously to explore the relationship between operation volumes and infection.", "In view of the accuracy of SSIs identification and the heterogeneity of definition and categorization methods, no existing studies have used different infection case identification nor definitions and categorization methods of operation volume simultaneously to explore the relationship between operation volumes and infection. The current study takes CABG SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, given different SSI cases identification, operation volume definitions and categorization methods. This retrospective and cross-sectional study adopted a multilevel design to examine the relationships between provider volumes and SSIs after adjusting for patient-, surgeon-, and hospital-level covariates.", "This retrospective and cross-sectional study adopted a multilevel design to examine the relationships between provider volumes and SSIs after adjusting for patient-, surgeon-, and hospital-level covariates. We used data from the Taiwan National Health Insurance Research Database NHIRD from 2005 and 2008. The NHIRD, published by the Taiwan National Health Research Institute, includes all the original claims data and registration files for beneficiaries enrolled under the National Health Insurance NHI program.", "The NHIRD, published by the Taiwan National Health Research Institute, includes all the original claims data and registration files for beneficiaries enrolled under the National Health Insurance NHI program. The database covers the 23 million Taiwanese enrollees approximately 98% of the population in the NHI program. It is a de-identified secondary database containing patient-level demographic and administrative information; however, treatment items are aggregated and without time-related and clinical information.", "It is a de-identified secondary database containing patient-level demographic and administrative information; however, treatment items are aggregated and without time-related and clinical information. The data is released for research purposes. The protocol for the study was approved by the Institutional Review Board of the National Taiwan University Hospital protocol #201001027R .", "The protocol for the study was approved by the Institutional Review Board of the National Taiwan University Hospital protocol #201001027R . The dataset we used in this study was secondary data; all information was de-identified by data owners. In this study, we adopted the ICD-9-CM SSI codes hereafter referred to as the ICD-9-CM based model and the Classification and Regression Trees CART model, which was developed in our previous work to identify SSI cases.", "In this study, we adopted the ICD-9-CM SSI codes hereafter referred to as the ICD-9-CM based model and the Classification and Regression Trees CART model, which was developed in our previous work to identify SSI cases. As we mentioned above, the ICD-9-CM SSI codes were the most popular tool to identify the SSI cases in claims data. In the ICD-9-CM based model, SSI cases were divided into two categories: index hospitalization events and post-discharge events i.e., SSIs that occurred within 1 year after discharge and required readmission to a hospital and/ or the use of ambulatory services .", "In the ICD-9-CM based model, SSI cases were divided into two categories: index hospitalization events and post-discharge events i.e., SSIs that occurred within 1 year after discharge and required readmission to a hospital and/ or the use of ambulatory services . Following Wu et al , this study adopted the secondary ICD-9-CM diagnosis codes for index hospitalization events ICD-9-CM code: 996.03, 996.61, 996.72, and 998.5 , and the primary and secondary diagnosis codes for post-discharge events ICD-9-CM code: 038.0-038. 4 as the criteria for SSI identification, in order to avoid cases in which infection existed prior to hospitalization.", "4 as the criteria for SSI identification, in order to avoid cases in which infection existed prior to hospitalization. If a case had an index hospitalization event or a post-discharge event, then he/ she will be identified as SSIs by the ICD-9-CM based model. In the CART model, we adopted the type of antibiotics, dose of cefazolin, length of stay, and number of vessels obstructed as a proxy indicator of duration of operation as the parameters to identify the SSIs, according to our previous findings.", "In the CART model, we adopted the type of antibiotics, dose of cefazolin, length of stay, and number of vessels obstructed as a proxy indicator of duration of operation as the parameters to identify the SSIs, according to our previous findings. In our previous work, we used the 2005-2008 National Health Insurance claims data and healthcare-associated infection surveillance data from two medical centers for model development and model verification. Infection cases based on surveillance were identified by infection control personnel if the patient met the Taiwan CDC's criteria, which are the same as those adopted in the U.S. CDC.", "Infection cases based on surveillance were identified by infection control personnel if the patient met the Taiwan CDC's criteria, which are the same as those adopted in the U.S. CDC. They manually review medical records of all patients at risk for the specified healthcare-associated infection. The classification algorithms, the multivariable regression model, and the data mining model were adopted to develop alternative models based on surrogate indicators to identify cases of CABG SSIs and to compare the performance among these models and the ICD-9-CMbased model.", "The classification algorithms, the multivariable regression model, and the data mining model were adopted to develop alternative models based on surrogate indicators to identify cases of CABG SSIs and to compare the performance among these models and the ICD-9-CMbased model. For the classification algorithms, researchers build up several criteria, and if a case satisfies or exceeds a specific number of criteria, then it will be identified as a case of infection. For the multivariable regression model, researchers usually calculated a risk score by the logistic regression model, and the optimal cutoff point was determined according to the resulting receiver operating characteristic curve.", "For the multivariable regression model, researchers usually calculated a risk score by the logistic regression model, and the optimal cutoff point was determined according to the resulting receiver operating characteristic curve. Concerning the data mining approach, which is widely used for predicting and classifying objects, the characteristics are: automatic discovery of patterns, prediction of likely outcomes, creation of actionable information, and focus on large data sets and databases. The classification and regression tree CART model, which is the most popular approach as applied in our work, and the growing, stopping, and pruning of the tree were determined by Gini improvement measures.", "The classification and regression tree CART model, which is the most popular approach as applied in our work, and the growing, stopping, and pruning of the tree were determined by Gini improvement measures. After referring to the literature and conferring with infectious disease specialists, we adopted the following seven parameters: type of antibiotic, doses of antibiotic, doses of cefazolin, use of second-line antibiotics, length of stay, and number of vessels obstructed. Additionally, cross-validation was also employed, where data from one medical center was used for model development, and another one was used for model validation.", "Additionally, cross-validation was also employed, where data from one medical center was used for model development, and another one was used for model validation. The results of our previous work revealed that the CART model offered better performance than that of the other identification models or the ICD-9-CM based model, especially in the positive predictive value >70% , which was only found to be 20% in the ICD-9-CM based model. Table 1 The findings also implied that the CART was a decidedly better tool for identifying cases of SSI in the Taiwan National Health Insurance database.", "Table 1 The findings also implied that the CART was a decidedly better tool for identifying cases of SSI in the Taiwan National Health Insurance database. Therefore, this study also adopted the CART model for identifying CABG SSIs. To ensure homogeneity, current study analyzed 7,007 patients from 19 medical centers in Taiwan who underwent CABG surgery ICD-9-CM procedure codes 36.1x-36.2x between 2006 and 2008.", "To ensure homogeneity, current study analyzed 7,007 patients from 19 medical centers in Taiwan who underwent CABG surgery ICD-9-CM procedure codes 36.1x-36.2x between 2006 and 2008. CABG patients under the age of 18 years or over 85 years were excluded in this study. A total of 302 cases were identified as SSIs by ICD-9-CM based model, and a total of 107 cases were identified as SSIs by CART model.", "A total of 302 cases were identified as SSIs by ICD-9-CM based model, and a total of 107 cases were identified as SSIs by CART model. In this study, we used the following two definitions to define operation volumes: . the cumulative operation volumes by each surgeon and hospital within the study period, which was the most common definition in the literature; and .", "the cumulative operation volumes by each surgeon and hospital within the study period, which was the most common definition in the literature; and . following Yasunaga et al. 's study, cumulative operation volumes by each surgeon and hospital in the previous one year for each surgery.", "'s study, cumulative operation volumes by each surgeon and hospital in the previous one year for each surgery. However, our data was skewed, which did not follow a normal distribution. Therefore, we conducted the log transformations on operation volumes. The current work treated operation volumes in three different ways: . a continuous variable; .", "a continuous variable; . a categorical variable based on the first and the third quartile as cutoff points the most common method to categorize service/ operation volumes ; and . a data-driven categorical variable based on k-means clustering algorithm.", "a data-driven categorical variable based on k-means clustering algorithm. This study categorized surgeon and hospital volumes into low, medium, and high volume groups by quartile method and kmeans clustering algorithm. In the quartile method, the cut-off value transformed by logarithm of the first quartile <25% for hospital volumes was 5.65, and the third quartile >75% was 6.43.", "In the quartile method, the cut-off value transformed by logarithm of the first quartile <25% for hospital volumes was 5.65, and the third quartile >75% was 6.43. In terms of surgeon volumes, the first quartile was 4.38, and the third was 5.35, when we used the cumulative operation volumes within the study period as the definition. While the definition changed, first quartile <25% for hospital volumes was 4.66, and the third quartile >75% was 5.31.", "While the definition changed, first quartile <25% for hospital volumes was 4.66, and the third quartile >75% was 5.31. In terms of surgeon volumes, the first quartile was 3.40, and the third was 4.32. K-means clustering is an unsupervised machine-learning algorithm introduced by MacQueen in 1960s.", "K-means clustering is an unsupervised machine-learning algorithm introduced by MacQueen in 1960s. This method is not only a simple and very reliable method in categorization/ classification, but is also recognized as one of the top 10 algorithms in data mining. This method has often been applied in many fields.", "This method has often been applied in many fields. Yu and his colleagues even applied it to define the quality of CABG care, and to explore the relationship among patient's income status, the level of quality of care, and inpatient mortality. The main idea of this method is to partition observed data points into k non-overlapping clusters by minimizing the within-group sum of squares.", "The main idea of this method is to partition observed data points into k non-overlapping clusters by minimizing the within-group sum of squares. Each point is assigned to the mean of its cluster using the Euclidian distance. Firstly, k cluster centers were randomly generated.", "Firstly, k cluster centers were randomly generated. Previous studies usually divided surgeons and hospitals into low-, medium-, and high-volume groups; therefore, we also predetermined the surgeon and hospital service volumes into 3 groups k = 3 . Then, participants were assigned to the cluster with the shortest distance to these cluster centers.", "Then, participants were assigned to the cluster with the shortest distance to these cluster centers. Finally, the cluster centers were recomputed using the new cluster assignment and these steps would be iterated until convergence was achieved. The cut-off values of hospital volumes were 5.21 and 5.69, and for surgeon's volumes were 2.40 and 4.38 respectively, when cumulative operation volumes within the study period was used as the definition.", "The cut-off values of hospital volumes were 5.21 and 5.69, and for surgeon's volumes were 2.40 and 4.38 respectively, when cumulative operation volumes within the study period was used as the definition. Likewise, when cumulative operation volumes before each surgery was used as definition, the cut-off values were 4.11 and 4.89 for hospital volumes, and 2.64 and 3.91 for surgeon's volumes. All cutoff values were transformed by logarithm.", "All cutoff values were transformed by logarithm. The results of k-means clustering are demonstrated in Figs 1-4. As the results show, the operation volumes were divided into three groups separately. In addition to surgeon and hospital volumes and SSI, we collected patient-, surgeon-, and hospital-level data.", "In addition to surgeon and hospital volumes and SSI, we collected patient-, surgeon-, and hospital-level data. Firstly, patient-level variables included age, gender, length of ICU stay, number of vessels obstructed that were involved in the surgical operation, and the presence of important underlying diseases e.g. diabetes mellitus, chronic obstructive pulmonary disease COPD , heart failure, renal failure and renal insufficiency, which were associated with SSI .", "diabetes mellitus, chronic obstructive pulmonary disease COPD , heart failure, renal failure and renal insufficiency, which were associated with SSI . Secondly, the surgeon-level variables included age and gender. Thirdly, the hospital-level variables included hospital ownership and geographic location.", "Thirdly, the hospital-level variables included hospital ownership and geographic location. All statistical analyses of volume-infection relationship were performed using SAS version 9.2, SAS Institution Inc., Cary, NC, USA . In statistical testing, a two-sided p value 0.05 was considered statistically significant.", "In statistical testing, a two-sided p value 0.05 was considered statistically significant. The distributional properties of continuous variables were expressed by mean ± standard deviation SD , whereas categorical variables were presented by frequency and percentage. In univariate analysis, the potential three-level predictors of SSI were examined using chi-square test or two-sample t-test as appropriate.", "In univariate analysis, the potential three-level predictors of SSI were examined using chi-square test or two-sample t-test as appropriate. Next, to account for the correlations within surgeon level-2 and hospital level-3 , multivariate analysis was conducted by fitting mixed-effects logistic regression models to each patient's data for estimating the effects of three-level predictors on the probability of post-operational SSI. Furthermore, subgroup analysis for comorbidities was also conducted.", "Furthermore, subgroup analysis for comorbidities was also conducted. Table 2 shows that there were 7,007 patients with CABG performed by 199 surgeons in 19 hospitals during 2006-2008 in Taiwan. The majority of patients were male 77.5% , and the mean age of patients was 65.3 years.", "The majority of patients were male 77.5% , and the mean age of patients was 65.3 years. The average ICU stay was 6.05 days, the mean level of number of vessels obstructed was around 1.6, while 51.8% of patients had diabetes mellitus, 33.3% had heart failure, 14.1% had renal failure and renal insufficiency, and 22.0% had COPD. Three hundred and two patients 4.31% were identified as having the ICD-9-CM SSI codes.", "Three hundred and two patients 4.31% were identified as having the ICD-9-CM SSI codes. However, identification by the CART model only revealed 107 infection cases, and 94 cases were identified in both models. Most cases received CABG surgery by male surgeons, with a mean age of 45.0 years, and the surgeon's average operation volumes within the study period was 151.64, while the average operation volumes before surgery was 52.18.", "Most cases received CABG surgery by male surgeons, with a mean age of 45.0 years, and the surgeon's average operation volumes within the study period was 151.64, while the average operation volumes before surgery was 52.18. More than half of the cases were performed with CABG in not-for-profit hospitals, and the hospitals' average operation volumes within the study period was 473.60, while the average operation volumes before each surgery was 158.79. Moreover, most of patients received their surgeries by high-volume surgeons and hospitals, when k-means algorithm was used for categorization, regardless of which definition of operation volumes were used.", "Moreover, most of patients received their surgeries by high-volume surgeons and hospitals, when k-means algorithm was used for categorization, regardless of which definition of operation volumes were used. Table 3 shows the results of multilevel mixed-effect models, with the SSIs being identified by ICD-9-CM codes, and the operation volumes defined as the cumulative volumes within the study period. The results of Model 1 continuous reveal that the surgeon's volumes were negatively associated with SSIs, while hospital's volumes were not associated with surgical site infection SSIs.", "The results of Model 1 continuous reveal that the surgeon's volumes were negatively associated with SSIs, while hospital's volumes were not associated with surgical site infection SSIs. Model 2 quartile suggests that low-volume surgeons had higher SSI risk OR = 2.220, p-value = 0.022 than high-volume surgeons. There were also no associations between hospital's operation volumes and SSIs.", "There were also no associations between hospital's operation volumes and SSIs. Model 3 k-means shows that the association did not exist between hospital's/ surgeon's volumes and SSIs. Table 4 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volumes within the study period.", "Table 4 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volumes within the study period. Model 1 again indicated a negative association between surgeon's volumes and SSIs, and hospital's volumes were not found to be associated with SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results revealed low-volume surgeons had higher risk OR = 1.691, p = 0.002 than high-volume surgeons. Table 5 displays the results of multilevel mixed-effect models, in which the SSIs were identified by ICD-9-CM codes, but the operation volumes were defined as the cumulative volume in the previous one year for each surgery.", "Table 5 displays the results of multilevel mixed-effect models, in which the SSIs were identified by ICD-9-CM codes, but the operation volumes were defined as the cumulative volume in the previous one year for each surgery. Model 1 also indicated a negative association between surgeon's volumes and SSIs, and hospital's volumes were not found to be associated with SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results also revealed low-volume surgeons had higher risk OR = 1.642, p = 0.040 than high-volume surgeons. Table 6 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volume in previous one year for each surgery.", "Table 6 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volume in previous one year for each surgery. In Model 1, different to the above findings, there was no association between hospital's/ surgeon's volumes and SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results also revealed low-volume surgeons had higher risk OR = 1.163, p = 0.020 than high-volume surgeons. We further examined the associations of surgeon and hospital volumes with SSIs in stratification analyses by underlying diseases.", "We further examined the associations of surgeon and hospital volumes with SSIs in stratification analyses by underlying diseases. When the operation volumes were defined as the cumulative operation volume within the study period, no relationships existed between hospital/ surgeon operation volumes and SSIs. Table 7 However, when the operation volumes were defined as the cumulative operation volumes in the previous one year for each surgery, the results suggested that there was a negative association between surgeon volumes and SSIs in the diabetes group, except that the volumes were treated as continuous variable and the infection cases were identified by ICD-9 codes.", "Table 7 However, when the operation volumes were defined as the cumulative operation volumes in the previous one year for each surgery, the results suggested that there was a negative association between surgeon volumes and SSIs in the diabetes group, except that the volumes were treated as continuous variable and the infection cases were identified by ICD-9 codes. In terms of hospital operation volumes, the association did not exist. Table 8 No studies have evaluated how different service/ operation volumes definitions and categorization methods affect volume-infection relationships.", "Table 8 No studies have evaluated how different service/ operation volumes definitions and categorization methods affect volume-infection relationships. Moreover, several studies have pointed out the inappropriateness of identifying infection cases using the ICD-9-CM codes in claims data. Given these reasons, this study adopted two approaches to identifying SSIs, two definitions of operation volumes, and three methods for categorizing operation volumes to examine the relationships between operation volumes and SSIs.", "Given these reasons, this study adopted two approaches to identifying SSIs, two definitions of operation volumes, and three methods for categorizing operation volumes to examine the relationships between operation volumes and SSIs. Our findings showed that the relationships between hospital volumes and SSIs did not exist, no matter which definitions, categorization mehods, or SSIs case identification approaches were used. On the contrary, the relationships between surgeon volumes and SSIs were not robust in our data.", "On the contrary, the relationships between surgeon volumes and SSIs were not robust in our data. It might be affected by different definitions and categorization methods of operation volumes, and also by different SSI cases identification approaches. In summary, most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons, and they also showed the risks were similar between medium-volume and high-volume surgeons.", "In summary, most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons, and they also showed the risks were similar between medium-volume and high-volume surgeons. However, why did surgeon volume relate to SSIs, but hospital volume did not? Except for those issues we were concerned about in this study, there are some disagreements in the literature.", "Except for those issues we were concerned about in this study, there are some disagreements in the literature. Such as \"Does provider volume really represent quality of care?\" Or \"Is provider volume the only one predictor for outcome of care?\"", "Or \"Is provider volume the only one predictor for outcome of care?\" These issues are worthy of further discussion, but are out of the scope of this study. Service/ operation volumes are treated as a proxy indicator for experiences; previous studies used it to examine whether practice makes perfect or not.", "Service/ operation volumes are treated as a proxy indicator for experiences; previous studies used it to examine whether practice makes perfect or not. But, except for provider's experiences, SSIs are also impacted by many factors, such as environmental and clinical factors. Wu et al once used Taiwan 2001 NHI claims data to explore the relationship between provider CABG operation volumes and SSIs.", "Wu et al once used Taiwan 2001 NHI claims data to explore the relationship between provider CABG operation volumes and SSIs. They found that hospital volumes had a greater effect than surgeon volumes and claimed that this may imply that hospital teamwork is more important than individual surgeon. However, our findings demonstrated that there was no relationship between hospital volumes and SSIs.", "However, our findings demonstrated that there was no relationship between hospital volumes and SSIs. Wu et al. adopted the cumulative operation volumes within the study period as the definition, and identified SSIs by ICD-9-CM codes.", "adopted the cumulative operation volumes within the study period as the definition, and identified SSIs by ICD-9-CM codes. Except, there were two differences between our work and Wu et al., which were the length and year of the data; our data was longer and more updated than theirs. Moreover, it is worth noting that there was an outbreak of severe acute respiratory syndrome SARS in Taiwan in 2003, after which the hospital infection control system in Taiwan was reviewed and re-designed.", "Moreover, it is worth noting that there was an outbreak of severe acute respiratory syndrome SARS in Taiwan in 2003, after which the hospital infection control system in Taiwan was reviewed and re-designed. Wu et al data was before SARS, so these efforts may also have improved the level of SSIs control in hospitals, leading to different findings in this study. In addition, although most models revealed that there were negative relationships between surgeon's volumes and surgical site infection, the relationships were not robust.", "In addition, although most models revealed that there were negative relationships between surgeon's volumes and surgical site infection, the relationships were not robust. The results varied between different definitions and categorization method of operation volumes, and between SSIs identification approaches. Researchers need to consider how to identify SSIs correctly, how to choose optimal cut-off values, and how to decide on which definition is appropriate.", "Researchers need to consider how to identify SSIs correctly, how to choose optimal cut-off values, and how to decide on which definition is appropriate. Finally, the results of stratification analyses showed that low-volume surgeon had higher risk than high-volume surgeon in the diabetes mellitus group, when the cumulative operation in the previous one year before surgery was used as definition. A large number of studies have indicated diabetes mellitus is associated with a higher risk of SSIs, and the findings of this study suggest that CABG patients with diabetes mellitus should be cared for by experienced surgeons.", "A large number of studies have indicated diabetes mellitus is associated with a higher risk of SSIs, and the findings of this study suggest that CABG patients with diabetes mellitus should be cared for by experienced surgeons. A multilevel analysis was applied to manage the nested factors, and two definitions of operation volume along with three different operation volume categorization methods were adopted to examine the relationship between volume and SSIs under two kinds of SSIs identification approaches. Nevertheless, the study suffered from several major limitations.", "Nevertheless, the study suffered from several major limitations. First, the accuracy of SSIs identification was still an issue. Although the performance of the CART model to identify CABG SSIs was better than ICD-9-CM codes in Taiwan NHI claims data, it did not reach the perfect scenario.", "Although the performance of the CART model to identify CABG SSIs was better than ICD-9-CM codes in Taiwan NHI claims data, it did not reach the perfect scenario. The accuracy of SSIs identification was still a challenge in our work. The second limitation relates to unmeasured variables, such as length of stay before operation, infection condition, hair removal, clinical information e.g.", "The second limitation relates to unmeasured variables, such as length of stay before operation, infection condition, hair removal, clinical information e.g. blood glucose level, causative microorganism , time-related information e.g. the duration of operation , the environment, surgical skills, use of post-operative drains, number of operations involved, and surgical site and wound care, etc.", "the duration of operation , the environment, surgical skills, use of post-operative drains, number of operations involved, and surgical site and wound care, etc. Furthermore, information about type elective or urgent and incision site for surgery was not available in the Taiwan NHI claims data. In conclusion, the findings of this study suggest that different definitions and categorization methods of operation volumes, and different SSIs identification approaches might lead to different findings, although surgeon volumes were more important than hospital volumes in exploring the relationships between CABG operation volumes and SSIs in Taiwan, but they were still not robust.", "In conclusion, the findings of this study suggest that different definitions and categorization methods of operation volumes, and different SSIs identification approaches might lead to different findings, although surgeon volumes were more important than hospital volumes in exploring the relationships between CABG operation volumes and SSIs in Taiwan, but they were still not robust. Definitions and categorization methods of operation volumes, and correct identification of SSIs are important issues for future research." ]

[ "BACKGROUND: Volume-infection relationships have been examined for high-risk surgical procedures, but the conclusions remain controversial. The inconsistency might be due to inaccurate identification of cases of infection and different methods of categorizing service volumes. This study takes coronary artery bypass graft CABG surgical site infections SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, when different SSIs case identification, definitions and categorization methods of operation volumes were implemented.", "This study takes coronary artery bypass graft CABG surgical site infections SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, when different SSIs case identification, definitions and categorization methods of operation volumes were implemented. METHODS: A population-based cross-sectional multilevel study was conducted. A total of 7,007 patients who received CABG surgery between 2006 and 2008 from19 medical centers in Taiwan were recruited.", "A total of 7,007 patients who received CABG surgery between 2006 and 2008 from19 medical centers in Taiwan were recruited. SSIs associated with CABG surgery were identified using International Classification of Diseases, 9th Revision, Clinical Modification ICD-9 CM codes and a Classification and Regression Trees CART model. Two definitions of surgeon and hospital operation volumes were used: .", "Two definitions of surgeon and hospital operation volumes were used: . the cumulative CABG operation volumes within the study period; and . the cumulative CABG operation volumes in the previous one year before each CABG surgery. Operation volumes were further treated in three different ways: . a continuous variable; .", "Operation volumes were further treated in three different ways: . a continuous variable; . a categorical variable based on the quartile; and . a data-driven categorical variable based on k-means clustering algorithm. Furthermore, subgroup analysis for comorbidities was also conducted.", "Furthermore, subgroup analysis for comorbidities was also conducted. RESULTS: This study showed that hospital volumes were not significantly associated with SSIs, no matter which definitions or categorization methods of operation volume, or SSIs case identification approaches were used. On the contrary, the relationships between surgeon’s volumes varied.", "On the contrary, the relationships between surgeon’s volumes varied. Most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons. CONCLUSION: Surgeon volumes were more important than hospital volumes in exploring the relationship between CABG operation volumes and SSIs in Taiwan. However, the relationships were not robust.", "However, the relationships were not robust. Definitions and categorization methods of operation volume and correct identification of SSIs are important issues for future research. Text: data, which should use hierarchical models, may result in biased estimation of the variation and also lead to incorrect conclusions.", "Text: data, which should use hierarchical models, may result in biased estimation of the variation and also lead to incorrect conclusions. SSIs following coronary artery bypass graft CABG procedures place a heavy burden on patients and healthcare systems. The total length of stay and expenditure for patients with SSIs after CABG surgery is significantly longer and higher than those without SSIs.", "The total length of stay and expenditure for patients with SSIs after CABG surgery is significantly longer and higher than those without SSIs. In 2008, the Centers for Medicare & Medicaid of the United States of America implemented the \"Never Event\" policy, where hospitals would no longer receive higher payments for the additional costs associated with treating patients for certain healthcare-acquired infections, including those related to CABG. In view of the accuracy of SSIs identification and the heterogeneity of definition and categorization methods, no existing studies have used different infection case identification nor definitions and categorization methods of operation volume simultaneously to explore the relationship between operation volumes and infection.", "In view of the accuracy of SSIs identification and the heterogeneity of definition and categorization methods, no existing studies have used different infection case identification nor definitions and categorization methods of operation volume simultaneously to explore the relationship between operation volumes and infection. The current study takes CABG SSIs as an example to examine whether a relationship exists between operation volumes and SSIs, given different SSI cases identification, operation volume definitions and categorization methods. This retrospective and cross-sectional study adopted a multilevel design to examine the relationships between provider volumes and SSIs after adjusting for patient-, surgeon-, and hospital-level covariates.", "This retrospective and cross-sectional study adopted a multilevel design to examine the relationships between provider volumes and SSIs after adjusting for patient-, surgeon-, and hospital-level covariates. We used data from the Taiwan National Health Insurance Research Database NHIRD from 2005 and 2008. The NHIRD, published by the Taiwan National Health Research Institute, includes all the original claims data and registration files for beneficiaries enrolled under the National Health Insurance NHI program.", "The NHIRD, published by the Taiwan National Health Research Institute, includes all the original claims data and registration files for beneficiaries enrolled under the National Health Insurance NHI program. The database covers the 23 million Taiwanese enrollees approximately 98% of the population in the NHI program. It is a de-identified secondary database containing patient-level demographic and administrative information; however, treatment items are aggregated and without time-related and clinical information.", "It is a de-identified secondary database containing patient-level demographic and administrative information; however, treatment items are aggregated and without time-related and clinical information. The data is released for research purposes. The protocol for the study was approved by the Institutional Review Board of the National Taiwan University Hospital protocol #201001027R .", "The protocol for the study was approved by the Institutional Review Board of the National Taiwan University Hospital protocol #201001027R . The dataset we used in this study was secondary data; all information was de-identified by data owners. In this study, we adopted the ICD-9-CM SSI codes hereafter referred to as the ICD-9-CM based model and the Classification and Regression Trees CART model, which was developed in our previous work to identify SSI cases.", "In this study, we adopted the ICD-9-CM SSI codes hereafter referred to as the ICD-9-CM based model and the Classification and Regression Trees CART model, which was developed in our previous work to identify SSI cases. As we mentioned above, the ICD-9-CM SSI codes were the most popular tool to identify the SSI cases in claims data. In the ICD-9-CM based model, SSI cases were divided into two categories: index hospitalization events and post-discharge events i.e., SSIs that occurred within 1 year after discharge and required readmission to a hospital and/ or the use of ambulatory services .", "In the ICD-9-CM based model, SSI cases were divided into two categories: index hospitalization events and post-discharge events i.e., SSIs that occurred within 1 year after discharge and required readmission to a hospital and/ or the use of ambulatory services . Following Wu et al , this study adopted the secondary ICD-9-CM diagnosis codes for index hospitalization events ICD-9-CM code: 996.03, 996.61, 996.72, and 998.5 , and the primary and secondary diagnosis codes for post-discharge events ICD-9-CM code: 038.0-038. 4 as the criteria for SSI identification, in order to avoid cases in which infection existed prior to hospitalization.", "4 as the criteria for SSI identification, in order to avoid cases in which infection existed prior to hospitalization. If a case had an index hospitalization event or a post-discharge event, then he/ she will be identified as SSIs by the ICD-9-CM based model. In the CART model, we adopted the type of antibiotics, dose of cefazolin, length of stay, and number of vessels obstructed as a proxy indicator of duration of operation as the parameters to identify the SSIs, according to our previous findings.", "In the CART model, we adopted the type of antibiotics, dose of cefazolin, length of stay, and number of vessels obstructed as a proxy indicator of duration of operation as the parameters to identify the SSIs, according to our previous findings. In our previous work, we used the 2005-2008 National Health Insurance claims data and healthcare-associated infection surveillance data from two medical centers for model development and model verification. Infection cases based on surveillance were identified by infection control personnel if the patient met the Taiwan CDC's criteria, which are the same as those adopted in the U.S. CDC.", "Infection cases based on surveillance were identified by infection control personnel if the patient met the Taiwan CDC's criteria, which are the same as those adopted in the U.S. CDC. They manually review medical records of all patients at risk for the specified healthcare-associated infection. The classification algorithms, the multivariable regression model, and the data mining model were adopted to develop alternative models based on surrogate indicators to identify cases of CABG SSIs and to compare the performance among these models and the ICD-9-CMbased model.", "The classification algorithms, the multivariable regression model, and the data mining model were adopted to develop alternative models based on surrogate indicators to identify cases of CABG SSIs and to compare the performance among these models and the ICD-9-CMbased model. For the classification algorithms, researchers build up several criteria, and if a case satisfies or exceeds a specific number of criteria, then it will be identified as a case of infection. For the multivariable regression model, researchers usually calculated a risk score by the logistic regression model, and the optimal cutoff point was determined according to the resulting receiver operating characteristic curve.", "For the multivariable regression model, researchers usually calculated a risk score by the logistic regression model, and the optimal cutoff point was determined according to the resulting receiver operating characteristic curve. Concerning the data mining approach, which is widely used for predicting and classifying objects, the characteristics are: automatic discovery of patterns, prediction of likely outcomes, creation of actionable information, and focus on large data sets and databases. The classification and regression tree CART model, which is the most popular approach as applied in our work, and the growing, stopping, and pruning of the tree were determined by Gini improvement measures.", "The classification and regression tree CART model, which is the most popular approach as applied in our work, and the growing, stopping, and pruning of the tree were determined by Gini improvement measures. After referring to the literature and conferring with infectious disease specialists, we adopted the following seven parameters: type of antibiotic, doses of antibiotic, doses of cefazolin, use of second-line antibiotics, length of stay, and number of vessels obstructed. Additionally, cross-validation was also employed, where data from one medical center was used for model development, and another one was used for model validation.", "Additionally, cross-validation was also employed, where data from one medical center was used for model development, and another one was used for model validation. The results of our previous work revealed that the CART model offered better performance than that of the other identification models or the ICD-9-CM based model, especially in the positive predictive value >70% , which was only found to be 20% in the ICD-9-CM based model. Table 1 The findings also implied that the CART was a decidedly better tool for identifying cases of SSI in the Taiwan National Health Insurance database.", "Table 1 The findings also implied that the CART was a decidedly better tool for identifying cases of SSI in the Taiwan National Health Insurance database. Therefore, this study also adopted the CART model for identifying CABG SSIs. To ensure homogeneity, current study analyzed 7,007 patients from 19 medical centers in Taiwan who underwent CABG surgery ICD-9-CM procedure codes 36.1x-36.2x between 2006 and 2008.", "To ensure homogeneity, current study analyzed 7,007 patients from 19 medical centers in Taiwan who underwent CABG surgery ICD-9-CM procedure codes 36.1x-36.2x between 2006 and 2008. CABG patients under the age of 18 years or over 85 years were excluded in this study. A total of 302 cases were identified as SSIs by ICD-9-CM based model, and a total of 107 cases were identified as SSIs by CART model.", "A total of 302 cases were identified as SSIs by ICD-9-CM based model, and a total of 107 cases were identified as SSIs by CART model. In this study, we used the following two definitions to define operation volumes: . the cumulative operation volumes by each surgeon and hospital within the study period, which was the most common definition in the literature; and .", "the cumulative operation volumes by each surgeon and hospital within the study period, which was the most common definition in the literature; and . following Yasunaga et al. 's study, cumulative operation volumes by each surgeon and hospital in the previous one year for each surgery.", "'s study, cumulative operation volumes by each surgeon and hospital in the previous one year for each surgery. However, our data was skewed, which did not follow a normal distribution. Therefore, we conducted the log transformations on operation volumes. The current work treated operation volumes in three different ways: . a continuous variable; .", "a continuous variable; . a categorical variable based on the first and the third quartile as cutoff points the most common method to categorize service/ operation volumes ; and . a data-driven categorical variable based on k-means clustering algorithm.", "a data-driven categorical variable based on k-means clustering algorithm. This study categorized surgeon and hospital volumes into low, medium, and high volume groups by quartile method and kmeans clustering algorithm. In the quartile method, the cut-off value transformed by logarithm of the first quartile <25% for hospital volumes was 5.65, and the third quartile >75% was 6.43.", "In the quartile method, the cut-off value transformed by logarithm of the first quartile <25% for hospital volumes was 5.65, and the third quartile >75% was 6.43. In terms of surgeon volumes, the first quartile was 4.38, and the third was 5.35, when we used the cumulative operation volumes within the study period as the definition. While the definition changed, first quartile <25% for hospital volumes was 4.66, and the third quartile >75% was 5.31.", "While the definition changed, first quartile <25% for hospital volumes was 4.66, and the third quartile >75% was 5.31. In terms of surgeon volumes, the first quartile was 3.40, and the third was 4.32. K-means clustering is an unsupervised machine-learning algorithm introduced by MacQueen in 1960s.", "K-means clustering is an unsupervised machine-learning algorithm introduced by MacQueen in 1960s. This method is not only a simple and very reliable method in categorization/ classification, but is also recognized as one of the top 10 algorithms in data mining. This method has often been applied in many fields.", "This method has often been applied in many fields. Yu and his colleagues even applied it to define the quality of CABG care, and to explore the relationship among patient's income status, the level of quality of care, and inpatient mortality. The main idea of this method is to partition observed data points into k non-overlapping clusters by minimizing the within-group sum of squares.", "The main idea of this method is to partition observed data points into k non-overlapping clusters by minimizing the within-group sum of squares. Each point is assigned to the mean of its cluster using the Euclidian distance. Firstly, k cluster centers were randomly generated.", "Firstly, k cluster centers were randomly generated. Previous studies usually divided surgeons and hospitals into low-, medium-, and high-volume groups; therefore, we also predetermined the surgeon and hospital service volumes into 3 groups k = 3 . Then, participants were assigned to the cluster with the shortest distance to these cluster centers.", "Then, participants were assigned to the cluster with the shortest distance to these cluster centers. Finally, the cluster centers were recomputed using the new cluster assignment and these steps would be iterated until convergence was achieved. The cut-off values of hospital volumes were 5.21 and 5.69, and for surgeon's volumes were 2.40 and 4.38 respectively, when cumulative operation volumes within the study period was used as the definition.", "The cut-off values of hospital volumes were 5.21 and 5.69, and for surgeon's volumes were 2.40 and 4.38 respectively, when cumulative operation volumes within the study period was used as the definition. Likewise, when cumulative operation volumes before each surgery was used as definition, the cut-off values were 4.11 and 4.89 for hospital volumes, and 2.64 and 3.91 for surgeon's volumes. All cutoff values were transformed by logarithm.", "All cutoff values were transformed by logarithm. The results of k-means clustering are demonstrated in Figs 1-4. As the results show, the operation volumes were divided into three groups separately. In addition to surgeon and hospital volumes and SSI, we collected patient-, surgeon-, and hospital-level data.", "In addition to surgeon and hospital volumes and SSI, we collected patient-, surgeon-, and hospital-level data. Firstly, patient-level variables included age, gender, length of ICU stay, number of vessels obstructed that were involved in the surgical operation, and the presence of important underlying diseases e.g. diabetes mellitus, chronic obstructive pulmonary disease COPD , heart failure, renal failure and renal insufficiency, which were associated with SSI .", "diabetes mellitus, chronic obstructive pulmonary disease COPD , heart failure, renal failure and renal insufficiency, which were associated with SSI . Secondly, the surgeon-level variables included age and gender. Thirdly, the hospital-level variables included hospital ownership and geographic location.", "Thirdly, the hospital-level variables included hospital ownership and geographic location. All statistical analyses of volume-infection relationship were performed using SAS version 9.2, SAS Institution Inc., Cary, NC, USA . In statistical testing, a two-sided p value 0.05 was considered statistically significant.", "In statistical testing, a two-sided p value 0.05 was considered statistically significant. The distributional properties of continuous variables were expressed by mean ± standard deviation SD , whereas categorical variables were presented by frequency and percentage. In univariate analysis, the potential three-level predictors of SSI were examined using chi-square test or two-sample t-test as appropriate.", "In univariate analysis, the potential three-level predictors of SSI were examined using chi-square test or two-sample t-test as appropriate. Next, to account for the correlations within surgeon level-2 and hospital level-3 , multivariate analysis was conducted by fitting mixed-effects logistic regression models to each patient's data for estimating the effects of three-level predictors on the probability of post-operational SSI. Furthermore, subgroup analysis for comorbidities was also conducted.", "Furthermore, subgroup analysis for comorbidities was also conducted. Table 2 shows that there were 7,007 patients with CABG performed by 199 surgeons in 19 hospitals during 2006-2008 in Taiwan. The majority of patients were male 77.5% , and the mean age of patients was 65.3 years.", "The majority of patients were male 77.5% , and the mean age of patients was 65.3 years. The average ICU stay was 6.05 days, the mean level of number of vessels obstructed was around 1.6, while 51.8% of patients had diabetes mellitus, 33.3% had heart failure, 14.1% had renal failure and renal insufficiency, and 22.0% had COPD. Three hundred and two patients 4.31% were identified as having the ICD-9-CM SSI codes.", "Three hundred and two patients 4.31% were identified as having the ICD-9-CM SSI codes. However, identification by the CART model only revealed 107 infection cases, and 94 cases were identified in both models. Most cases received CABG surgery by male surgeons, with a mean age of 45.0 years, and the surgeon's average operation volumes within the study period was 151.64, while the average operation volumes before surgery was 52.18.", "Most cases received CABG surgery by male surgeons, with a mean age of 45.0 years, and the surgeon's average operation volumes within the study period was 151.64, while the average operation volumes before surgery was 52.18. More than half of the cases were performed with CABG in not-for-profit hospitals, and the hospitals' average operation volumes within the study period was 473.60, while the average operation volumes before each surgery was 158.79. Moreover, most of patients received their surgeries by high-volume surgeons and hospitals, when k-means algorithm was used for categorization, regardless of which definition of operation volumes were used.", "Moreover, most of patients received their surgeries by high-volume surgeons and hospitals, when k-means algorithm was used for categorization, regardless of which definition of operation volumes were used. Table 3 shows the results of multilevel mixed-effect models, with the SSIs being identified by ICD-9-CM codes, and the operation volumes defined as the cumulative volumes within the study period. The results of Model 1 continuous reveal that the surgeon's volumes were negatively associated with SSIs, while hospital's volumes were not associated with surgical site infection SSIs.", "The results of Model 1 continuous reveal that the surgeon's volumes were negatively associated with SSIs, while hospital's volumes were not associated with surgical site infection SSIs. Model 2 quartile suggests that low-volume surgeons had higher SSI risk OR = 2.220, p-value = 0.022 than high-volume surgeons. There were also no associations between hospital's operation volumes and SSIs.", "There were also no associations between hospital's operation volumes and SSIs. Model 3 k-means shows that the association did not exist between hospital's/ surgeon's volumes and SSIs. Table 4 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volumes within the study period.", "Table 4 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volumes within the study period. Model 1 again indicated a negative association between surgeon's volumes and SSIs, and hospital's volumes were not found to be associated with SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results revealed low-volume surgeons had higher risk OR = 1.691, p = 0.002 than high-volume surgeons. Table 5 displays the results of multilevel mixed-effect models, in which the SSIs were identified by ICD-9-CM codes, but the operation volumes were defined as the cumulative volume in the previous one year for each surgery.", "Table 5 displays the results of multilevel mixed-effect models, in which the SSIs were identified by ICD-9-CM codes, but the operation volumes were defined as the cumulative volume in the previous one year for each surgery. Model 1 also indicated a negative association between surgeon's volumes and SSIs, and hospital's volumes were not found to be associated with SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results also revealed low-volume surgeons had higher risk OR = 1.642, p = 0.040 than high-volume surgeons. Table 6 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volume in previous one year for each surgery.", "Table 6 displays the results of multilevel mixed-effect models, in which the SSIs were identified by the CART model, and the operation volumes were also defined as the cumulative volume in previous one year for each surgery. In Model 1, different to the above findings, there was no association between hospital's/ surgeon's volumes and SSIs. In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist.", "In Model 2, the results showed that the relationship between hospital's/ surgeon's volumes and SSIs did not exist. In Model 3, results also revealed low-volume surgeons had higher risk OR = 1.163, p = 0.020 than high-volume surgeons. We further examined the associations of surgeon and hospital volumes with SSIs in stratification analyses by underlying diseases.", "We further examined the associations of surgeon and hospital volumes with SSIs in stratification analyses by underlying diseases. When the operation volumes were defined as the cumulative operation volume within the study period, no relationships existed between hospital/ surgeon operation volumes and SSIs. Table 7 However, when the operation volumes were defined as the cumulative operation volumes in the previous one year for each surgery, the results suggested that there was a negative association between surgeon volumes and SSIs in the diabetes group, except that the volumes were treated as continuous variable and the infection cases were identified by ICD-9 codes.", "Table 7 However, when the operation volumes were defined as the cumulative operation volumes in the previous one year for each surgery, the results suggested that there was a negative association between surgeon volumes and SSIs in the diabetes group, except that the volumes were treated as continuous variable and the infection cases were identified by ICD-9 codes. In terms of hospital operation volumes, the association did not exist. Table 8 No studies have evaluated how different service/ operation volumes definitions and categorization methods affect volume-infection relationships.", "Table 8 No studies have evaluated how different service/ operation volumes definitions and categorization methods affect volume-infection relationships. Moreover, several studies have pointed out the inappropriateness of identifying infection cases using the ICD-9-CM codes in claims data. Given these reasons, this study adopted two approaches to identifying SSIs, two definitions of operation volumes, and three methods for categorizing operation volumes to examine the relationships between operation volumes and SSIs.", "Given these reasons, this study adopted two approaches to identifying SSIs, two definitions of operation volumes, and three methods for categorizing operation volumes to examine the relationships between operation volumes and SSIs. Our findings showed that the relationships between hospital volumes and SSIs did not exist, no matter which definitions, categorization mehods, or SSIs case identification approaches were used. On the contrary, the relationships between surgeon volumes and SSIs were not robust in our data.", "On the contrary, the relationships between surgeon volumes and SSIs were not robust in our data. It might be affected by different definitions and categorization methods of operation volumes, and also by different SSI cases identification approaches. In summary, most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons, and they also showed the risks were similar between medium-volume and high-volume surgeons.", "In summary, most of the models demonstrated that the low-volume surgeons had higher risk than high-volume surgeons, and they also showed the risks were similar between medium-volume and high-volume surgeons. However, why did surgeon volume relate to SSIs, but hospital volume did not? Except for those issues we were concerned about in this study, there are some disagreements in the literature.", "Except for those issues we were concerned about in this study, there are some disagreements in the literature. Such as \"Does provider volume really represent quality of care?\" Or \"Is provider volume the only one predictor for outcome of care?\"", "Or \"Is provider volume the only one predictor for outcome of care?\" These issues are worthy of further discussion, but are out of the scope of this study. Service/ operation volumes are treated as a proxy indicator for experiences; previous studies used it to examine whether practice makes perfect or not.", "Service/ operation volumes are treated as a proxy indicator for experiences; previous studies used it to examine whether practice makes perfect or not. But, except for provider's experiences, SSIs are also impacted by many factors, such as environmental and clinical factors. Wu et al once used Taiwan 2001 NHI claims data to explore the relationship between provider CABG operation volumes and SSIs.", "Wu et al once used Taiwan 2001 NHI claims data to explore the relationship between provider CABG operation volumes and SSIs. They found that hospital volumes had a greater effect than surgeon volumes and claimed that this may imply that hospital teamwork is more important than individual surgeon. However, our findings demonstrated that there was no relationship between hospital volumes and SSIs.", "However, our findings demonstrated that there was no relationship between hospital volumes and SSIs. Wu et al. adopted the cumulative operation volumes within the study period as the definition, and identified SSIs by ICD-9-CM codes.", "adopted the cumulative operation volumes within the study period as the definition, and identified SSIs by ICD-9-CM codes. Except, there were two differences between our work and Wu et al., which were the length and year of the data; our data was longer and more updated than theirs. Moreover, it is worth noting that there was an outbreak of severe acute respiratory syndrome SARS in Taiwan in 2003, after which the hospital infection control system in Taiwan was reviewed and re-designed.", "Moreover, it is worth noting that there was an outbreak of severe acute respiratory syndrome SARS in Taiwan in 2003, after which the hospital infection control system in Taiwan was reviewed and re-designed. Wu et al data was before SARS, so these efforts may also have improved the level of SSIs control in hospitals, leading to different findings in this study. In addition, although most models revealed that there were negative relationships between surgeon's volumes and surgical site infection, the relationships were not robust.", "In addition, although most models revealed that there were negative relationships between surgeon's volumes and surgical site infection, the relationships were not robust. The results varied between different definitions and categorization method of operation volumes, and between SSIs identification approaches. Researchers need to consider how to identify SSIs correctly, how to choose optimal cut-off values, and how to decide on which definition is appropriate.", "Researchers need to consider how to identify SSIs correctly, how to choose optimal cut-off values, and how to decide on which definition is appropriate. Finally, the results of stratification analyses showed that low-volume surgeon had higher risk than high-volume surgeon in the diabetes mellitus group, when the cumulative operation in the previous one year before surgery was used as definition. A large number of studies have indicated diabetes mellitus is associated with a higher risk of SSIs, and the findings of this study suggest that CABG patients with diabetes mellitus should be cared for by experienced surgeons.", "A large number of studies have indicated diabetes mellitus is associated with a higher risk of SSIs, and the findings of this study suggest that CABG patients with diabetes mellitus should be cared for by experienced surgeons. A multilevel analysis was applied to manage the nested factors, and two definitions of operation volume along with three different operation volume categorization methods were adopted to examine the relationship between volume and SSIs under two kinds of SSIs identification approaches. Nevertheless, the study suffered from several major limitations.", "Nevertheless, the study suffered from several major limitations. First, the accuracy of SSIs identification was still an issue. Although the performance of the CART model to identify CABG SSIs was better than ICD-9-CM codes in Taiwan NHI claims data, it did not reach the perfect scenario.", "Although the performance of the CART model to identify CABG SSIs was better than ICD-9-CM codes in Taiwan NHI claims data, it did not reach the perfect scenario. The accuracy of SSIs identification was still a challenge in our work. The second limitation relates to unmeasured variables, such as length of stay before operation, infection condition, hair removal, clinical information e.g.", "The second limitation relates to unmeasured variables, such as length of stay before operation, infection condition, hair removal, clinical information e.g. blood glucose level, causative microorganism , time-related information e.g. the duration of operation , the environment, surgical skills, use of post-operative drains, number of operations involved, and surgical site and wound care, etc.", "the duration of operation , the environment, surgical skills, use of post-operative drains, number of operations involved, and surgical site and wound care, etc. Furthermore, information about type elective or urgent and incision site for surgery was not available in the Taiwan NHI claims data. In conclusion, the findings of this study suggest that different definitions and categorization methods of operation volumes, and different SSIs identification approaches might lead to different findings, although surgeon volumes were more important than hospital volumes in exploring the relationships between CABG operation volumes and SSIs in Taiwan, but they were still not robust.", "In conclusion, the findings of this study suggest that different definitions and categorization methods of operation volumes, and different SSIs identification approaches might lead to different findings, although surgeon volumes were more important than hospital volumes in exploring the relationships between CABG operation volumes and SSIs in Taiwan, but they were still not robust. Definitions and categorization methods of operation volumes, and correct identification of SSIs are important issues for future research." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "In December 2019, a novel coronavirus, called COVID-19, was discovered in Wuhan, China, and has spread to different cities in China as well as to 24 other countries. The number of confirmed cases is increasing daily and reached 34,598 on 8 February 2020. In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China.", "In the current study, we present a new forecasting model to estimate and forecast the number of confirmed cases of COVID-19 in the upcoming ten days based on the previously confirmed cases recorded in China. The proposed model is an improved adaptive neuro-fuzzy inference system ANFIS using an enhanced flower pollination algorithm FPA by using the salp swarm algorithm SSA . In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima .", "In general, SSA is employed to improve FPA to avoid its drawbacks i.e., getting trapped at the local optima . The main idea of the proposed model, called FPASSA-ANFIS, is to improve the performance of ANFIS by determining the parameters of ANFIS using FPASSA. The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days.", "The FPASSA-ANFIS model is evaluated using the World Health Organization WHO official data of the outbreak of the COVID-19 to forecast the confirmed cases of the upcoming ten days. More so, the FPASSA-ANFIS model is compared to several existing models, and it showed better performance in terms of Mean Absolute Percentage Error MAPE , Root Mean Squared Relative Error RMSRE , Root Mean Squared Relative Error RMSRE , coefficient of determination R 2 , and computing time. Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China.", "Furthermore, we tested the proposed model using two different datasets of weekly influenza confirmed cases in two countries, namely the USA and China. The outcomes also showed good performances. Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases.", "Text: A large family of viruses, called coronaviruses, are severe pathogens for human beings, which infect respiratory, hepatic, gastrointestinal, and neurologic diseases. They are distributed among humans, birds, livestock, mice, bats, and other wild animals . The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human .", "The outbreaks of two previous coronaviruses, SARS-CoV and MERS-CoV in 2003 and 2012, respectively, have approved the transmission from animal to animal, and human to human . In December 2019, the World Health Organization WHO received notifications from China for many cases of respiratory illness that were linked to some people who had visited a seafood market in Wuhan . Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV .", "Currently, Wuhan city suffers from the spreading of a novel coronavirus, called COVID-19 previously, it was called 2019-nCoV . In , the authors concluded that COVID-19 likely originated in bats, because it is more similar to two bat-derived coronavirus strains. However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively.", "However, the source of the COVID-19 is not confirmed yet, and it communities, Hong Kong and Toronto, were 1.2 and 1.32, respectively. Ong et al. proposed a monitoring and forecasting model for influenza A H1N1-2009 . Furthermore, Nah et al. proposed a probability-based model to predict the spread of the MERS.", "proposed a probability-based model to predict the spread of the MERS. The Adaptive Neuro-Fuzzy Inference System ANFIS is widely applied in time series prediction and forecasting problems, and it showed good performance in many existing applications. It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems.", "It offers flexibility in determining nonlinearity in the time series data, as well as combining the properties of both artificial neural networks ANN and fuzzy logic systems. It has been applied in various forecasting applications, for example, in , a stock price forecasting model was proposed using ANFIS and empirical mode decomposition. Chen et al.", "Chen et al. proposed a TAIEX time series forecasting model based on a hybrid of ANFIS and ordered weighted averaging OWA . In , another time series forecasting method was presented for electricity prices based on ANFIS. Svalina et al. proposed an ANFIS based forecasting model for close price indices for a stock market for five days.", "proposed an ANFIS based forecasting model for close price indices for a stock market for five days. Ekici and Aksoy presented an ANFIS based building energy consumption forecasting model. More so, ANFIS is also applied to forecast electricity loads . Kumar et al. proposed an ANFIS based model to forecast return products.", "Kumar et al. proposed an ANFIS based model to forecast return products. Ho and Tsai applied ANFIS to forecast product development performance. However, estimating ANFIS parameters is a challenge that needs to be improved.", "However, estimating ANFIS parameters is a challenge that needs to be improved. Therefore, in previous studies, some individual swarm intelligence SI methods have been applied to the ANFIS parameters to enhance time series forecasting because these parameters have a significant effect on the performance of ANFIS. The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO .", "The SI methods include the particle swarm optimization PSO , social-spider optimization , sine-cosine algorithm SCA , and multi-verse optimizer MVO . For example, in SCA algorithm was applied to improve the ANFIS model to forecast oil consumption in three countries, namely, Canada, Germany, and Japan. In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries.", "In the same context, in , The MVO algorithm was used to enhance the ANFIS model to forecast oil consumption in two countries. In addition, in the PSO was used with ANFIS to predict biochar yield. However, individual SI algorithms may stock at local optima.", "However, individual SI algorithms may stock at local optima. Therefore, one solution is to apply hybrid SI algorithms to avoid this problem. In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model.", "In , a hybrid of two SI algorithms, namely GA and SSA, was presented to improve the ANFIS model. The proposed new model called GA-SSA-ANFIS was applied to forecast crude oil prices for long-term time series data. However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output.", "However, the previously mentioned methods suffer from some limitations that can affect the performance of the forecasting output such as slow convergence and the ability to balance between exploration and exploitation phases can influence the quality of the final output. This motivated us to propose an alternative forecasting method dependent on the hybridization concept. This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones.", "This concept avoids the limitations of traditional SI techniques by combining the strengths of different techniques, and this produces new SI techniques that are better than traditional ones. In the current study, we propose an improved ANFIS model based on a modified flower pollination algorithm FPA using the salp swarm algorithm SSA . The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants.", "The FPA is an optimization algorithm proposed by Yang , which was inspired by the flow pollination process of the flowering plants. The FPA was employed in various optimization applications, for example to estimate solar PV parameter , solving sudoku puzzles , feature selection , antenna design , and other applications . Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al.", "Moreover, SSA is also an optimization algorithm proposed by Mirjalili et al. inspired by the behavior of salp chains. In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others .", "In recent years, the SSA was utilized to solve different optimization problems, such as feature selection , data classification , image segmentation , and others . The proposed method called FPASSA is a hybrid of FPA and SSA, in which the SSA is applied as a local search method for FPA. The proposed FPASSA starts by receiving the historical COVID-19 dataset.", "The proposed FPASSA starts by receiving the historical COVID-19 dataset. Then a set of solutions is generated where each of them represents the value for the parameters of the ANFIS model. Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution.", "Then the quality of each solution is calculated using the fitness value, and the solution that has the best fitness value is chosen to represent the best solution. Then the probability of each solution is computed. Then the current solution will be updated, either using global or local strategy in FPA.", "Then the current solution will be updated, either using global or local strategy in FPA. However, in the case of local strategy, the operators of SSA or FPA will be used according to the probability of the fitness value for each solution. The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19.", "The process of updating the solutions is repeated until reaching the stop condition, and the best parameter configurations are used to forecast the number of confirmed cases of COVID-19. The main contribution points of the current study are as follows: 1. We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases.", "We propose an efficient forecasting model to forecast the confirmed cases of the COVID-19 in China for the upcoming ten days based on previously confirmed cases. An improved ANFIS model is proposed using a modified FPA algorithm, using SSA. We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA.", "We compare the proposed model with the original ANFIS and existing modified ANFIS models, such as PSO, GA, ABC, and FPA. The rest of this study is organized as follows. The preliminaries of ANFIS, FPA, and SSA are described in Section 2.", "The preliminaries of ANFIS, FPA, and SSA are described in Section 2. Section 3 presents the proposed FPASSA, and Section 4 presents the experimental setup and results. We conclude this study in Section 5. The principles of the ANFIS are given in this section. The ANFIS model links the fuzzy logic and neural networks .", "The ANFIS model links the fuzzy logic and neural networks . It generates a mapping between the input and output by applying IF-THEN rules it is also called Takagi-Sugeno inference model . Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions.", "Figure 1 illustrates the ANFIS model where, y and x define the inputs to Layer 1 whereas, O 1i is its output of node i that is computed as follows: where µ denotes the generalized Gaussian membership functions. A i and B i define the membership values of µ. α i and ρ i denote the premise parameters set. The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang .", "The output of Layer 2 it is also known as the firing strength of a rule is calculated as follows: Meanwhile, the output of Layer 3 it is also known as the normalized firing strength is calculated as follows: The output of Layer 4 it is also known as an adaptive node is calculated as follows: where r i , q i , and p i define the consequent parameters of the node i. Layer 5 contains only one node; its output is computed as: Flower Pollination Algorithm is an optimization method proposed by Yang . It simulates the transfer of flowers' pollen by pollinators in nature. This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination .", "This algorithm utilizes the two types of pollination i.e., self-pollination and cross-pollination . In self-pollination, the pollination occurs with no pollinators, whereas, in cross-pollination, the pollens are moved between different plants. In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination.", "In more detail, the self-pollination can be represented as a local pollination while the cross-pollination can be called global pollination. The global pollination or cross-pollination can be mathematically formed as follows: where x t i defines the pollen i at iteration t. L denotes the pollination's strength or the step size. F * is the target position or best solution.", "F * is the target position or best solution. In some cases, insects can fly with different distance steps for a long space; therefore, Levy fly distribution is applied to simulate this movement. where λ = 1.5. Γ λ denotes the gamma function. This distribution is available for large steps s > 0.", "This distribution is available for large steps s > 0. The self-pollination or local pollination can be mathematically formed as follows: where x t i and x k i represent pollens from different flower in the same plant. in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination.", "in the range 0,1 The process of pollination can be done using cross-pollination or self-pollination. Therefore, the random variable p, in the range , is used to determine this process. SSA is an optimization technique introduced by . It simulates the Salps' behavior in nature. This behavior is called salp chain.", "It simulates the Salps' behavior in nature. This behavior is called salp chain. The mathematical model of SSA begins by splinting its population into a leader group and followers group. The leader is the front salp, whereas, the followers are the other salps. The search space is determined in n-dimensions with n variables. Equation .", "The search space is determined in n-dimensions with n variables. Equation . works to update the salps' positions. where x 1 j denotes the leader's position in j-th dimension. F j is the target position. ub j and lb j represent the max and min bounds, respectively.", "ub j and lb j represent the max and min bounds, respectively. c 2 and c 3 denote random numbers in . c 1 is an important parameter; it balances between the exploration and exploitation phases. It is computed as follows: where the current loop number is t and the max loop' number is t max .", "It is computed as follows: where the current loop number is t and the max loop' number is t max . Then, the followers' position is updated as follows: where x i j defines the i-th position of the follower in j-th dimension. i > 1. This section explains the proposed FPASSA-ANFIS method.", "i > 1. This section explains the proposed FPASSA-ANFIS method. It is a time series method for forecasting the confirmed cases of the COVID-19, as given in Figure 2 . The FPASSA-ANFIS utilizes the improved FPA to train the ANFIS model by optimizing its parameters. The FPASSA-ANFIS contains five layers as the classic ANFIS model.", "The FPASSA-ANFIS contains five layers as the classic ANFIS model. Layer 1 contains the input variables the historical COVID-19 confirmed cases . Whereas Layer 5 produces the forecasted values. In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5.", "In the learning phase, the FPASSA is used to select the best weights between Layer 4 and Layer 5. The FPASSA-ANFIS starts by formatting the input data in a time series form. In our case, the autocorrelation function ACF was considered.", "In our case, the autocorrelation function ACF was considered. ACF is one of the methods applied to find patterns in the data; it presents information about the correlation between points separated by various time lags. Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags.", "Therefore, in this paper, the variables with ACF greater than 0.2 are considered i.e., 5-lags. Besides, the training data contains 75% of the dataset, whereas the testing data contains 25% of them. The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model.", "The number of clusters is defined by the fuzzy c-mean FCM method to construct the ANFIS model. The parameters of the ANFIS model are prepared by the FPASSA algorithm. In the training phase, the calculation error as in Equation . between the real data and the predicted data is used to evaluate the parameters' quality.", "between the real data and the predicted data is used to evaluate the parameters' quality. where T is the real data, and P is the predicted data. N s is the sample length. The smaller values of the objective function indicate good ANFIS's parameter.", "The smaller values of the objective function indicate good ANFIS's parameter. On the other hand, the updating phase of the followers' positions in the SSA algorithm is applied to improve the global pollination phase in the FPA algorithm. In this improvement, there is a random variable r used to switch between both phases.", "In this improvement, there is a random variable r used to switch between both phases. If r > 0.5, then the operators of the SSA is used; otherwise, the operators of the FPA are used. In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution.", "In general, The FPASSA starts by constructing the population X ; afterward, the objective function is calculated for each solution. The solution with the lowest error value is saved to the next iteration. This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations.", "This sequence is repeated until meeting the stop condition, which in this paper, is the maximum number of iterations. Then the best solution is passed to train the parameters of the ANFIS model. After finishing the training phase, the testing phase is started with the best solution to compute the final output.", "After finishing the training phase, the testing phase is started with the best solution to compute the final output. The performance of the proposed method is evaluated by comparing the real data with the predicted data using the performance measures. Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day.", "Finally, the FPASSA produces a foretasted value for confirmed cases of COVID-19 in China in the next day. The steps of the proposed FPASSA are presented in Algorithm 1. Input: Historical COVID-19 dataset, size of population N, total number of iterations t max . Divide the data into training and testing sets.", "Divide the data into training and testing sets. Using Fuzzy c-mean method to determine the number of membership functions. Constructing the ANFIS network. Set the initial value for N solutions X . Return the best solution that represents the best configuration for ANFIS. Apply the testing set to the best ANFIS model.", "Apply the testing set to the best ANFIS model. Forecasting the COVID-19 for the next ten days. This section presents the description of the used dataset, the performance measures, the parameter setting for all methods, the experiment results, and discussions. The main dataset of this study is COVID-19 dataset.", "The main dataset of this study is COVID-19 dataset. It was collected from the WHO website https: //.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/ . It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 .", "It contains the daily confirmed cases in China from 21 January 2020 to 18 February 2020, as shown in Table 1 . We used 75% from the dataset to train the model while the rest is used to test it. Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases.", "Moreover, we evaluated the performance of the proposed method using two datasets of weekly influenza confirmed cases. The first one is called DS1; it was collected from the Centers for Disease Control and Prevention CDC It starts from week number 40 in 2015 and continues until week number 6 in 2020. Whereas, the second one is called DS2.", "Whereas, the second one is called DS2. It was collected from the WHO website It contains the data of weekly influenza confirmed cases in China from week number 1 in 2016 to week number 8 in 2020. The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively.", "The quality of the proposed method is evaluated using a set of performance metrics as follows: • Root Mean Square Error RMSE : where Yp and Y are the predicted and original values, respectively. • Mean Absolute Error MAE : • Mean Absolute Percentage Error MAPE : • Root Mean Squared Relative Error RMSRE : N s represents the sample size of the data. • Coefficient of Determination R 2 : where Y represents the average of Y.", "• Coefficient of Determination R 2 : where Y represents the average of Y. The lowest value of RMSE, MAE, MAPE, and RMSRE refers to the best method. The higher value of R 2 indicates better correlation for the method.", "The higher value of R 2 indicates better correlation for the method. This paper aims to assess the ability of the FPASSA to forecast the COVID-19 by comparing its performance with other methods, namely the ANFIS and the trained ANFIS models using PSO, GA, ABC, FPA, and FPASSA. The parameters' setting for these models is listed in Table 2 .", "The parameters' setting for these models is listed in Table 2 . The common parameters, such as population size, are set to 25 and 100 iterations are applied. Besides, each algorithm is performed for 30 independent runs to fair comparisons. The selected parameters are chosen because they produced good behavior in previous experiments, such as .", "The selected parameters are chosen because they produced good behavior in previous experiments, such as . Table 2 . Parameters' setting. Parameters Setting Max. epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1.", "epochs = 100, Error goal = 0, Initial step = 0.01, Decrease rate = 0.9, Increase rate = 1. In this section, the performance of the proposed FPASSA to predict the DS1 and DS2 is discussed. It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second.", "It can be concluded from Table 3 that the performance of FPASSA outperformed the compared methods in all measures, whereas the FPA is ranked second. The results of DS2 indicate that the FPASSA is ranked first in terms of RMSE, MAPE, R 2 , and the CPU time. Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC.", "Whereas, the PSO is ranked second, followed by the FPA, GA, then ABC. These results denote that the proposed method can optimize the parameters of the ANFIS model effectively and produce good results in terms of the performance measures. Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 .", "Comparison results between the proposed FPASSA and other models to forecast COVID-19 are given in Table 4 . It can be concluded that the FPASSA outperforms other models. For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA.", "For example, by analyzing the results of RMSE, MAE, MAPE, RMSRE, and CPU time s it can be observed that the FPASSA achieves the smallest value among the comparison algorithms, and this indicates the high quality of the FPASSA. Meanwhile, the FPA allocates the second rank, which provides better results than the rest of the methods. Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97.", "Moreover, the value of R 2 refers to the high correlation between the prediction obtained by the proposed FPASSA method and the original COVID-19, which has nearly 0.97. This can also be noticed from Figure 3 , which depicts the training of the algorithms using the historical data of the COVID-19 as well as their forecasting values for ten days. Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020.", "Table 5 depicts the forecasting value for the confirmed cases of the COVID-19 in China from 19/2/2020 to 28/2/2020. From these results, it can be noticed that the outbreak will reach its highest level on the day 28/2/2020. The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020.", "The average percentage of the increase over the forecasted period is 10%, the highest percentage is 12% on 28/2/2020, and the lowest percentage is 8.7% on 19/2/2020. From the previous results, it can be concluded that the proposed FPASSA-ANFIS has a high ability to forecast the COVID-19 dataset. These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method.", "These results avoid the limitations of traditional ANFIS because of the combination with the modified FPA method. Moreover, the operators of SSA are combined with the local strategy of FPA to enhance their exploitation ability. However, the time computational of the proposed FPASSA method still requires more improvements.", "However, the time computational of the proposed FPASSA method still requires more improvements. This paper proposed a modified version for the flower pollination algorithm FPA using the salp swarm algorithm SSA . This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters.", "This modified version, called FPASSA, is applied to improve the performance of the ANFIS through determining the optimal value for its parameters. The developed FPASSA-ANFIS model is applied as a forecasting technique for a novel coronavirus, called COVID-19, that was discovered in Wuhan, China at the end of last year and January of the current year. The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days.", "The proposed FPASSA-ANFIS model has a high ability to predict the number of confirmed cases within ten days. Besides, FPASSA-ANFIS outperforms other forecasting models in terms of RMSE, MAE, MAPE, RMSRE, and R 2 . Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance.", "Furthermore, two datasets of weekly influenza confirmed cases in the USA and China were used to evaluate the proposed method, and the evaluation outcomes showed its good performance. According to the promising results obtained by the proposed FPASSA-ANFIS, it can be applied in different forecasting applications." ]

[ "The vacuolar-type H + -ATPase v-ATPase is the major proton pump that acidifies intracellular compartments of eukaryotic cells. Since the inhibition of v-ATPase resulted in anti-tumor and anti-metastatic effects in different tumor models, this enzyme has emerged as promising strategy against cancer. Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far.", "Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far. Human endothelial cells treated with archazolid showed an increased adhesion of tumor cells, whereas the transendothelial migration of tumor cells was reduced. The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin.", "The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin. Instead, the adhesion was mediated by β1-integrins expressed on tumor cells, as blocking of the integrin β1 subunit reversed this process. Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs.", "Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs. The accumulation of collagen was accompanied by a strong decrease of the expression and activity of the protease cathepsin B. Overexpression of cathepsin B in ECs prevented the capability of archazolid to increase the adhesion of tumor cells onto ECs. Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced.", "Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced. These findings further support archazolid as a promising anti-metastatic compound. Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells .", "Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells . The enzyme consists of two multi-subunit complexes, the soluble V 1 transmembrane V o subcomplex required for the proton transport across membranes . In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles .", "In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles . The function of v-ATPases is essential for cellular processes such as vesicular trafficking, receptor-mediated endocytosis and protein degradation and processing. In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space .", "In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space . In cancer cells v-ATPases are expressed on the plasma membrane in order to eliminate toxic cytosolic H + . Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis .", "Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis . Since the inhibition of v-ATPase was shown to reduce the invasiveness of cancer cells and metastasis formation , this enzyme has emerged as a promising drug target in the recent years. Archazolid A and B are highly potent and specific inhibitors of v-ATPases .", "Archazolid A and B are highly potent and specific inhibitors of v-ATPases . They were first isolated from the myxobacterium Archangium gephyra . These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex.", "These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex. As their biological activity is comparable to the v-ATPase inhibitors bafilomycin and concanamycin , archazolids are natural compounds of high interest that can be used both as a tool to study the consequences of v-ATPase inhibition and as a lead for drug development. Archazolids can be either produced by fermentation or by total synthesis .", "Archazolids can be either produced by fermentation or by total synthesis . In the field of cancer research several studies reported on interesting pharmacological effects of archazolid: It reduced the migration of different invasive tumor cells in vitro and cancer cell metastasis in vivo in a breast tumor mouse model . Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells .", "Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells . In classically activated macrophages, archazolid selectively induced the generation of tumor necrosis factor α TNFα , which may indirectly promote tumor suppression . Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated.", "Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated. The endothelium plays a crucial role in the pathogenesis and progression of cancer: The metastatic cascade includes local angiogenesis at the site of the primary tumor and adhesion of tumor cells at the site of metastasis . Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells .", "Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells . This process ensures the nutrient supply of the tumor and its growth . Circulating cancer cells can adhere to the endothelium at distant sites.", "Circulating cancer cells can adhere to the endothelium at distant sites. This adhesive interaction is mediated by receptors and corresponding ligands expressed on tumor and endothelial cells . V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells .", "V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells . A recent study showed that the inhibition of v-ATPase by concanamycin prevented proliferation, reduced migration and impaired angiogenesis-related signaling in endothelial cells . So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium.", "So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium. Thus, we were interested in the consequences of the inhibition of endothelial v-ATPase by archazolid on the interaction between endothelial and cancer cells. Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells .", "Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells . Accordingly, we focused on these cell adhesion molecules and integrins. For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells.", "For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells. CellTiter-Blue Cell Viability Assay Promega, Mannheim, Germany was performed according to the manufacturer's protocol for determining the cell viability of cells after treatment with archazolid. This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin.", "This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin. The CellTiter-Blue Reagent was added to the cells 4 h before the endpoint of treatment. Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission .", "Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission . CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega was performed according to the manufacturer's instructions for determining the lactate dehydrogenase LDH release after treatment with archazolid. Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme.", "Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme. LDH is a cytosolic enzyme that is released by leaky cells. Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase.", "Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase. The absorbance was measured with a Varioskan Flash microplate reader Thermo Fisher Scientific at 490 nm. LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells.", "LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells. HUVECs were cultured to confluence on collagen G-coated μ-slides 80826, ibidi, Martinsried, Germany before they were treated with archazolid for 24 h. 1 μg/ ml Hoechst 33342 Sigma-Aldrich, Munich, Germany was used to visualize the nuclei and 50 nM LysoTracker Red DND-99 was used to visualize the acidic compartments which correspond to the lysosomes. Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany .", "Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany . HUVECs were seeded in collagen G-coated 24-well plates and grown to confluence for two days before treatment. The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C.", "The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C. Non-adherent tumor cells were washed off three times with PBS containing Ca 2+ and Mg 2+ . Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission .", "Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission . For blocking the integrin β1 subunit on MDA-MB-231 or PC-3 cells, CellTracker Greenlabeled MDA-MB-231 or PC-3 cells were incubated with an anti-integrin β1 antibody P5D2, ab24693, Abcam, Cambridge, United Kingdom at a concentration of 1 μg antibody per one million cells in 1 ml DMEM. Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM.", "Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM. For blocking the integrin β1 subunit on HUVECs, the cells were incubated with the anti-integrin β1 antibody 0.1 μg/well in ECGM . HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs.", "HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs. For the adhesion of MDA-MB-231 or PC-3 cells onto extracellular matrix ECM components 24-well plates were coated with collagen G 10 μg/ml in PBS , human plasma fibronectin 10 μg/ml PBS or laminin-411 10 μg/ml in Dulbecco's PBS DPBS containing Ca 2+ and Mg 2+ at 4˚C overnight. The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C .", "The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C . HUVECs were grown on a porous filter membrane Transwell insert, polycarbonate membrane, 8 μm pores; Corning, New York, USA for 48 h and were treated as indicated. Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA.", "Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA. HUVECs were washed twice with medium 199 containing 0.1% BSA before MDA-MB-231 cells were allowed to transmigrate through the endothelial monolayer for 24 h. Medium 199 containing 0.1% BSA was used as negative control and medium 199 containing 20% FCS was used as chemoattractant for transmigration in the lower compartment. Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab.", "Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab. Transmigrated cells were lysed in radioimmunoprecipitation assay RIPA buffer and transmigration was quantified by measuring the fluorescence signal at 485 nm excitation and 535 nm emission . HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα.", "HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα. RNA was isolated using the RNeasy Mini Kit from Qiagen Hilden, Germany according to the manufacturer's protocol. On-column DNase digestion was performed to remove genomic DNA.", "On-column DNase digestion was performed to remove genomic DNA. RNA was transcribed into cDNA by Superscript II Life Technologies, Thermo Fisher Scientific . qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3.", "qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3. Power SYBR Green PCR Master Mix Life Technologies and the comparative C T quantitation method 2 -ΔΔCT were used. HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules.", "HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules. Subsequently, the cells were detached with HyClone HyQTase GE Healthcare, Freiburg, Germany . In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min.", "In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min. For all other proteins, the cells were not fixed and washed once with PBS before incubating with the antibodies phycoerythrin PE -labeled anti-human CD106 mouse, VCAM-1 , PE-labeled anti-human CD62E mouse, E-selectin and PE-labeled anti-human CD325 mouse, N-cadherin from Becton Dickinson on ice for 45 min. These antibodies were diluted in PBS containing 0.2% BSA.", "These antibodies were diluted in PBS containing 0.2% BSA. The surface expression of cell adhesion molecules was measured by flow cytometry FACSVerse, Becton Dickinson, Heidelberg, Germany . To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min.", "To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min. The staining procedure was performed on ice to ensure that surface proteins or antibodies are not endocytosed. The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth .", "The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth . Alexa Fluor 488-conjugated anti-rabbit antibody goat, 1:400, A11008, Life Technologies was used as secondary antibody and Hoechst 33342 1 μg/ml, Sigma-Aldrich was used to visualize nuclei. Confluent HUVECs in 6-well plates were treated as indicated.", "Confluent HUVECs in 6-well plates were treated as indicated. Cells were washed with ice-cold PBS and lysed with RIPA buffer supplemented with protease inhibitors Complete Mini EDTA-free; Roche, Mannheim, Germany , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride, β-glycerophosphate, sodium pyrophosphate and H 2 O 2 . Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific .", "Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific . Equal amounts of proteins 10-20 μg were separated by sodium dodecyl sulfatepolyacrylamide gel electrophoresis SDS-PAGE; Bio-Rad Laboratories, Munich, Germany . Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection.", "Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection. Membranes were blocked with 5% boltinggrade milk powder Carl Roth in TBS containing 0.1% Tween 20 Sigma-Aldrich . The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 .", "The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 . ImageJ version 1.49m was used for densitometric analysis. Cathepsin B activity assay was performed as described in the publication by Kubisch et al.", "Cathepsin B activity assay was performed as described in the publication by Kubisch et al. . Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated.", ". Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated. Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride.", "Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride. The fluorogenic cathepsin B substrate Z-Arg-Arg-7-amido-4-methylcoumarin hydrochloride C5429, Sigma-Aldrich was added to 30 μg of the cell lysate diluted in assay buffer supplemented with 2 mM L-cysteine C7880, Sigma-Aldrich and incubated for 30 min at 40˚C. Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific .", "Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific . The intensity of the fluorescence signal corresponded to the cathepsin B enzyme activity. For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction.", "For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction. The HUVEC Nucleofector Kit Lonza, Cologne, Germany was used to transfect HUVECs. The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza .", "The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza . 48 h after transfection the cells were treated for further experiments. The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe .", "The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe . hCathepsin B was digested with PmeI and XbaI and the linear DNA fragment not corresponding to the human CTSB gene was religated to generate the empty pcDNA3.1 - delta MCS plasmid that was used for control transfections. The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific.", "The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific. The control vector pcDNA3.1 - delta MCS used for our transfections was cloned on the basis of hCathepsin B and is therefore lacking almost the whole part of the multiple cloning site of the pcDNA3.1 - . Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA .", "Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA . One-way ANOVA followed by Tukey's post-hoc test or unpaired t-test was used for the evaluation of a minimum of three independent experiments. The numbers of independently performed experiments n are stated in the corresponding figure legends. p 0.05 was considered as statistically significant.", "p 0.05 was considered as statistically significant. Data are expressed as mean ± standard error of the mean SEM . Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays.", "Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays. We treated confluent HUVECs with up to 1 nM archazolid for 24 and 48 h and observed that this treatment has neither an influence on the metabolic activity nor on the release of LDH after 24 h Fig 1A and 1B, left panels . The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels .", "The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels . Consequently, the following experiments were all carried out after 24 h or less of archazolid treatment in order to exclude any cytotoxic effects of archazolid within our experimental settings. Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors .", "Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors . This effect was obvious both in subconfluent and in confluent cells Fig 2A . Inhibition of v-ATPase prevents the acidification of lysosomes .", "Inhibition of v-ATPase prevents the acidification of lysosomes . Using the cell-permeable dye LysoTracker Red DND-99, it is possible to label the acidic lysosomes in living cells. Thus, this dye can serve as an indicator of v-ATPase inhibition.", "Thus, this dye can serve as an indicator of v-ATPase inhibition. To proof that archazolid is also functionally active as a v-ATPase inhibitor in HUVECs, cells were treated with 1 nM archazolid before they were incubated with LysoTracker Red DND-99 and Hoechst 33342. As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid.", "As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid. In summary, archazolid treatment for 24 h was not cytotoxic to quiescent HUVECs, but inhibited the functionality of the v-ATPase. We analyzed the adhesion of MDA-MB-231 cells onto HUVECs.", "We analyzed the adhesion of MDA-MB-231 cells onto HUVECs. Confluent HUVECs were treated with up to 1 nM archazolid for 24 h. Untreated MDA-MB-231 cells were labeled with Cell-Tracker Green CMFDA Dye. Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B .", "Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B . We also investigated the influence of archazolid on the transendothelial migration of MDA-MB-231 cells. HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells.", "HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells. The influence of archazolid on tumor cell adhesion was not only studied in HUVECs, which represent macrovascular endothelial cells, but also in microvascular HMEC-1 cells. Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line.", "Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line. Archazolid treatment of endothelial cells increased the attachment of MDA-MB-231 cells onto the HMEC-1 monolayer after 120 min of adhesion Fig 4A and increased the attachment of PC-3 cells onto the HUVEC monolayer after 30 and 60 min of adhesion Fig 4B . Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig .", "Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig . Taken together, archazolid treatment augmented the adhesive properties of both micro-and macrovascular endothelial cells for metastatic tumor cells, but not for non-metastatic ones. Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion.", "Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion. The adhesion of tumor cells onto the endothelium is in principle similar to that of leukocytes, but slightly differs in the molecules that mediate the adhesion process. Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction .", "Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction . Inhibition of the v-ATPase might affect the expression of endothelial cell adhesion molecules on mRNA or protein levels. To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control.", "To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control. Quantitative real-time PCR showed that v-ATPase inhibition in HUVECs did not alter the mRNA levels of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5A . The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry.", "The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry. Archazolid 1 nM, 24 h did not affect the cell surface expression of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5B . Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion .", "Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion . Since none of the cell adhesion molecules expressed on HUVECs were regulated upon archazolid treatment, we considered integrins as potential interaction partners. Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells .", "Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells . In order to elucidate the role of β1-integrins for the archazolid-induced tumor cell adhesion, the integrin β1-subunit was blocked either on MDA-MB-231 cells, PC-3 cells or on HUVECs. Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid.", "Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid. After blocking β1-integrins on MDA-MB-231 or PC-3 cells, the archazolid-induced tumor cell adhesion was reduced almost to control level Fig 6A and 6B , left panels , whereas blocking of β1-integrins on HUVECs had no significant effect on the increase of tumor cell adhesion by v-ATPase inhibition Fig 6A and 6B , right panels . Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin .", "Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin . Therefore, we hypothesized that archazolid treatment of endothelial cells might lead to an upregulation of these components. MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components.", "MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components. This cell adhesion assay revealed that MDA-MB-231 as well as PC-3 cells favor the interaction with the ECM component collagen, as the adhesion onto collagen is much higher than onto the uncoated plastic control Fig 7A . MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating.", "MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating. Therefore, we focused on the interaction between these two tumor cell lines and collagen. Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins.", "Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins. Since collagen is the major ECM component MDA-MB-231 and PC-3 cells interact with, the next step was to prove whether v-ATPase inhibition influences the amount of collagen expressed by HUVECs as extracellular matrix. To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen.", "To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen. Interestingly, archazolid increased the amount of surface collagen on HUVECs by about 50% Fig 7C . Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig .", "Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig . It was reported that v-ATPase inhibition by archazolid impairs the activity of cathepsin B , a lysosomal enzyme that degrades extracellular matrix components including collagen . As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B.", "As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B. Therefore, an enzyme activity assay based on the proteolysis of a fluorogenic cathepsin B substrate was performed. In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin.", "In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin. Inhibition of endothelial vATPase increases tumor cell adhesion to endothelial cells strongly decreased by approximately 50% compared to control cells at an archazolid concentration of 1 nM Fig 8A . In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B .", "In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B . To proof whether the archazolid-induced tumor cell adhesion is a consequence of the decreased amount of cathepsin B, HUVECs were transfected with a plasmid coding for human cathepsin B or with the empty vector as control. After 48 h, the transfected cells were treated with 1 nM archazolid.", "After 48 h, the transfected cells were treated with 1 nM archazolid. The level of cathepsin B after transfection and treatment was assessed by western blot analysis Fig 9A . Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B .", "Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B . Targeting the proton pump v-ATPase for cancer therapy has gained great interest since its inhibition was reported to reduce the invasiveness of cancer cells and, most importantly, also metastasis . Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis .", "Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis . In the present study we used the myxobacterial natural product archazolid to investigate the consequences of v-ATPase inhibition in the endothelium on tumor-endothelial cell interactions. For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium.", "For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium. Inhibition of the v-ATPase in endothelial cells by archazolid significantly increased the adhesion of metastatic cancer cells and decreased the transendothelial migration of cancer cells which was attributed to augmented collagen levels on the surface on archazolid-treated endothelial cells. Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected.", "Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected. The archazolidinduced adhesion of tumor cells was independent from the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin, as their expression was not regulated by the compound. However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid.", "However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid. In adhesion experiments on plastic coated with extracellular matrix components, we could show that MDA-MB-231 and PC-3 cells clearly favored the interaction with collagen, whereas the adhesion of non-metastatic Jurkat cells was largely independent from extracellular matrix proteins S1B Fig . The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line.", "The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line. MDA-MB-231 and PC-3 cells express α2β1-and α3β1-integrins, which represent collagen receptors , while Jurkat cells express α4β1-integrins but lack α2β1-, α3β1-integrins . α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 .", "α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 . Our results are in line with previous studies showing that α2β1-and α3β1-integrin expressing MDA-MB-231 and PC-3 cells were able to rapidly attach to collagen in the cortical bone matrix. In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins.", "In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins. α2β1-and α3β1-integrins can additionally act as laminin receptors and at least α3β1integrins recognize fibronectin . Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components.", "Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components. Importantly, v-ATPase inhibition by archazolid increased the surface levels of the extracellular matrix component collagen, which might explain that the increase of MDA-MB-231 and PC-3 cells onto archazolid-treated HUVECs is independent of endothelial cell adhesion molecules. By performing a live cell proteolysis assay, Cavallo-Medved et al.", "By performing a live cell proteolysis assay, Cavallo-Medved et al. demonstrated ECM degradation, in particular of gelatin and collagen IV, in association with active cathepsin B in caveolae of endothelial cells during tube formation . In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells .", "In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells . Therefore, we suggested that the accumulation of collagen on the endothelial surface might be a consequence of impaired cathepsin B activity or expression in endothelial cells. In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced.", "In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced. Cathepsin B is synthesized as preprocathepsin B on membrane-bound ribosomes. Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides.", "Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides. The targeting of procathepsin B to lysosomes is mannose-6-phosphate receptor-dependent and its dissociation from the receptor as well as its proteolytic processing into mature cathepsin B requires acidification of the compartment . In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B .", "In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B . We assumed that the archazolid-induced decrease in cathepsin B activity and expression was based on the same mechanism. Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B.", "Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B. As cathepsin B can also degrade other extracellular matrix components such as fibronectin and laminin , v-ATPase inhibition could lead to an accumulation of these proteins and an increased adhesion of cells expressing fibronectin or laminin receptors. However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells.", "However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells. These cells predominantly adhered to collagen, while the adhesion of Jurkat cells is mostly independent from the ECM proteins collagen, fibronectin or laminin S1B Fig . Interestingly .", "Interestingly . In hepatic cancer cells, archazolid reduces Ras/Raf/MEK/ERK signaling by altering the membrane composition and fluidity . We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells.", "We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells. Taken together, our study shows that archazolid reduces the activity and expression of cathepsin B in endothelial cells. As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected.", "As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected. This study shows that the v-ATPase plays an important role in regulating the adhesion of cells expressing receptors for extracellular matrix components. Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells.", "Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells. Moreover, we for the first time linked the function of v-ATPase to the adhesion and transmigration of tumor cells onto endothelial cells as well as to the remodeling of the extracellular matrix on the surface of endothelial cells. The fact that the adhesion of metastatic tumor cells onto endothelial cells is increased while their transendothelial migration is reduced upon inhibition of endothelial v-ATPase by archazolid further supports the view of archazolid as a potential anti-metastatic compound." ]

[ "The vacuolar-type H + -ATPase v-ATPase is the major proton pump that acidifies intracellular compartments of eukaryotic cells. Since the inhibition of v-ATPase resulted in anti-tumor and anti-metastatic effects in different tumor models, this enzyme has emerged as promising strategy against cancer. Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far.", "Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far. Human endothelial cells treated with archazolid showed an increased adhesion of tumor cells, whereas the transendothelial migration of tumor cells was reduced. The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin.", "The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin. Instead, the adhesion was mediated by β1-integrins expressed on tumor cells, as blocking of the integrin β1 subunit reversed this process. Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs.", "Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs. The accumulation of collagen was accompanied by a strong decrease of the expression and activity of the protease cathepsin B. Overexpression of cathepsin B in ECs prevented the capability of archazolid to increase the adhesion of tumor cells onto ECs. Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced.", "Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced. These findings further support archazolid as a promising anti-metastatic compound. Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells .", "Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells . The enzyme consists of two multi-subunit complexes, the soluble V 1 transmembrane V o subcomplex required for the proton transport across membranes . In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles .", "In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles . The function of v-ATPases is essential for cellular processes such as vesicular trafficking, receptor-mediated endocytosis and protein degradation and processing. In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space .", "In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space . In cancer cells v-ATPases are expressed on the plasma membrane in order to eliminate toxic cytosolic H + . Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis .", "Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis . Since the inhibition of v-ATPase was shown to reduce the invasiveness of cancer cells and metastasis formation , this enzyme has emerged as a promising drug target in the recent years. Archazolid A and B are highly potent and specific inhibitors of v-ATPases .", "Archazolid A and B are highly potent and specific inhibitors of v-ATPases . They were first isolated from the myxobacterium Archangium gephyra . These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex.", "These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex. As their biological activity is comparable to the v-ATPase inhibitors bafilomycin and concanamycin , archazolids are natural compounds of high interest that can be used both as a tool to study the consequences of v-ATPase inhibition and as a lead for drug development. Archazolids can be either produced by fermentation or by total synthesis .", "Archazolids can be either produced by fermentation or by total synthesis . In the field of cancer research several studies reported on interesting pharmacological effects of archazolid: It reduced the migration of different invasive tumor cells in vitro and cancer cell metastasis in vivo in a breast tumor mouse model . Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells .", "Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells . In classically activated macrophages, archazolid selectively induced the generation of tumor necrosis factor α TNFα , which may indirectly promote tumor suppression . Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated.", "Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated. The endothelium plays a crucial role in the pathogenesis and progression of cancer: The metastatic cascade includes local angiogenesis at the site of the primary tumor and adhesion of tumor cells at the site of metastasis . Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells .", "Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells . This process ensures the nutrient supply of the tumor and its growth . Circulating cancer cells can adhere to the endothelium at distant sites.", "Circulating cancer cells can adhere to the endothelium at distant sites. This adhesive interaction is mediated by receptors and corresponding ligands expressed on tumor and endothelial cells . V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells .", "V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells . A recent study showed that the inhibition of v-ATPase by concanamycin prevented proliferation, reduced migration and impaired angiogenesis-related signaling in endothelial cells . So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium.", "So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium. Thus, we were interested in the consequences of the inhibition of endothelial v-ATPase by archazolid on the interaction between endothelial and cancer cells. Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells .", "Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells . Accordingly, we focused on these cell adhesion molecules and integrins. For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells.", "For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells. CellTiter-Blue Cell Viability Assay Promega, Mannheim, Germany was performed according to the manufacturer's protocol for determining the cell viability of cells after treatment with archazolid. This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin.", "This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin. The CellTiter-Blue Reagent was added to the cells 4 h before the endpoint of treatment. Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission .", "Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission . CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega was performed according to the manufacturer's instructions for determining the lactate dehydrogenase LDH release after treatment with archazolid. Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme.", "Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme. LDH is a cytosolic enzyme that is released by leaky cells. Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase.", "Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase. The absorbance was measured with a Varioskan Flash microplate reader Thermo Fisher Scientific at 490 nm. LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells.", "LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells. HUVECs were cultured to confluence on collagen G-coated μ-slides 80826, ibidi, Martinsried, Germany before they were treated with archazolid for 24 h. 1 μg/ ml Hoechst 33342 Sigma-Aldrich, Munich, Germany was used to visualize the nuclei and 50 nM LysoTracker Red DND-99 was used to visualize the acidic compartments which correspond to the lysosomes. Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany .", "Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany . HUVECs were seeded in collagen G-coated 24-well plates and grown to confluence for two days before treatment. The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C.", "The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C. Non-adherent tumor cells were washed off three times with PBS containing Ca 2+ and Mg 2+ . Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission .", "Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission . For blocking the integrin β1 subunit on MDA-MB-231 or PC-3 cells, CellTracker Greenlabeled MDA-MB-231 or PC-3 cells were incubated with an anti-integrin β1 antibody P5D2, ab24693, Abcam, Cambridge, United Kingdom at a concentration of 1 μg antibody per one million cells in 1 ml DMEM. Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM.", "Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM. For blocking the integrin β1 subunit on HUVECs, the cells were incubated with the anti-integrin β1 antibody 0.1 μg/well in ECGM . HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs.", "HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs. For the adhesion of MDA-MB-231 or PC-3 cells onto extracellular matrix ECM components 24-well plates were coated with collagen G 10 μg/ml in PBS , human plasma fibronectin 10 μg/ml PBS or laminin-411 10 μg/ml in Dulbecco's PBS DPBS containing Ca 2+ and Mg 2+ at 4˚C overnight. The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C .", "The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C . HUVECs were grown on a porous filter membrane Transwell insert, polycarbonate membrane, 8 μm pores; Corning, New York, USA for 48 h and were treated as indicated. Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA.", "Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA. HUVECs were washed twice with medium 199 containing 0.1% BSA before MDA-MB-231 cells were allowed to transmigrate through the endothelial monolayer for 24 h. Medium 199 containing 0.1% BSA was used as negative control and medium 199 containing 20% FCS was used as chemoattractant for transmigration in the lower compartment. Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab.", "Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab. Transmigrated cells were lysed in radioimmunoprecipitation assay RIPA buffer and transmigration was quantified by measuring the fluorescence signal at 485 nm excitation and 535 nm emission . HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα.", "HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα. RNA was isolated using the RNeasy Mini Kit from Qiagen Hilden, Germany according to the manufacturer's protocol. On-column DNase digestion was performed to remove genomic DNA.", "On-column DNase digestion was performed to remove genomic DNA. RNA was transcribed into cDNA by Superscript II Life Technologies, Thermo Fisher Scientific . qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3.", "qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3. Power SYBR Green PCR Master Mix Life Technologies and the comparative C T quantitation method 2 -ΔΔCT were used. HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules.", "HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules. Subsequently, the cells were detached with HyClone HyQTase GE Healthcare, Freiburg, Germany . In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min.", "In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min. For all other proteins, the cells were not fixed and washed once with PBS before incubating with the antibodies phycoerythrin PE -labeled anti-human CD106 mouse, VCAM-1 , PE-labeled anti-human CD62E mouse, E-selectin and PE-labeled anti-human CD325 mouse, N-cadherin from Becton Dickinson on ice for 45 min. These antibodies were diluted in PBS containing 0.2% BSA.", "These antibodies were diluted in PBS containing 0.2% BSA. The surface expression of cell adhesion molecules was measured by flow cytometry FACSVerse, Becton Dickinson, Heidelberg, Germany . To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min.", "To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min. The staining procedure was performed on ice to ensure that surface proteins or antibodies are not endocytosed. The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth .", "The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth . Alexa Fluor 488-conjugated anti-rabbit antibody goat, 1:400, A11008, Life Technologies was used as secondary antibody and Hoechst 33342 1 μg/ml, Sigma-Aldrich was used to visualize nuclei. Confluent HUVECs in 6-well plates were treated as indicated.", "Confluent HUVECs in 6-well plates were treated as indicated. Cells were washed with ice-cold PBS and lysed with RIPA buffer supplemented with protease inhibitors Complete Mini EDTA-free; Roche, Mannheim, Germany , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride, β-glycerophosphate, sodium pyrophosphate and H 2 O 2 . Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific .", "Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific . Equal amounts of proteins 10-20 μg were separated by sodium dodecyl sulfatepolyacrylamide gel electrophoresis SDS-PAGE; Bio-Rad Laboratories, Munich, Germany . Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection.", "Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection. Membranes were blocked with 5% boltinggrade milk powder Carl Roth in TBS containing 0.1% Tween 20 Sigma-Aldrich . The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 .", "The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 . ImageJ version 1.49m was used for densitometric analysis. Cathepsin B activity assay was performed as described in the publication by Kubisch et al.", "Cathepsin B activity assay was performed as described in the publication by Kubisch et al. . Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated.", ". Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated. Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride.", "Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride. The fluorogenic cathepsin B substrate Z-Arg-Arg-7-amido-4-methylcoumarin hydrochloride C5429, Sigma-Aldrich was added to 30 μg of the cell lysate diluted in assay buffer supplemented with 2 mM L-cysteine C7880, Sigma-Aldrich and incubated for 30 min at 40˚C. Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific .", "Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific . The intensity of the fluorescence signal corresponded to the cathepsin B enzyme activity. For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction.", "For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction. The HUVEC Nucleofector Kit Lonza, Cologne, Germany was used to transfect HUVECs. The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza .", "The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza . 48 h after transfection the cells were treated for further experiments. The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe .", "The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe . hCathepsin B was digested with PmeI and XbaI and the linear DNA fragment not corresponding to the human CTSB gene was religated to generate the empty pcDNA3.1 - delta MCS plasmid that was used for control transfections. The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific.", "The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific. The control vector pcDNA3.1 - delta MCS used for our transfections was cloned on the basis of hCathepsin B and is therefore lacking almost the whole part of the multiple cloning site of the pcDNA3.1 - . Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA .", "Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA . One-way ANOVA followed by Tukey's post-hoc test or unpaired t-test was used for the evaluation of a minimum of three independent experiments. The numbers of independently performed experiments n are stated in the corresponding figure legends. p 0.05 was considered as statistically significant.", "p 0.05 was considered as statistically significant. Data are expressed as mean ± standard error of the mean SEM . Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays.", "Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays. We treated confluent HUVECs with up to 1 nM archazolid for 24 and 48 h and observed that this treatment has neither an influence on the metabolic activity nor on the release of LDH after 24 h Fig 1A and 1B, left panels . The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels .", "The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels . Consequently, the following experiments were all carried out after 24 h or less of archazolid treatment in order to exclude any cytotoxic effects of archazolid within our experimental settings. Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors .", "Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors . This effect was obvious both in subconfluent and in confluent cells Fig 2A . Inhibition of v-ATPase prevents the acidification of lysosomes .", "Inhibition of v-ATPase prevents the acidification of lysosomes . Using the cell-permeable dye LysoTracker Red DND-99, it is possible to label the acidic lysosomes in living cells. Thus, this dye can serve as an indicator of v-ATPase inhibition.", "Thus, this dye can serve as an indicator of v-ATPase inhibition. To proof that archazolid is also functionally active as a v-ATPase inhibitor in HUVECs, cells were treated with 1 nM archazolid before they were incubated with LysoTracker Red DND-99 and Hoechst 33342. As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid.", "As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid. In summary, archazolid treatment for 24 h was not cytotoxic to quiescent HUVECs, but inhibited the functionality of the v-ATPase. We analyzed the adhesion of MDA-MB-231 cells onto HUVECs.", "We analyzed the adhesion of MDA-MB-231 cells onto HUVECs. Confluent HUVECs were treated with up to 1 nM archazolid for 24 h. Untreated MDA-MB-231 cells were labeled with Cell-Tracker Green CMFDA Dye. Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B .", "Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B . We also investigated the influence of archazolid on the transendothelial migration of MDA-MB-231 cells. HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells.", "HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells. The influence of archazolid on tumor cell adhesion was not only studied in HUVECs, which represent macrovascular endothelial cells, but also in microvascular HMEC-1 cells. Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line.", "Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line. Archazolid treatment of endothelial cells increased the attachment of MDA-MB-231 cells onto the HMEC-1 monolayer after 120 min of adhesion Fig 4A and increased the attachment of PC-3 cells onto the HUVEC monolayer after 30 and 60 min of adhesion Fig 4B . Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig .", "Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig . Taken together, archazolid treatment augmented the adhesive properties of both micro-and macrovascular endothelial cells for metastatic tumor cells, but not for non-metastatic ones. Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion.", "Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion. The adhesion of tumor cells onto the endothelium is in principle similar to that of leukocytes, but slightly differs in the molecules that mediate the adhesion process. Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction .", "Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction . Inhibition of the v-ATPase might affect the expression of endothelial cell adhesion molecules on mRNA or protein levels. To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control.", "To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control. Quantitative real-time PCR showed that v-ATPase inhibition in HUVECs did not alter the mRNA levels of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5A . The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry.", "The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry. Archazolid 1 nM, 24 h did not affect the cell surface expression of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5B . Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion .", "Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion . Since none of the cell adhesion molecules expressed on HUVECs were regulated upon archazolid treatment, we considered integrins as potential interaction partners. Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells .", "Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells . In order to elucidate the role of β1-integrins for the archazolid-induced tumor cell adhesion, the integrin β1-subunit was blocked either on MDA-MB-231 cells, PC-3 cells or on HUVECs. Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid.", "Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid. After blocking β1-integrins on MDA-MB-231 or PC-3 cells, the archazolid-induced tumor cell adhesion was reduced almost to control level Fig 6A and 6B , left panels , whereas blocking of β1-integrins on HUVECs had no significant effect on the increase of tumor cell adhesion by v-ATPase inhibition Fig 6A and 6B , right panels . Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin .", "Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin . Therefore, we hypothesized that archazolid treatment of endothelial cells might lead to an upregulation of these components. MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components.", "MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components. This cell adhesion assay revealed that MDA-MB-231 as well as PC-3 cells favor the interaction with the ECM component collagen, as the adhesion onto collagen is much higher than onto the uncoated plastic control Fig 7A . MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating.", "MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating. Therefore, we focused on the interaction between these two tumor cell lines and collagen. Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins.", "Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins. Since collagen is the major ECM component MDA-MB-231 and PC-3 cells interact with, the next step was to prove whether v-ATPase inhibition influences the amount of collagen expressed by HUVECs as extracellular matrix. To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen.", "To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen. Interestingly, archazolid increased the amount of surface collagen on HUVECs by about 50% Fig 7C . Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig .", "Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig . It was reported that v-ATPase inhibition by archazolid impairs the activity of cathepsin B , a lysosomal enzyme that degrades extracellular matrix components including collagen . As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B.", "As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B. Therefore, an enzyme activity assay based on the proteolysis of a fluorogenic cathepsin B substrate was performed. In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin.", "In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin. Inhibition of endothelial vATPase increases tumor cell adhesion to endothelial cells strongly decreased by approximately 50% compared to control cells at an archazolid concentration of 1 nM Fig 8A . In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B .", "In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B . To proof whether the archazolid-induced tumor cell adhesion is a consequence of the decreased amount of cathepsin B, HUVECs were transfected with a plasmid coding for human cathepsin B or with the empty vector as control. After 48 h, the transfected cells were treated with 1 nM archazolid.", "After 48 h, the transfected cells were treated with 1 nM archazolid. The level of cathepsin B after transfection and treatment was assessed by western blot analysis Fig 9A . Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B .", "Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B . Targeting the proton pump v-ATPase for cancer therapy has gained great interest since its inhibition was reported to reduce the invasiveness of cancer cells and, most importantly, also metastasis . Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis .", "Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis . In the present study we used the myxobacterial natural product archazolid to investigate the consequences of v-ATPase inhibition in the endothelium on tumor-endothelial cell interactions. For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium.", "For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium. Inhibition of the v-ATPase in endothelial cells by archazolid significantly increased the adhesion of metastatic cancer cells and decreased the transendothelial migration of cancer cells which was attributed to augmented collagen levels on the surface on archazolid-treated endothelial cells. Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected.", "Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected. The archazolidinduced adhesion of tumor cells was independent from the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin, as their expression was not regulated by the compound. However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid.", "However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid. In adhesion experiments on plastic coated with extracellular matrix components, we could show that MDA-MB-231 and PC-3 cells clearly favored the interaction with collagen, whereas the adhesion of non-metastatic Jurkat cells was largely independent from extracellular matrix proteins S1B Fig . The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line.", "The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line. MDA-MB-231 and PC-3 cells express α2β1-and α3β1-integrins, which represent collagen receptors , while Jurkat cells express α4β1-integrins but lack α2β1-, α3β1-integrins . α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 .", "α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 . Our results are in line with previous studies showing that α2β1-and α3β1-integrin expressing MDA-MB-231 and PC-3 cells were able to rapidly attach to collagen in the cortical bone matrix. In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins.", "In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins. α2β1-and α3β1-integrins can additionally act as laminin receptors and at least α3β1integrins recognize fibronectin . Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components.", "Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components. Importantly, v-ATPase inhibition by archazolid increased the surface levels of the extracellular matrix component collagen, which might explain that the increase of MDA-MB-231 and PC-3 cells onto archazolid-treated HUVECs is independent of endothelial cell adhesion molecules. By performing a live cell proteolysis assay, Cavallo-Medved et al.", "By performing a live cell proteolysis assay, Cavallo-Medved et al. demonstrated ECM degradation, in particular of gelatin and collagen IV, in association with active cathepsin B in caveolae of endothelial cells during tube formation . In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells .", "In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells . Therefore, we suggested that the accumulation of collagen on the endothelial surface might be a consequence of impaired cathepsin B activity or expression in endothelial cells. In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced.", "In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced. Cathepsin B is synthesized as preprocathepsin B on membrane-bound ribosomes. Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides.", "Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides. The targeting of procathepsin B to lysosomes is mannose-6-phosphate receptor-dependent and its dissociation from the receptor as well as its proteolytic processing into mature cathepsin B requires acidification of the compartment . In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B .", "In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B . We assumed that the archazolid-induced decrease in cathepsin B activity and expression was based on the same mechanism. Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B.", "Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B. As cathepsin B can also degrade other extracellular matrix components such as fibronectin and laminin , v-ATPase inhibition could lead to an accumulation of these proteins and an increased adhesion of cells expressing fibronectin or laminin receptors. However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells.", "However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells. These cells predominantly adhered to collagen, while the adhesion of Jurkat cells is mostly independent from the ECM proteins collagen, fibronectin or laminin S1B Fig . Interestingly .", "Interestingly . In hepatic cancer cells, archazolid reduces Ras/Raf/MEK/ERK signaling by altering the membrane composition and fluidity . We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells.", "We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells. Taken together, our study shows that archazolid reduces the activity and expression of cathepsin B in endothelial cells. As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected.", "As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected. This study shows that the v-ATPase plays an important role in regulating the adhesion of cells expressing receptors for extracellular matrix components. Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells.", "Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells. Moreover, we for the first time linked the function of v-ATPase to the adhesion and transmigration of tumor cells onto endothelial cells as well as to the remodeling of the extracellular matrix on the surface of endothelial cells. The fact that the adhesion of metastatic tumor cells onto endothelial cells is increased while their transendothelial migration is reduced upon inhibition of endothelial v-ATPase by archazolid further supports the view of archazolid as a potential anti-metastatic compound." ]

[ "The vacuolar-type H + -ATPase v-ATPase is the major proton pump that acidifies intracellular compartments of eukaryotic cells. Since the inhibition of v-ATPase resulted in anti-tumor and anti-metastatic effects in different tumor models, this enzyme has emerged as promising strategy against cancer. Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far.", "Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far. Human endothelial cells treated with archazolid showed an increased adhesion of tumor cells, whereas the transendothelial migration of tumor cells was reduced. The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin.", "The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin. Instead, the adhesion was mediated by β1-integrins expressed on tumor cells, as blocking of the integrin β1 subunit reversed this process. Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs.", "Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs. The accumulation of collagen was accompanied by a strong decrease of the expression and activity of the protease cathepsin B. Overexpression of cathepsin B in ECs prevented the capability of archazolid to increase the adhesion of tumor cells onto ECs. Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced.", "Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced. These findings further support archazolid as a promising anti-metastatic compound. Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells .", "Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells . The enzyme consists of two multi-subunit complexes, the soluble V 1 transmembrane V o subcomplex required for the proton transport across membranes . In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles .", "In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles . The function of v-ATPases is essential for cellular processes such as vesicular trafficking, receptor-mediated endocytosis and protein degradation and processing. In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space .", "In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space . In cancer cells v-ATPases are expressed on the plasma membrane in order to eliminate toxic cytosolic H + . Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis .", "Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis . Since the inhibition of v-ATPase was shown to reduce the invasiveness of cancer cells and metastasis formation , this enzyme has emerged as a promising drug target in the recent years. Archazolid A and B are highly potent and specific inhibitors of v-ATPases .", "Archazolid A and B are highly potent and specific inhibitors of v-ATPases . They were first isolated from the myxobacterium Archangium gephyra . These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex.", "These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex. As their biological activity is comparable to the v-ATPase inhibitors bafilomycin and concanamycin , archazolids are natural compounds of high interest that can be used both as a tool to study the consequences of v-ATPase inhibition and as a lead for drug development. Archazolids can be either produced by fermentation or by total synthesis .", "Archazolids can be either produced by fermentation or by total synthesis . In the field of cancer research several studies reported on interesting pharmacological effects of archazolid: It reduced the migration of different invasive tumor cells in vitro and cancer cell metastasis in vivo in a breast tumor mouse model . Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells .", "Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells . In classically activated macrophages, archazolid selectively induced the generation of tumor necrosis factor α TNFα , which may indirectly promote tumor suppression . Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated.", "Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated. The endothelium plays a crucial role in the pathogenesis and progression of cancer: The metastatic cascade includes local angiogenesis at the site of the primary tumor and adhesion of tumor cells at the site of metastasis . Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells .", "Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells . This process ensures the nutrient supply of the tumor and its growth . Circulating cancer cells can adhere to the endothelium at distant sites.", "Circulating cancer cells can adhere to the endothelium at distant sites. This adhesive interaction is mediated by receptors and corresponding ligands expressed on tumor and endothelial cells . V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells .", "V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells . A recent study showed that the inhibition of v-ATPase by concanamycin prevented proliferation, reduced migration and impaired angiogenesis-related signaling in endothelial cells . So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium.", "So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium. Thus, we were interested in the consequences of the inhibition of endothelial v-ATPase by archazolid on the interaction between endothelial and cancer cells. Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells .", "Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells . Accordingly, we focused on these cell adhesion molecules and integrins. For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells.", "For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells. CellTiter-Blue Cell Viability Assay Promega, Mannheim, Germany was performed according to the manufacturer's protocol for determining the cell viability of cells after treatment with archazolid. This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin.", "This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin. The CellTiter-Blue Reagent was added to the cells 4 h before the endpoint of treatment. Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission .", "Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission . CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega was performed according to the manufacturer's instructions for determining the lactate dehydrogenase LDH release after treatment with archazolid. Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme.", "Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme. LDH is a cytosolic enzyme that is released by leaky cells. Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase.", "Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase. The absorbance was measured with a Varioskan Flash microplate reader Thermo Fisher Scientific at 490 nm. LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells.", "LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells. HUVECs were cultured to confluence on collagen G-coated μ-slides 80826, ibidi, Martinsried, Germany before they were treated with archazolid for 24 h. 1 μg/ ml Hoechst 33342 Sigma-Aldrich, Munich, Germany was used to visualize the nuclei and 50 nM LysoTracker Red DND-99 was used to visualize the acidic compartments which correspond to the lysosomes. Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany .", "Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany . HUVECs were seeded in collagen G-coated 24-well plates and grown to confluence for two days before treatment. The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C.", "The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C. Non-adherent tumor cells were washed off three times with PBS containing Ca 2+ and Mg 2+ . Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission .", "Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission . For blocking the integrin β1 subunit on MDA-MB-231 or PC-3 cells, CellTracker Greenlabeled MDA-MB-231 or PC-3 cells were incubated with an anti-integrin β1 antibody P5D2, ab24693, Abcam, Cambridge, United Kingdom at a concentration of 1 μg antibody per one million cells in 1 ml DMEM. Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM.", "Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM. For blocking the integrin β1 subunit on HUVECs, the cells were incubated with the anti-integrin β1 antibody 0.1 μg/well in ECGM . HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs.", "HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs. For the adhesion of MDA-MB-231 or PC-3 cells onto extracellular matrix ECM components 24-well plates were coated with collagen G 10 μg/ml in PBS , human plasma fibronectin 10 μg/ml PBS or laminin-411 10 μg/ml in Dulbecco's PBS DPBS containing Ca 2+ and Mg 2+ at 4˚C overnight. The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C .", "The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C . HUVECs were grown on a porous filter membrane Transwell insert, polycarbonate membrane, 8 μm pores; Corning, New York, USA for 48 h and were treated as indicated. Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA.", "Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA. HUVECs were washed twice with medium 199 containing 0.1% BSA before MDA-MB-231 cells were allowed to transmigrate through the endothelial monolayer for 24 h. Medium 199 containing 0.1% BSA was used as negative control and medium 199 containing 20% FCS was used as chemoattractant for transmigration in the lower compartment. Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab.", "Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab. Transmigrated cells were lysed in radioimmunoprecipitation assay RIPA buffer and transmigration was quantified by measuring the fluorescence signal at 485 nm excitation and 535 nm emission . HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα.", "HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα. RNA was isolated using the RNeasy Mini Kit from Qiagen Hilden, Germany according to the manufacturer's protocol. On-column DNase digestion was performed to remove genomic DNA.", "On-column DNase digestion was performed to remove genomic DNA. RNA was transcribed into cDNA by Superscript II Life Technologies, Thermo Fisher Scientific . qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3.", "qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3. Power SYBR Green PCR Master Mix Life Technologies and the comparative C T quantitation method 2 -ΔΔCT were used. HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules.", "HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules. Subsequently, the cells were detached with HyClone HyQTase GE Healthcare, Freiburg, Germany . In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min.", "In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min. For all other proteins, the cells were not fixed and washed once with PBS before incubating with the antibodies phycoerythrin PE -labeled anti-human CD106 mouse, VCAM-1 , PE-labeled anti-human CD62E mouse, E-selectin and PE-labeled anti-human CD325 mouse, N-cadherin from Becton Dickinson on ice for 45 min. These antibodies were diluted in PBS containing 0.2% BSA.", "These antibodies were diluted in PBS containing 0.2% BSA. The surface expression of cell adhesion molecules was measured by flow cytometry FACSVerse, Becton Dickinson, Heidelberg, Germany . To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min.", "To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min. The staining procedure was performed on ice to ensure that surface proteins or antibodies are not endocytosed. The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth .", "The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth . Alexa Fluor 488-conjugated anti-rabbit antibody goat, 1:400, A11008, Life Technologies was used as secondary antibody and Hoechst 33342 1 μg/ml, Sigma-Aldrich was used to visualize nuclei. Confluent HUVECs in 6-well plates were treated as indicated.", "Confluent HUVECs in 6-well plates were treated as indicated. Cells were washed with ice-cold PBS and lysed with RIPA buffer supplemented with protease inhibitors Complete Mini EDTA-free; Roche, Mannheim, Germany , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride, β-glycerophosphate, sodium pyrophosphate and H 2 O 2 . Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific .", "Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific . Equal amounts of proteins 10-20 μg were separated by sodium dodecyl sulfatepolyacrylamide gel electrophoresis SDS-PAGE; Bio-Rad Laboratories, Munich, Germany . Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection.", "Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection. Membranes were blocked with 5% boltinggrade milk powder Carl Roth in TBS containing 0.1% Tween 20 Sigma-Aldrich . The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 .", "The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 . ImageJ version 1.49m was used for densitometric analysis. Cathepsin B activity assay was performed as described in the publication by Kubisch et al.", "Cathepsin B activity assay was performed as described in the publication by Kubisch et al. . Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated.", ". Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated. Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride.", "Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride. The fluorogenic cathepsin B substrate Z-Arg-Arg-7-amido-4-methylcoumarin hydrochloride C5429, Sigma-Aldrich was added to 30 μg of the cell lysate diluted in assay buffer supplemented with 2 mM L-cysteine C7880, Sigma-Aldrich and incubated for 30 min at 40˚C. Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific .", "Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific . The intensity of the fluorescence signal corresponded to the cathepsin B enzyme activity. For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction.", "For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction. The HUVEC Nucleofector Kit Lonza, Cologne, Germany was used to transfect HUVECs. The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza .", "The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza . 48 h after transfection the cells were treated for further experiments. The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe .", "The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe . hCathepsin B was digested with PmeI and XbaI and the linear DNA fragment not corresponding to the human CTSB gene was religated to generate the empty pcDNA3.1 - delta MCS plasmid that was used for control transfections. The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific.", "The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific. The control vector pcDNA3.1 - delta MCS used for our transfections was cloned on the basis of hCathepsin B and is therefore lacking almost the whole part of the multiple cloning site of the pcDNA3.1 - . Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA .", "Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA . One-way ANOVA followed by Tukey's post-hoc test or unpaired t-test was used for the evaluation of a minimum of three independent experiments. The numbers of independently performed experiments n are stated in the corresponding figure legends. p 0.05 was considered as statistically significant.", "p 0.05 was considered as statistically significant. Data are expressed as mean ± standard error of the mean SEM . Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays.", "Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays. We treated confluent HUVECs with up to 1 nM archazolid for 24 and 48 h and observed that this treatment has neither an influence on the metabolic activity nor on the release of LDH after 24 h Fig 1A and 1B, left panels . The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels .", "The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels . Consequently, the following experiments were all carried out after 24 h or less of archazolid treatment in order to exclude any cytotoxic effects of archazolid within our experimental settings. Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors .", "Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors . This effect was obvious both in subconfluent and in confluent cells Fig 2A . Inhibition of v-ATPase prevents the acidification of lysosomes .", "Inhibition of v-ATPase prevents the acidification of lysosomes . Using the cell-permeable dye LysoTracker Red DND-99, it is possible to label the acidic lysosomes in living cells. Thus, this dye can serve as an indicator of v-ATPase inhibition.", "Thus, this dye can serve as an indicator of v-ATPase inhibition. To proof that archazolid is also functionally active as a v-ATPase inhibitor in HUVECs, cells were treated with 1 nM archazolid before they were incubated with LysoTracker Red DND-99 and Hoechst 33342. As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid.", "As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid. In summary, archazolid treatment for 24 h was not cytotoxic to quiescent HUVECs, but inhibited the functionality of the v-ATPase. We analyzed the adhesion of MDA-MB-231 cells onto HUVECs.", "We analyzed the adhesion of MDA-MB-231 cells onto HUVECs. Confluent HUVECs were treated with up to 1 nM archazolid for 24 h. Untreated MDA-MB-231 cells were labeled with Cell-Tracker Green CMFDA Dye. Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B .", "Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B . We also investigated the influence of archazolid on the transendothelial migration of MDA-MB-231 cells. HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells.", "HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells. The influence of archazolid on tumor cell adhesion was not only studied in HUVECs, which represent macrovascular endothelial cells, but also in microvascular HMEC-1 cells. Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line.", "Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line. Archazolid treatment of endothelial cells increased the attachment of MDA-MB-231 cells onto the HMEC-1 monolayer after 120 min of adhesion Fig 4A and increased the attachment of PC-3 cells onto the HUVEC monolayer after 30 and 60 min of adhesion Fig 4B . Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig .", "Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig . Taken together, archazolid treatment augmented the adhesive properties of both micro-and macrovascular endothelial cells for metastatic tumor cells, but not for non-metastatic ones. Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion.", "Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion. The adhesion of tumor cells onto the endothelium is in principle similar to that of leukocytes, but slightly differs in the molecules that mediate the adhesion process. Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction .", "Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction . Inhibition of the v-ATPase might affect the expression of endothelial cell adhesion molecules on mRNA or protein levels. To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control.", "To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control. Quantitative real-time PCR showed that v-ATPase inhibition in HUVECs did not alter the mRNA levels of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5A . The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry.", "The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry. Archazolid 1 nM, 24 h did not affect the cell surface expression of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5B . Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion .", "Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion . Since none of the cell adhesion molecules expressed on HUVECs were regulated upon archazolid treatment, we considered integrins as potential interaction partners. Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells .", "Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells . In order to elucidate the role of β1-integrins for the archazolid-induced tumor cell adhesion, the integrin β1-subunit was blocked either on MDA-MB-231 cells, PC-3 cells or on HUVECs. Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid.", "Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid. After blocking β1-integrins on MDA-MB-231 or PC-3 cells, the archazolid-induced tumor cell adhesion was reduced almost to control level Fig 6A and 6B , left panels , whereas blocking of β1-integrins on HUVECs had no significant effect on the increase of tumor cell adhesion by v-ATPase inhibition Fig 6A and 6B , right panels . Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin .", "Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin . Therefore, we hypothesized that archazolid treatment of endothelial cells might lead to an upregulation of these components. MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components.", "MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components. This cell adhesion assay revealed that MDA-MB-231 as well as PC-3 cells favor the interaction with the ECM component collagen, as the adhesion onto collagen is much higher than onto the uncoated plastic control Fig 7A . MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating.", "MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating. Therefore, we focused on the interaction between these two tumor cell lines and collagen. Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins.", "Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins. Since collagen is the major ECM component MDA-MB-231 and PC-3 cells interact with, the next step was to prove whether v-ATPase inhibition influences the amount of collagen expressed by HUVECs as extracellular matrix. To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen.", "To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen. Interestingly, archazolid increased the amount of surface collagen on HUVECs by about 50% Fig 7C . Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig .", "Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig . It was reported that v-ATPase inhibition by archazolid impairs the activity of cathepsin B , a lysosomal enzyme that degrades extracellular matrix components including collagen . As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B.", "As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B. Therefore, an enzyme activity assay based on the proteolysis of a fluorogenic cathepsin B substrate was performed. In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin.", "In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin. Inhibition of endothelial vATPase increases tumor cell adhesion to endothelial cells strongly decreased by approximately 50% compared to control cells at an archazolid concentration of 1 nM Fig 8A . In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B .", "In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B . To proof whether the archazolid-induced tumor cell adhesion is a consequence of the decreased amount of cathepsin B, HUVECs were transfected with a plasmid coding for human cathepsin B or with the empty vector as control. After 48 h, the transfected cells were treated with 1 nM archazolid.", "After 48 h, the transfected cells were treated with 1 nM archazolid. The level of cathepsin B after transfection and treatment was assessed by western blot analysis Fig 9A . Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B .", "Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B . Targeting the proton pump v-ATPase for cancer therapy has gained great interest since its inhibition was reported to reduce the invasiveness of cancer cells and, most importantly, also metastasis . Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis .", "Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis . In the present study we used the myxobacterial natural product archazolid to investigate the consequences of v-ATPase inhibition in the endothelium on tumor-endothelial cell interactions. For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium.", "For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium. Inhibition of the v-ATPase in endothelial cells by archazolid significantly increased the adhesion of metastatic cancer cells and decreased the transendothelial migration of cancer cells which was attributed to augmented collagen levels on the surface on archazolid-treated endothelial cells. Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected.", "Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected. The archazolidinduced adhesion of tumor cells was independent from the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin, as their expression was not regulated by the compound. However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid.", "However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid. In adhesion experiments on plastic coated with extracellular matrix components, we could show that MDA-MB-231 and PC-3 cells clearly favored the interaction with collagen, whereas the adhesion of non-metastatic Jurkat cells was largely independent from extracellular matrix proteins S1B Fig . The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line.", "The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line. MDA-MB-231 and PC-3 cells express α2β1-and α3β1-integrins, which represent collagen receptors , while Jurkat cells express α4β1-integrins but lack α2β1-, α3β1-integrins . α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 .", "α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 . Our results are in line with previous studies showing that α2β1-and α3β1-integrin expressing MDA-MB-231 and PC-3 cells were able to rapidly attach to collagen in the cortical bone matrix. In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins.", "In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins. α2β1-and α3β1-integrins can additionally act as laminin receptors and at least α3β1integrins recognize fibronectin . Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components.", "Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components. Importantly, v-ATPase inhibition by archazolid increased the surface levels of the extracellular matrix component collagen, which might explain that the increase of MDA-MB-231 and PC-3 cells onto archazolid-treated HUVECs is independent of endothelial cell adhesion molecules. By performing a live cell proteolysis assay, Cavallo-Medved et al.", "By performing a live cell proteolysis assay, Cavallo-Medved et al. demonstrated ECM degradation, in particular of gelatin and collagen IV, in association with active cathepsin B in caveolae of endothelial cells during tube formation . In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells .", "In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells . Therefore, we suggested that the accumulation of collagen on the endothelial surface might be a consequence of impaired cathepsin B activity or expression in endothelial cells. In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced.", "In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced. Cathepsin B is synthesized as preprocathepsin B on membrane-bound ribosomes. Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides.", "Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides. The targeting of procathepsin B to lysosomes is mannose-6-phosphate receptor-dependent and its dissociation from the receptor as well as its proteolytic processing into mature cathepsin B requires acidification of the compartment . In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B .", "In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B . We assumed that the archazolid-induced decrease in cathepsin B activity and expression was based on the same mechanism. Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B.", "Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B. As cathepsin B can also degrade other extracellular matrix components such as fibronectin and laminin , v-ATPase inhibition could lead to an accumulation of these proteins and an increased adhesion of cells expressing fibronectin or laminin receptors. However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells.", "However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells. These cells predominantly adhered to collagen, while the adhesion of Jurkat cells is mostly independent from the ECM proteins collagen, fibronectin or laminin S1B Fig . Interestingly .", "Interestingly . In hepatic cancer cells, archazolid reduces Ras/Raf/MEK/ERK signaling by altering the membrane composition and fluidity . We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells.", "We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells. Taken together, our study shows that archazolid reduces the activity and expression of cathepsin B in endothelial cells. As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected.", "As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected. This study shows that the v-ATPase plays an important role in regulating the adhesion of cells expressing receptors for extracellular matrix components. Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells.", "Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells. Moreover, we for the first time linked the function of v-ATPase to the adhesion and transmigration of tumor cells onto endothelial cells as well as to the remodeling of the extracellular matrix on the surface of endothelial cells. The fact that the adhesion of metastatic tumor cells onto endothelial cells is increased while their transendothelial migration is reduced upon inhibition of endothelial v-ATPase by archazolid further supports the view of archazolid as a potential anti-metastatic compound." ]

[ "The vacuolar-type H + -ATPase v-ATPase is the major proton pump that acidifies intracellular compartments of eukaryotic cells. Since the inhibition of v-ATPase resulted in anti-tumor and anti-metastatic effects in different tumor models, this enzyme has emerged as promising strategy against cancer. Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far.", "Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far. Human endothelial cells treated with archazolid showed an increased adhesion of tumor cells, whereas the transendothelial migration of tumor cells was reduced. The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin.", "The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin. Instead, the adhesion was mediated by β1-integrins expressed on tumor cells, as blocking of the integrin β1 subunit reversed this process. Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs.", "Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs. The accumulation of collagen was accompanied by a strong decrease of the expression and activity of the protease cathepsin B. Overexpression of cathepsin B in ECs prevented the capability of archazolid to increase the adhesion of tumor cells onto ECs. Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced.", "Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced. These findings further support archazolid as a promising anti-metastatic compound. Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells .", "Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells . The enzyme consists of two multi-subunit complexes, the soluble V 1 transmembrane V o subcomplex required for the proton transport across membranes . In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles .", "In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles . The function of v-ATPases is essential for cellular processes such as vesicular trafficking, receptor-mediated endocytosis and protein degradation and processing. In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space .", "In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space . In cancer cells v-ATPases are expressed on the plasma membrane in order to eliminate toxic cytosolic H + . Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis .", "Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis . Since the inhibition of v-ATPase was shown to reduce the invasiveness of cancer cells and metastasis formation , this enzyme has emerged as a promising drug target in the recent years. Archazolid A and B are highly potent and specific inhibitors of v-ATPases .", "Archazolid A and B are highly potent and specific inhibitors of v-ATPases . They were first isolated from the myxobacterium Archangium gephyra . These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex.", "These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex. As their biological activity is comparable to the v-ATPase inhibitors bafilomycin and concanamycin , archazolids are natural compounds of high interest that can be used both as a tool to study the consequences of v-ATPase inhibition and as a lead for drug development. Archazolids can be either produced by fermentation or by total synthesis .", "Archazolids can be either produced by fermentation or by total synthesis . In the field of cancer research several studies reported on interesting pharmacological effects of archazolid: It reduced the migration of different invasive tumor cells in vitro and cancer cell metastasis in vivo in a breast tumor mouse model . Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells .", "Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells . In classically activated macrophages, archazolid selectively induced the generation of tumor necrosis factor α TNFα , which may indirectly promote tumor suppression . Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated.", "Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated. The endothelium plays a crucial role in the pathogenesis and progression of cancer: The metastatic cascade includes local angiogenesis at the site of the primary tumor and adhesion of tumor cells at the site of metastasis . Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells .", "Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells . This process ensures the nutrient supply of the tumor and its growth . Circulating cancer cells can adhere to the endothelium at distant sites.", "Circulating cancer cells can adhere to the endothelium at distant sites. This adhesive interaction is mediated by receptors and corresponding ligands expressed on tumor and endothelial cells . V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells .", "V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells . A recent study showed that the inhibition of v-ATPase by concanamycin prevented proliferation, reduced migration and impaired angiogenesis-related signaling in endothelial cells . So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium.", "So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium. Thus, we were interested in the consequences of the inhibition of endothelial v-ATPase by archazolid on the interaction between endothelial and cancer cells. Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells .", "Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells . Accordingly, we focused on these cell adhesion molecules and integrins. For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells.", "For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells. CellTiter-Blue Cell Viability Assay Promega, Mannheim, Germany was performed according to the manufacturer's protocol for determining the cell viability of cells after treatment with archazolid. This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin.", "This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin. The CellTiter-Blue Reagent was added to the cells 4 h before the endpoint of treatment. Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission .", "Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission . CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega was performed according to the manufacturer's instructions for determining the lactate dehydrogenase LDH release after treatment with archazolid. Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme.", "Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme. LDH is a cytosolic enzyme that is released by leaky cells. Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase.", "Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase. The absorbance was measured with a Varioskan Flash microplate reader Thermo Fisher Scientific at 490 nm. LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells.", "LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells. HUVECs were cultured to confluence on collagen G-coated μ-slides 80826, ibidi, Martinsried, Germany before they were treated with archazolid for 24 h. 1 μg/ ml Hoechst 33342 Sigma-Aldrich, Munich, Germany was used to visualize the nuclei and 50 nM LysoTracker Red DND-99 was used to visualize the acidic compartments which correspond to the lysosomes. Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany .", "Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany . HUVECs were seeded in collagen G-coated 24-well plates and grown to confluence for two days before treatment. The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C.", "The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C. Non-adherent tumor cells were washed off three times with PBS containing Ca 2+ and Mg 2+ . Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission .", "Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission . For blocking the integrin β1 subunit on MDA-MB-231 or PC-3 cells, CellTracker Greenlabeled MDA-MB-231 or PC-3 cells were incubated with an anti-integrin β1 antibody P5D2, ab24693, Abcam, Cambridge, United Kingdom at a concentration of 1 μg antibody per one million cells in 1 ml DMEM. Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM.", "Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM. For blocking the integrin β1 subunit on HUVECs, the cells were incubated with the anti-integrin β1 antibody 0.1 μg/well in ECGM . HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs.", "HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs. For the adhesion of MDA-MB-231 or PC-3 cells onto extracellular matrix ECM components 24-well plates were coated with collagen G 10 μg/ml in PBS , human plasma fibronectin 10 μg/ml PBS or laminin-411 10 μg/ml in Dulbecco's PBS DPBS containing Ca 2+ and Mg 2+ at 4˚C overnight. The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C .", "The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C . HUVECs were grown on a porous filter membrane Transwell insert, polycarbonate membrane, 8 μm pores; Corning, New York, USA for 48 h and were treated as indicated. Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA.", "Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA. HUVECs were washed twice with medium 199 containing 0.1% BSA before MDA-MB-231 cells were allowed to transmigrate through the endothelial monolayer for 24 h. Medium 199 containing 0.1% BSA was used as negative control and medium 199 containing 20% FCS was used as chemoattractant for transmigration in the lower compartment. Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab.", "Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab. Transmigrated cells were lysed in radioimmunoprecipitation assay RIPA buffer and transmigration was quantified by measuring the fluorescence signal at 485 nm excitation and 535 nm emission . HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα.", "HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα. RNA was isolated using the RNeasy Mini Kit from Qiagen Hilden, Germany according to the manufacturer's protocol. On-column DNase digestion was performed to remove genomic DNA.", "On-column DNase digestion was performed to remove genomic DNA. RNA was transcribed into cDNA by Superscript II Life Technologies, Thermo Fisher Scientific . qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3.", "qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3. Power SYBR Green PCR Master Mix Life Technologies and the comparative C T quantitation method 2 -ΔΔCT were used. HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules.", "HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules. Subsequently, the cells were detached with HyClone HyQTase GE Healthcare, Freiburg, Germany . In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min.", "In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min. For all other proteins, the cells were not fixed and washed once with PBS before incubating with the antibodies phycoerythrin PE -labeled anti-human CD106 mouse, VCAM-1 , PE-labeled anti-human CD62E mouse, E-selectin and PE-labeled anti-human CD325 mouse, N-cadherin from Becton Dickinson on ice for 45 min. These antibodies were diluted in PBS containing 0.2% BSA.", "These antibodies were diluted in PBS containing 0.2% BSA. The surface expression of cell adhesion molecules was measured by flow cytometry FACSVerse, Becton Dickinson, Heidelberg, Germany . To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min.", "To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min. The staining procedure was performed on ice to ensure that surface proteins or antibodies are not endocytosed. The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth .", "The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth . Alexa Fluor 488-conjugated anti-rabbit antibody goat, 1:400, A11008, Life Technologies was used as secondary antibody and Hoechst 33342 1 μg/ml, Sigma-Aldrich was used to visualize nuclei. Confluent HUVECs in 6-well plates were treated as indicated.", "Confluent HUVECs in 6-well plates were treated as indicated. Cells were washed with ice-cold PBS and lysed with RIPA buffer supplemented with protease inhibitors Complete Mini EDTA-free; Roche, Mannheim, Germany , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride, β-glycerophosphate, sodium pyrophosphate and H 2 O 2 . Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific .", "Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific . Equal amounts of proteins 10-20 μg were separated by sodium dodecyl sulfatepolyacrylamide gel electrophoresis SDS-PAGE; Bio-Rad Laboratories, Munich, Germany . Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection.", "Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection. Membranes were blocked with 5% boltinggrade milk powder Carl Roth in TBS containing 0.1% Tween 20 Sigma-Aldrich . The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 .", "The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 . ImageJ version 1.49m was used for densitometric analysis. Cathepsin B activity assay was performed as described in the publication by Kubisch et al.", "Cathepsin B activity assay was performed as described in the publication by Kubisch et al. . Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated.", ". Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated. Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride.", "Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride. The fluorogenic cathepsin B substrate Z-Arg-Arg-7-amido-4-methylcoumarin hydrochloride C5429, Sigma-Aldrich was added to 30 μg of the cell lysate diluted in assay buffer supplemented with 2 mM L-cysteine C7880, Sigma-Aldrich and incubated for 30 min at 40˚C. Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific .", "Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific . The intensity of the fluorescence signal corresponded to the cathepsin B enzyme activity. For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction.", "For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction. The HUVEC Nucleofector Kit Lonza, Cologne, Germany was used to transfect HUVECs. The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza .", "The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza . 48 h after transfection the cells were treated for further experiments. The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe .", "The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe . hCathepsin B was digested with PmeI and XbaI and the linear DNA fragment not corresponding to the human CTSB gene was religated to generate the empty pcDNA3.1 - delta MCS plasmid that was used for control transfections. The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific.", "The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific. The control vector pcDNA3.1 - delta MCS used for our transfections was cloned on the basis of hCathepsin B and is therefore lacking almost the whole part of the multiple cloning site of the pcDNA3.1 - . Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA .", "Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA . One-way ANOVA followed by Tukey's post-hoc test or unpaired t-test was used for the evaluation of a minimum of three independent experiments. The numbers of independently performed experiments n are stated in the corresponding figure legends. p 0.05 was considered as statistically significant.", "p 0.05 was considered as statistically significant. Data are expressed as mean ± standard error of the mean SEM . Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays.", "Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays. We treated confluent HUVECs with up to 1 nM archazolid for 24 and 48 h and observed that this treatment has neither an influence on the metabolic activity nor on the release of LDH after 24 h Fig 1A and 1B, left panels . The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels .", "The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels . Consequently, the following experiments were all carried out after 24 h or less of archazolid treatment in order to exclude any cytotoxic effects of archazolid within our experimental settings. Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors .", "Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors . This effect was obvious both in subconfluent and in confluent cells Fig 2A . Inhibition of v-ATPase prevents the acidification of lysosomes .", "Inhibition of v-ATPase prevents the acidification of lysosomes . Using the cell-permeable dye LysoTracker Red DND-99, it is possible to label the acidic lysosomes in living cells. Thus, this dye can serve as an indicator of v-ATPase inhibition.", "Thus, this dye can serve as an indicator of v-ATPase inhibition. To proof that archazolid is also functionally active as a v-ATPase inhibitor in HUVECs, cells were treated with 1 nM archazolid before they were incubated with LysoTracker Red DND-99 and Hoechst 33342. As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid.", "As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid. In summary, archazolid treatment for 24 h was not cytotoxic to quiescent HUVECs, but inhibited the functionality of the v-ATPase. We analyzed the adhesion of MDA-MB-231 cells onto HUVECs.", "We analyzed the adhesion of MDA-MB-231 cells onto HUVECs. Confluent HUVECs were treated with up to 1 nM archazolid for 24 h. Untreated MDA-MB-231 cells were labeled with Cell-Tracker Green CMFDA Dye. Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B .", "Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B . We also investigated the influence of archazolid on the transendothelial migration of MDA-MB-231 cells. HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells.", "HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells. The influence of archazolid on tumor cell adhesion was not only studied in HUVECs, which represent macrovascular endothelial cells, but also in microvascular HMEC-1 cells. Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line.", "Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line. Archazolid treatment of endothelial cells increased the attachment of MDA-MB-231 cells onto the HMEC-1 monolayer after 120 min of adhesion Fig 4A and increased the attachment of PC-3 cells onto the HUVEC monolayer after 30 and 60 min of adhesion Fig 4B . Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig .", "Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig . Taken together, archazolid treatment augmented the adhesive properties of both micro-and macrovascular endothelial cells for metastatic tumor cells, but not for non-metastatic ones. Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion.", "Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion. The adhesion of tumor cells onto the endothelium is in principle similar to that of leukocytes, but slightly differs in the molecules that mediate the adhesion process. Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction .", "Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction . Inhibition of the v-ATPase might affect the expression of endothelial cell adhesion molecules on mRNA or protein levels. To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control.", "To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control. Quantitative real-time PCR showed that v-ATPase inhibition in HUVECs did not alter the mRNA levels of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5A . The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry.", "The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry. Archazolid 1 nM, 24 h did not affect the cell surface expression of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5B . Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion .", "Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion . Since none of the cell adhesion molecules expressed on HUVECs were regulated upon archazolid treatment, we considered integrins as potential interaction partners. Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells .", "Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells . In order to elucidate the role of β1-integrins for the archazolid-induced tumor cell adhesion, the integrin β1-subunit was blocked either on MDA-MB-231 cells, PC-3 cells or on HUVECs. Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid.", "Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid. After blocking β1-integrins on MDA-MB-231 or PC-3 cells, the archazolid-induced tumor cell adhesion was reduced almost to control level Fig 6A and 6B , left panels , whereas blocking of β1-integrins on HUVECs had no significant effect on the increase of tumor cell adhesion by v-ATPase inhibition Fig 6A and 6B , right panels . Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin .", "Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin . Therefore, we hypothesized that archazolid treatment of endothelial cells might lead to an upregulation of these components. MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components.", "MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components. This cell adhesion assay revealed that MDA-MB-231 as well as PC-3 cells favor the interaction with the ECM component collagen, as the adhesion onto collagen is much higher than onto the uncoated plastic control Fig 7A . MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating.", "MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating. Therefore, we focused on the interaction between these two tumor cell lines and collagen. Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins.", "Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins. Since collagen is the major ECM component MDA-MB-231 and PC-3 cells interact with, the next step was to prove whether v-ATPase inhibition influences the amount of collagen expressed by HUVECs as extracellular matrix. To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen.", "To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen. Interestingly, archazolid increased the amount of surface collagen on HUVECs by about 50% Fig 7C . Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig .", "Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig . It was reported that v-ATPase inhibition by archazolid impairs the activity of cathepsin B , a lysosomal enzyme that degrades extracellular matrix components including collagen . As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B.", "As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B. Therefore, an enzyme activity assay based on the proteolysis of a fluorogenic cathepsin B substrate was performed. In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin.", "In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin. Inhibition of endothelial vATPase increases tumor cell adhesion to endothelial cells strongly decreased by approximately 50% compared to control cells at an archazolid concentration of 1 nM Fig 8A . In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B .", "In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B . To proof whether the archazolid-induced tumor cell adhesion is a consequence of the decreased amount of cathepsin B, HUVECs were transfected with a plasmid coding for human cathepsin B or with the empty vector as control. After 48 h, the transfected cells were treated with 1 nM archazolid.", "After 48 h, the transfected cells were treated with 1 nM archazolid. The level of cathepsin B after transfection and treatment was assessed by western blot analysis Fig 9A . Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B .", "Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B . Targeting the proton pump v-ATPase for cancer therapy has gained great interest since its inhibition was reported to reduce the invasiveness of cancer cells and, most importantly, also metastasis . Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis .", "Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis . In the present study we used the myxobacterial natural product archazolid to investigate the consequences of v-ATPase inhibition in the endothelium on tumor-endothelial cell interactions. For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium.", "For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium. Inhibition of the v-ATPase in endothelial cells by archazolid significantly increased the adhesion of metastatic cancer cells and decreased the transendothelial migration of cancer cells which was attributed to augmented collagen levels on the surface on archazolid-treated endothelial cells. Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected.", "Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected. The archazolidinduced adhesion of tumor cells was independent from the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin, as their expression was not regulated by the compound. However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid.", "However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid. In adhesion experiments on plastic coated with extracellular matrix components, we could show that MDA-MB-231 and PC-3 cells clearly favored the interaction with collagen, whereas the adhesion of non-metastatic Jurkat cells was largely independent from extracellular matrix proteins S1B Fig . The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line.", "The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line. MDA-MB-231 and PC-3 cells express α2β1-and α3β1-integrins, which represent collagen receptors , while Jurkat cells express α4β1-integrins but lack α2β1-, α3β1-integrins . α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 .", "α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 . Our results are in line with previous studies showing that α2β1-and α3β1-integrin expressing MDA-MB-231 and PC-3 cells were able to rapidly attach to collagen in the cortical bone matrix. In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins.", "In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins. α2β1-and α3β1-integrins can additionally act as laminin receptors and at least α3β1integrins recognize fibronectin . Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components.", "Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components. Importantly, v-ATPase inhibition by archazolid increased the surface levels of the extracellular matrix component collagen, which might explain that the increase of MDA-MB-231 and PC-3 cells onto archazolid-treated HUVECs is independent of endothelial cell adhesion molecules. By performing a live cell proteolysis assay, Cavallo-Medved et al.", "By performing a live cell proteolysis assay, Cavallo-Medved et al. demonstrated ECM degradation, in particular of gelatin and collagen IV, in association with active cathepsin B in caveolae of endothelial cells during tube formation . In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells .", "In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells . Therefore, we suggested that the accumulation of collagen on the endothelial surface might be a consequence of impaired cathepsin B activity or expression in endothelial cells. In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced.", "In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced. Cathepsin B is synthesized as preprocathepsin B on membrane-bound ribosomes. Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides.", "Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides. The targeting of procathepsin B to lysosomes is mannose-6-phosphate receptor-dependent and its dissociation from the receptor as well as its proteolytic processing into mature cathepsin B requires acidification of the compartment . In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B .", "In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B . We assumed that the archazolid-induced decrease in cathepsin B activity and expression was based on the same mechanism. Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B.", "Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B. As cathepsin B can also degrade other extracellular matrix components such as fibronectin and laminin , v-ATPase inhibition could lead to an accumulation of these proteins and an increased adhesion of cells expressing fibronectin or laminin receptors. However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells.", "However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells. These cells predominantly adhered to collagen, while the adhesion of Jurkat cells is mostly independent from the ECM proteins collagen, fibronectin or laminin S1B Fig . Interestingly .", "Interestingly . In hepatic cancer cells, archazolid reduces Ras/Raf/MEK/ERK signaling by altering the membrane composition and fluidity . We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells.", "We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells. Taken together, our study shows that archazolid reduces the activity and expression of cathepsin B in endothelial cells. As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected.", "As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected. This study shows that the v-ATPase plays an important role in regulating the adhesion of cells expressing receptors for extracellular matrix components. Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells.", "Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells. Moreover, we for the first time linked the function of v-ATPase to the adhesion and transmigration of tumor cells onto endothelial cells as well as to the remodeling of the extracellular matrix on the surface of endothelial cells. The fact that the adhesion of metastatic tumor cells onto endothelial cells is increased while their transendothelial migration is reduced upon inhibition of endothelial v-ATPase by archazolid further supports the view of archazolid as a potential anti-metastatic compound." ]

[ "The vacuolar-type H + -ATPase v-ATPase is the major proton pump that acidifies intracellular compartments of eukaryotic cells. Since the inhibition of v-ATPase resulted in anti-tumor and anti-metastatic effects in different tumor models, this enzyme has emerged as promising strategy against cancer. Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far.", "Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far. Human endothelial cells treated with archazolid showed an increased adhesion of tumor cells, whereas the transendothelial migration of tumor cells was reduced. The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin.", "The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin. Instead, the adhesion was mediated by β1-integrins expressed on tumor cells, as blocking of the integrin β1 subunit reversed this process. Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs.", "Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs. The accumulation of collagen was accompanied by a strong decrease of the expression and activity of the protease cathepsin B. Overexpression of cathepsin B in ECs prevented the capability of archazolid to increase the adhesion of tumor cells onto ECs. Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced.", "Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced. These findings further support archazolid as a promising anti-metastatic compound. Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells .", "Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells . The enzyme consists of two multi-subunit complexes, the soluble V 1 transmembrane V o subcomplex required for the proton transport across membranes . In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles .", "In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles . The function of v-ATPases is essential for cellular processes such as vesicular trafficking, receptor-mediated endocytosis and protein degradation and processing. In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space .", "In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space . In cancer cells v-ATPases are expressed on the plasma membrane in order to eliminate toxic cytosolic H + . Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis .", "Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis . Since the inhibition of v-ATPase was shown to reduce the invasiveness of cancer cells and metastasis formation , this enzyme has emerged as a promising drug target in the recent years. Archazolid A and B are highly potent and specific inhibitors of v-ATPases .", "Archazolid A and B are highly potent and specific inhibitors of v-ATPases . They were first isolated from the myxobacterium Archangium gephyra . These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex.", "These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex. As their biological activity is comparable to the v-ATPase inhibitors bafilomycin and concanamycin , archazolids are natural compounds of high interest that can be used both as a tool to study the consequences of v-ATPase inhibition and as a lead for drug development. Archazolids can be either produced by fermentation or by total synthesis .", "Archazolids can be either produced by fermentation or by total synthesis . In the field of cancer research several studies reported on interesting pharmacological effects of archazolid: It reduced the migration of different invasive tumor cells in vitro and cancer cell metastasis in vivo in a breast tumor mouse model . Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells .", "Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells . In classically activated macrophages, archazolid selectively induced the generation of tumor necrosis factor α TNFα , which may indirectly promote tumor suppression . Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated.", "Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated. The endothelium plays a crucial role in the pathogenesis and progression of cancer: The metastatic cascade includes local angiogenesis at the site of the primary tumor and adhesion of tumor cells at the site of metastasis . Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells .", "Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells . This process ensures the nutrient supply of the tumor and its growth . Circulating cancer cells can adhere to the endothelium at distant sites.", "Circulating cancer cells can adhere to the endothelium at distant sites. This adhesive interaction is mediated by receptors and corresponding ligands expressed on tumor and endothelial cells . V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells .", "V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells . A recent study showed that the inhibition of v-ATPase by concanamycin prevented proliferation, reduced migration and impaired angiogenesis-related signaling in endothelial cells . So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium.", "So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium. Thus, we were interested in the consequences of the inhibition of endothelial v-ATPase by archazolid on the interaction between endothelial and cancer cells. Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells .", "Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells . Accordingly, we focused on these cell adhesion molecules and integrins. For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells.", "For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells. CellTiter-Blue Cell Viability Assay Promega, Mannheim, Germany was performed according to the manufacturer's protocol for determining the cell viability of cells after treatment with archazolid. This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin.", "This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin. The CellTiter-Blue Reagent was added to the cells 4 h before the endpoint of treatment. Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission .", "Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission . CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega was performed according to the manufacturer's instructions for determining the lactate dehydrogenase LDH release after treatment with archazolid. Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme.", "Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme. LDH is a cytosolic enzyme that is released by leaky cells. Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase.", "Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase. The absorbance was measured with a Varioskan Flash microplate reader Thermo Fisher Scientific at 490 nm. LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells.", "LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells. HUVECs were cultured to confluence on collagen G-coated μ-slides 80826, ibidi, Martinsried, Germany before they were treated with archazolid for 24 h. 1 μg/ ml Hoechst 33342 Sigma-Aldrich, Munich, Germany was used to visualize the nuclei and 50 nM LysoTracker Red DND-99 was used to visualize the acidic compartments which correspond to the lysosomes. Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany .", "Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany . HUVECs were seeded in collagen G-coated 24-well plates and grown to confluence for two days before treatment. The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C.", "The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C. Non-adherent tumor cells were washed off three times with PBS containing Ca 2+ and Mg 2+ . Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission .", "Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission . For blocking the integrin β1 subunit on MDA-MB-231 or PC-3 cells, CellTracker Greenlabeled MDA-MB-231 or PC-3 cells were incubated with an anti-integrin β1 antibody P5D2, ab24693, Abcam, Cambridge, United Kingdom at a concentration of 1 μg antibody per one million cells in 1 ml DMEM. Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM.", "Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM. For blocking the integrin β1 subunit on HUVECs, the cells were incubated with the anti-integrin β1 antibody 0.1 μg/well in ECGM . HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs.", "HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs. For the adhesion of MDA-MB-231 or PC-3 cells onto extracellular matrix ECM components 24-well plates were coated with collagen G 10 μg/ml in PBS , human plasma fibronectin 10 μg/ml PBS or laminin-411 10 μg/ml in Dulbecco's PBS DPBS containing Ca 2+ and Mg 2+ at 4˚C overnight. The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C .", "The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C . HUVECs were grown on a porous filter membrane Transwell insert, polycarbonate membrane, 8 μm pores; Corning, New York, USA for 48 h and were treated as indicated. Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA.", "Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA. HUVECs were washed twice with medium 199 containing 0.1% BSA before MDA-MB-231 cells were allowed to transmigrate through the endothelial monolayer for 24 h. Medium 199 containing 0.1% BSA was used as negative control and medium 199 containing 20% FCS was used as chemoattractant for transmigration in the lower compartment. Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab.", "Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab. Transmigrated cells were lysed in radioimmunoprecipitation assay RIPA buffer and transmigration was quantified by measuring the fluorescence signal at 485 nm excitation and 535 nm emission . HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα.", "HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα. RNA was isolated using the RNeasy Mini Kit from Qiagen Hilden, Germany according to the manufacturer's protocol. On-column DNase digestion was performed to remove genomic DNA.", "On-column DNase digestion was performed to remove genomic DNA. RNA was transcribed into cDNA by Superscript II Life Technologies, Thermo Fisher Scientific . qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3.", "qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3. Power SYBR Green PCR Master Mix Life Technologies and the comparative C T quantitation method 2 -ΔΔCT were used. HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules.", "HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules. Subsequently, the cells were detached with HyClone HyQTase GE Healthcare, Freiburg, Germany . In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min.", "In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min. For all other proteins, the cells were not fixed and washed once with PBS before incubating with the antibodies phycoerythrin PE -labeled anti-human CD106 mouse, VCAM-1 , PE-labeled anti-human CD62E mouse, E-selectin and PE-labeled anti-human CD325 mouse, N-cadherin from Becton Dickinson on ice for 45 min. These antibodies were diluted in PBS containing 0.2% BSA.", "These antibodies were diluted in PBS containing 0.2% BSA. The surface expression of cell adhesion molecules was measured by flow cytometry FACSVerse, Becton Dickinson, Heidelberg, Germany . To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min.", "To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min. The staining procedure was performed on ice to ensure that surface proteins or antibodies are not endocytosed. The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth .", "The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth . Alexa Fluor 488-conjugated anti-rabbit antibody goat, 1:400, A11008, Life Technologies was used as secondary antibody and Hoechst 33342 1 μg/ml, Sigma-Aldrich was used to visualize nuclei. Confluent HUVECs in 6-well plates were treated as indicated.", "Confluent HUVECs in 6-well plates were treated as indicated. Cells were washed with ice-cold PBS and lysed with RIPA buffer supplemented with protease inhibitors Complete Mini EDTA-free; Roche, Mannheim, Germany , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride, β-glycerophosphate, sodium pyrophosphate and H 2 O 2 . Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific .", "Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific . Equal amounts of proteins 10-20 μg were separated by sodium dodecyl sulfatepolyacrylamide gel electrophoresis SDS-PAGE; Bio-Rad Laboratories, Munich, Germany . Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection.", "Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection. Membranes were blocked with 5% boltinggrade milk powder Carl Roth in TBS containing 0.1% Tween 20 Sigma-Aldrich . The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 .", "The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 . ImageJ version 1.49m was used for densitometric analysis. Cathepsin B activity assay was performed as described in the publication by Kubisch et al.", "Cathepsin B activity assay was performed as described in the publication by Kubisch et al. . Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated.", ". Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated. Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride.", "Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride. The fluorogenic cathepsin B substrate Z-Arg-Arg-7-amido-4-methylcoumarin hydrochloride C5429, Sigma-Aldrich was added to 30 μg of the cell lysate diluted in assay buffer supplemented with 2 mM L-cysteine C7880, Sigma-Aldrich and incubated for 30 min at 40˚C. Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific .", "Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific . The intensity of the fluorescence signal corresponded to the cathepsin B enzyme activity. For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction.", "For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction. The HUVEC Nucleofector Kit Lonza, Cologne, Germany was used to transfect HUVECs. The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza .", "The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza . 48 h after transfection the cells were treated for further experiments. The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe .", "The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe . hCathepsin B was digested with PmeI and XbaI and the linear DNA fragment not corresponding to the human CTSB gene was religated to generate the empty pcDNA3.1 - delta MCS plasmid that was used for control transfections. The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific.", "The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific. The control vector pcDNA3.1 - delta MCS used for our transfections was cloned on the basis of hCathepsin B and is therefore lacking almost the whole part of the multiple cloning site of the pcDNA3.1 - . Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA .", "Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA . One-way ANOVA followed by Tukey's post-hoc test or unpaired t-test was used for the evaluation of a minimum of three independent experiments. The numbers of independently performed experiments n are stated in the corresponding figure legends. p 0.05 was considered as statistically significant.", "p 0.05 was considered as statistically significant. Data are expressed as mean ± standard error of the mean SEM . Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays.", "Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays. We treated confluent HUVECs with up to 1 nM archazolid for 24 and 48 h and observed that this treatment has neither an influence on the metabolic activity nor on the release of LDH after 24 h Fig 1A and 1B, left panels . The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels .", "The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels . Consequently, the following experiments were all carried out after 24 h or less of archazolid treatment in order to exclude any cytotoxic effects of archazolid within our experimental settings. Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors .", "Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors . This effect was obvious both in subconfluent and in confluent cells Fig 2A . Inhibition of v-ATPase prevents the acidification of lysosomes .", "Inhibition of v-ATPase prevents the acidification of lysosomes . Using the cell-permeable dye LysoTracker Red DND-99, it is possible to label the acidic lysosomes in living cells. Thus, this dye can serve as an indicator of v-ATPase inhibition.", "Thus, this dye can serve as an indicator of v-ATPase inhibition. To proof that archazolid is also functionally active as a v-ATPase inhibitor in HUVECs, cells were treated with 1 nM archazolid before they were incubated with LysoTracker Red DND-99 and Hoechst 33342. As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid.", "As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid. In summary, archazolid treatment for 24 h was not cytotoxic to quiescent HUVECs, but inhibited the functionality of the v-ATPase. We analyzed the adhesion of MDA-MB-231 cells onto HUVECs.", "We analyzed the adhesion of MDA-MB-231 cells onto HUVECs. Confluent HUVECs were treated with up to 1 nM archazolid for 24 h. Untreated MDA-MB-231 cells were labeled with Cell-Tracker Green CMFDA Dye. Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B .", "Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B . We also investigated the influence of archazolid on the transendothelial migration of MDA-MB-231 cells. HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells.", "HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells. The influence of archazolid on tumor cell adhesion was not only studied in HUVECs, which represent macrovascular endothelial cells, but also in microvascular HMEC-1 cells. Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line.", "Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line. Archazolid treatment of endothelial cells increased the attachment of MDA-MB-231 cells onto the HMEC-1 monolayer after 120 min of adhesion Fig 4A and increased the attachment of PC-3 cells onto the HUVEC monolayer after 30 and 60 min of adhesion Fig 4B . Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig .", "Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig . Taken together, archazolid treatment augmented the adhesive properties of both micro-and macrovascular endothelial cells for metastatic tumor cells, but not for non-metastatic ones. Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion.", "Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion. The adhesion of tumor cells onto the endothelium is in principle similar to that of leukocytes, but slightly differs in the molecules that mediate the adhesion process. Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction .", "Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction . Inhibition of the v-ATPase might affect the expression of endothelial cell adhesion molecules on mRNA or protein levels. To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control.", "To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control. Quantitative real-time PCR showed that v-ATPase inhibition in HUVECs did not alter the mRNA levels of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5A . The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry.", "The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry. Archazolid 1 nM, 24 h did not affect the cell surface expression of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5B . Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion .", "Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion . Since none of the cell adhesion molecules expressed on HUVECs were regulated upon archazolid treatment, we considered integrins as potential interaction partners. Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells .", "Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells . In order to elucidate the role of β1-integrins for the archazolid-induced tumor cell adhesion, the integrin β1-subunit was blocked either on MDA-MB-231 cells, PC-3 cells or on HUVECs. Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid.", "Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid. After blocking β1-integrins on MDA-MB-231 or PC-3 cells, the archazolid-induced tumor cell adhesion was reduced almost to control level Fig 6A and 6B , left panels , whereas blocking of β1-integrins on HUVECs had no significant effect on the increase of tumor cell adhesion by v-ATPase inhibition Fig 6A and 6B , right panels . Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin .", "Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin . Therefore, we hypothesized that archazolid treatment of endothelial cells might lead to an upregulation of these components. MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components.", "MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components. This cell adhesion assay revealed that MDA-MB-231 as well as PC-3 cells favor the interaction with the ECM component collagen, as the adhesion onto collagen is much higher than onto the uncoated plastic control Fig 7A . MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating.", "MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating. Therefore, we focused on the interaction between these two tumor cell lines and collagen. Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins.", "Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins. Since collagen is the major ECM component MDA-MB-231 and PC-3 cells interact with, the next step was to prove whether v-ATPase inhibition influences the amount of collagen expressed by HUVECs as extracellular matrix. To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen.", "To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen. Interestingly, archazolid increased the amount of surface collagen on HUVECs by about 50% Fig 7C . Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig .", "Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig . It was reported that v-ATPase inhibition by archazolid impairs the activity of cathepsin B , a lysosomal enzyme that degrades extracellular matrix components including collagen . As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B.", "As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B. Therefore, an enzyme activity assay based on the proteolysis of a fluorogenic cathepsin B substrate was performed. In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin.", "In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin. Inhibition of endothelial vATPase increases tumor cell adhesion to endothelial cells strongly decreased by approximately 50% compared to control cells at an archazolid concentration of 1 nM Fig 8A . In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B .", "In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B . To proof whether the archazolid-induced tumor cell adhesion is a consequence of the decreased amount of cathepsin B, HUVECs were transfected with a plasmid coding for human cathepsin B or with the empty vector as control. After 48 h, the transfected cells were treated with 1 nM archazolid.", "After 48 h, the transfected cells were treated with 1 nM archazolid. The level of cathepsin B after transfection and treatment was assessed by western blot analysis Fig 9A . Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B .", "Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B . Targeting the proton pump v-ATPase for cancer therapy has gained great interest since its inhibition was reported to reduce the invasiveness of cancer cells and, most importantly, also metastasis . Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis .", "Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis . In the present study we used the myxobacterial natural product archazolid to investigate the consequences of v-ATPase inhibition in the endothelium on tumor-endothelial cell interactions. For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium.", "For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium. Inhibition of the v-ATPase in endothelial cells by archazolid significantly increased the adhesion of metastatic cancer cells and decreased the transendothelial migration of cancer cells which was attributed to augmented collagen levels on the surface on archazolid-treated endothelial cells. Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected.", "Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected. The archazolidinduced adhesion of tumor cells was independent from the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin, as their expression was not regulated by the compound. However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid.", "However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid. In adhesion experiments on plastic coated with extracellular matrix components, we could show that MDA-MB-231 and PC-3 cells clearly favored the interaction with collagen, whereas the adhesion of non-metastatic Jurkat cells was largely independent from extracellular matrix proteins S1B Fig . The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line.", "The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line. MDA-MB-231 and PC-3 cells express α2β1-and α3β1-integrins, which represent collagen receptors , while Jurkat cells express α4β1-integrins but lack α2β1-, α3β1-integrins . α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 .", "α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 . Our results are in line with previous studies showing that α2β1-and α3β1-integrin expressing MDA-MB-231 and PC-3 cells were able to rapidly attach to collagen in the cortical bone matrix. In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins.", "In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins. α2β1-and α3β1-integrins can additionally act as laminin receptors and at least α3β1integrins recognize fibronectin . Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components.", "Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components. Importantly, v-ATPase inhibition by archazolid increased the surface levels of the extracellular matrix component collagen, which might explain that the increase of MDA-MB-231 and PC-3 cells onto archazolid-treated HUVECs is independent of endothelial cell adhesion molecules. By performing a live cell proteolysis assay, Cavallo-Medved et al.", "By performing a live cell proteolysis assay, Cavallo-Medved et al. demonstrated ECM degradation, in particular of gelatin and collagen IV, in association with active cathepsin B in caveolae of endothelial cells during tube formation . In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells .", "In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells . Therefore, we suggested that the accumulation of collagen on the endothelial surface might be a consequence of impaired cathepsin B activity or expression in endothelial cells. In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced.", "In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced. Cathepsin B is synthesized as preprocathepsin B on membrane-bound ribosomes. Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides.", "Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides. The targeting of procathepsin B to lysosomes is mannose-6-phosphate receptor-dependent and its dissociation from the receptor as well as its proteolytic processing into mature cathepsin B requires acidification of the compartment . In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B .", "In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B . We assumed that the archazolid-induced decrease in cathepsin B activity and expression was based on the same mechanism. Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B.", "Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B. As cathepsin B can also degrade other extracellular matrix components such as fibronectin and laminin , v-ATPase inhibition could lead to an accumulation of these proteins and an increased adhesion of cells expressing fibronectin or laminin receptors. However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells.", "However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells. These cells predominantly adhered to collagen, while the adhesion of Jurkat cells is mostly independent from the ECM proteins collagen, fibronectin or laminin S1B Fig . Interestingly .", "Interestingly . In hepatic cancer cells, archazolid reduces Ras/Raf/MEK/ERK signaling by altering the membrane composition and fluidity . We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells.", "We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells. Taken together, our study shows that archazolid reduces the activity and expression of cathepsin B in endothelial cells. As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected.", "As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected. This study shows that the v-ATPase plays an important role in regulating the adhesion of cells expressing receptors for extracellular matrix components. Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells.", "Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells. Moreover, we for the first time linked the function of v-ATPase to the adhesion and transmigration of tumor cells onto endothelial cells as well as to the remodeling of the extracellular matrix on the surface of endothelial cells. The fact that the adhesion of metastatic tumor cells onto endothelial cells is increased while their transendothelial migration is reduced upon inhibition of endothelial v-ATPase by archazolid further supports the view of archazolid as a potential anti-metastatic compound." ]

[ "The vacuolar-type H + -ATPase v-ATPase is the major proton pump that acidifies intracellular compartments of eukaryotic cells. Since the inhibition of v-ATPase resulted in anti-tumor and anti-metastatic effects in different tumor models, this enzyme has emerged as promising strategy against cancer. Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far.", "Here, we used the well-established v-ATPase inhibitor archazolid, a natural product first isolated from the myxobacterium Archangium gephyra, to study the consequences of v-ATPase inhibition in endothelial cells ECs , in particular on the interaction between ECs and cancer cells, which has been neglected so far. Human endothelial cells treated with archazolid showed an increased adhesion of tumor cells, whereas the transendothelial migration of tumor cells was reduced. The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin.", "The adhesion process was independent from the EC adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin. Instead, the adhesion was mediated by β1-integrins expressed on tumor cells, as blocking of the integrin β1 subunit reversed this process. Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs.", "Tumor cells preferentially adhered to the β1-integrin ligand collagen and archazolid led to an increase in the amount of collagen on the surface of ECs. The accumulation of collagen was accompanied by a strong decrease of the expression and activity of the protease cathepsin B. Overexpression of cathepsin B in ECs prevented the capability of archazolid to increase the adhesion of tumor cells onto ECs. Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced.", "Our study demonstrates that the inhibition of v-ATPase by archazolid induces a pro-adhesive phenotype in endothelial cells that promotes their interaction with cancer cells, whereas the transmigration of tumor cells was reduced. These findings further support archazolid as a promising anti-metastatic compound. Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells .", "Text: The vacuolar-type H + -ATPase v-ATPase is the major proton pump responsible for acidification of intracellular compartments in eukaryotic cells . The enzyme consists of two multi-subunit complexes, the soluble V 1 transmembrane V o subcomplex required for the proton transport across membranes . In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles .", "In most cell types v-ATPases are only expressed in the endomembrane system to regulate and maintain the acidic pH of intracellular compartments such as lysosomes, endosomes, the Golgi apparatus, secretory granules and coated vesicles . The function of v-ATPases is essential for cellular processes such as vesicular trafficking, receptor-mediated endocytosis and protein degradation and processing. In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space .", "In specialized cell types including osteoclasts and renal epithelial cells, v-ATPases can also be expressed on the plasma membrane, where they pump protons into the extracellular space . In cancer cells v-ATPases are expressed on the plasma membrane in order to eliminate toxic cytosolic H + . Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis .", "Most importantly, v-ATPases contribute to the acidic tumor microenvironment, which leads to the activation of proteases, thus facilitating tumor cell migration, invasion and angiogenesis . Since the inhibition of v-ATPase was shown to reduce the invasiveness of cancer cells and metastasis formation , this enzyme has emerged as a promising drug target in the recent years. Archazolid A and B are highly potent and specific inhibitors of v-ATPases .", "Archazolid A and B are highly potent and specific inhibitors of v-ATPases . They were first isolated from the myxobacterium Archangium gephyra . These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex.", "These compounds inhibit v-ATPase at low nanomolar concentrations by binding to the subunit c of the V o complex. As their biological activity is comparable to the v-ATPase inhibitors bafilomycin and concanamycin , archazolids are natural compounds of high interest that can be used both as a tool to study the consequences of v-ATPase inhibition and as a lead for drug development. Archazolids can be either produced by fermentation or by total synthesis .", "Archazolids can be either produced by fermentation or by total synthesis . In the field of cancer research several studies reported on interesting pharmacological effects of archazolid: It reduced the migration of different invasive tumor cells in vitro and cancer cell metastasis in vivo in a breast tumor mouse model . Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells .", "Furthermore, archazolid activated pathways of cellular stress response and apoptosis in highly invasive tumor cells . In classically activated macrophages, archazolid selectively induced the generation of tumor necrosis factor α TNFα , which may indirectly promote tumor suppression . Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated.", "Up to now, the role of v-ATPases in endothelial cells has only rarely been investigated. The endothelium plays a crucial role in the pathogenesis and progression of cancer: The metastatic cascade includes local angiogenesis at the site of the primary tumor and adhesion of tumor cells at the site of metastasis . Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells .", "Angiogenesis, the development of new blood vessels out of existing ones, depends on the proliferation, migration and differentiation of endothelial cells . This process ensures the nutrient supply of the tumor and its growth . Circulating cancer cells can adhere to the endothelium at distant sites.", "Circulating cancer cells can adhere to the endothelium at distant sites. This adhesive interaction is mediated by receptors and corresponding ligands expressed on tumor and endothelial cells . V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells .", "V-ATPases have been reported to regulate intracellular pH and cell migration in microvascular endothelial cells . A recent study showed that the inhibition of v-ATPase by concanamycin prevented proliferation, reduced migration and impaired angiogenesis-related signaling in endothelial cells . So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium.", "So far, there are no investigations on the role of endothelial v-ATPases for the process of tumor cell adhesion onto the endothelium. Thus, we were interested in the consequences of the inhibition of endothelial v-ATPase by archazolid on the interaction between endothelial and cancer cells. Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells .", "Various cell adhesion molecules on the endothelium, such as intercellular adhesion molecule 1 ICAM-1 , vascular cell adhesion protein VCAM-1 , E-selectin or N-cadherin as well as integrins expressed on cancer cells have been reported to mediate cell adhesion of cancer cells onto endothelial cells . Accordingly, we focused on these cell adhesion molecules and integrins. For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells.", "For the first time, our study revealed a link between the function of v-ATPases and the adhesion and transmigration properties of endothelial cells. CellTiter-Blue Cell Viability Assay Promega, Mannheim, Germany was performed according to the manufacturer's protocol for determining the cell viability of cells after treatment with archazolid. This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin.", "This assay is based on the ability of metabolically active cells to reduce resazurin which results in fluorescent resorufin. The CellTiter-Blue Reagent was added to the cells 4 h before the endpoint of treatment. Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission .", "Fluorescence was measured with an Infinite F200 pro microplate reader Tecan, Männedorf, Switzerland at 560 nm excitation and 590 nm emission . CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega was performed according to the manufacturer's instructions for determining the lactate dehydrogenase LDH release after treatment with archazolid. Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme.", "Lysis buffer was added to untreated cells 45 min before the end of treatment to induce the release of this enzyme. LDH is a cytosolic enzyme that is released by leaky cells. Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase.", "Released LDH catalyzes the enzymatic conversion of lactate to pyruvate which provides NADH for the conversion of iodonitrotetrazolium violet into a red formazan product in the presence of diaphorase. The absorbance was measured with a Varioskan Flash microplate reader Thermo Fisher Scientific at 490 nm. LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells.", "LysoTracker Red DND-99 Life Technologies, Thermo Fisher Scientific is a dye to measure pH values in viable cells. HUVECs were cultured to confluence on collagen G-coated μ-slides 80826, ibidi, Martinsried, Germany before they were treated with archazolid for 24 h. 1 μg/ ml Hoechst 33342 Sigma-Aldrich, Munich, Germany was used to visualize the nuclei and 50 nM LysoTracker Red DND-99 was used to visualize the acidic compartments which correspond to the lysosomes. Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany .", "Both dyes were incubated for 10 min at 37˚C before acquisition of single images by a Leica DMI6000 B fluorescence microscope Leica Microsystems, Wetzlar, Germany . HUVECs were seeded in collagen G-coated 24-well plates and grown to confluence for two days before treatment. The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C.", "The cells were incubated with indicated concentrations of archazolid for 24 h. Untreated MDA-MB-231 or PC-3 cells were labeled with CellTracker Green CMFDA Dye 5 μM in serum-free DMEM, 37˚C for 30 min before 100,000 cells per well were added to HUVECs and were allowed to adhere for various time points at 37˚C. Non-adherent tumor cells were washed off three times with PBS containing Ca 2+ and Mg 2+ . Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission .", "Tumor cell adhesion was determined by fluorescence measurements with an Infinite F200 pro microplate reader Tecan at 485 nm excitation and 535 nm emission . For blocking the integrin β1 subunit on MDA-MB-231 or PC-3 cells, CellTracker Greenlabeled MDA-MB-231 or PC-3 cells were incubated with an anti-integrin β1 antibody P5D2, ab24693, Abcam, Cambridge, United Kingdom at a concentration of 1 μg antibody per one million cells in 1 ml DMEM. Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM.", "Before adding to archazolid-treated HUVECs, MDA-MB-231 or PC-3 cells were washed once with DMEM. For blocking the integrin β1 subunit on HUVECs, the cells were incubated with the anti-integrin β1 antibody 0.1 μg/well in ECGM . HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs.", "HUVECs were washed once with ECGM before untreated MDA-MB-231 or PC-3 cells were added to HUVECs. For the adhesion of MDA-MB-231 or PC-3 cells onto extracellular matrix ECM components 24-well plates were coated with collagen G 10 μg/ml in PBS , human plasma fibronectin 10 μg/ml PBS or laminin-411 10 μg/ml in Dulbecco's PBS DPBS containing Ca 2+ and Mg 2+ at 4˚C overnight. The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C .", "The adhesion of MDA-MB-231 and PC-3 cells onto these three most prominent ECM components was carried out as described above 10 min adhesion at 37˚C . HUVECs were grown on a porous filter membrane Transwell insert, polycarbonate membrane, 8 μm pores; Corning, New York, USA for 48 h and were treated as indicated. Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA.", "Untreated MDA-MB-231 cells were labeled with CellTracker Green CMFDA Dye as described in the section cell adhesion assay and resuspended in medium 199 PAN-Biotech containing 0.1% BSA. HUVECs were washed twice with medium 199 containing 0.1% BSA before MDA-MB-231 cells were allowed to transmigrate through the endothelial monolayer for 24 h. Medium 199 containing 0.1% BSA was used as negative control and medium 199 containing 20% FCS was used as chemoattractant for transmigration in the lower compartment. Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab.", "Non-migrated cells remaining in the upper compartment were carefully removed using a cotton swab. Transmigrated cells were lysed in radioimmunoprecipitation assay RIPA buffer and transmigration was quantified by measuring the fluorescence signal at 485 nm excitation and 535 nm emission . HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα.", "HUVECs were grown to confluence on 6-well plates before they were treated with archazolid for 12 h. The cells were induced to upregulate the gene expression of cell adhesion molecules by TNFα. RNA was isolated using the RNeasy Mini Kit from Qiagen Hilden, Germany according to the manufacturer's protocol. On-column DNase digestion was performed to remove genomic DNA.", "On-column DNase digestion was performed to remove genomic DNA. RNA was transcribed into cDNA by Superscript II Life Technologies, Thermo Fisher Scientific . qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3.", "qPCR experiments were performed using a StepOnePlus System Applied Biosystems, Thermo Fisher Scientific and data was analyzed by the StepOne and Ste-pOnePlus Software v2.3. Power SYBR Green PCR Master Mix Life Technologies and the comparative C T quantitation method 2 -ΔΔCT were used. HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules.", "HUVECs were grown to confluence on 12-well plates before they were treated with archazolid for 24 h. Cells were treated with TNFα for 24 h to induce the expression of cell adhesion molecules. Subsequently, the cells were detached with HyClone HyQTase GE Healthcare, Freiburg, Germany . In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min.", "In the case of ICAM-1 the detached cells were fixed with 4% formaldehyde Polysciences, Hirschberg an der Bergstraße, Germany in PBS for 10 min and washed once with PBS before incubating with the fluorescein isothiocyanate FITC -labeled anti-human CD54 mouse, ICAM-1 antibody MCA1615F, Biozol, Eching, Germany at room temperature for 45 min. For all other proteins, the cells were not fixed and washed once with PBS before incubating with the antibodies phycoerythrin PE -labeled anti-human CD106 mouse, VCAM-1 , PE-labeled anti-human CD62E mouse, E-selectin and PE-labeled anti-human CD325 mouse, N-cadherin from Becton Dickinson on ice for 45 min. These antibodies were diluted in PBS containing 0.2% BSA.", "These antibodies were diluted in PBS containing 0.2% BSA. The surface expression of cell adhesion molecules was measured by flow cytometry FACSVerse, Becton Dickinson, Heidelberg, Germany . To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min.", "To stain the surface collagen on HUVECs, cells were incubated with an anti-human collagen antibody rabbit, 1:40, ab36064, Abcam on ice for 30 min. The staining procedure was performed on ice to ensure that surface proteins or antibodies are not endocytosed. The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth .", "The cells were washed once with PBS containing Ca 2+ and Mg 2+ before they were fixed with Roti-Histofix Carl Roth . Alexa Fluor 488-conjugated anti-rabbit antibody goat, 1:400, A11008, Life Technologies was used as secondary antibody and Hoechst 33342 1 μg/ml, Sigma-Aldrich was used to visualize nuclei. Confluent HUVECs in 6-well plates were treated as indicated.", "Confluent HUVECs in 6-well plates were treated as indicated. Cells were washed with ice-cold PBS and lysed with RIPA buffer supplemented with protease inhibitors Complete Mini EDTA-free; Roche, Mannheim, Germany , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride, β-glycerophosphate, sodium pyrophosphate and H 2 O 2 . Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific .", "Protein determination was performed using the Pierce BCA Protein Assay Kit Thermo Fisher Scientific . Equal amounts of proteins 10-20 μg were separated by sodium dodecyl sulfatepolyacrylamide gel electrophoresis SDS-PAGE; Bio-Rad Laboratories, Munich, Germany . Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection.", "Separated proteins were transferred onto polyvinylidene difluoride membranes by tank blotting Bio-Rad Laboratories for immunodetection. Membranes were blocked with 5% boltinggrade milk powder Carl Roth in TBS containing 0.1% Tween 20 Sigma-Aldrich . The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 .", "The following antibodies were used: mouse anti-human cathepsin B antibody IM27L, Merck 1:500 , mouse anti-β-actin-peroxidase antibody A3854, Sigma-Aldrich 1:100,000 and antimouse IgG horse radish peroxidase HRP -linked antibody 7076, Cell Signaling, Frankfurt, Germany 1:5,000 . ImageJ version 1.49m was used for densitometric analysis. Cathepsin B activity assay was performed as described in the publication by Kubisch et al.", "Cathepsin B activity assay was performed as described in the publication by Kubisch et al. . Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated.", ". Confluent HUVECs or HMEC-1 seeded in 6-well plates were treated as indicated. Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride.", "Cells were washed with PBS and lysed with the non-denaturating M-PER mammalian protein extraction reagent 78501, Thermo Fisher Scientific supplemented with protease inhibitors Complete Mini EDTA-free, Roche , sodium orthovanadate, sodium fluoride, phenylmethylsulphonyl fluoride. The fluorogenic cathepsin B substrate Z-Arg-Arg-7-amido-4-methylcoumarin hydrochloride C5429, Sigma-Aldrich was added to 30 μg of the cell lysate diluted in assay buffer supplemented with 2 mM L-cysteine C7880, Sigma-Aldrich and incubated for 30 min at 40˚C. Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific .", "Fluorescence was measured at 348 nm excitation and 440 nm emission with a microplate reader Varioskan Flash, Thermo Fisher Scientific . The intensity of the fluorescence signal corresponded to the cathepsin B enzyme activity. For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction.", "For background subtraction the cathepsin B inhibitor CA-074Me Enzo Life Sciences, Lörrach, Germany was added to an additional reaction. The HUVEC Nucleofector Kit Lonza, Cologne, Germany was used to transfect HUVECs. The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza .", "The transfection was performed according to the manufacturer's protocol using 2.5 μg plasmid DNA for 500,000 cells Nucleofector 2b Device, Lonza . 48 h after transfection the cells were treated for further experiments. The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe .", "The addgene plasmid #11249 hCathepsin B was kindly provided by Hyeryun Choe . hCathepsin B was digested with PmeI and XbaI and the linear DNA fragment not corresponding to the human CTSB gene was religated to generate the empty pcDNA3.1 - delta MCS plasmid that was used for control transfections. The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific.", "The original backbone of hCathepsin B is the pcDNA3.1 - from Thermo Fisher Scientific. The control vector pcDNA3.1 - delta MCS used for our transfections was cloned on the basis of hCathepsin B and is therefore lacking almost the whole part of the multiple cloning site of the pcDNA3.1 - . Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA .", "Statistical analyses were performed using GraphPad Prism 5.0 San Diego, USA . One-way ANOVA followed by Tukey's post-hoc test or unpaired t-test was used for the evaluation of a minimum of three independent experiments. The numbers of independently performed experiments n are stated in the corresponding figure legends. p 0.05 was considered as statistically significant.", "p 0.05 was considered as statistically significant. Data are expressed as mean ± standard error of the mean SEM . Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays.", "Since the v-ATPase inhibitor archazolid has never been used for studies in endothelial cells, we first performed cytotoxicity assays. We treated confluent HUVECs with up to 1 nM archazolid for 24 and 48 h and observed that this treatment has neither an influence on the metabolic activity nor on the release of LDH after 24 h Fig 1A and 1B, left panels . The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels .", "The metabolic activity and the release of LDH were only slightly affected by the highest concentration of archazolid after 48 h Fig 1A and 1B, right panels . Consequently, the following experiments were all carried out after 24 h or less of archazolid treatment in order to exclude any cytotoxic effects of archazolid within our experimental settings. Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors .", "Microscopic analysis revealed that also the integrity of the endothelial monolayer was not affected by archazolid, but the cells showed a slightly different morphology Fig 2A : Archazolid-treated cells were swollen compared to control cells, which was not unexpected, as vacuolation of the endoplasmic reticulum ER has been described for other cell types and is typical for v-ATPase inhibitors . This effect was obvious both in subconfluent and in confluent cells Fig 2A . Inhibition of v-ATPase prevents the acidification of lysosomes .", "Inhibition of v-ATPase prevents the acidification of lysosomes . Using the cell-permeable dye LysoTracker Red DND-99, it is possible to label the acidic lysosomes in living cells. Thus, this dye can serve as an indicator of v-ATPase inhibition.", "Thus, this dye can serve as an indicator of v-ATPase inhibition. To proof that archazolid is also functionally active as a v-ATPase inhibitor in HUVECs, cells were treated with 1 nM archazolid before they were incubated with LysoTracker Red DND-99 and Hoechst 33342. As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid.", "As shown in Fig 2B, the red vesicular staining corresponding to acidified lysosomes in control cells disappeared completely after treatment with archazolid. In summary, archazolid treatment for 24 h was not cytotoxic to quiescent HUVECs, but inhibited the functionality of the v-ATPase. We analyzed the adhesion of MDA-MB-231 cells onto HUVECs.", "We analyzed the adhesion of MDA-MB-231 cells onto HUVECs. Confluent HUVECs were treated with up to 1 nM archazolid for 24 h. Untreated MDA-MB-231 cells were labeled with Cell-Tracker Green CMFDA Dye. Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B .", "Interestingly, v-ATPase inhibition strongly increased the attachment of the metastatic breast carcinoma cell line MDA-MB-231 onto HUVECs after 10 and 120 min of adhesion Fig 3A and 3B . We also investigated the influence of archazolid on the transendothelial migration of MDA-MB-231 cells. HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells.", "HUVECs seeded in a Boyden chamber were treated with 1 nM archazolid for 24 h. CellTracker Green-labeled MDA-MB-231 cells not treated with archazolid were allowed to transmigrate through the endothelial monolayer for 24 h. As shown in Fig 3C, archazolid significantly decreased the transendothelial migration of MDA-MB-231 cells. The influence of archazolid on tumor cell adhesion was not only studied in HUVECs, which represent macrovascular endothelial cells, but also in microvascular HMEC-1 cells. Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line.", "Moreover, besides the breast cancer cell line MDA-MB-231, also PC-3 prostate cancer cells were used as a second metastatic cancer cell line. Archazolid treatment of endothelial cells increased the attachment of MDA-MB-231 cells onto the HMEC-1 monolayer after 120 min of adhesion Fig 4A and increased the attachment of PC-3 cells onto the HUVEC monolayer after 30 and 60 min of adhesion Fig 4B . Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig .", "Of note, the adhesion of non-metastatic Jurkat cells, an acute T cell leukemia cell line, remained unaffected after treatment of HUVECs with archazolid S1A Fig . Taken together, archazolid treatment augmented the adhesive properties of both micro-and macrovascular endothelial cells for metastatic tumor cells, but not for non-metastatic ones. Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion.", "Of note, cancer cell adhesion onto archazolid-activated endothelial cells increased with the time of adhesion. The adhesion of tumor cells onto the endothelium is in principle similar to that of leukocytes, but slightly differs in the molecules that mediate the adhesion process. Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction .", "Ligands for the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin were found to be expressed on tumor cells and to mediate tumor-endothelial cell interaction . Inhibition of the v-ATPase might affect the expression of endothelial cell adhesion molecules on mRNA or protein levels. To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control.", "To determine the mRNA expression of ICAM-1, VCAM-1, E-selectin and Ncadherin, HUVECs were treated with archazolid for 12 h. TNFα is known to upregulate the expression of ICAM-1, VCAM-1 and E-selectin and, thus, served as positive control. Quantitative real-time PCR showed that v-ATPase inhibition in HUVECs did not alter the mRNA levels of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5A . The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry.", "The protein expression of these adhesion molecules on the surface of endothelial cells was analyzed by flow cytometry. Archazolid 1 nM, 24 h did not affect the cell surface expression of ICAM-1, VCAM-1, E-selectin and N-cadherin Fig 5B . Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion .", "Besides ICAM-1, VCAM-1, E-selectin and N-cadherin, also integrins are able to mediate the process of cell adhesion . Since none of the cell adhesion molecules expressed on HUVECs were regulated upon archazolid treatment, we considered integrins as potential interaction partners. Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells .", "Within this protein family β1-integrins have been reported to mediate tumor cell adhesion onto quiescent endothelial cells . In order to elucidate the role of β1-integrins for the archazolid-induced tumor cell adhesion, the integrin β1-subunit was blocked either on MDA-MB-231 cells, PC-3 cells or on HUVECs. Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid.", "Of note, as in all experiments throughout this study, only endothelial cells were treated with archazolid. After blocking β1-integrins on MDA-MB-231 or PC-3 cells, the archazolid-induced tumor cell adhesion was reduced almost to control level Fig 6A and 6B , left panels , whereas blocking of β1-integrins on HUVECs had no significant effect on the increase of tumor cell adhesion by v-ATPase inhibition Fig 6A and 6B , right panels . Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin .", "Depending on their α subunit, β1-integrins have a variety of ligands including extracellular matrix ECM components such as collagen, fibronectin and laminin . Therefore, we hypothesized that archazolid treatment of endothelial cells might lead to an upregulation of these components. MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components.", "MDA-MB-231 and PC-3 cells were allowed to adhere onto plastic that was coated with these ECM components. This cell adhesion assay revealed that MDA-MB-231 as well as PC-3 cells favor the interaction with the ECM component collagen, as the adhesion onto collagen is much higher than onto the uncoated plastic control Fig 7A . MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating.", "MDA-MB-231 and PC-3 cells also adhered to fibronectin-coated plastic, but to a much lesser extent compared to the collagen coating. Therefore, we focused on the interaction between these two tumor cell lines and collagen. Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins.", "Blocking of the integrin β1 subunit on MDA-MB-231 and PC-3 cells clearly abolished the interaction with collagen Fig 7B , indicating that the attachment of these tumor cells to collagen is mediated by β1-integrins. Since collagen is the major ECM component MDA-MB-231 and PC-3 cells interact with, the next step was to prove whether v-ATPase inhibition influences the amount of collagen expressed by HUVECs as extracellular matrix. To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen.", "To detect collagen on the endothelial surface, archazolid-treated HUVECs were labeled with an antibody against collagen type I-IV on ice to prevent endocytosis and to ensure that the antibody does not bind to intracellular collagen. Interestingly, archazolid increased the amount of surface collagen on HUVECs by about 50% Fig 7C . Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig .", "Control stainings were performed using an antibody against the cytosolic p65 subunit of the transcription factor nuclear factor κB NFκB to show that intracellular proteins were not detected by this staining method S2 Fig . It was reported that v-ATPase inhibition by archazolid impairs the activity of cathepsin B , a lysosomal enzyme that degrades extracellular matrix components including collagen . As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B.", "As collagen is degraded by cathepsin B and the activation of cathepsin B depends on v-ATPase activity 28, 42 , we suggested that an accumulation of collagen on the surface of endothelial cells might be a consequence of an impaired functionality of cathepsin B. Therefore, an enzyme activity assay based on the proteolysis of a fluorogenic cathepsin B substrate was performed. In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin.", "In archazolid-treated HUVECs and HMEC-1 the activity of cathepsin B was induce both the mRNA 1 ng/ml TNF and the cell surface expression 10 ng/ml TNF of ICAM-1, VCAM-1, E-selectin and Ncadherin. Inhibition of endothelial vATPase increases tumor cell adhesion to endothelial cells strongly decreased by approximately 50% compared to control cells at an archazolid concentration of 1 nM Fig 8A . In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B .", "In line with this result, western blot analysis showed that archazolid 1 nM reduces the protein expression of the mature, active form of cathepsin B to less than 40% of the control in HUVECs Fig 8B . To proof whether the archazolid-induced tumor cell adhesion is a consequence of the decreased amount of cathepsin B, HUVECs were transfected with a plasmid coding for human cathepsin B or with the empty vector as control. After 48 h, the transfected cells were treated with 1 nM archazolid.", "After 48 h, the transfected cells were treated with 1 nM archazolid. The level of cathepsin B after transfection and treatment was assessed by western blot analysis Fig 9A . Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B .", "Overexpression of cathepsin B strongly diminished both the basal and the archazolid-induced adhesion of MDA-MB-231 cells Fig 9B . Targeting the proton pump v-ATPase for cancer therapy has gained great interest since its inhibition was reported to reduce the invasiveness of cancer cells and, most importantly, also metastasis . Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis .", "Thus, intensive research related to v-ATPases was done in cancer cells, whereas there are only few studies investigating v-ATPases in endothelial cells indicating a role in migration, proliferation and possibly angiogenesis . In the present study we used the myxobacterial natural product archazolid to investigate the consequences of v-ATPase inhibition in the endothelium on tumor-endothelial cell interactions. For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium.", "For the first time, we were able to show a link between v-ATPase and the adhesion and transmigration properties of the endothelium. Inhibition of the v-ATPase in endothelial cells by archazolid significantly increased the adhesion of metastatic cancer cells and decreased the transendothelial migration of cancer cells which was attributed to augmented collagen levels on the surface on archazolid-treated endothelial cells. Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected.", "Of note, adhesion of the non-metastatic Jurkat cell line onto archazolid-treated endothelial cells remained unaffected. The archazolidinduced adhesion of tumor cells was independent from the endothelial cell adhesion molecules ICAM-1, VCAM-1, E-selectin and N-cadherin, as their expression was not regulated by the compound. However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid.", "However, we found that the archazolid-induced tumor cell adhesion was mediated by β1-integrins expressed on MDA-MB-231 breast cancer and PC-3 prostate cancer cells as blocking of the integrin β1 subunit on these tumor cells reversed the pro-adhesive effect of archazolid. In adhesion experiments on plastic coated with extracellular matrix components, we could show that MDA-MB-231 and PC-3 cells clearly favored the interaction with collagen, whereas the adhesion of non-metastatic Jurkat cells was largely independent from extracellular matrix proteins S1B Fig . The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line.", "The different adhesion properties of metastatic cancer cells and Jurkat cells might be a result of the distinct integrin expression pattern of each cell line. MDA-MB-231 and PC-3 cells express α2β1-and α3β1-integrins, which represent collagen receptors , while Jurkat cells express α4β1-integrins but lack α2β1-, α3β1-integrins . α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 .", "α4β1integrins are receptors for VCAM-1 and fibronectin and it has been shown that Jurkat cells interact with human endothelial cells that express VCAM-1 after cytokine treatment or cells transfected with VCAM-1 . Our results are in line with previous studies showing that α2β1-and α3β1-integrin expressing MDA-MB-231 and PC-3 cells were able to rapidly attach to collagen in the cortical bone matrix. In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins.", "In contrast, Jurkat cells were not able to adhere and might preferentially interact with cell adhesion molecules rather than with ECM proteins. α2β1-and α3β1-integrins can additionally act as laminin receptors and at least α3β1integrins recognize fibronectin . Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components.", "Though expressing receptors for fibronectin and laminin, MDA-MB-231 and PC-3 cells adhered to fibronectin to a much lesser extent and did not adhere to laminin, probably due to lower affinities to these extracellular matrix components. Importantly, v-ATPase inhibition by archazolid increased the surface levels of the extracellular matrix component collagen, which might explain that the increase of MDA-MB-231 and PC-3 cells onto archazolid-treated HUVECs is independent of endothelial cell adhesion molecules. By performing a live cell proteolysis assay, Cavallo-Medved et al.", "By performing a live cell proteolysis assay, Cavallo-Medved et al. demonstrated ECM degradation, in particular of gelatin and collagen IV, in association with active cathepsin B in caveolae of endothelial cells during tube formation . In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells .", "In addition, recent studies reported that v-ATPase inhibition impairs the activity of cathepsin B in cancer cells . Therefore, we suggested that the accumulation of collagen on the endothelial surface might be a consequence of impaired cathepsin B activity or expression in endothelial cells. In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced.", "In fact, we confirmed the impairment of cathepsin B activity by archazolid as the expression levels of the mature active form of this enzyme was strongly reduced. Cathepsin B is synthesized as preprocathepsin B on membrane-bound ribosomes. Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides.", "Following transport to the Golgi apparatus, the preprocathepsin B is glycosylated with mannose-containing oligosaccharides. The targeting of procathepsin B to lysosomes is mannose-6-phosphate receptor-dependent and its dissociation from the receptor as well as its proteolytic processing into mature cathepsin B requires acidification of the compartment . In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B .", "In cancer cells v-ATPase inhibition by archazolid impaired the mannose-6-phosphate receptor-mediated trafficking from the trans-Golgi network to prelysosomal compartments resulting in a decrease of active lysosomal proteases like cathepsin B . We assumed that the archazolid-induced decrease in cathepsin B activity and expression was based on the same mechanism. Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B.", "Interestingly, overexpression of cathepsin B attenuated the archazolid-induced adhesion of breast cancer cells onto endothelial cells, indicating that the adhesion negatively correlates with the expression of cathepsin B. As cathepsin B can also degrade other extracellular matrix components such as fibronectin and laminin , v-ATPase inhibition could lead to an accumulation of these proteins and an increased adhesion of cells expressing fibronectin or laminin receptors. However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells.", "However, we did not focus on these ECM components since they were not relevant for the adhesion of MDA-MB-231 and PC-3 cells. These cells predominantly adhered to collagen, while the adhesion of Jurkat cells is mostly independent from the ECM proteins collagen, fibronectin or laminin S1B Fig . Interestingly .", "Interestingly . In hepatic cancer cells, archazolid reduces Ras/Raf/MEK/ERK signaling by altering the membrane composition and fluidity . We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells.", "We assume that archazolid affects endothelial cells in a similar way leading to inhibition of Ras signaling and, therefore, reduced transendothelial migration of MDA-MB-231 cells. Taken together, our study shows that archazolid reduces the activity and expression of cathepsin B in endothelial cells. As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected.", "As a result, the amount of collagen on the surface of endothelial cells was significantly upregulated, which finally resulted in an increased adhesion of the β1-integrin-expressing metastatic cancer cell lines MDA-MB-231 and PC-3 onto archazolidtreated endothelial cells, whereas the adhesion of non-metastatic Jurkat cells was unaffected. This study shows that the v-ATPase plays an important role in regulating the adhesion of cells expressing receptors for extracellular matrix components. Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells.", "Archazolid represents a promising tool to elucidate the role of v-ATPase in endothelial cells. Moreover, we for the first time linked the function of v-ATPase to the adhesion and transmigration of tumor cells onto endothelial cells as well as to the remodeling of the extracellular matrix on the surface of endothelial cells. The fact that the adhesion of metastatic tumor cells onto endothelial cells is increased while their transendothelial migration is reduced upon inhibition of endothelial v-ATPase by archazolid further supports the view of archazolid as a potential anti-metastatic compound." ]

[ "BACKGROUND: Gastroenteritis GE and respiratory tract infection RTI outbreaks are a significant issue in nursing homes. This study aimed to describe GE and RTI outbreaks with infection and all-cause lethality rates according to the individual characteristics of nursing home residents. METHODS: Clinical and virological surveillance were conducted 2007 to 2018 .", "METHODS: Clinical and virological surveillance were conducted 2007 to 2018 . Virus stratifications for the analysis were: outbreaks with positive norovirus or influenza identifications respectively NoV+ or Flu+ , episodes with no NoV or influenza identification or testing respectively NoV- or Flu- . Associations between individual variables sex, age, length of stay LOS , autonomy status and infection and lethality rates were tested with univariate and Mantel-Haenszel MH methods.", "Associations between individual variables sex, age, length of stay LOS , autonomy status and infection and lethality rates were tested with univariate and Mantel-Haenszel MH methods. RESULTS: 61 GE outbreaks and 76 RTI oubreaks total 137 outbreaks were recorded involving respectively 4309 and 5862 residents. In univariate analysis, higher infection rates and age were associated in NoV+, NoV-, and Flu+ contexts, and lower infection rates were associated with longer stays NoV+ and NoV- .", "In univariate analysis, higher infection rates and age were associated in NoV+, NoV-, and Flu+ contexts, and lower infection rates were associated with longer stays NoV+ and NoV- . In MH stratified analysis virus, sex female/male adjusted for LOS <4 or ≥4 years , the odds of being infected remained significant among older residents ≥86 years : NoV+/male Odds ratio OR MH : 1.64, 95% confidence interval CI : 1.16–2.30 and Flu+/female and male respectively OR MH : 1.50, CI: 1.27–1.79 and 1.73, CI: 1.28–2.33 . In univariate analysis, lower autonomy status NoV+, Flu+ and Flu- and increased age Flu+ were associated with higher lethality.", "In univariate analysis, lower autonomy status NoV+, Flu+ and Flu- and increased age Flu+ were associated with higher lethality. In MH adjusted analysis, significant OR age adjusted for autonomy was: Flu+/ ≥86 years compared with <86 years, 1.97 1.19–3.25 and OR autonomy adjusted for age for the more autonomous group compared with the less autonomous group was: Flu+, 0.41 0.24–0.69 ; Flu-, 0.42 0.20, 0.90 . CONCLUSION: The residents of nursing homes are increasingly elderly and dependent.", "CONCLUSION: The residents of nursing homes are increasingly elderly and dependent. The specific infection and lethality risks according to these two factors indicate that surveillance and infection control measures are essential and of high priority. Text: Introduction Gastroenteritis GE and respiratory tract infection RTI outbreaks represent a significant burden of illness in nursing homes.", "Text: Introduction Gastroenteritis GE and respiratory tract infection RTI outbreaks represent a significant burden of illness in nursing homes. Viruses cause the majority of these outbreaks, and noroviruses and influenza viruses are the most common pathogens . Previous studies have suggested that viral respiratory infections and norovirus outbreaks are a common cause of hospitalization or death, particularly among elderly individuals .", "Previous studies have suggested that viral respiratory infections and norovirus outbreaks are a common cause of hospitalization or death, particularly among elderly individuals . The impact of outbreaks has been described in terms of both frequency and epidemiology, but little is known about infection rates and all-cause lethality in GE and RTI nursing home outbreaks in relation to the individual characteristics of the residents . The residents of these institutions are increasingly elderly and dependent, and the impact of this trend on the seasonal outbreak burden requires in-depth investigation.", "The residents of these institutions are increasingly elderly and dependent, and the impact of this trend on the seasonal outbreak burden requires in-depth investigation. The results of studies focused on this issue could yield valuable information for nursing homes, allowing them to adapt their infection control strategies, in particular for improved assessment of infection risk. Our objective was to describe GE and RTI infection and all-cause lethality rates according to the individual characteristics of nursing home residents sex, age, length of stay, autonomy status , and to identify specific susceptibility patterns related to these types of viral outbreaks in these facilities.", "Our objective was to describe GE and RTI infection and all-cause lethality rates according to the individual characteristics of nursing home residents sex, age, length of stay, autonomy status , and to identify specific susceptibility patterns related to these types of viral outbreaks in these facilities. The present study explored outbreaks in 14 sites 28 units with geriatric nursing home activities for a total of 1121 beds caring for dependent people in southern Alsace an area in northeastern France . Data were collected between September 2007 and August 2018 .", "Data were collected between September 2007 and August 2018 . Each site was geographically independent and autonomous for social and care management. Units were located within the larger sites and were defined as a place having a dedicated team at one location. During outbreaks at one site, only the residents in the units with confirmed cases were included.", "During outbreaks at one site, only the residents in the units with confirmed cases were included. Outbreak inclusion depended on institutional alert to the hygiene team. Surveillance was done in each unit independently, and the members of staff had to inform a physician or charge nurse when two or more potential related cases of pneumonia or GE were observed within four days and when three or more cases were observed for other RTI.", "Surveillance was done in each unit independently, and the members of staff had to inform a physician or charge nurse when two or more potential related cases of pneumonia or GE were observed within four days and when three or more cases were observed for other RTI. Units also had to inform the hygiene team when these threshold values were exceeded. For influenza, the first suspected case led to a local alert and the hygiene team was contacted.", "For influenza, the first suspected case led to a local alert and the hygiene team was contacted. A practitioner from the hygiene team collected the information and evaluated the clinical signs, the virology information and the epidemiological context with the physician in the affected unit. The detected cluster was only put under surveillance if the hygiene team considered that there was a potential outbreak phenomenon.", "The detected cluster was only put under surveillance if the hygiene team considered that there was a potential outbreak phenomenon. The duration of 4 days was in relation with the national protocol with alert to the authorities when 5 cases occurred within 4 days . On a local level and in addition to the clusters reported to the authorities, clusters with at least 3 cases within a period of seven days in one unit could be recorded if they were reported to the hygiene team.", "On a local level and in addition to the clusters reported to the authorities, clusters with at least 3 cases within a period of seven days in one unit could be recorded if they were reported to the hygiene team. Because several outbreaks could potentially occur in the same unit during the surveillance period, a resident could be included repeatedly in different clusters. As a result, the observed patterns reflected the characteristics of an institutional population with longitudinal and pluriannual exposures.", "As a result, the observed patterns reflected the characteristics of an institutional population with longitudinal and pluriannual exposures. Personal information and clinical information was collected by a practitioner from the hygiene team directly from the residents' health care records. Personal information was collected for all those present the first day of the outbreak.", "Personal information was collected for all those present the first day of the outbreak. The collected information included: month and year of birth, sex, date of arrival at the nursing home and autonomy status. The autonomy status of residents in French nursing homes is assessed using the AGGIR scale Autonomy Gerontology Groups Iso-Resources , which is the legal instrument for evaluating dependency in the elderly and whose primary purpose is the allocation of means and resources .", "The autonomy status of residents in French nursing homes is assessed using the AGGIR scale Autonomy Gerontology Groups Iso-Resources , which is the legal instrument for evaluating dependency in the elderly and whose primary purpose is the allocation of means and resources . With the AGGIR scale, autonomy is classified into 6 Iso-Resource Groups GIR : GIR 1 bedridden or armchair-bound persons, mental functions seriously altered and requiring continuous presence , GIR 2 bedridden or armchair-bound persons, mental functions not totally altered and requiring assistance in most activities of daily living, or mental functions altered with preserved ability to get around , GIR 3 preserved mental autonomy with partially preserved motor autonomy and assistance several times a day for physical autonomy , GIR 4 moves around the home and sometimes assistance for washing, dressing, physical activities or eating , GIR 5 only occasional assistance for washing, meal preparation, and housework , GIR 6 autonomy for essential tasks of daily living . In outbreaks where the influenza virus was identified, influenza vaccination status and oseltamivir prescriptions were recorded as well.", "In outbreaks where the influenza virus was identified, influenza vaccination status and oseltamivir prescriptions were recorded as well. A file is transmitted in the Supporting Information with all previous data S1 Data . GE was defined as the sudden onset of vomiting and/or diarrhea over a 24 h period: i diarrhea �3 episodes, ii and/or vomiting �3 episodes, iii or diarrhea or vomiting <3 episodes with two or more other symptoms diarrhea, vomiting, stomach ache, abdominal cramps, nausea, fever, mucus in stools .", "GE was defined as the sudden onset of vomiting and/or diarrhea over a 24 h period: i diarrhea �3 episodes, ii and/or vomiting �3 episodes, iii or diarrhea or vomiting <3 episodes with two or more other symptoms diarrhea, vomiting, stomach ache, abdominal cramps, nausea, fever, mucus in stools . RTI presentation in older adults may be atypical, like for other acute illnesses in this age group . We used the recommended definitions for RTI surveillance in geriatric units, divided in 3 subcategories: i common cold syndromes or pharyngitis at least two of the following criteria: runny nose or sneezing, stuffy nose i.e.", "We used the recommended definitions for RTI surveillance in geriatric units, divided in 3 subcategories: i common cold syndromes or pharyngitis at least two of the following criteria: runny nose or sneezing, stuffy nose i.e. congestion , sore throat or hoarseness or difficulty swallowing, dry cough, swollen or tender glands in the neck cervical lymphadenopathy , ii influenza-like illness both the following criteria must be met: fever AND at least three other symptoms chills, new headache or eye pain, myalgia or body aches, malaise or loss of appetite, sore throat, new or increased dry cough and iii lower respiratory tract infection both of the following criteria must be met: at least two respiratory signs or symptoms new or increased cough, new/increased sputum production, O 2 saturation <94% or reduced >3% from baseline, abnormal lung examination new or changed , pleuritic chest pain, respiratory rate �25 breaths/min AND one or more constitutional signs/symptoms fever, leukocytosis, confusion, acute functional decline . Infection corresponding to one of these three subcategories was included in this study and classified as RTI.", "Infection corresponding to one of these three subcategories was included in this study and classified as RTI. For both infection types, the practitioner from the hygiene team obtained clinical information from the patient's health care records, and members of the health care team were consulted if necessary to complete any missing information. At the end of the episode within seven days after the last identified case , case inclusion as exposed and not infected ENI or exposed and infected EI was determined with a resident physician.", "At the end of the episode within seven days after the last identified case , case inclusion as exposed and not infected ENI or exposed and infected EI was determined with a resident physician. In order to study the lethality, the presence of each infected resident was evaluated once at least 56 days after the last case of each outbreak. Each resident was followed up retrospectively during eighth 7-day interval I n, n = 1 to 8, total 56 days, between the date of onset of symptoms and the fifty-sixth day of the studied period with three different possibilities: present alive and officially residing in the institution , lost to follow-up alive at the date of departure but no longer residing in the institution return home, transfer to another institution or death death recorded in the health care record .", "Each resident was followed up retrospectively during eighth 7-day interval I n, n = 1 to 8, total 56 days, between the date of onset of symptoms and the fifty-sixth day of the studied period with three different possibilities: present alive and officially residing in the institution , lost to follow-up alive at the date of departure but no longer residing in the institution return home, transfer to another institution or death death recorded in the health care record . The dates of death and lost to follow-up were recorded. Testing for the virus was not systematic and was decided by the physicians in each institution in the presence of clinical signs.", "Testing for the virus was not systematic and was decided by the physicians in each institution in the presence of clinical signs. For GE, stool samples were sent to the National Reference Centre for Gastroenteritis Viruses in Dijon for laboratory testing, as previously described . For RTI surveillance, rapid tests were used to identify the influenza virus.", "For RTI surveillance, rapid tests were used to identify the influenza virus. The rapid immunoassay diagnosis tests used for influenza detection were: Clearview1 Exact Influenza A and B Inverness Medical, Cologne, Germany from 2007 to 2014 and InfluenzaTop1 Alldiag, Strasbourg, France from 2014 to 2018. Given the low sensitivity of influenza rapid tests, they were no longer used once the control measures had been implemented and the influenza outbreak was under control.", "Given the low sensitivity of influenza rapid tests, they were no longer used once the control measures had been implemented and the influenza outbreak was under control. Samples were also occasionally sent to hospital laboratories or to the National Reference Centre for Influenza Viruses to detect viruses with real-time RT-PCR . Most testing targeted the norovirus NoV and influenza virus, but other tests were occasionally performed by the National Reference Centre for Influenza Viruses rhinovirus, respiratory syncytial virus, human metapneumovirus, parainfluenza 1, 2, 3 and 4, and coronavirus and the National Reference Centre for Enteric Viruses rotavirus, astrovirus, and adenovirus .", "Most testing targeted the norovirus NoV and influenza virus, but other tests were occasionally performed by the National Reference Centre for Influenza Viruses rhinovirus, respiratory syncytial virus, human metapneumovirus, parainfluenza 1, 2, 3 and 4, and coronavirus and the National Reference Centre for Enteric Viruses rotavirus, astrovirus, and adenovirus . Because testing for the viruses was variable from one institution/physician to another, not used in some outbreaks, types of virus sought and considering the poor sensitivity of the rapid influenza tests, these two sources of data were used to define the epidemiological context of confirmed outbreaks. Consequently, individual cases were included consistently in all episodes according to clinical signs and medical evaluation.", "Consequently, individual cases were included consistently in all episodes according to clinical signs and medical evaluation. When virus testing was negative, the clinical signs were recorded and medical evaluation was used as previously to classify the included residents as infected or not infected. The epidemiological context of each outbreak was defined according to whether the virus had been identified or not.", "The epidemiological context of each outbreak was defined according to whether the virus had been identified or not. One or more positive samples led to the qualification of a NoV NoV+ or flu Flu+ context. The other episodes were qualified as flu or NoV outbreaks with no specific identification or testing NoV-and Flu- .", "The other episodes were qualified as flu or NoV outbreaks with no specific identification or testing NoV-and Flu- . Flu and NoV contexts did not eliminate other potential enteric or respiratory pathogens. Sex, age, length of stay LOS, in years and autonomy status were described for all exposed residents.", "Sex, age, length of stay LOS, in years and autonomy status were described for all exposed residents. Influenza vaccination and oseltamivir administration rates were calculated for confirmed influenza outbreaks. Dichotomous or categorical variables were expressed as percentages.", "Dichotomous or categorical variables were expressed as percentages. In univariate analysis, the categories were specific in order to obtain a precise description of the age and LOS variables. Class intervals were 5 years for age and one year for LOS.", "Class intervals were 5 years for age and one year for LOS. The residents classified as GIR 4 to 6 sometimes, occasional and no assistance were grouped together because they were few. For the multi-level analysis with 2x2 tables, a median value was used to define the two-level age categories.", "For the multi-level analysis with 2x2 tables, a median value was used to define the two-level age categories. For LOS, assessing the longest stays was necessary to identify the effect of longer exposure in a nursing home. Consequently, a four-year cutoff was chosen to create the two categories.", "Consequently, a four-year cutoff was chosen to create the two categories. For autonomy, the two most dependent categories GIR � 2 were grouped together and compared with the more autonomous categories GIR � 3 . The outbreak epidemiological contexts were used with the four categories: NoV+, Flu+, NoV-and flu-.", "The outbreak epidemiological contexts were used with the four categories: NoV+, Flu+, NoV-and flu-. Other GE or RTI viruses were occasionally identified, but the number of results was too limited to develop separate analyses. However, all the results are available in the tables about the virus investigations along with NoV and influenza identifications.", "However, all the results are available in the tables about the virus investigations along with NoV and influenza identifications. For the different categories, infection rate EI/Exposed Residents ER , in percentage was calculated according to sex, age group, LOS and autonomy status. To investigate all-cause lethality and define the appropriate period for the 56-day monitoring D 1 to 56 , the all-cause lethality rate per 7-day interval LR n /I n, n = 1 to 8 was calculated: number of deaths during interval I n / EI alive the first day of n th studied interval minus lost to follow-up EI during the interval I n � 100 .", "To investigate all-cause lethality and define the appropriate period for the 56-day monitoring D 1 to 56 , the all-cause lethality rate per 7-day interval LR n /I n, n = 1 to 8 was calculated: number of deaths during interval I n / EI alive the first day of n th studied interval minus lost to follow-up EI during the interval I n � 100 . Seeing as successive clusters could occur within the same site, potentially influencing allcause lethality, the serial interval in days SI d was calculated. The SI d was the time period between the onset of symptoms of the last case in initial outbreak N and the onset of symptoms of the first case in the following outbreak N+1 .", "The SI d was the time period between the onset of symptoms of the last case in initial outbreak N and the onset of symptoms of the first case in the following outbreak N+1 . Investigations were performed when SI d was shorter or equal to the length of the previous D 1 to 56 and the following parameters were evaluated for these specific situations: number of episodes, residents infected in both outbreaks, and death among the identified individuals. Finally, according to the death rate and the impact of successive outbreaks, the number of 7-day intervals N.I n to take into account was defined, and the all-cause lethality rate was analyzed during these periods I 1 to N th .I n or D 1 to 7 � N .", "Finally, according to the death rate and the impact of successive outbreaks, the number of 7-day intervals N.I n to take into account was defined, and the all-cause lethality rate was analyzed during these periods I 1 to N th .I n or D 1 to 7 � N . All-cause lethality rates were calculated with the following formula: number of deaths from D 1 to 7 � N / EI number at D 1 minus lost to follow-up among EI during the period D 1 to 7 � N � 100 . Estimation of the turnover rate per 7-day interval among the infected residents was calculated on the base of the LOS median in years with the following formula: proportion of discharged residents: 50.0% in the case of the median / median LOS � 365 /7 .", "Estimation of the turnover rate per 7-day interval among the infected residents was calculated on the base of the LOS median in years with the following formula: proportion of discharged residents: 50.0% in the case of the median / median LOS � 365 /7 . The average rate of residents discharged per 7-day period was calculated: number of lost to follow up during the period D 1 to 7 � N /number of exposed and infected residents at D 1 /N 7-day interval � 100. As some residents were included in several outbreaks during the surveillance, the observations were not completely independent; non-parametric tests were used as a result.", "As some residents were included in several outbreaks during the surveillance, the observations were not completely independent; non-parametric tests were used as a result. In univariate analysis, Chi-square or Fisher exact tests expected number of frequencies fewer than 5 were used to compare infection and lethality rates according to the studied parameters and the odds ratio was calculated by median-unbiased estimation. The Kruskal-Wallis test was used to compare median values.", "The Kruskal-Wallis test was used to compare median values. Confidence intervals for medians were calculated with bootstrap methods. Covariate adjusted analyses were performed with two tables 2x2 . The respective impact of each individual factor was tested with Mantel-Haenszel chi-squared tests. The equality of the stratum odds ratios was tested with the Woolf test of homogeneity.", "The equality of the stratum odds ratios was tested with the Woolf test of homogeneity. Finally, for each virus context, multiple tables 2x2 were generated and tested with confounding variables, effect modifiers or covariables. Statistical analyses were done using R for Mas OS X version R 3.4.1 software with RStudio version 1.0.153.", "Statistical analyses were done using R for Mas OS X version R 3.4.1 software with RStudio version 1.0.153. A file is transmitted in the Supporting Information with all R codes and the packages used S1 R Codes . Differences were considered significant at p � 0.05.", "Differences were considered significant at p � 0.05. The French Data Protection Authority approved data collection and analysis DE-2013-074 and the local ethics committee Espace Local de Réflexion Ethique, Centre Hospitalier de Rouffach approved the study protocol ERLE-32 . According to the French law for biomedical research and human experimentation, individual written consent was not required from the patients or their relatives for data collection.", "According to the French law for biomedical research and human experimentation, individual written consent was not required from the patients or their relatives for data collection. Each year, the referring local practitioner of the study coordinated with the doctors working in the nursing home. At the beginning of the surveillance period, information regarding participation in the study was displayed in the family vising area, including a document about their right to access and rectify personal data.", "At the beginning of the surveillance period, information regarding participation in the study was displayed in the family vising area, including a document about their right to access and rectify personal data. After collection, data were rendered anonymous. No specific authorization was needed to retrospectively analyze anonymous data collected during routine care in the context of routine surveillance.", "No specific authorization was needed to retrospectively analyze anonymous data collected during routine care in the context of routine surveillance. A total of 137 outbreaks were recorded in the 14 sites. RTI outbreaks were more frequent than GE outbreaks 76 outbreaks and 5862 exposed residents vs. 61 outbreaks and 4309 exposed residents, respectively .", "RTI outbreaks were more frequent than GE outbreaks 76 outbreaks and 5862 exposed residents vs. 61 outbreaks and 4309 exposed residents, respectively . Overall, 7643 of the exposed residents were women and 2528 were men. The median age was 86.7 years old interquartile range: 81.1-91.0 years .", "The median age was 86.7 years old interquartile range: 81.1-91.0 years . Virus investigations respectively 389 samples for RTI and 143 for GE with all the detailed results in S1-S4 Tables confirmed a considerable number of norovirus-related GE outbreaks 34/61 and influenza-related RTI outbreaks 46/76 . For GE outbreaks, 2524 residents were in a NoV+ context versus 1785 in a NoV-context, and for RTI outbreaks, 3479 residents were in a Flu+ context versus 2383 in a Flu-context.", "For GE outbreaks, 2524 residents were in a NoV+ context versus 1785 in a NoV-context, and for RTI outbreaks, 3479 residents were in a Flu+ context versus 2383 in a Flu-context. For GE surveillance in the NoV+ context, there were 1093 EI residents versus 1431 ENI residents, whereas in the NoV-context, there were 583 EI residents versus 1202 ENI residents. Therefore, the infection rate was higher in the NoV+ context 43.3% than in the NoV-context 32.7%, odds ratio OR : 0.63, 95% confidence interval CI : 0.56-0.72 , p < 0.001 .", "Therefore, the infection rate was higher in the NoV+ context 43.3% than in the NoV-context 32.7%, odds ratio OR : 0.63, 95% confidence interval CI : 0.56-0.72 , p < 0.001 . For RTI surveillance, the rates of infection were similar with and without confirmed influenza: 31.5% N = 1095 EI residents /3479 exposed residents vs. 30.5% N = 728 EI residents/ 2383 exposed residents, OR: 0.96, CI: 0.85-1.07, p = 0.47 . Moreover, infection rate in the NoV + context was higher than the three other contexts: NoV- OR: 0.63, CI: 0.56-0.72 , Flu+ OR: 0.60, CI:0.54-0.67 and Flu- OR: 0.58, CI: 0.51-0.65 .", "Moreover, infection rate in the NoV + context was higher than the three other contexts: NoV- OR: 0.63, CI: 0.56-0.72 , Flu+ OR: 0.60, CI:0.54-0.67 and Flu- OR: 0.58, CI: 0.51-0.65 . In univariate analysis, certain individual characteristics were associated with significant variations in the infection rate S5 Table . The infection rate increased with age except in the Flucontext and, decreased with LOS during GE outbreaks.", "The infection rate increased with age except in the Flucontext and, decreased with LOS during GE outbreaks. The covariate adjusted analysis revealed specific significant effect modification according to sex NoV+ and LOS NoV- S6 Table . In analyses stratified according to virus and sex, age adjusted for LOS remained significant for Flu+ and NoV+ outbreaks males .", "In analyses stratified according to virus and sex, age adjusted for LOS remained significant for Flu+ and NoV+ outbreaks males . In NoV-context, the effect modification of LOS remained significant Table 1 . Finally, when autonomy was included and adjusted for age virus, sex, LOS stratification , the less autonomous residents female/LOS<4 years/age<86/ GIR 1-2 were affected more severely by Flu+ outbreaks with specific effect modification according to age S7 Table .", "Finally, when autonomy was included and adjusted for age virus, sex, LOS stratification , the less autonomous residents female/LOS<4 years/age<86/ GIR 1-2 were affected more severely by Flu+ outbreaks with specific effect modification according to age S7 Table . The study of lethality rates in infected residents over the 56 days after onset indicated that there were significant variations for RTI but no change for GE Table 2 . Significant differences appeared after 28 days in the context of Flu+ outbreaks and other RTI outbreaks.", "Significant differences appeared after 28 days in the context of Flu+ outbreaks and other RTI outbreaks. The analysis of successive or simultaneous clusters in the same institutions was performed when the time period between the onset of symptoms of the last case in outbreak N and the onset of symptoms of the first case in outbreak N+1 was �56 days S8 Table . 44 of the 137 outbreaks 32.12% were identified, and 194 of the 3499 exposed and infected residents contracted multiple infections.", "44 of the 137 outbreaks 32.12% were identified, and 194 of the 3499 exposed and infected residents contracted multiple infections. The percentage of exposed and infected residents implicated in more than one virus stratification was 11.09% 194 � 2 /3499 . Moreover, two deceased residents were included in the NoV-Na and Flu lethality analyses because death occurred within 56 days for both infections.", "Moreover, two deceased residents were included in the NoV-Na and Flu lethality analyses because death occurred within 56 days for both infections. The analysis of virus stratification of the 44 outbreaks showed the absence of successive clusters for the same category. The same analysis for the first four 7-day intervals Days 1 to 28 showed the respective values: 26 outbreaks 18.98% , 117 residents 6.69% 117 � 2 /3499 , one dead resident.", "The same analysis for the first four 7-day intervals Days 1 to 28 showed the respective values: 26 outbreaks 18.98% , 117 residents 6.69% 117 � 2 /3499 , one dead resident. Finally, according to the higher lethality impact during the first four 7-day intervals and to limit the impact of successive clusters in the same site, all cause lethality rates were studied according to individual parameters for the four 7 days intervals with the respective number of According to the surveillance type GE or RTI , the lethality rates differed significantly: 1.6% versus 3.4% respectively NoV+ and NoV-contexts, OR: 2.24, CI: 1.16-4.39, p = 0.02 and 8.3% versus 5.6% respectively Flu+ and Flu-, OR: 0.67, CI: 0.45-0.97, p = 0.04 . In univariate analysis S9 Table , low autonomy status in the NoV+, Flu+ and Flu-contexts was most significantly associated with increased all-cause lethality, and age was associated with higher lethality in the Flu+ context.", "In univariate analysis S9 Table , low autonomy status in the NoV+, Flu+ and Flu-contexts was most significantly associated with increased all-cause lethality, and age was associated with higher lethality in the Flu+ context. In the adjusted analysis, no significant statistical differences were identified in GE outbreaks. For RTI episodes, the adjusted analysis showed that autonomy had a significant impact when adjusted for sex, age or LOS Flu+ and Flu-NA and that age had a significant impact when adjusted for sex, autonomy or LOS Flu+ S10 Table .", "For RTI episodes, the adjusted analysis showed that autonomy had a significant impact when adjusted for sex, age or LOS Flu+ and Flu-NA and that age had a significant impact when adjusted for sex, autonomy or LOS Flu+ S10 Table . In Table 3 , the specific effects of age or autonomy were tested. Significant OR age adjusted for autonomy were: Flu+/age �86 years compared with the <86 group , 1.97 1.19-3.25 .", "Significant OR age adjusted for autonomy were: Flu+/age �86 years compared with the <86 group , 1.97 1.19-3.25 . OR autonomy adjusted for age were for GIR 3-6 compared with GIR 1-2 : Flu+, 0.41 0.24-0.69 ; Flu-, 0.42 0.20, 0.90 . Finally, despite the low number of residents and deaths per category, and consequently the limited robustness of the results, autonomy adjusted for age with stratification according to virus, sex and LOS showed that the effects were higher among subgroups of less autonomous residents female or male/LOS<4 years/GIR 1-2 in Flu+ outbreaks, and there was also higher mortality in the small subgroup of autonomous men with LOS � 4 years higher mortality S11 Table .", "Finally, despite the low number of residents and deaths per category, and consequently the limited robustness of the results, autonomy adjusted for age with stratification according to virus, sex and LOS showed that the effects were higher among subgroups of less autonomous residents female or male/LOS<4 years/GIR 1-2 in Flu+ outbreaks, and there was also higher mortality in the small subgroup of autonomous men with LOS � 4 years higher mortality S11 Table . In the Flu+ context, data regarding vaccination status and oseltamivir prescriptions were available but not used in this study. In the present study, surveillance data obtained during GE and RTI outbreaks in nursing homes were used to construct stratified analyses and to identify specific infection and all-cause lethality rates according to the residents' individual characteristics.", "In the present study, surveillance data obtained during GE and RTI outbreaks in nursing homes were used to construct stratified analyses and to identify specific infection and all-cause lethality rates according to the residents' individual characteristics. The infection rates observed here were similar to those found in previous studies of NoV and Influenza outbreaks odds of being infected during a Flu+ outbreak were around 40% less than during a NoV+ outbreak . Reported infection rates were close to 30.0% in influenza outbreaks and 40.0% in NoV outbreaks .", "Reported infection rates were close to 30.0% in influenza outbreaks and 40.0% in NoV outbreaks . Older age appeared to increase the likelihood of GE and influenza infection, with increasing rates among older residents. Age is a well-known factor for influenza and norovirus severity in the elderly and in nursing homes .", "Age is a well-known factor for influenza and norovirus severity in the elderly and in nursing homes . For NoV, the highest incidence estimates 5-year age strata was found in the �85 year-category approximately 800 men and for 1,400 women per 100,000 inhabitants . In our study, univariate analysis NoV+ showed that the odds of being infected were 1.5 to 1.6 times higher if a resident was older than 85.", "In our study, univariate analysis NoV+ showed that the odds of being infected were 1.5 to 1.6 times higher if a resident was older than 85. Moreover, an adjusted analysis of GE outbreaks highlighted different effects among subgroups of residents according to sex and LOS. Indeed, multiple and/or repeated exposure to GE viruses while institutionalized may lead to susceptibility or possible increased immunity in some residents .", "Indeed, multiple and/or repeated exposure to GE viruses while institutionalized may lead to susceptibility or possible increased immunity in some residents . For the sex variable, two factors could explain the effect: a possible selection bias with men reporting mild infections less than women particularly in the <86 years subgroup or that male susceptibility was different age, LOS, immunity,. .", ". . . A German study from 2013 also reported a greater impact in women . Moreover, when age analysis was stratified by sex and LOS, no Epidemic impacts in nursing homes significant impact was observed in women; the only significant differences were fewer infections in men in the <86-subgroup except in the NoV-with LOS <4 years .", "Moreover, when age analysis was stratified by sex and LOS, no Epidemic impacts in nursing homes significant impact was observed in women; the only significant differences were fewer infections in men in the <86-subgroup except in the NoV-with LOS <4 years . For the RTI outbreaks, sex and LOS variables did not have a significant effect. In residents older than 86, the odds of being infected in Flu+ context were 1.5 times higher for women and 1.7 for men.", "In residents older than 86, the odds of being infected in Flu+ context were 1.5 times higher for women and 1.7 for men. In univariate analysis, contrary to the other virus contexts where odds ratios were rarely above 2, residents over 95 years old had increased odds of infection of � 2.8 compared with the 70-year-old category, and for the 100 year-old group the odds were approximately 3.8. In the Flu+ context, autonomy adjusted for age virus, sex and LOS stratification revealed a possible increase in infection rates among less autonomous residents.", "In the Flu+ context, autonomy adjusted for age virus, sex and LOS stratification revealed a possible increase in infection rates among less autonomous residents. A previous study found that when elderly residents were exposed to the A H3N2 virus, there were higher rates of infection and reinfection, and more significant effects on the institution than with other influenza types/subtypes. In the community, the relative illness ratio RIR in the .", "In the community, the relative illness ratio RIR in the . The incidence of influenza infection and the associated risks were well described by age group, but the specific impact according to age was not studied. The results of this work highlighted the specific age distribution of influenza illnesses among the nursing home residents and the more significant impact among the older residents.", "The results of this work highlighted the specific age distribution of influenza illnesses among the nursing home residents and the more significant impact among the older residents. This specific susceptibility could be a critical factor in the institutional exposure and dissemination of influenza and could partly explain the high infection impact in the elderly institutional population. In this work, autonomy status was not the main factor associated with infection no significant impact in GE and in Flu-contexts .", "In this work, autonomy status was not the main factor associated with infection no significant impact in GE and in Flu-contexts . However, in Flu+ outbreaks, a high level of dependency was associated with a higher risk of falling ill. This observation implies that staff could play a role in the spread of infection highly dependent and less mobile residents are less likely to contaminate themselves or that the more active residents may be less fragile and/or have a greater involvement in the recommended infection control measures.", "This observation implies that staff could play a role in the spread of infection highly dependent and less mobile residents are less likely to contaminate themselves or that the more active residents may be less fragile and/or have a greater involvement in the recommended infection control measures. Finally, improving compliance with personal hygiene measures both for nursing staff and residents might be expected to have a beneficial effect on infection rates. Previous studies identified higher NoV infection rates in highly dependent individuals, but the results were not adjusted for age and LOS to take into account the potential correlation with the autonomy status .", "Previous studies identified higher NoV infection rates in highly dependent individuals, but the results were not adjusted for age and LOS to take into account the potential correlation with the autonomy status . Lethality is difficult to assess in nursing homes because death is frequent. Our GE and RTI episodes occurred during the winter seasons, and there are possible interactions between outbreaks and increased mortality at this time of the year .", "Our GE and RTI episodes occurred during the winter seasons, and there are possible interactions between outbreaks and increased mortality at this time of the year . The all-cause lethality rate of the infected residents in our study reflected global mortality including GE and RTI outbreaks and the global epidemiological context. Not surprisingly, a higher all-cause lethality rate was observed in the influenza contexts, as reported in previous studies .", "Not surprisingly, a higher all-cause lethality rate was observed in the influenza contexts, as reported in previous studies . Age and autonomy had similar effects in the different contexts, but in GE and to a lesser degree in Flu-outbreaks, the relatively small number of deaths could have limited the power of the statistical tests. In nursing homes, residents are generally discharged due to death.", "In nursing homes, residents are generally discharged due to death. The number of residents lost to follow up was low 0.14% in the first 28 days , so the 7-day interval turnover rate calculated on the base of the median LOS provides a good indication of the average case fatality rate. The lethality rate for NoV+ outbreaks was similar to the estimated 7-day interval turnover rate 1.6% indicating that this context had a limited impact on the death rate.", "The lethality rate for NoV+ outbreaks was similar to the estimated 7-day interval turnover rate 1.6% indicating that this context had a limited impact on the death rate. The all-cause lethality rate was most affected by age and autonomy. Both individual characteristics were significant in the Flu+ outbreaks, and autonomy adjusted for age was significant in the Flu-episodes.", "Both individual characteristics were significant in the Flu+ outbreaks, and autonomy adjusted for age was significant in the Flu-episodes. The influence of age on mortality in a context of influenza has already been described: a very high mortality rate 831/100,000 inhabitants was reported in persons 90 years of age and older compared with those aged 65-69 years 23/100,000 inhabitants . In our univariate analysis, the higher risk was observed in the �90 group whose risk of death was at least 2.6 higher than the <70 group.", "In our univariate analysis, the higher risk was observed in the �90 group whose risk of death was at least 2.6 higher than the <70 group. When adjusted for autonomy, the impact of age was not significant in more autonomous residents in the Flu+ context and not at all in the Flucontext. The opposite analysis autonomy adjusted for age showed higher global impact in the less autonomous group Flu- or only in the �86 age group Flu+ .", "The opposite analysis autonomy adjusted for age showed higher global impact in the less autonomous group Flu- or only in the �86 age group Flu+ . Age and autonomy are a reflection of resident's level of frailty. Clinical frailty scores were not used in this study, but in a previous study of patients with critical illness, they were associated with greater mortality, regardless of age .", "Clinical frailty scores were not used in this study, but in a previous study of patients with critical illness, they were associated with greater mortality, regardless of age . This suggests that in addition to age, autonomy can be a valuable indicator for the assessment of outbreak impact in outbreak surveillance. Other studies have suggested that age and certain comorbidities are independent risk factors for the influenza mortality rate or that mortality increase according to the number of risk factors .", "Other studies have suggested that age and certain comorbidities are independent risk factors for the influenza mortality rate or that mortality increase according to the number of risk factors . Comorbidities and underlying diseases of various severities could reflect overall frailty and consequently the risk of death. In nursing homes, information about autonomy and age are easier to collect and interpret than data on comorbidities.", "In nursing homes, information about autonomy and age are easier to collect and interpret than data on comorbidities. These various approaches should be evaluated and compared in the goal of optimizing risk assessment among nursing home residents. The present work has two main limitations.", "The present work has two main limitations. First, the virus information was incomplete limited identification, mainly influenza rapid tests for the RTI . Consequently, some episodes in the levels with no available identification may also have been associated with influenza or norovirus, and multiple contaminations could have been underestimated or not taken into account.", "Consequently, some episodes in the levels with no available identification may also have been associated with influenza or norovirus, and multiple contaminations could have been underestimated or not taken into account. Moreover, vaccination and oseltamivir prescriptions were recorded but not included because the influenza genotype was not determined and identification was limited. Secondly, the deaths of uninfected residents were not recorded in this protocol even though such data would have provided valuable information about the global epidemiological context.", "Secondly, the deaths of uninfected residents were not recorded in this protocol even though such data would have provided valuable information about the global epidemiological context. In conclusion, specific susceptibility patterns were observed among exposed residents. In this cohort of nursing homes, infection rates varied according to virus, sex, length of stay and age, and there were major differences in lethality depending on virus, age and autonomy score.", "In this cohort of nursing homes, infection rates varied according to virus, sex, length of stay and age, and there were major differences in lethality depending on virus, age and autonomy score. The collected data were easy to record and could be used to improve the characterization of seasonal outbreaks in nursing homes, whose residents are particularly vulnerable. Finally, as the average age and dependency level of residents continues to increase, subsequently increasing the risk of infection and death, health care staff will have to be increasingly vigilant during seasonal outbreaks and targeted interventions should be implemented.", "Finally, as the average age and dependency level of residents continues to increase, subsequently increasing the risk of infection and death, health care staff will have to be increasingly vigilant during seasonal outbreaks and targeted interventions should be implemented. Supporting information S1 Data. CSV S1 R Codes. R S1 Table. XLSX S10 Table.", "CSV S1 R Codes. R S1 Table. XLSX S10 Table. XLSX S11 Table. XLSX" ]

[ "BACKGROUND: Gastroenteritis GE and respiratory tract infection RTI outbreaks are a significant issue in nursing homes. This study aimed to describe GE and RTI outbreaks with infection and all-cause lethality rates according to the individual characteristics of nursing home residents. METHODS: Clinical and virological surveillance were conducted 2007 to 2018 .", "METHODS: Clinical and virological surveillance were conducted 2007 to 2018 . Virus stratifications for the analysis were: outbreaks with positive norovirus or influenza identifications respectively NoV+ or Flu+ , episodes with no NoV or influenza identification or testing respectively NoV- or Flu- . Associations between individual variables sex, age, length of stay LOS , autonomy status and infection and lethality rates were tested with univariate and Mantel-Haenszel MH methods.", "Associations between individual variables sex, age, length of stay LOS , autonomy status and infection and lethality rates were tested with univariate and Mantel-Haenszel MH methods. RESULTS: 61 GE outbreaks and 76 RTI oubreaks total 137 outbreaks were recorded involving respectively 4309 and 5862 residents. In univariate analysis, higher infection rates and age were associated in NoV+, NoV-, and Flu+ contexts, and lower infection rates were associated with longer stays NoV+ and NoV- .", "In univariate analysis, higher infection rates and age were associated in NoV+, NoV-, and Flu+ contexts, and lower infection rates were associated with longer stays NoV+ and NoV- . In MH stratified analysis virus, sex female/male adjusted for LOS <4 or ≥4 years , the odds of being infected remained significant among older residents ≥86 years : NoV+/male Odds ratio OR MH : 1.64, 95% confidence interval CI : 1.16–2.30 and Flu+/female and male respectively OR MH : 1.50, CI: 1.27–1.79 and 1.73, CI: 1.28–2.33 . In univariate analysis, lower autonomy status NoV+, Flu+ and Flu- and increased age Flu+ were associated with higher lethality.", "In univariate analysis, lower autonomy status NoV+, Flu+ and Flu- and increased age Flu+ were associated with higher lethality. In MH adjusted analysis, significant OR age adjusted for autonomy was: Flu+/ ≥86 years compared with <86 years, 1.97 1.19–3.25 and OR autonomy adjusted for age for the more autonomous group compared with the less autonomous group was: Flu+, 0.41 0.24–0.69 ; Flu-, 0.42 0.20, 0.90 . CONCLUSION: The residents of nursing homes are increasingly elderly and dependent.", "CONCLUSION: The residents of nursing homes are increasingly elderly and dependent. The specific infection and lethality risks according to these two factors indicate that surveillance and infection control measures are essential and of high priority. Text: Introduction Gastroenteritis GE and respiratory tract infection RTI outbreaks represent a significant burden of illness in nursing homes.", "Text: Introduction Gastroenteritis GE and respiratory tract infection RTI outbreaks represent a significant burden of illness in nursing homes. Viruses cause the majority of these outbreaks, and noroviruses and influenza viruses are the most common pathogens . Previous studies have suggested that viral respiratory infections and norovirus outbreaks are a common cause of hospitalization or death, particularly among elderly individuals .", "Previous studies have suggested that viral respiratory infections and norovirus outbreaks are a common cause of hospitalization or death, particularly among elderly individuals . The impact of outbreaks has been described in terms of both frequency and epidemiology, but little is known about infection rates and all-cause lethality in GE and RTI nursing home outbreaks in relation to the individual characteristics of the residents . The residents of these institutions are increasingly elderly and dependent, and the impact of this trend on the seasonal outbreak burden requires in-depth investigation.", "The residents of these institutions are increasingly elderly and dependent, and the impact of this trend on the seasonal outbreak burden requires in-depth investigation. The results of studies focused on this issue could yield valuable information for nursing homes, allowing them to adapt their infection control strategies, in particular for improved assessment of infection risk. Our objective was to describe GE and RTI infection and all-cause lethality rates according to the individual characteristics of nursing home residents sex, age, length of stay, autonomy status , and to identify specific susceptibility patterns related to these types of viral outbreaks in these facilities.", "Our objective was to describe GE and RTI infection and all-cause lethality rates according to the individual characteristics of nursing home residents sex, age, length of stay, autonomy status , and to identify specific susceptibility patterns related to these types of viral outbreaks in these facilities. The present study explored outbreaks in 14 sites 28 units with geriatric nursing home activities for a total of 1121 beds caring for dependent people in southern Alsace an area in northeastern France . Data were collected between September 2007 and August 2018 .", "Data were collected between September 2007 and August 2018 . Each site was geographically independent and autonomous for social and care management. Units were located within the larger sites and were defined as a place having a dedicated team at one location. During outbreaks at one site, only the residents in the units with confirmed cases were included.", "During outbreaks at one site, only the residents in the units with confirmed cases were included. Outbreak inclusion depended on institutional alert to the hygiene team. Surveillance was done in each unit independently, and the members of staff had to inform a physician or charge nurse when two or more potential related cases of pneumonia or GE were observed within four days and when three or more cases were observed for other RTI.", "Surveillance was done in each unit independently, and the members of staff had to inform a physician or charge nurse when two or more potential related cases of pneumonia or GE were observed within four days and when three or more cases were observed for other RTI. Units also had to inform the hygiene team when these threshold values were exceeded. For influenza, the first suspected case led to a local alert and the hygiene team was contacted.", "For influenza, the first suspected case led to a local alert and the hygiene team was contacted. A practitioner from the hygiene team collected the information and evaluated the clinical signs, the virology information and the epidemiological context with the physician in the affected unit. The detected cluster was only put under surveillance if the hygiene team considered that there was a potential outbreak phenomenon.", "The detected cluster was only put under surveillance if the hygiene team considered that there was a potential outbreak phenomenon. The duration of 4 days was in relation with the national protocol with alert to the authorities when 5 cases occurred within 4 days . On a local level and in addition to the clusters reported to the authorities, clusters with at least 3 cases within a period of seven days in one unit could be recorded if they were reported to the hygiene team.", "On a local level and in addition to the clusters reported to the authorities, clusters with at least 3 cases within a period of seven days in one unit could be recorded if they were reported to the hygiene team. Because several outbreaks could potentially occur in the same unit during the surveillance period, a resident could be included repeatedly in different clusters. As a result, the observed patterns reflected the characteristics of an institutional population with longitudinal and pluriannual exposures.", "As a result, the observed patterns reflected the characteristics of an institutional population with longitudinal and pluriannual exposures. Personal information and clinical information was collected by a practitioner from the hygiene team directly from the residents' health care records. Personal information was collected for all those present the first day of the outbreak.", "Personal information was collected for all those present the first day of the outbreak. The collected information included: month and year of birth, sex, date of arrival at the nursing home and autonomy status. The autonomy status of residents in French nursing homes is assessed using the AGGIR scale Autonomy Gerontology Groups Iso-Resources , which is the legal instrument for evaluating dependency in the elderly and whose primary purpose is the allocation of means and resources .", "The autonomy status of residents in French nursing homes is assessed using the AGGIR scale Autonomy Gerontology Groups Iso-Resources , which is the legal instrument for evaluating dependency in the elderly and whose primary purpose is the allocation of means and resources . With the AGGIR scale, autonomy is classified into 6 Iso-Resource Groups GIR : GIR 1 bedridden or armchair-bound persons, mental functions seriously altered and requiring continuous presence , GIR 2 bedridden or armchair-bound persons, mental functions not totally altered and requiring assistance in most activities of daily living, or mental functions altered with preserved ability to get around , GIR 3 preserved mental autonomy with partially preserved motor autonomy and assistance several times a day for physical autonomy , GIR 4 moves around the home and sometimes assistance for washing, dressing, physical activities or eating , GIR 5 only occasional assistance for washing, meal preparation, and housework , GIR 6 autonomy for essential tasks of daily living . In outbreaks where the influenza virus was identified, influenza vaccination status and oseltamivir prescriptions were recorded as well.", "In outbreaks where the influenza virus was identified, influenza vaccination status and oseltamivir prescriptions were recorded as well. A file is transmitted in the Supporting Information with all previous data S1 Data . GE was defined as the sudden onset of vomiting and/or diarrhea over a 24 h period: i diarrhea �3 episodes, ii and/or vomiting �3 episodes, iii or diarrhea or vomiting <3 episodes with two or more other symptoms diarrhea, vomiting, stomach ache, abdominal cramps, nausea, fever, mucus in stools .", "GE was defined as the sudden onset of vomiting and/or diarrhea over a 24 h period: i diarrhea �3 episodes, ii and/or vomiting �3 episodes, iii or diarrhea or vomiting <3 episodes with two or more other symptoms diarrhea, vomiting, stomach ache, abdominal cramps, nausea, fever, mucus in stools . RTI presentation in older adults may be atypical, like for other acute illnesses in this age group . We used the recommended definitions for RTI surveillance in geriatric units, divided in 3 subcategories: i common cold syndromes or pharyngitis at least two of the following criteria: runny nose or sneezing, stuffy nose i.e.", "We used the recommended definitions for RTI surveillance in geriatric units, divided in 3 subcategories: i common cold syndromes or pharyngitis at least two of the following criteria: runny nose or sneezing, stuffy nose i.e. congestion , sore throat or hoarseness or difficulty swallowing, dry cough, swollen or tender glands in the neck cervical lymphadenopathy , ii influenza-like illness both the following criteria must be met: fever AND at least three other symptoms chills, new headache or eye pain, myalgia or body aches, malaise or loss of appetite, sore throat, new or increased dry cough and iii lower respiratory tract infection both of the following criteria must be met: at least two respiratory signs or symptoms new or increased cough, new/increased sputum production, O 2 saturation <94% or reduced >3% from baseline, abnormal lung examination new or changed , pleuritic chest pain, respiratory rate �25 breaths/min AND one or more constitutional signs/symptoms fever, leukocytosis, confusion, acute functional decline . Infection corresponding to one of these three subcategories was included in this study and classified as RTI.", "Infection corresponding to one of these three subcategories was included in this study and classified as RTI. For both infection types, the practitioner from the hygiene team obtained clinical information from the patient's health care records, and members of the health care team were consulted if necessary to complete any missing information. At the end of the episode within seven days after the last identified case , case inclusion as exposed and not infected ENI or exposed and infected EI was determined with a resident physician.", "At the end of the episode within seven days after the last identified case , case inclusion as exposed and not infected ENI or exposed and infected EI was determined with a resident physician. In order to study the lethality, the presence of each infected resident was evaluated once at least 56 days after the last case of each outbreak. Each resident was followed up retrospectively during eighth 7-day interval I n, n = 1 to 8, total 56 days, between the date of onset of symptoms and the fifty-sixth day of the studied period with three different possibilities: present alive and officially residing in the institution , lost to follow-up alive at the date of departure but no longer residing in the institution return home, transfer to another institution or death death recorded in the health care record .", "Each resident was followed up retrospectively during eighth 7-day interval I n, n = 1 to 8, total 56 days, between the date of onset of symptoms and the fifty-sixth day of the studied period with three different possibilities: present alive and officially residing in the institution , lost to follow-up alive at the date of departure but no longer residing in the institution return home, transfer to another institution or death death recorded in the health care record . The dates of death and lost to follow-up were recorded. Testing for the virus was not systematic and was decided by the physicians in each institution in the presence of clinical signs.", "Testing for the virus was not systematic and was decided by the physicians in each institution in the presence of clinical signs. For GE, stool samples were sent to the National Reference Centre for Gastroenteritis Viruses in Dijon for laboratory testing, as previously described . For RTI surveillance, rapid tests were used to identify the influenza virus.", "For RTI surveillance, rapid tests were used to identify the influenza virus. The rapid immunoassay diagnosis tests used for influenza detection were: Clearview1 Exact Influenza A and B Inverness Medical, Cologne, Germany from 2007 to 2014 and InfluenzaTop1 Alldiag, Strasbourg, France from 2014 to 2018. Given the low sensitivity of influenza rapid tests, they were no longer used once the control measures had been implemented and the influenza outbreak was under control.", "Given the low sensitivity of influenza rapid tests, they were no longer used once the control measures had been implemented and the influenza outbreak was under control. Samples were also occasionally sent to hospital laboratories or to the National Reference Centre for Influenza Viruses to detect viruses with real-time RT-PCR . Most testing targeted the norovirus NoV and influenza virus, but other tests were occasionally performed by the National Reference Centre for Influenza Viruses rhinovirus, respiratory syncytial virus, human metapneumovirus, parainfluenza 1, 2, 3 and 4, and coronavirus and the National Reference Centre for Enteric Viruses rotavirus, astrovirus, and adenovirus .", "Most testing targeted the norovirus NoV and influenza virus, but other tests were occasionally performed by the National Reference Centre for Influenza Viruses rhinovirus, respiratory syncytial virus, human metapneumovirus, parainfluenza 1, 2, 3 and 4, and coronavirus and the National Reference Centre for Enteric Viruses rotavirus, astrovirus, and adenovirus . Because testing for the viruses was variable from one institution/physician to another, not used in some outbreaks, types of virus sought and considering the poor sensitivity of the rapid influenza tests, these two sources of data were used to define the epidemiological context of confirmed outbreaks. Consequently, individual cases were included consistently in all episodes according to clinical signs and medical evaluation.", "Consequently, individual cases were included consistently in all episodes according to clinical signs and medical evaluation. When virus testing was negative, the clinical signs were recorded and medical evaluation was used as previously to classify the included residents as infected or not infected. The epidemiological context of each outbreak was defined according to whether the virus had been identified or not.", "The epidemiological context of each outbreak was defined according to whether the virus had been identified or not. One or more positive samples led to the qualification of a NoV NoV+ or flu Flu+ context. The other episodes were qualified as flu or NoV outbreaks with no specific identification or testing NoV-and Flu- .", "The other episodes were qualified as flu or NoV outbreaks with no specific identification or testing NoV-and Flu- . Flu and NoV contexts did not eliminate other potential enteric or respiratory pathogens. Sex, age, length of stay LOS, in years and autonomy status were described for all exposed residents.", "Sex, age, length of stay LOS, in years and autonomy status were described for all exposed residents. Influenza vaccination and oseltamivir administration rates were calculated for confirmed influenza outbreaks. Dichotomous or categorical variables were expressed as percentages.", "Dichotomous or categorical variables were expressed as percentages. In univariate analysis, the categories were specific in order to obtain a precise description of the age and LOS variables. Class intervals were 5 years for age and one year for LOS.", "Class intervals were 5 years for age and one year for LOS. The residents classified as GIR 4 to 6 sometimes, occasional and no assistance were grouped together because they were few. For the multi-level analysis with 2x2 tables, a median value was used to define the two-level age categories.", "For the multi-level analysis with 2x2 tables, a median value was used to define the two-level age categories. For LOS, assessing the longest stays was necessary to identify the effect of longer exposure in a nursing home. Consequently, a four-year cutoff was chosen to create the two categories.", "Consequently, a four-year cutoff was chosen to create the two categories. For autonomy, the two most dependent categories GIR � 2 were grouped together and compared with the more autonomous categories GIR � 3 . The outbreak epidemiological contexts were used with the four categories: NoV+, Flu+, NoV-and flu-.", "The outbreak epidemiological contexts were used with the four categories: NoV+, Flu+, NoV-and flu-. Other GE or RTI viruses were occasionally identified, but the number of results was too limited to develop separate analyses. However, all the results are available in the tables about the virus investigations along with NoV and influenza identifications.", "However, all the results are available in the tables about the virus investigations along with NoV and influenza identifications. For the different categories, infection rate EI/Exposed Residents ER , in percentage was calculated according to sex, age group, LOS and autonomy status. To investigate all-cause lethality and define the appropriate period for the 56-day monitoring D 1 to 56 , the all-cause lethality rate per 7-day interval LR n /I n, n = 1 to 8 was calculated: number of deaths during interval I n / EI alive the first day of n th studied interval minus lost to follow-up EI during the interval I n � 100 .", "To investigate all-cause lethality and define the appropriate period for the 56-day monitoring D 1 to 56 , the all-cause lethality rate per 7-day interval LR n /I n, n = 1 to 8 was calculated: number of deaths during interval I n / EI alive the first day of n th studied interval minus lost to follow-up EI during the interval I n � 100 . Seeing as successive clusters could occur within the same site, potentially influencing allcause lethality, the serial interval in days SI d was calculated. The SI d was the time period between the onset of symptoms of the last case in initial outbreak N and the onset of symptoms of the first case in the following outbreak N+1 .", "The SI d was the time period between the onset of symptoms of the last case in initial outbreak N and the onset of symptoms of the first case in the following outbreak N+1 . Investigations were performed when SI d was shorter or equal to the length of the previous D 1 to 56 and the following parameters were evaluated for these specific situations: number of episodes, residents infected in both outbreaks, and death among the identified individuals. Finally, according to the death rate and the impact of successive outbreaks, the number of 7-day intervals N.I n to take into account was defined, and the all-cause lethality rate was analyzed during these periods I 1 to N th .I n or D 1 to 7 � N .", "Finally, according to the death rate and the impact of successive outbreaks, the number of 7-day intervals N.I n to take into account was defined, and the all-cause lethality rate was analyzed during these periods I 1 to N th .I n or D 1 to 7 � N . All-cause lethality rates were calculated with the following formula: number of deaths from D 1 to 7 � N / EI number at D 1 minus lost to follow-up among EI during the period D 1 to 7 � N � 100 . Estimation of the turnover rate per 7-day interval among the infected residents was calculated on the base of the LOS median in years with the following formula: proportion of discharged residents: 50.0% in the case of the median / median LOS � 365 /7 .", "Estimation of the turnover rate per 7-day interval among the infected residents was calculated on the base of the LOS median in years with the following formula: proportion of discharged residents: 50.0% in the case of the median / median LOS � 365 /7 . The average rate of residents discharged per 7-day period was calculated: number of lost to follow up during the period D 1 to 7 � N /number of exposed and infected residents at D 1 /N 7-day interval � 100. As some residents were included in several outbreaks during the surveillance, the observations were not completely independent; non-parametric tests were used as a result.", "As some residents were included in several outbreaks during the surveillance, the observations were not completely independent; non-parametric tests were used as a result. In univariate analysis, Chi-square or Fisher exact tests expected number of frequencies fewer than 5 were used to compare infection and lethality rates according to the studied parameters and the odds ratio was calculated by median-unbiased estimation. The Kruskal-Wallis test was used to compare median values.", "The Kruskal-Wallis test was used to compare median values. Confidence intervals for medians were calculated with bootstrap methods. Covariate adjusted analyses were performed with two tables 2x2 . The respective impact of each individual factor was tested with Mantel-Haenszel chi-squared tests. The equality of the stratum odds ratios was tested with the Woolf test of homogeneity.", "The equality of the stratum odds ratios was tested with the Woolf test of homogeneity. Finally, for each virus context, multiple tables 2x2 were generated and tested with confounding variables, effect modifiers or covariables. Statistical analyses were done using R for Mas OS X version R 3.4.1 software with RStudio version 1.0.153.", "Statistical analyses were done using R for Mas OS X version R 3.4.1 software with RStudio version 1.0.153. A file is transmitted in the Supporting Information with all R codes and the packages used S1 R Codes . Differences were considered significant at p � 0.05.", "Differences were considered significant at p � 0.05. The French Data Protection Authority approved data collection and analysis DE-2013-074 and the local ethics committee Espace Local de Réflexion Ethique, Centre Hospitalier de Rouffach approved the study protocol ERLE-32 . According to the French law for biomedical research and human experimentation, individual written consent was not required from the patients or their relatives for data collection.", "According to the French law for biomedical research and human experimentation, individual written consent was not required from the patients or their relatives for data collection. Each year, the referring local practitioner of the study coordinated with the doctors working in the nursing home. At the beginning of the surveillance period, information regarding participation in the study was displayed in the family vising area, including a document about their right to access and rectify personal data.", "At the beginning of the surveillance period, information regarding participation in the study was displayed in the family vising area, including a document about their right to access and rectify personal data. After collection, data were rendered anonymous. No specific authorization was needed to retrospectively analyze anonymous data collected during routine care in the context of routine surveillance.", "No specific authorization was needed to retrospectively analyze anonymous data collected during routine care in the context of routine surveillance. A total of 137 outbreaks were recorded in the 14 sites. RTI outbreaks were more frequent than GE outbreaks 76 outbreaks and 5862 exposed residents vs. 61 outbreaks and 4309 exposed residents, respectively .", "RTI outbreaks were more frequent than GE outbreaks 76 outbreaks and 5862 exposed residents vs. 61 outbreaks and 4309 exposed residents, respectively . Overall, 7643 of the exposed residents were women and 2528 were men. The median age was 86.7 years old interquartile range: 81.1-91.0 years .", "The median age was 86.7 years old interquartile range: 81.1-91.0 years . Virus investigations respectively 389 samples for RTI and 143 for GE with all the detailed results in S1-S4 Tables confirmed a considerable number of norovirus-related GE outbreaks 34/61 and influenza-related RTI outbreaks 46/76 . For GE outbreaks, 2524 residents were in a NoV+ context versus 1785 in a NoV-context, and for RTI outbreaks, 3479 residents were in a Flu+ context versus 2383 in a Flu-context.", "For GE outbreaks, 2524 residents were in a NoV+ context versus 1785 in a NoV-context, and for RTI outbreaks, 3479 residents were in a Flu+ context versus 2383 in a Flu-context. For GE surveillance in the NoV+ context, there were 1093 EI residents versus 1431 ENI residents, whereas in the NoV-context, there were 583 EI residents versus 1202 ENI residents. Therefore, the infection rate was higher in the NoV+ context 43.3% than in the NoV-context 32.7%, odds ratio OR : 0.63, 95% confidence interval CI : 0.56-0.72 , p < 0.001 .", "Therefore, the infection rate was higher in the NoV+ context 43.3% than in the NoV-context 32.7%, odds ratio OR : 0.63, 95% confidence interval CI : 0.56-0.72 , p < 0.001 . For RTI surveillance, the rates of infection were similar with and without confirmed influenza: 31.5% N = 1095 EI residents /3479 exposed residents vs. 30.5% N = 728 EI residents/ 2383 exposed residents, OR: 0.96, CI: 0.85-1.07, p = 0.47 . Moreover, infection rate in the NoV + context was higher than the three other contexts: NoV- OR: 0.63, CI: 0.56-0.72 , Flu+ OR: 0.60, CI:0.54-0.67 and Flu- OR: 0.58, CI: 0.51-0.65 .", "Moreover, infection rate in the NoV + context was higher than the three other contexts: NoV- OR: 0.63, CI: 0.56-0.72 , Flu+ OR: 0.60, CI:0.54-0.67 and Flu- OR: 0.58, CI: 0.51-0.65 . In univariate analysis, certain individual characteristics were associated with significant variations in the infection rate S5 Table . The infection rate increased with age except in the Flucontext and, decreased with LOS during GE outbreaks.", "The infection rate increased with age except in the Flucontext and, decreased with LOS during GE outbreaks. The covariate adjusted analysis revealed specific significant effect modification according to sex NoV+ and LOS NoV- S6 Table . In analyses stratified according to virus and sex, age adjusted for LOS remained significant for Flu+ and NoV+ outbreaks males .", "In analyses stratified according to virus and sex, age adjusted for LOS remained significant for Flu+ and NoV+ outbreaks males . In NoV-context, the effect modification of LOS remained significant Table 1 . Finally, when autonomy was included and adjusted for age virus, sex, LOS stratification , the less autonomous residents female/LOS<4 years/age<86/ GIR 1-2 were affected more severely by Flu+ outbreaks with specific effect modification according to age S7 Table .", "Finally, when autonomy was included and adjusted for age virus, sex, LOS stratification , the less autonomous residents female/LOS<4 years/age<86/ GIR 1-2 were affected more severely by Flu+ outbreaks with specific effect modification according to age S7 Table . The study of lethality rates in infected residents over the 56 days after onset indicated that there were significant variations for RTI but no change for GE Table 2 . Significant differences appeared after 28 days in the context of Flu+ outbreaks and other RTI outbreaks.", "Significant differences appeared after 28 days in the context of Flu+ outbreaks and other RTI outbreaks. The analysis of successive or simultaneous clusters in the same institutions was performed when the time period between the onset of symptoms of the last case in outbreak N and the onset of symptoms of the first case in outbreak N+1 was �56 days S8 Table . 44 of the 137 outbreaks 32.12% were identified, and 194 of the 3499 exposed and infected residents contracted multiple infections.", "44 of the 137 outbreaks 32.12% were identified, and 194 of the 3499 exposed and infected residents contracted multiple infections. The percentage of exposed and infected residents implicated in more than one virus stratification was 11.09% 194 � 2 /3499 . Moreover, two deceased residents were included in the NoV-Na and Flu lethality analyses because death occurred within 56 days for both infections.", "Moreover, two deceased residents were included in the NoV-Na and Flu lethality analyses because death occurred within 56 days for both infections. The analysis of virus stratification of the 44 outbreaks showed the absence of successive clusters for the same category. The same analysis for the first four 7-day intervals Days 1 to 28 showed the respective values: 26 outbreaks 18.98% , 117 residents 6.69% 117 � 2 /3499 , one dead resident.", "The same analysis for the first four 7-day intervals Days 1 to 28 showed the respective values: 26 outbreaks 18.98% , 117 residents 6.69% 117 � 2 /3499 , one dead resident. Finally, according to the higher lethality impact during the first four 7-day intervals and to limit the impact of successive clusters in the same site, all cause lethality rates were studied according to individual parameters for the four 7 days intervals with the respective number of According to the surveillance type GE or RTI , the lethality rates differed significantly: 1.6% versus 3.4% respectively NoV+ and NoV-contexts, OR: 2.24, CI: 1.16-4.39, p = 0.02 and 8.3% versus 5.6% respectively Flu+ and Flu-, OR: 0.67, CI: 0.45-0.97, p = 0.04 . In univariate analysis S9 Table , low autonomy status in the NoV+, Flu+ and Flu-contexts was most significantly associated with increased all-cause lethality, and age was associated with higher lethality in the Flu+ context.", "In univariate analysis S9 Table , low autonomy status in the NoV+, Flu+ and Flu-contexts was most significantly associated with increased all-cause lethality, and age was associated with higher lethality in the Flu+ context. In the adjusted analysis, no significant statistical differences were identified in GE outbreaks. For RTI episodes, the adjusted analysis showed that autonomy had a significant impact when adjusted for sex, age or LOS Flu+ and Flu-NA and that age had a significant impact when adjusted for sex, autonomy or LOS Flu+ S10 Table .", "For RTI episodes, the adjusted analysis showed that autonomy had a significant impact when adjusted for sex, age or LOS Flu+ and Flu-NA and that age had a significant impact when adjusted for sex, autonomy or LOS Flu+ S10 Table . In Table 3 , the specific effects of age or autonomy were tested. Significant OR age adjusted for autonomy were: Flu+/age �86 years compared with the <86 group , 1.97 1.19-3.25 .", "Significant OR age adjusted for autonomy were: Flu+/age �86 years compared with the <86 group , 1.97 1.19-3.25 . OR autonomy adjusted for age were for GIR 3-6 compared with GIR 1-2 : Flu+, 0.41 0.24-0.69 ; Flu-, 0.42 0.20, 0.90 . Finally, despite the low number of residents and deaths per category, and consequently the limited robustness of the results, autonomy adjusted for age with stratification according to virus, sex and LOS showed that the effects were higher among subgroups of less autonomous residents female or male/LOS<4 years/GIR 1-2 in Flu+ outbreaks, and there was also higher mortality in the small subgroup of autonomous men with LOS � 4 years higher mortality S11 Table .", "Finally, despite the low number of residents and deaths per category, and consequently the limited robustness of the results, autonomy adjusted for age with stratification according to virus, sex and LOS showed that the effects were higher among subgroups of less autonomous residents female or male/LOS<4 years/GIR 1-2 in Flu+ outbreaks, and there was also higher mortality in the small subgroup of autonomous men with LOS � 4 years higher mortality S11 Table . In the Flu+ context, data regarding vaccination status and oseltamivir prescriptions were available but not used in this study. In the present study, surveillance data obtained during GE and RTI outbreaks in nursing homes were used to construct stratified analyses and to identify specific infection and all-cause lethality rates according to the residents' individual characteristics.", "In the present study, surveillance data obtained during GE and RTI outbreaks in nursing homes were used to construct stratified analyses and to identify specific infection and all-cause lethality rates according to the residents' individual characteristics. The infection rates observed here were similar to those found in previous studies of NoV and Influenza outbreaks odds of being infected during a Flu+ outbreak were around 40% less than during a NoV+ outbreak . Reported infection rates were close to 30.0% in influenza outbreaks and 40.0% in NoV outbreaks .", "Reported infection rates were close to 30.0% in influenza outbreaks and 40.0% in NoV outbreaks . Older age appeared to increase the likelihood of GE and influenza infection, with increasing rates among older residents. Age is a well-known factor for influenza and norovirus severity in the elderly and in nursing homes .", "Age is a well-known factor for influenza and norovirus severity in the elderly and in nursing homes . For NoV, the highest incidence estimates 5-year age strata was found in the �85 year-category approximately 800 men and for 1,400 women per 100,000 inhabitants . In our study, univariate analysis NoV+ showed that the odds of being infected were 1.5 to 1.6 times higher if a resident was older than 85.", "In our study, univariate analysis NoV+ showed that the odds of being infected were 1.5 to 1.6 times higher if a resident was older than 85. Moreover, an adjusted analysis of GE outbreaks highlighted different effects among subgroups of residents according to sex and LOS. Indeed, multiple and/or repeated exposure to GE viruses while institutionalized may lead to susceptibility or possible increased immunity in some residents .", "Indeed, multiple and/or repeated exposure to GE viruses while institutionalized may lead to susceptibility or possible increased immunity in some residents . For the sex variable, two factors could explain the effect: a possible selection bias with men reporting mild infections less than women particularly in the <86 years subgroup or that male susceptibility was different age, LOS, immunity,. .", ". . . A German study from 2013 also reported a greater impact in women . Moreover, when age analysis was stratified by sex and LOS, no Epidemic impacts in nursing homes significant impact was observed in women; the only significant differences were fewer infections in men in the <86-subgroup except in the NoV-with LOS <4 years .", "Moreover, when age analysis was stratified by sex and LOS, no Epidemic impacts in nursing homes significant impact was observed in women; the only significant differences were fewer infections in men in the <86-subgroup except in the NoV-with LOS <4 years . For the RTI outbreaks, sex and LOS variables did not have a significant effect. In residents older than 86, the odds of being infected in Flu+ context were 1.5 times higher for women and 1.7 for men.", "In residents older than 86, the odds of being infected in Flu+ context were 1.5 times higher for women and 1.7 for men. In univariate analysis, contrary to the other virus contexts where odds ratios were rarely above 2, residents over 95 years old had increased odds of infection of � 2.8 compared with the 70-year-old category, and for the 100 year-old group the odds were approximately 3.8. In the Flu+ context, autonomy adjusted for age virus, sex and LOS stratification revealed a possible increase in infection rates among less autonomous residents.", "In the Flu+ context, autonomy adjusted for age virus, sex and LOS stratification revealed a possible increase in infection rates among less autonomous residents. A previous study found that when elderly residents were exposed to the A H3N2 virus, there were higher rates of infection and reinfection, and more significant effects on the institution than with other influenza types/subtypes. In the community, the relative illness ratio RIR in the .", "In the community, the relative illness ratio RIR in the . The incidence of influenza infection and the associated risks were well described by age group, but the specific impact according to age was not studied. The results of this work highlighted the specific age distribution of influenza illnesses among the nursing home residents and the more significant impact among the older residents.", "The results of this work highlighted the specific age distribution of influenza illnesses among the nursing home residents and the more significant impact among the older residents. This specific susceptibility could be a critical factor in the institutional exposure and dissemination of influenza and could partly explain the high infection impact in the elderly institutional population. In this work, autonomy status was not the main factor associated with infection no significant impact in GE and in Flu-contexts .", "In this work, autonomy status was not the main factor associated with infection no significant impact in GE and in Flu-contexts . However, in Flu+ outbreaks, a high level of dependency was associated with a higher risk of falling ill. This observation implies that staff could play a role in the spread of infection highly dependent and less mobile residents are less likely to contaminate themselves or that the more active residents may be less fragile and/or have a greater involvement in the recommended infection control measures.", "This observation implies that staff could play a role in the spread of infection highly dependent and less mobile residents are less likely to contaminate themselves or that the more active residents may be less fragile and/or have a greater involvement in the recommended infection control measures. Finally, improving compliance with personal hygiene measures both for nursing staff and residents might be expected to have a beneficial effect on infection rates. Previous studies identified higher NoV infection rates in highly dependent individuals, but the results were not adjusted for age and LOS to take into account the potential correlation with the autonomy status .", "Previous studies identified higher NoV infection rates in highly dependent individuals, but the results were not adjusted for age and LOS to take into account the potential correlation with the autonomy status . Lethality is difficult to assess in nursing homes because death is frequent. Our GE and RTI episodes occurred during the winter seasons, and there are possible interactions between outbreaks and increased mortality at this time of the year .", "Our GE and RTI episodes occurred during the winter seasons, and there are possible interactions between outbreaks and increased mortality at this time of the year . The all-cause lethality rate of the infected residents in our study reflected global mortality including GE and RTI outbreaks and the global epidemiological context. Not surprisingly, a higher all-cause lethality rate was observed in the influenza contexts, as reported in previous studies .", "Not surprisingly, a higher all-cause lethality rate was observed in the influenza contexts, as reported in previous studies . Age and autonomy had similar effects in the different contexts, but in GE and to a lesser degree in Flu-outbreaks, the relatively small number of deaths could have limited the power of the statistical tests. In nursing homes, residents are generally discharged due to death.", "In nursing homes, residents are generally discharged due to death. The number of residents lost to follow up was low 0.14% in the first 28 days , so the 7-day interval turnover rate calculated on the base of the median LOS provides a good indication of the average case fatality rate. The lethality rate for NoV+ outbreaks was similar to the estimated 7-day interval turnover rate 1.6% indicating that this context had a limited impact on the death rate.", "The lethality rate for NoV+ outbreaks was similar to the estimated 7-day interval turnover rate 1.6% indicating that this context had a limited impact on the death rate. The all-cause lethality rate was most affected by age and autonomy. Both individual characteristics were significant in the Flu+ outbreaks, and autonomy adjusted for age was significant in the Flu-episodes.", "Both individual characteristics were significant in the Flu+ outbreaks, and autonomy adjusted for age was significant in the Flu-episodes. The influence of age on mortality in a context of influenza has already been described: a very high mortality rate 831/100,000 inhabitants was reported in persons 90 years of age and older compared with those aged 65-69 years 23/100,000 inhabitants . In our univariate analysis, the higher risk was observed in the �90 group whose risk of death was at least 2.6 higher than the <70 group.", "In our univariate analysis, the higher risk was observed in the �90 group whose risk of death was at least 2.6 higher than the <70 group. When adjusted for autonomy, the impact of age was not significant in more autonomous residents in the Flu+ context and not at all in the Flucontext. The opposite analysis autonomy adjusted for age showed higher global impact in the less autonomous group Flu- or only in the �86 age group Flu+ .", "The opposite analysis autonomy adjusted for age showed higher global impact in the less autonomous group Flu- or only in the �86 age group Flu+ . Age and autonomy are a reflection of resident's level of frailty. Clinical frailty scores were not used in this study, but in a previous study of patients with critical illness, they were associated with greater mortality, regardless of age .", "Clinical frailty scores were not used in this study, but in a previous study of patients with critical illness, they were associated with greater mortality, regardless of age . This suggests that in addition to age, autonomy can be a valuable indicator for the assessment of outbreak impact in outbreak surveillance. Other studies have suggested that age and certain comorbidities are independent risk factors for the influenza mortality rate or that mortality increase according to the number of risk factors .", "Other studies have suggested that age and certain comorbidities are independent risk factors for the influenza mortality rate or that mortality increase according to the number of risk factors . Comorbidities and underlying diseases of various severities could reflect overall frailty and consequently the risk of death. In nursing homes, information about autonomy and age are easier to collect and interpret than data on comorbidities.", "In nursing homes, information about autonomy and age are easier to collect and interpret than data on comorbidities. These various approaches should be evaluated and compared in the goal of optimizing risk assessment among nursing home residents. The present work has two main limitations.", "The present work has two main limitations. First, the virus information was incomplete limited identification, mainly influenza rapid tests for the RTI . Consequently, some episodes in the levels with no available identification may also have been associated with influenza or norovirus, and multiple contaminations could have been underestimated or not taken into account.", "Consequently, some episodes in the levels with no available identification may also have been associated with influenza or norovirus, and multiple contaminations could have been underestimated or not taken into account. Moreover, vaccination and oseltamivir prescriptions were recorded but not included because the influenza genotype was not determined and identification was limited. Secondly, the deaths of uninfected residents were not recorded in this protocol even though such data would have provided valuable information about the global epidemiological context.", "Secondly, the deaths of uninfected residents were not recorded in this protocol even though such data would have provided valuable information about the global epidemiological context. In conclusion, specific susceptibility patterns were observed among exposed residents. In this cohort of nursing homes, infection rates varied according to virus, sex, length of stay and age, and there were major differences in lethality depending on virus, age and autonomy score.", "In this cohort of nursing homes, infection rates varied according to virus, sex, length of stay and age, and there were major differences in lethality depending on virus, age and autonomy score. The collected data were easy to record and could be used to improve the characterization of seasonal outbreaks in nursing homes, whose residents are particularly vulnerable. Finally, as the average age and dependency level of residents continues to increase, subsequently increasing the risk of infection and death, health care staff will have to be increasingly vigilant during seasonal outbreaks and targeted interventions should be implemented.", "Finally, as the average age and dependency level of residents continues to increase, subsequently increasing the risk of infection and death, health care staff will have to be increasingly vigilant during seasonal outbreaks and targeted interventions should be implemented. Supporting information S1 Data. CSV S1 R Codes. R S1 Table. XLSX S10 Table.", "CSV S1 R Codes. R S1 Table. XLSX S10 Table. XLSX S11 Table. XLSX" ]

[ "BACKGROUND: Gastroenteritis GE and respiratory tract infection RTI outbreaks are a significant issue in nursing homes. This study aimed to describe GE and RTI outbreaks with infection and all-cause lethality rates according to the individual characteristics of nursing home residents. METHODS: Clinical and virological surveillance were conducted 2007 to 2018 .", "METHODS: Clinical and virological surveillance were conducted 2007 to 2018 . Virus stratifications for the analysis were: outbreaks with positive norovirus or influenza identifications respectively NoV+ or Flu+ , episodes with no NoV or influenza identification or testing respectively NoV- or Flu- . Associations between individual variables sex, age, length of stay LOS , autonomy status and infection and lethality rates were tested with univariate and Mantel-Haenszel MH methods.", "Associations between individual variables sex, age, length of stay LOS , autonomy status and infection and lethality rates were tested with univariate and Mantel-Haenszel MH methods. RESULTS: 61 GE outbreaks and 76 RTI oubreaks total 137 outbreaks were recorded involving respectively 4309 and 5862 residents. In univariate analysis, higher infection rates and age were associated in NoV+, NoV-, and Flu+ contexts, and lower infection rates were associated with longer stays NoV+ and NoV- .", "In univariate analysis, higher infection rates and age were associated in NoV+, NoV-, and Flu+ contexts, and lower infection rates were associated with longer stays NoV+ and NoV- . In MH stratified analysis virus, sex female/male adjusted for LOS <4 or ≥4 years , the odds of being infected remained significant among older residents ≥86 years : NoV+/male Odds ratio OR MH : 1.64, 95% confidence interval CI : 1.16–2.30 and Flu+/female and male respectively OR MH : 1.50, CI: 1.27–1.79 and 1.73, CI: 1.28–2.33 . In univariate analysis, lower autonomy status NoV+, Flu+ and Flu- and increased age Flu+ were associated with higher lethality.", "In univariate analysis, lower autonomy status NoV+, Flu+ and Flu- and increased age Flu+ were associated with higher lethality. In MH adjusted analysis, significant OR age adjusted for autonomy was: Flu+/ ≥86 years compared with <86 years, 1.97 1.19–3.25 and OR autonomy adjusted for age for the more autonomous group compared with the less autonomous group was: Flu+, 0.41 0.24–0.69 ; Flu-, 0.42 0.20, 0.90 . CONCLUSION: The residents of nursing homes are increasingly elderly and dependent.", "CONCLUSION: The residents of nursing homes are increasingly elderly and dependent. The specific infection and lethality risks according to these two factors indicate that surveillance and infection control measures are essential and of high priority. Text: Introduction Gastroenteritis GE and respiratory tract infection RTI outbreaks represent a significant burden of illness in nursing homes.", "Text: Introduction Gastroenteritis GE and respiratory tract infection RTI outbreaks represent a significant burden of illness in nursing homes. Viruses cause the majority of these outbreaks, and noroviruses and influenza viruses are the most common pathogens . Previous studies have suggested that viral respiratory infections and norovirus outbreaks are a common cause of hospitalization or death, particularly among elderly individuals .", "Previous studies have suggested that viral respiratory infections and norovirus outbreaks are a common cause of hospitalization or death, particularly among elderly individuals . The impact of outbreaks has been described in terms of both frequency and epidemiology, but little is known about infection rates and all-cause lethality in GE and RTI nursing home outbreaks in relation to the individual characteristics of the residents . The residents of these institutions are increasingly elderly and dependent, and the impact of this trend on the seasonal outbreak burden requires in-depth investigation.", "The residents of these institutions are increasingly elderly and dependent, and the impact of this trend on the seasonal outbreak burden requires in-depth investigation. The results of studies focused on this issue could yield valuable information for nursing homes, allowing them to adapt their infection control strategies, in particular for improved assessment of infection risk. Our objective was to describe GE and RTI infection and all-cause lethality rates according to the individual characteristics of nursing home residents sex, age, length of stay, autonomy status , and to identify specific susceptibility patterns related to these types of viral outbreaks in these facilities.", "Our objective was to describe GE and RTI infection and all-cause lethality rates according to the individual characteristics of nursing home residents sex, age, length of stay, autonomy status , and to identify specific susceptibility patterns related to these types of viral outbreaks in these facilities. The present study explored outbreaks in 14 sites 28 units with geriatric nursing home activities for a total of 1121 beds caring for dependent people in southern Alsace an area in northeastern France . Data were collected between September 2007 and August 2018 .", "Data were collected between September 2007 and August 2018 . Each site was geographically independent and autonomous for social and care management. Units were located within the larger sites and were defined as a place having a dedicated team at one location. During outbreaks at one site, only the residents in the units with confirmed cases were included.", "During outbreaks at one site, only the residents in the units with confirmed cases were included. Outbreak inclusion depended on institutional alert to the hygiene team. Surveillance was done in each unit independently, and the members of staff had to inform a physician or charge nurse when two or more potential related cases of pneumonia or GE were observed within four days and when three or more cases were observed for other RTI.", "Surveillance was done in each unit independently, and the members of staff had to inform a physician or charge nurse when two or more potential related cases of pneumonia or GE were observed within four days and when three or more cases were observed for other RTI. Units also had to inform the hygiene team when these threshold values were exceeded. For influenza, the first suspected case led to a local alert and the hygiene team was contacted.", "For influenza, the first suspected case led to a local alert and the hygiene team was contacted. A practitioner from the hygiene team collected the information and evaluated the clinical signs, the virology information and the epidemiological context with the physician in the affected unit. The detected cluster was only put under surveillance if the hygiene team considered that there was a potential outbreak phenomenon.", "The detected cluster was only put under surveillance if the hygiene team considered that there was a potential outbreak phenomenon. The duration of 4 days was in relation with the national protocol with alert to the authorities when 5 cases occurred within 4 days . On a local level and in addition to the clusters reported to the authorities, clusters with at least 3 cases within a period of seven days in one unit could be recorded if they were reported to the hygiene team.", "On a local level and in addition to the clusters reported to the authorities, clusters with at least 3 cases within a period of seven days in one unit could be recorded if they were reported to the hygiene team. Because several outbreaks could potentially occur in the same unit during the surveillance period, a resident could be included repeatedly in different clusters. As a result, the observed patterns reflected the characteristics of an institutional population with longitudinal and pluriannual exposures.", "As a result, the observed patterns reflected the characteristics of an institutional population with longitudinal and pluriannual exposures. Personal information and clinical information was collected by a practitioner from the hygiene team directly from the residents' health care records. Personal information was collected for all those present the first day of the outbreak.", "Personal information was collected for all those present the first day of the outbreak. The collected information included: month and year of birth, sex, date of arrival at the nursing home and autonomy status. The autonomy status of residents in French nursing homes is assessed using the AGGIR scale Autonomy Gerontology Groups Iso-Resources , which is the legal instrument for evaluating dependency in the elderly and whose primary purpose is the allocation of means and resources .", "The autonomy status of residents in French nursing homes is assessed using the AGGIR scale Autonomy Gerontology Groups Iso-Resources , which is the legal instrument for evaluating dependency in the elderly and whose primary purpose is the allocation of means and resources . With the AGGIR scale, autonomy is classified into 6 Iso-Resource Groups GIR : GIR 1 bedridden or armchair-bound persons, mental functions seriously altered and requiring continuous presence , GIR 2 bedridden or armchair-bound persons, mental functions not totally altered and requiring assistance in most activities of daily living, or mental functions altered with preserved ability to get around , GIR 3 preserved mental autonomy with partially preserved motor autonomy and assistance several times a day for physical autonomy , GIR 4 moves around the home and sometimes assistance for washing, dressing, physical activities or eating , GIR 5 only occasional assistance for washing, meal preparation, and housework , GIR 6 autonomy for essential tasks of daily living . In outbreaks where the influenza virus was identified, influenza vaccination status and oseltamivir prescriptions were recorded as well.", "In outbreaks where the influenza virus was identified, influenza vaccination status and oseltamivir prescriptions were recorded as well. A file is transmitted in the Supporting Information with all previous data S1 Data . GE was defined as the sudden onset of vomiting and/or diarrhea over a 24 h period: i diarrhea �3 episodes, ii and/or vomiting �3 episodes, iii or diarrhea or vomiting <3 episodes with two or more other symptoms diarrhea, vomiting, stomach ache, abdominal cramps, nausea, fever, mucus in stools .", "GE was defined as the sudden onset of vomiting and/or diarrhea over a 24 h period: i diarrhea �3 episodes, ii and/or vomiting �3 episodes, iii or diarrhea or vomiting <3 episodes with two or more other symptoms diarrhea, vomiting, stomach ache, abdominal cramps, nausea, fever, mucus in stools . RTI presentation in older adults may be atypical, like for other acute illnesses in this age group . We used the recommended definitions for RTI surveillance in geriatric units, divided in 3 subcategories: i common cold syndromes or pharyngitis at least two of the following criteria: runny nose or sneezing, stuffy nose i.e.", "We used the recommended definitions for RTI surveillance in geriatric units, divided in 3 subcategories: i common cold syndromes or pharyngitis at least two of the following criteria: runny nose or sneezing, stuffy nose i.e. congestion , sore throat or hoarseness or difficulty swallowing, dry cough, swollen or tender glands in the neck cervical lymphadenopathy , ii influenza-like illness both the following criteria must be met: fever AND at least three other symptoms chills, new headache or eye pain, myalgia or body aches, malaise or loss of appetite, sore throat, new or increased dry cough and iii lower respiratory tract infection both of the following criteria must be met: at least two respiratory signs or symptoms new or increased cough, new/increased sputum production, O 2 saturation <94% or reduced >3% from baseline, abnormal lung examination new or changed , pleuritic chest pain, respiratory rate �25 breaths/min AND one or more constitutional signs/symptoms fever, leukocytosis, confusion, acute functional decline . Infection corresponding to one of these three subcategories was included in this study and classified as RTI.", "Infection corresponding to one of these three subcategories was included in this study and classified as RTI. For both infection types, the practitioner from the hygiene team obtained clinical information from the patient's health care records, and members of the health care team were consulted if necessary to complete any missing information. At the end of the episode within seven days after the last identified case , case inclusion as exposed and not infected ENI or exposed and infected EI was determined with a resident physician.", "At the end of the episode within seven days after the last identified case , case inclusion as exposed and not infected ENI or exposed and infected EI was determined with a resident physician. In order to study the lethality, the presence of each infected resident was evaluated once at least 56 days after the last case of each outbreak. Each resident was followed up retrospectively during eighth 7-day interval I n, n = 1 to 8, total 56 days, between the date of onset of symptoms and the fifty-sixth day of the studied period with three different possibilities: present alive and officially residing in the institution , lost to follow-up alive at the date of departure but no longer residing in the institution return home, transfer to another institution or death death recorded in the health care record .", "Each resident was followed up retrospectively during eighth 7-day interval I n, n = 1 to 8, total 56 days, between the date of onset of symptoms and the fifty-sixth day of the studied period with three different possibilities: present alive and officially residing in the institution , lost to follow-up alive at the date of departure but no longer residing in the institution return home, transfer to another institution or death death recorded in the health care record . The dates of death and lost to follow-up were recorded. Testing for the virus was not systematic and was decided by the physicians in each institution in the presence of clinical signs.", "Testing for the virus was not systematic and was decided by the physicians in each institution in the presence of clinical signs. For GE, stool samples were sent to the National Reference Centre for Gastroenteritis Viruses in Dijon for laboratory testing, as previously described . For RTI surveillance, rapid tests were used to identify the influenza virus.", "For RTI surveillance, rapid tests were used to identify the influenza virus. The rapid immunoassay diagnosis tests used for influenza detection were: Clearview1 Exact Influenza A and B Inverness Medical, Cologne, Germany from 2007 to 2014 and InfluenzaTop1 Alldiag, Strasbourg, France from 2014 to 2018. Given the low sensitivity of influenza rapid tests, they were no longer used once the control measures had been implemented and the influenza outbreak was under control.", "Given the low sensitivity of influenza rapid tests, they were no longer used once the control measures had been implemented and the influenza outbreak was under control. Samples were also occasionally sent to hospital laboratories or to the National Reference Centre for Influenza Viruses to detect viruses with real-time RT-PCR . Most testing targeted the norovirus NoV and influenza virus, but other tests were occasionally performed by the National Reference Centre for Influenza Viruses rhinovirus, respiratory syncytial virus, human metapneumovirus, parainfluenza 1, 2, 3 and 4, and coronavirus and the National Reference Centre for Enteric Viruses rotavirus, astrovirus, and adenovirus .", "Most testing targeted the norovirus NoV and influenza virus, but other tests were occasionally performed by the National Reference Centre for Influenza Viruses rhinovirus, respiratory syncytial virus, human metapneumovirus, parainfluenza 1, 2, 3 and 4, and coronavirus and the National Reference Centre for Enteric Viruses rotavirus, astrovirus, and adenovirus . Because testing for the viruses was variable from one institution/physician to another, not used in some outbreaks, types of virus sought and considering the poor sensitivity of the rapid influenza tests, these two sources of data were used to define the epidemiological context of confirmed outbreaks. Consequently, individual cases were included consistently in all episodes according to clinical signs and medical evaluation.", "Consequently, individual cases were included consistently in all episodes according to clinical signs and medical evaluation. When virus testing was negative, the clinical signs were recorded and medical evaluation was used as previously to classify the included residents as infected or not infected. The epidemiological context of each outbreak was defined according to whether the virus had been identified or not.", "The epidemiological context of each outbreak was defined according to whether the virus had been identified or not. One or more positive samples led to the qualification of a NoV NoV+ or flu Flu+ context. The other episodes were qualified as flu or NoV outbreaks with no specific identification or testing NoV-and Flu- .", "The other episodes were qualified as flu or NoV outbreaks with no specific identification or testing NoV-and Flu- . Flu and NoV contexts did not eliminate other potential enteric or respiratory pathogens. Sex, age, length of stay LOS, in years and autonomy status were described for all exposed residents.", "Sex, age, length of stay LOS, in years and autonomy status were described for all exposed residents. Influenza vaccination and oseltamivir administration rates were calculated for confirmed influenza outbreaks. Dichotomous or categorical variables were expressed as percentages.", "Dichotomous or categorical variables were expressed as percentages. In univariate analysis, the categories were specific in order to obtain a precise description of the age and LOS variables. Class intervals were 5 years for age and one year for LOS.", "Class intervals were 5 years for age and one year for LOS. The residents classified as GIR 4 to 6 sometimes, occasional and no assistance were grouped together because they were few. For the multi-level analysis with 2x2 tables, a median value was used to define the two-level age categories.", "For the multi-level analysis with 2x2 tables, a median value was used to define the two-level age categories. For LOS, assessing the longest stays was necessary to identify the effect of longer exposure in a nursing home. Consequently, a four-year cutoff was chosen to create the two categories.", "Consequently, a four-year cutoff was chosen to create the two categories. For autonomy, the two most dependent categories GIR � 2 were grouped together and compared with the more autonomous categories GIR � 3 . The outbreak epidemiological contexts were used with the four categories: NoV+, Flu+, NoV-and flu-.", "The outbreak epidemiological contexts were used with the four categories: NoV+, Flu+, NoV-and flu-. Other GE or RTI viruses were occasionally identified, but the number of results was too limited to develop separate analyses. However, all the results are available in the tables about the virus investigations along with NoV and influenza identifications.", "However, all the results are available in the tables about the virus investigations along with NoV and influenza identifications. For the different categories, infection rate EI/Exposed Residents ER , in percentage was calculated according to sex, age group, LOS and autonomy status. To investigate all-cause lethality and define the appropriate period for the 56-day monitoring D 1 to 56 , the all-cause lethality rate per 7-day interval LR n /I n, n = 1 to 8 was calculated: number of deaths during interval I n / EI alive the first day of n th studied interval minus lost to follow-up EI during the interval I n � 100 .", "To investigate all-cause lethality and define the appropriate period for the 56-day monitoring D 1 to 56 , the all-cause lethality rate per 7-day interval LR n /I n, n = 1 to 8 was calculated: number of deaths during interval I n / EI alive the first day of n th studied interval minus lost to follow-up EI during the interval I n � 100 . Seeing as successive clusters could occur within the same site, potentially influencing allcause lethality, the serial interval in days SI d was calculated. The SI d was the time period between the onset of symptoms of the last case in initial outbreak N and the onset of symptoms of the first case in the following outbreak N+1 .", "The SI d was the time period between the onset of symptoms of the last case in initial outbreak N and the onset of symptoms of the first case in the following outbreak N+1 . Investigations were performed when SI d was shorter or equal to the length of the previous D 1 to 56 and the following parameters were evaluated for these specific situations: number of episodes, residents infected in both outbreaks, and death among the identified individuals. Finally, according to the death rate and the impact of successive outbreaks, the number of 7-day intervals N.I n to take into account was defined, and the all-cause lethality rate was analyzed during these periods I 1 to N th .I n or D 1 to 7 � N .", "Finally, according to the death rate and the impact of successive outbreaks, the number of 7-day intervals N.I n to take into account was defined, and the all-cause lethality rate was analyzed during these periods I 1 to N th .I n or D 1 to 7 � N . All-cause lethality rates were calculated with the following formula: number of deaths from D 1 to 7 � N / EI number at D 1 minus lost to follow-up among EI during the period D 1 to 7 � N � 100 . Estimation of the turnover rate per 7-day interval among the infected residents was calculated on the base of the LOS median in years with the following formula: proportion of discharged residents: 50.0% in the case of the median / median LOS � 365 /7 .", "Estimation of the turnover rate per 7-day interval among the infected residents was calculated on the base of the LOS median in years with the following formula: proportion of discharged residents: 50.0% in the case of the median / median LOS � 365 /7 . The average rate of residents discharged per 7-day period was calculated: number of lost to follow up during the period D 1 to 7 � N /number of exposed and infected residents at D 1 /N 7-day interval � 100. As some residents were included in several outbreaks during the surveillance, the observations were not completely independent; non-parametric tests were used as a result.", "As some residents were included in several outbreaks during the surveillance, the observations were not completely independent; non-parametric tests were used as a result. In univariate analysis, Chi-square or Fisher exact tests expected number of frequencies fewer than 5 were used to compare infection and lethality rates according to the studied parameters and the odds ratio was calculated by median-unbiased estimation. The Kruskal-Wallis test was used to compare median values.", "The Kruskal-Wallis test was used to compare median values. Confidence intervals for medians were calculated with bootstrap methods. Covariate adjusted analyses were performed with two tables 2x2 . The respective impact of each individual factor was tested with Mantel-Haenszel chi-squared tests. The equality of the stratum odds ratios was tested with the Woolf test of homogeneity.", "The equality of the stratum odds ratios was tested with the Woolf test of homogeneity. Finally, for each virus context, multiple tables 2x2 were generated and tested with confounding variables, effect modifiers or covariables. Statistical analyses were done using R for Mas OS X version R 3.4.1 software with RStudio version 1.0.153.", "Statistical analyses were done using R for Mas OS X version R 3.4.1 software with RStudio version 1.0.153. A file is transmitted in the Supporting Information with all R codes and the packages used S1 R Codes . Differences were considered significant at p � 0.05.", "Differences were considered significant at p � 0.05. The French Data Protection Authority approved data collection and analysis DE-2013-074 and the local ethics committee Espace Local de Réflexion Ethique, Centre Hospitalier de Rouffach approved the study protocol ERLE-32 . According to the French law for biomedical research and human experimentation, individual written consent was not required from the patients or their relatives for data collection.", "According to the French law for biomedical research and human experimentation, individual written consent was not required from the patients or their relatives for data collection. Each year, the referring local practitioner of the study coordinated with the doctors working in the nursing home. At the beginning of the surveillance period, information regarding participation in the study was displayed in the family vising area, including a document about their right to access and rectify personal data.", "At the beginning of the surveillance period, information regarding participation in the study was displayed in the family vising area, including a document about their right to access and rectify personal data. After collection, data were rendered anonymous. No specific authorization was needed to retrospectively analyze anonymous data collected during routine care in the context of routine surveillance.", "No specific authorization was needed to retrospectively analyze anonymous data collected during routine care in the context of routine surveillance. A total of 137 outbreaks were recorded in the 14 sites. RTI outbreaks were more frequent than GE outbreaks 76 outbreaks and 5862 exposed residents vs. 61 outbreaks and 4309 exposed residents, respectively .", "RTI outbreaks were more frequent than GE outbreaks 76 outbreaks and 5862 exposed residents vs. 61 outbreaks and 4309 exposed residents, respectively . Overall, 7643 of the exposed residents were women and 2528 were men. The median age was 86.7 years old interquartile range: 81.1-91.0 years .", "The median age was 86.7 years old interquartile range: 81.1-91.0 years . Virus investigations respectively 389 samples for RTI and 143 for GE with all the detailed results in S1-S4 Tables confirmed a considerable number of norovirus-related GE outbreaks 34/61 and influenza-related RTI outbreaks 46/76 . For GE outbreaks, 2524 residents were in a NoV+ context versus 1785 in a NoV-context, and for RTI outbreaks, 3479 residents were in a Flu+ context versus 2383 in a Flu-context.", "For GE outbreaks, 2524 residents were in a NoV+ context versus 1785 in a NoV-context, and for RTI outbreaks, 3479 residents were in a Flu+ context versus 2383 in a Flu-context. For GE surveillance in the NoV+ context, there were 1093 EI residents versus 1431 ENI residents, whereas in the NoV-context, there were 583 EI residents versus 1202 ENI residents. Therefore, the infection rate was higher in the NoV+ context 43.3% than in the NoV-context 32.7%, odds ratio OR : 0.63, 95% confidence interval CI : 0.56-0.72 , p < 0.001 .", "Therefore, the infection rate was higher in the NoV+ context 43.3% than in the NoV-context 32.7%, odds ratio OR : 0.63, 95% confidence interval CI : 0.56-0.72 , p < 0.001 . For RTI surveillance, the rates of infection were similar with and without confirmed influenza: 31.5% N = 1095 EI residents /3479 exposed residents vs. 30.5% N = 728 EI residents/ 2383 exposed residents, OR: 0.96, CI: 0.85-1.07, p = 0.47 . Moreover, infection rate in the NoV + context was higher than the three other contexts: NoV- OR: 0.63, CI: 0.56-0.72 , Flu+ OR: 0.60, CI:0.54-0.67 and Flu- OR: 0.58, CI: 0.51-0.65 .", "Moreover, infection rate in the NoV + context was higher than the three other contexts: NoV- OR: 0.63, CI: 0.56-0.72 , Flu+ OR: 0.60, CI:0.54-0.67 and Flu- OR: 0.58, CI: 0.51-0.65 . In univariate analysis, certain individual characteristics were associated with significant variations in the infection rate S5 Table . The infection rate increased with age except in the Flucontext and, decreased with LOS during GE outbreaks.", "The infection rate increased with age except in the Flucontext and, decreased with LOS during GE outbreaks. The covariate adjusted analysis revealed specific significant effect modification according to sex NoV+ and LOS NoV- S6 Table . In analyses stratified according to virus and sex, age adjusted for LOS remained significant for Flu+ and NoV+ outbreaks males .", "In analyses stratified according to virus and sex, age adjusted for LOS remained significant for Flu+ and NoV+ outbreaks males . In NoV-context, the effect modification of LOS remained significant Table 1 . Finally, when autonomy was included and adjusted for age virus, sex, LOS stratification , the less autonomous residents female/LOS<4 years/age<86/ GIR 1-2 were affected more severely by Flu+ outbreaks with specific effect modification according to age S7 Table .", "Finally, when autonomy was included and adjusted for age virus, sex, LOS stratification , the less autonomous residents female/LOS<4 years/age<86/ GIR 1-2 were affected more severely by Flu+ outbreaks with specific effect modification according to age S7 Table . The study of lethality rates in infected residents over the 56 days after onset indicated that there were significant variations for RTI but no change for GE Table 2 . Significant differences appeared after 28 days in the context of Flu+ outbreaks and other RTI outbreaks.", "Significant differences appeared after 28 days in the context of Flu+ outbreaks and other RTI outbreaks. The analysis of successive or simultaneous clusters in the same institutions was performed when the time period between the onset of symptoms of the last case in outbreak N and the onset of symptoms of the first case in outbreak N+1 was �56 days S8 Table . 44 of the 137 outbreaks 32.12% were identified, and 194 of the 3499 exposed and infected residents contracted multiple infections.", "44 of the 137 outbreaks 32.12% were identified, and 194 of the 3499 exposed and infected residents contracted multiple infections. The percentage of exposed and infected residents implicated in more than one virus stratification was 11.09% 194 � 2 /3499 . Moreover, two deceased residents were included in the NoV-Na and Flu lethality analyses because death occurred within 56 days for both infections.", "Moreover, two deceased residents were included in the NoV-Na and Flu lethality analyses because death occurred within 56 days for both infections. The analysis of virus stratification of the 44 outbreaks showed the absence of successive clusters for the same category. The same analysis for the first four 7-day intervals Days 1 to 28 showed the respective values: 26 outbreaks 18.98% , 117 residents 6.69% 117 � 2 /3499 , one dead resident.", "The same analysis for the first four 7-day intervals Days 1 to 28 showed the respective values: 26 outbreaks 18.98% , 117 residents 6.69% 117 � 2 /3499 , one dead resident. Finally, according to the higher lethality impact during the first four 7-day intervals and to limit the impact of successive clusters in the same site, all cause lethality rates were studied according to individual parameters for the four 7 days intervals with the respective number of According to the surveillance type GE or RTI , the lethality rates differed significantly: 1.6% versus 3.4% respectively NoV+ and NoV-contexts, OR: 2.24, CI: 1.16-4.39, p = 0.02 and 8.3% versus 5.6% respectively Flu+ and Flu-, OR: 0.67, CI: 0.45-0.97, p = 0.04 . In univariate analysis S9 Table , low autonomy status in the NoV+, Flu+ and Flu-contexts was most significantly associated with increased all-cause lethality, and age was associated with higher lethality in the Flu+ context.", "In univariate analysis S9 Table , low autonomy status in the NoV+, Flu+ and Flu-contexts was most significantly associated with increased all-cause lethality, and age was associated with higher lethality in the Flu+ context. In the adjusted analysis, no significant statistical differences were identified in GE outbreaks. For RTI episodes, the adjusted analysis showed that autonomy had a significant impact when adjusted for sex, age or LOS Flu+ and Flu-NA and that age had a significant impact when adjusted for sex, autonomy or LOS Flu+ S10 Table .", "For RTI episodes, the adjusted analysis showed that autonomy had a significant impact when adjusted for sex, age or LOS Flu+ and Flu-NA and that age had a significant impact when adjusted for sex, autonomy or LOS Flu+ S10 Table . In Table 3 , the specific effects of age or autonomy were tested. Significant OR age adjusted for autonomy were: Flu+/age �86 years compared with the <86 group , 1.97 1.19-3.25 .", "Significant OR age adjusted for autonomy were: Flu+/age �86 years compared with the <86 group , 1.97 1.19-3.25 . OR autonomy adjusted for age were for GIR 3-6 compared with GIR 1-2 : Flu+, 0.41 0.24-0.69 ; Flu-, 0.42 0.20, 0.90 . Finally, despite the low number of residents and deaths per category, and consequently the limited robustness of the results, autonomy adjusted for age with stratification according to virus, sex and LOS showed that the effects were higher among subgroups of less autonomous residents female or male/LOS<4 years/GIR 1-2 in Flu+ outbreaks, and there was also higher mortality in the small subgroup of autonomous men with LOS � 4 years higher mortality S11 Table .", "Finally, despite the low number of residents and deaths per category, and consequently the limited robustness of the results, autonomy adjusted for age with stratification according to virus, sex and LOS showed that the effects were higher among subgroups of less autonomous residents female or male/LOS<4 years/GIR 1-2 in Flu+ outbreaks, and there was also higher mortality in the small subgroup of autonomous men with LOS � 4 years higher mortality S11 Table . In the Flu+ context, data regarding vaccination status and oseltamivir prescriptions were available but not used in this study. In the present study, surveillance data obtained during GE and RTI outbreaks in nursing homes were used to construct stratified analyses and to identify specific infection and all-cause lethality rates according to the residents' individual characteristics.", "In the present study, surveillance data obtained during GE and RTI outbreaks in nursing homes were used to construct stratified analyses and to identify specific infection and all-cause lethality rates according to the residents' individual characteristics. The infection rates observed here were similar to those found in previous studies of NoV and Influenza outbreaks odds of being infected during a Flu+ outbreak were around 40% less than during a NoV+ outbreak . Reported infection rates were close to 30.0% in influenza outbreaks and 40.0% in NoV outbreaks .", "Reported infection rates were close to 30.0% in influenza outbreaks and 40.0% in NoV outbreaks . Older age appeared to increase the likelihood of GE and influenza infection, with increasing rates among older residents. Age is a well-known factor for influenza and norovirus severity in the elderly and in nursing homes .", "Age is a well-known factor for influenza and norovirus severity in the elderly and in nursing homes . For NoV, the highest incidence estimates 5-year age strata was found in the �85 year-category approximately 800 men and for 1,400 women per 100,000 inhabitants . In our study, univariate analysis NoV+ showed that the odds of being infected were 1.5 to 1.6 times higher if a resident was older than 85.", "In our study, univariate analysis NoV+ showed that the odds of being infected were 1.5 to 1.6 times higher if a resident was older than 85. Moreover, an adjusted analysis of GE outbreaks highlighted different effects among subgroups of residents according to sex and LOS. Indeed, multiple and/or repeated exposure to GE viruses while institutionalized may lead to susceptibility or possible increased immunity in some residents .", "Indeed, multiple and/or repeated exposure to GE viruses while institutionalized may lead to susceptibility or possible increased immunity in some residents . For the sex variable, two factors could explain the effect: a possible selection bias with men reporting mild infections less than women particularly in the <86 years subgroup or that male susceptibility was different age, LOS, immunity,. .", ". . . A German study from 2013 also reported a greater impact in women . Moreover, when age analysis was stratified by sex and LOS, no Epidemic impacts in nursing homes significant impact was observed in women; the only significant differences were fewer infections in men in the <86-subgroup except in the NoV-with LOS <4 years .", "Moreover, when age analysis was stratified by sex and LOS, no Epidemic impacts in nursing homes significant impact was observed in women; the only significant differences were fewer infections in men in the <86-subgroup except in the NoV-with LOS <4 years . For the RTI outbreaks, sex and LOS variables did not have a significant effect. In residents older than 86, the odds of being infected in Flu+ context were 1.5 times higher for women and 1.7 for men.", "In residents older than 86, the odds of being infected in Flu+ context were 1.5 times higher for women and 1.7 for men. In univariate analysis, contrary to the other virus contexts where odds ratios were rarely above 2, residents over 95 years old had increased odds of infection of � 2.8 compared with the 70-year-old category, and for the 100 year-old group the odds were approximately 3.8. In the Flu+ context, autonomy adjusted for age virus, sex and LOS stratification revealed a possible increase in infection rates among less autonomous residents.", "In the Flu+ context, autonomy adjusted for age virus, sex and LOS stratification revealed a possible increase in infection rates among less autonomous residents. A previous study found that when elderly residents were exposed to the A H3N2 virus, there were higher rates of infection and reinfection, and more significant effects on the institution than with other influenza types/subtypes. In the community, the relative illness ratio RIR in the .", "In the community, the relative illness ratio RIR in the . The incidence of influenza infection and the associated risks were well described by age group, but the specific impact according to age was not studied. The results of this work highlighted the specific age distribution of influenza illnesses among the nursing home residents and the more significant impact among the older residents.", "The results of this work highlighted the specific age distribution of influenza illnesses among the nursing home residents and the more significant impact among the older residents. This specific susceptibility could be a critical factor in the institutional exposure and dissemination of influenza and could partly explain the high infection impact in the elderly institutional population. In this work, autonomy status was not the main factor associated with infection no significant impact in GE and in Flu-contexts .", "In this work, autonomy status was not the main factor associated with infection no significant impact in GE and in Flu-contexts . However, in Flu+ outbreaks, a high level of dependency was associated with a higher risk of falling ill. This observation implies that staff could play a role in the spread of infection highly dependent and less mobile residents are less likely to contaminate themselves or that the more active residents may be less fragile and/or have a greater involvement in the recommended infection control measures.", "This observation implies that staff could play a role in the spread of infection highly dependent and less mobile residents are less likely to contaminate themselves or that the more active residents may be less fragile and/or have a greater involvement in the recommended infection control measures. Finally, improving compliance with personal hygiene measures both for nursing staff and residents might be expected to have a beneficial effect on infection rates. Previous studies identified higher NoV infection rates in highly dependent individuals, but the results were not adjusted for age and LOS to take into account the potential correlation with the autonomy status .", "Previous studies identified higher NoV infection rates in highly dependent individuals, but the results were not adjusted for age and LOS to take into account the potential correlation with the autonomy status . Lethality is difficult to assess in nursing homes because death is frequent. Our GE and RTI episodes occurred during the winter seasons, and there are possible interactions between outbreaks and increased mortality at this time of the year .", "Our GE and RTI episodes occurred during the winter seasons, and there are possible interactions between outbreaks and increased mortality at this time of the year . The all-cause lethality rate of the infected residents in our study reflected global mortality including GE and RTI outbreaks and the global epidemiological context. Not surprisingly, a higher all-cause lethality rate was observed in the influenza contexts, as reported in previous studies .", "Not surprisingly, a higher all-cause lethality rate was observed in the influenza contexts, as reported in previous studies . Age and autonomy had similar effects in the different contexts, but in GE and to a lesser degree in Flu-outbreaks, the relatively small number of deaths could have limited the power of the statistical tests. In nursing homes, residents are generally discharged due to death.", "In nursing homes, residents are generally discharged due to death. The number of residents lost to follow up was low 0.14% in the first 28 days , so the 7-day interval turnover rate calculated on the base of the median LOS provides a good indication of the average case fatality rate. The lethality rate for NoV+ outbreaks was similar to the estimated 7-day interval turnover rate 1.6% indicating that this context had a limited impact on the death rate.", "The lethality rate for NoV+ outbreaks was similar to the estimated 7-day interval turnover rate 1.6% indicating that this context had a limited impact on the death rate. The all-cause lethality rate was most affected by age and autonomy. Both individual characteristics were significant in the Flu+ outbreaks, and autonomy adjusted for age was significant in the Flu-episodes.", "Both individual characteristics were significant in the Flu+ outbreaks, and autonomy adjusted for age was significant in the Flu-episodes. The influence of age on mortality in a context of influenza has already been described: a very high mortality rate 831/100,000 inhabitants was reported in persons 90 years of age and older compared with those aged 65-69 years 23/100,000 inhabitants . In our univariate analysis, the higher risk was observed in the �90 group whose risk of death was at least 2.6 higher than the <70 group.", "In our univariate analysis, the higher risk was observed in the �90 group whose risk of death was at least 2.6 higher than the <70 group. When adjusted for autonomy, the impact of age was not significant in more autonomous residents in the Flu+ context and not at all in the Flucontext. The opposite analysis autonomy adjusted for age showed higher global impact in the less autonomous group Flu- or only in the �86 age group Flu+ .", "The opposite analysis autonomy adjusted for age showed higher global impact in the less autonomous group Flu- or only in the �86 age group Flu+ . Age and autonomy are a reflection of resident's level of frailty. Clinical frailty scores were not used in this study, but in a previous study of patients with critical illness, they were associated with greater mortality, regardless of age .", "Clinical frailty scores were not used in this study, but in a previous study of patients with critical illness, they were associated with greater mortality, regardless of age . This suggests that in addition to age, autonomy can be a valuable indicator for the assessment of outbreak impact in outbreak surveillance. Other studies have suggested that age and certain comorbidities are independent risk factors for the influenza mortality rate or that mortality increase according to the number of risk factors .", "Other studies have suggested that age and certain comorbidities are independent risk factors for the influenza mortality rate or that mortality increase according to the number of risk factors . Comorbidities and underlying diseases of various severities could reflect overall frailty and consequently the risk of death. In nursing homes, information about autonomy and age are easier to collect and interpret than data on comorbidities.", "In nursing homes, information about autonomy and age are easier to collect and interpret than data on comorbidities. These various approaches should be evaluated and compared in the goal of optimizing risk assessment among nursing home residents. The present work has two main limitations.", "The present work has two main limitations. First, the virus information was incomplete limited identification, mainly influenza rapid tests for the RTI . Consequently, some episodes in the levels with no available identification may also have been associated with influenza or norovirus, and multiple contaminations could have been underestimated or not taken into account.", "Consequently, some episodes in the levels with no available identification may also have been associated with influenza or norovirus, and multiple contaminations could have been underestimated or not taken into account. Moreover, vaccination and oseltamivir prescriptions were recorded but not included because the influenza genotype was not determined and identification was limited. Secondly, the deaths of uninfected residents were not recorded in this protocol even though such data would have provided valuable information about the global epidemiological context.", "Secondly, the deaths of uninfected residents were not recorded in this protocol even though such data would have provided valuable information about the global epidemiological context. In conclusion, specific susceptibility patterns were observed among exposed residents. In this cohort of nursing homes, infection rates varied according to virus, sex, length of stay and age, and there were major differences in lethality depending on virus, age and autonomy score.", "In this cohort of nursing homes, infection rates varied according to virus, sex, length of stay and age, and there were major differences in lethality depending on virus, age and autonomy score. The collected data were easy to record and could be used to improve the characterization of seasonal outbreaks in nursing homes, whose residents are particularly vulnerable. Finally, as the average age and dependency level of residents continues to increase, subsequently increasing the risk of infection and death, health care staff will have to be increasingly vigilant during seasonal outbreaks and targeted interventions should be implemented.", "Finally, as the average age and dependency level of residents continues to increase, subsequently increasing the risk of infection and death, health care staff will have to be increasingly vigilant during seasonal outbreaks and targeted interventions should be implemented. Supporting information S1 Data. CSV S1 R Codes. R S1 Table. XLSX S10 Table.", "CSV S1 R Codes. R S1 Table. XLSX S10 Table. XLSX S11 Table. XLSX" ]

[ "The objective of this clinical trial was to evaluate the effectiveness of zinc supplementation on diarrhea and average daily weight gain ADG in pre-weaned dairy calves. A total of 1,482 healthy Holstein heifer and bull calves from a large California dairy were enrolled at 24 to 48 hours of age until hutch exit at approximately 90 days of age. Calves were block-randomized by time to one of three treatments: 1 placebo, 2 zinc methionine ZM , or 3 zinc sulfate ZS administered in milk once daily for 14 days.", "Calves were block-randomized by time to one of three treatments: 1 placebo, 2 zinc methionine ZM , or 3 zinc sulfate ZS administered in milk once daily for 14 days. Serum total protein at enrollment and body weight at birth, treatment end, and hutch exit were measured. Fecal consistency was assessed daily for 28 days post-enrollment.", "Fecal consistency was assessed daily for 28 days post-enrollment. For a random sample of 127 calves, serum zinc concentrations before and after treatment and a fecal antigen ELISA at diarrhea start and resolution for Escherichia coli K99, rotavirus, coronavirus, and Cryptosporidium parvum were performed. Linear regression showed that ZM-treated bull calves had 22 g increased ADG compared to placebo-treated bulls P = 0.042 .", "Linear regression showed that ZM-treated bull calves had 22 g increased ADG compared to placebo-treated bulls P = 0.042 . ZM-treated heifers had 9 g decreased ADG compared to placebo-treated heifers P = 0.037 , after adjusting for average birth weight. Sex-stratified models showed that high birth weight heifers treated with ZM gained more than placebo-treated heifers of the same birth weight, which suggests a dose-response effect rather than a true sex-specific effect of ZM on ADG.", "Sex-stratified models showed that high birth weight heifers treated with ZM gained more than placebo-treated heifers of the same birth weight, which suggests a dose-response effect rather than a true sex-specific effect of ZM on ADG. Cox regression showed that ZM and ZS-treated calves had a 14.7% P = 0.015 and 13.9% P = 0.022 reduced hazard of diarrhea, respectively, compared to placebo-treated calves. Calves supplemented for at least the first five days of diarrhea with ZM and ZS had a 21.4% P = 0.027 and 13.0% P = 0.040 increased hazard of cure from diarrhea, respectively, compared to placebo-treated calves.", "Calves supplemented for at least the first five days of diarrhea with ZM and ZS had a 21.4% P = 0.027 and 13.0% P = 0.040 increased hazard of cure from diarrhea, respectively, compared to placebo-treated calves. Logistic regression showed that the odds of microbiological cure at diarrhea resolution for rotavirus, C. parvum, or any single fecal pathogen was not different between treatment groups. Zinc supplementation delayed diarrhea and expedited diarrhea recovery in pre-weaned calves.", "Zinc supplementation delayed diarrhea and expedited diarrhea recovery in pre-weaned calves. Additionally, zinc improved weight gain differentially in bulls compared to heifers, indicating a research need for sex-specific dosing. Text: Introduction Diarrhea is the leading cause of morbidity and mortality and the most common reason for antimicrobial drug treatments in pre-weaned dairy heifers .", "Text: Introduction Diarrhea is the leading cause of morbidity and mortality and the most common reason for antimicrobial drug treatments in pre-weaned dairy heifers . A USDA survey of preweaned dairy heifers reported that 24% experienced diarrhea and 18% received antimicrobial treatment for it . Diarrhea is also a leading cause of morbidity and the second foremost cause of mortality in children with over 1 billion cases and a half a million deaths annually .", "Diarrhea is also a leading cause of morbidity and the second foremost cause of mortality in children with over 1 billion cases and a half a million deaths annually . Zinc supplementation in children decreases the incidence, duration, and severity of diarrhea, increases recovery rates, decreases the use of antibiotics and antidiarrheal medications, and reduces mortality . In a clinical trial that established a non-toxic zinc dose and investigated its therapeutic use for diarrhea in neonatal dairy calves, zinc-treated calves had numerically quicker clinical recovery, increased weight gain, and higher odds of fecal clearance of Cryptosporidium parvum between diarrhea onset and recovery compared with placebotreated calves .", "In a clinical trial that established a non-toxic zinc dose and investigated its therapeutic use for diarrhea in neonatal dairy calves, zinc-treated calves had numerically quicker clinical recovery, increased weight gain, and higher odds of fecal clearance of Cryptosporidium parvum between diarrhea onset and recovery compared with placebotreated calves . As a result, zinc supplementation may be beneficial for prevention of diarrhea in dairy calves and, thus, minimize antimicrobial use. However, studies investigating zinc's potential effectiveness are lacking.", "However, studies investigating zinc's potential effectiveness are lacking. In children, both organic zinc acetate, zinc gluconate, and zinc methionine and inorganic zinc sulfate and zinc oxide zinc formulations are beneficial in the prevention and treatment of childhood diarrhea . However, differing bioavailability was observed in several animal studies .", "However, differing bioavailability was observed in several animal studies . In addition, the underlying mechanism of action of oral zinc is unknown . Hence, contrasting the effect, if any, of organic compared to inorganic zinc formulations in pre-weaned calves may help identify differences in mode of action.", "Hence, contrasting the effect, if any, of organic compared to inorganic zinc formulations in pre-weaned calves may help identify differences in mode of action. The objective of this clinical trial was to compare average daily weight gain ADG and the incidence and duration of diarrhea in pre-weaned dairy calves randomly assigned to receive either organic zinc methionine ZM , inorganic zinc sulfate ZS , or a placebo in milk once daily for 14 days. By elucidating the potential role of zinc supplementation in prevention of diarrhea in preweaned dairy calves, calf morbidity, mortality, and antimicrobial usage may be mitigated.", "By elucidating the potential role of zinc supplementation in prevention of diarrhea in preweaned dairy calves, calf morbidity, mortality, and antimicrobial usage may be mitigated. A double-blind, block randomized, placebo-controlled clinical trial was conducted between December 14, 2015 and June 15, 2016 on a large dairy in California's San Joaquin Valley. The dairy was selected based on the owner and calf manager's willingness to participate in the study.", "The dairy was selected based on the owner and calf manager's willingness to participate in the study. The dairy herd was composed of 5,500 lactating cows, predominantly Holsteins, and housed approximately 1,600 pre-weaned calves. Approximately 75% of the calves were born on the participating dairy and 25% were born on an affiliated dairy located approximately 10 miles away.", "Approximately 75% of the calves were born on the participating dairy and 25% were born on an affiliated dairy located approximately 10 miles away. Calves enrolled in the trial included healthy Holstein heifer or bull calves 24 to 48 hours of age. Calves were determined to be healthy via visual examination by a veterinarian HF or a trained researcher.", "Calves were determined to be healthy via visual examination by a veterinarian HF or a trained researcher. Calves were excluded if they had obvious morbidities or congenital defects, were non-Holstein, born on the affiliated dairy, younger than 24 hours of age or older than 48 hours of age at the time of enrollment. Calves from the affiliated dairy were excluded due to differences in physical location and management practices of pre-partum cows.", "Calves from the affiliated dairy were excluded due to differences in physical location and management practices of pre-partum cows. All procedures were approved by the University of California Davis Institutional Animal Care and Use Committee protocol number 18067 Approved: March 6, 2014 . 107 g between treatment groups Stata, College Station, TX .", "107 g between treatment groups Stata, College Station, TX . After allowing for 15% attrition and assuming 50% incidence of diarrhea based on study authors expert opinion, and a difference in ADG of 107g , a sample size of 500 calves per treatment group n = 1500 total was deemed required. Newborn calves were removed from the dam within an hour of birth and placed in a strawbedded, group calf pen where their navels were dipped in an iodine-based solution.", "Newborn calves were removed from the dam within an hour of birth and placed in a strawbedded, group calf pen where their navels were dipped in an iodine-based solution. Each calf received 4 liters of colostrum within 1 hour of birth and a second colostrum feeding 2 liters 6-10 hours after birth. Colostrum was refrigerated for < 48 hours and heated in a hot water bath prior to feeding using an esophageal tube feeder.", "Colostrum was refrigerated for < 48 hours and heated in a hot water bath prior to feeding using an esophageal tube feeder. Within 18 hours of birth, pre-weaned calves were transported to individual metal hutches initially bedded with almond shells. Straw hay was later added to wet and muddy hutches throughout the pre-weaning period.", "Straw hay was later added to wet and muddy hutches throughout the pre-weaning period. For the first 14 days of life, pre-weaned calves were bottle-fed 1.9 liters of milk twice daily and 1.9 liters of a commercial oral electrolyte solution Calva Lyte; Calva Products, Inc., Acampo, CA once daily between milk feedings. Milk consisted of a combination of pasteurized waste milk, rehydrated commercial milk replacer powder Strauss Feeds LLC, Watertown, WI , tetracycline and neomycin powder, and additional supplements S1 Table .", "Milk consisted of a combination of pasteurized waste milk, rehydrated commercial milk replacer powder Strauss Feeds LLC, Watertown, WI , tetracycline and neomycin powder, and additional supplements S1 Table . The proportion of pasteurized waste milk to milk replacer varied with each feeding, as the volume of waste milk varied with changes in the number and production of cows contributing to the waste milk tank. After 14 days of age, calves were bottle-fed 2.8 liters of milk twice daily.", "After 14 days of age, calves were bottle-fed 2.8 liters of milk twice daily. Calves with clinical diarrhea received 1.9 liters of a commercial oral electrolyte solution NuLife; Genex Cooperative, Inc., Shawano, WI once daily between milk feedings. A list of ingredients that make up the two oral electrolyte solutions can be found in S2 Table.", "A list of ingredients that make up the two oral electrolyte solutions can be found in S2 Table. All pre-weaned calves had free choice access to water and a calf starter grain mix. Calves were gradually weaned over a 10-day period, starting at approximately 60 days of age after which calves received a grower grain mix until 90 days of age when they were moved to group pens.", "Calves were gradually weaned over a 10-day period, starting at approximately 60 days of age after which calves received a grower grain mix until 90 days of age when they were moved to group pens. Each calf received 1 mL of a selenium supplement MU-SE; Merck Animal Health, Boxmeer, Netherlands intramuscularly within 24 hours of age and an intranasal vaccine Inforce 3, Zoetis, Inc., Florham Park, NJ within 48 hours of age and again near the time of weaning. Approximately 8.3% n = 126 of all enrolled calves were also vaccinated using an autogenous Moraxella bovis/bovoculi bacterin vaccine Newport Laboratories, Inc., Worthington, MN for the prevention of pinkeye at 5 and 7 weeks of age.", "Approximately 8.3% n = 126 of all enrolled calves were also vaccinated using an autogenous Moraxella bovis/bovoculi bacterin vaccine Newport Laboratories, Inc., Worthington, MN for the prevention of pinkeye at 5 and 7 weeks of age. All pre-weaned calves were evaluated daily by dairy personnel for calfhood diseases and treated according to standard on-farm treatment protocols. With regard to diarrhea therapy, calves less than two weeks of age with clinical diarrhea received an oral mixture of 118.5 mL 2.08 g bismuth subsalicylate Bismusal Suspension, Durvet, Inc., Blue Springs, MO and 31.5 mL 1575 mg spectinomycin SpectoGard, Bimeda, Inc., Le Sueur, MN once daily for two days.", "With regard to diarrhea therapy, calves less than two weeks of age with clinical diarrhea received an oral mixture of 118.5 mL 2.08 g bismuth subsalicylate Bismusal Suspension, Durvet, Inc., Blue Springs, MO and 31.5 mL 1575 mg spectinomycin SpectoGard, Bimeda, Inc., Le Sueur, MN once daily for two days. Calves older than two weeks of age with clinical diarrhea received oral sulfamethoxazole 1600 mg /trimethoprim 320 mg Amneal Pharmaceuticls of NY, Hauppauge, NY once daily for 2 to 3 days. Repeated treatment was at the discretion of the calf manager.", "Repeated treatment was at the discretion of the calf manager. inductively coupled plasma mass spectrometry . Financial limitations restricted the ability to test more than two samples of each dietary component.", "Financial limitations restricted the ability to test more than two samples of each dietary component. Due to variation of zinc content in duplicate samples, the maximum concentration was used to estimate the daily zinc intake during the first 14 days of life S3 Table . In blocks of 36, enrolled calves were randomized using a random number generator Microsoft Corporation, Redmond, WA to one of three treatment groups: 1 placebo, 2 ZM, or 3 ZS to be administered in the morning milk feeding once daily for 14 days, starting on the day after enrollment.", "In blocks of 36, enrolled calves were randomized using a random number generator Microsoft Corporation, Redmond, WA to one of three treatment groups: 1 placebo, 2 ZM, or 3 ZS to be administered in the morning milk feeding once daily for 14 days, starting on the day after enrollment. During the 14-day zinc treatment period, study calves that did not drink the entire milk bottle were tube-fed the remaining milk by trained technicians using an esophageal feeder disinfected between uses. The ZM treatment group received 0.45 g zinc methionine complex equivalent to 80 mg of elemental zinc as the product Zinpro180 Zinpro Corporation, Eden Prairie, MN combined with 0.44 g milk replacer powder.", "The ZM treatment group received 0.45 g zinc methionine complex equivalent to 80 mg of elemental zinc as the product Zinpro180 Zinpro Corporation, Eden Prairie, MN combined with 0.44 g milk replacer powder. The ZS treatment group received 0.22 g zinc sulfate monohydrate equivalent to 80 mg of elemental zinc Sigma-Aldrich Company, St. Louis, MO combined with 0.44 g milk replacer powder. The placebo treatment group received approximately 0.44 g fresh milk replacer powder.", "The placebo treatment group received approximately 0.44 g fresh milk replacer powder. Zinc supplementation was based on a previously published clinical trial, toxicological studies, and nutritional guidelines 11, . The milk replacer powder used in treatment preparation was the same product used in the pre-weaned calf milk ration.", "The milk replacer powder used in treatment preparation was the same product used in the pre-weaned calf milk ration. Treatments were weighed GX-2000 precision scale; A&D Co Ltd., San Jose, CA at the Dairy Epidemiology Laboratory at the University of California, Davis Veterinary Medicine Teaching and Research Center VMTRC; Aly Lab in Tulare, CA and placed in 2.0 mL microcentrifuge tubes with polypropylene snap caps Fisher Scientific, Pittsburgh, PA . Prior to study commencement, a color was randomly and permanently assigned to each treatment group, after which treatment tubes, calf milk bottles and calf hutches were marked with either pink, orange, or yellow ink.", "Prior to study commencement, a color was randomly and permanently assigned to each treatment group, after which treatment tubes, calf milk bottles and calf hutches were marked with either pink, orange, or yellow ink. The study investigators and technicians responsible for treatment preparation, allocation, administration and data collection were blinded to the color assignment until completion of the trial. For each calf, the study period started at enrollment 24 to 48 hours of age and ended when the calf exited the hutch approximately 90 days of age and from here onwards will be referred to as the \"pre-weaning period.\"", "For each calf, the study period started at enrollment 24 to 48 hours of age and ended when the calf exited the hutch approximately 90 days of age and from here onwards will be referred to as the \"pre-weaning period.\" Calf enrollment and study procedures were performed daily at the time of morning feeding. At enrollment, calf characteristics, including sex, birth date, time of first colostrum feeding, and treatment color were recorded.", "At enrollment, calf characteristics, including sex, birth date, time of first colostrum feeding, and treatment color were recorded. Attitude and feces were assessed daily until 28 days post-enrollment using previously published methods by two study investigators, a veterinarian and a trained researcher. Attitude scoring was based on a threepoint scale.", "Attitude scoring was based on a threepoint scale. A calf with an attitude score of 1 was bright, alert, and readily stood with stimulation; a calf with a score of 2 was quiet, alert, and stood only with moderate stimulation; a calf with a score of 3 exhibited a dull mentation and remained recumbent in response to stimulation. Fecal scoring was performed only on fresh feces and was also based on a three-point scale, as 1 solid , 2 semi-formed/loose , or 3 watery .", "Fecal scoring was performed only on fresh feces and was also based on a three-point scale, as 1 solid , 2 semi-formed/loose , or 3 watery . If no fresh feces were observed in the hutch, \"none seen\" NS was recorded. Body weight was measured using a digital scale at birth, end of treatment, and hutch exit by farm employees with the exception of end of treatment weights, which were recorded by study investigators.", "Body weight was measured using a digital scale at birth, end of treatment, and hutch exit by farm employees with the exception of end of treatment weights, which were recorded by study investigators. Treatments for farm-diagnosed illnesses were performed and recorded on hutch cards by the calf manager. Study investigators regularly recorded this information from cards in addition to extracting treatment event reports from DairyComp 305 Valley Agricultural Software, Tulare, CA .", "Study investigators regularly recorded this information from cards in addition to extracting treatment event reports from DairyComp 305 Valley Agricultural Software, Tulare, CA . Though daily diagnosis and treatment of study calves was performed and recorded by the calf manager, a veterinarian was responsible for examining and determining whether study calves met specific criteria for euthanasia. A calf was euthanized if morbidity was severe enough to significantly depress appetite, hydration status, attitude, mentation, and/or ambulatory capability and the calf showed limited to no immediate response to therapy or supportive care.", "A calf was euthanized if morbidity was severe enough to significantly depress appetite, hydration status, attitude, mentation, and/or ambulatory capability and the calf showed limited to no immediate response to therapy or supportive care. Study calves were euthanized by the calf manager using an on-farm captive bolt protocol established by the herd veterinarian within 3 hours of the decision to euthanize. Enrolled calves that died prior to hutch exit were necropsied within 24 hours of death by a veterinarian.", "Enrolled calves that died prior to hutch exit were necropsied within 24 hours of death by a veterinarian. All calves were monitored throughout the study period for evidence of zinc toxicity. At the end of the study period, calves were cared for at the dairy in accordance with standard commercial operations.", "At the end of the study period, calves were cared for at the dairy in accordance with standard commercial operations. Using the same random number generator, a random sample of 127 calves was selected for additional biologic sampling. Approximately 8 to 10% of the study population was selected due to the financial constraints of additional laboratory testing.", "Approximately 8 to 10% of the study population was selected due to the financial constraints of additional laboratory testing. Serum zinc concentration at baseline and in response to treatment were evaluated for the three treatment groups. Feces collected on the first day of diarrhea and at diarrhea resolution were evaluated for four fecal pathogens Escherichia.", "Feces collected on the first day of diarrhea and at diarrhea resolution were evaluated for four fecal pathogens Escherichia. coli K99, bovine rotavirus and coronavirus, and Cryptosporidium parvum oocysts . Serum total protein.", "Serum total protein. At enrollment, blood from each calf was collected from the jugular vein using a 20 gauge 1-inch multi-sample needle Exelint International Co., Redondo Beach, CA and placed into a 10 mL red top serum tube BD Vacutainer, Franklin Lakes, NJ for determination of total protein. Samples remained at room temperature for up to 12 hours until clotting and were then centrifuged International Equipment Company, CRU-5000, Needham Heights, MA for 15 minutes.", "Samples remained at room temperature for up to 12 hours until clotting and were then centrifuged International Equipment Company, CRU-5000, Needham Heights, MA for 15 minutes. Total protein g/dL was measured by a single investigator HF on decanted serum using a handheld refractometer Sper Scientific, Model 300005, Scottsdale, AZ . Serum zinc.", "Serum zinc. For the 127 randomly-sampled calves, additional blood was collected at enrollment and on the last day of treatment, as described above, and placed into 6.0 mL trace element tubes BD Vacutainer, Franklin Lakes, NJ . Serum was extracted, as described above, and placed in a 2.0 mL microcentrifuge tube with a polypropylene snap cap Fisher Scientific, Pittsburgh, PA and stored at −20˚C until analysis.", "Serum was extracted, as described above, and placed in a 2.0 mL microcentrifuge tube with a polypropylene snap cap Fisher Scientific, Pittsburgh, PA and stored at −20˚C until analysis. Using the same random number generator, 36 of the 127 sampled calves were randomly selected for analysis due to limited financial resources. The pre-and post-zinc supplementation serum samples from each calf n = 72 were analyzed for zinc concentration ppm by ICP-OES inductively coupled plasma-optical emission spectroscopy at the CAHFS Laboratory.", "The pre-and post-zinc supplementation serum samples from each calf n = 72 were analyzed for zinc concentration ppm by ICP-OES inductively coupled plasma-optical emission spectroscopy at the CAHFS Laboratory. Quality control samples, including method blanks, laboratory control spikes, and reference Sigma serum, were run with each set of study samples. Fecal analysis.", "Fecal analysis. For 127 randomly-sampled calves at the first diarrhea episode, fecal samples were collected at two time points, the first day of diarrhea fecal score > 1 and the day diarrhea resolved second day of fecal score = 1 . Using new gloves and sterile lubricant, fresh feces was collected by digital rectal stimulation into 20 mL polypropylene twist-top jars The Cary Company, Addison, IL and stored at -20˚C until analysis.", "Using new gloves and sterile lubricant, fresh feces was collected by digital rectal stimulation into 20 mL polypropylene twist-top jars The Cary Company, Addison, IL and stored at -20˚C until analysis. Fecal samples were tested at the Dairy Epidemiology Laboratory, VMTRC by a veterinarian for E. coli K99, bovine rotavirus and coronavirus, and C. parvum oocysts using a commercial kit Pathasure Enteritis 4; Biovet, Quebec, Canada that is highly specific > 90% and sensitive E. coli K99, 93%; rotavirus, 100%; coronavirus, 77% . For calves with a first-day diarrhea sample on or before 7 days of age, both fecal samples were tested for all four pathogens.", "For calves with a first-day diarrhea sample on or before 7 days of age, both fecal samples were tested for all four pathogens. For calves with a first-day diarrhea sample after 7 days of age, both fecal samples were tested for three pathogens C. parvum, bovine rotavirus and coronavirus . Samples from calves older than 7 days of age were not tested for E. coli K99 based on calves' susceptibility .", "Samples from calves older than 7 days of age were not tested for E. coli K99 based on calves' susceptibility . Testing was performed according to kit manufacturer guidelines, and a low-temperature incubator Fisher Scientific, Model 146, Pittsburgh, PA was used during incubation periods. Test results were recorded as positive or negative using control wells for color comparison.", "Test results were recorded as positive or negative using control wells for color comparison. If the color change was darker than the negative control, the sample was considered positive. Milk zinc.", "Milk zinc. For each of the 107 study days December 15, 2015 to March 31, 2016 of zinc supplementation, approximately 1.5 mL of treated milk from two bottles of each treatment group were randomly collected into 2.0 mL microcentrifuge tubes with polypropylene snap caps Fisher Scientific, Pittsburgh, PA , and stored at −20˚C until analysis. At the time of analysis, milk samples were thawed at 4˚C, vortexed, pooled by week and treatment group, and analyzed for zinc concentration ppm by ICP-MS inductively coupled plasma mass spectrometry at the CAHFS Laboratory.", "At the time of analysis, milk samples were thawed at 4˚C, vortexed, pooled by week and treatment group, and analyzed for zinc concentration ppm by ICP-MS inductively coupled plasma mass spectrometry at the CAHFS Laboratory. Quality control samples, including method blanks, laboratory control spikes, National Institute of Standards and Technology NIST reference materials NIST 1640 , and a spiked milk sample, were run with each set of study samples. Data analysis was performed using R Statistic Software version 3.3.1 and Stata IC 14.2 College Station, TX .", "Data analysis was performed using R Statistic Software version 3.3.1 and Stata IC 14.2 College Station, TX . Statistical differences were determined at the 5% level of significance using per protocol analysis. An ANOVA was used to compare calves in each treatment group at enrollment with respect to birth weight kg , serum total protein g/dL , attitude score, and fecal score.", "An ANOVA was used to compare calves in each treatment group at enrollment with respect to birth weight kg , serum total protein g/dL , attitude score, and fecal score. Oral zinc dose at the start and end of treatment was calculated as the zinc supplementation dose 80 mg divided by calf body weight kg at birth and on the last day of treatment, respectively. An ANOVA was used to compare oral zinc dose mg/kg at treatment start and end as well as mean body weight kg at birth, end of treatment, and hutch exit between treatment groups and between bulls and heifers.", "An ANOVA was used to compare oral zinc dose mg/kg at treatment start and end as well as mean body weight kg at birth, end of treatment, and hutch exit between treatment groups and between bulls and heifers. A Chi-Square test of Independence was used to compare the proportions of calves by sex as well as mortality between treatment groups. For all analyses, Tukey's Honest Significant Difference method was used to generate pairwise comparisons to further characterize significant differences identified by ANOVA.", "For all analyses, Tukey's Honest Significant Difference method was used to generate pairwise comparisons to further characterize significant differences identified by ANOVA. Residual diagnostics, including Residuals vs. Fitted, Scale-Location, Normal Q-Q, and Cook's distances plots, were used to validate all ANOVA model assumptions. The non-parametric Kruskal-Wallis Rank Sum test was used when assumptions were violated.", "The non-parametric Kruskal-Wallis Rank Sum test was used when assumptions were violated. For the randomly-sampled calves, Fisher exact tests were used to compare fecal pathogen prevalence on the first day of diarrhea and at diarrhea resolution between treatment groups. Pairwise comparisons with Bonferroni adjustment were used to identify specific differences in pathogen prevalence.", "Pairwise comparisons with Bonferroni adjustment were used to identify specific differences in pathogen prevalence. An ANOVA was used to compare serum zinc concentration before and after treatment between treatment groups and between bulls and heifers. A Kruskal-Wallis Rank Sum test was used to compare rank sums of zinc concentrations in pooled milk samples from different treatment groups.", "A Kruskal-Wallis Rank Sum test was used to compare rank sums of zinc concentrations in pooled milk samples from different treatment groups. Post-hoc Nemenyi-tests for pairwise multiple comparisons of ranked data were used to identify specific differences in zinc concentrations between groups. For all regression models in this study, univariate regression was first used to evaluate associations between individual predictor variables and outcomes.", "For all regression models in this study, univariate regression was first used to evaluate associations between individual predictor variables and outcomes. All variables with statistical and/or biological significance were initially included in multivariate regression models. The final models were built using a manual backwards elimination procedure, with a significance level of P > 0.05 as the removal criterion.", "The final models were built using a manual backwards elimination procedure, with a significance level of P > 0.05 as the removal criterion. Confounding was assessed using the method of change of estimates, where a 10% or greater change in the estimate of the treatment group regression coefficient between the models with and without the confounder variable was used as evidence of confounding . Variables identified as confounders were included in the final model.", "Variables identified as confounders were included in the final model. All possible interactions between treatment group and predictor variables were explored and retained in the final model if statistically significant. Microbiological cure. For the randomly-sampled calves, logistic regression was used to evaluate associations between microbiological cure and treatment group.", "For the randomly-sampled calves, logistic regression was used to evaluate associations between microbiological cure and treatment group. Other predictor variables of interest included sex, serum total protein, and age on the first day of diarrhea. Microbiological cure was defined as a negative fecal ELISA test at resolution of clinical diarrhea for calves with a positive ELISA test on the first day of diarrhea for at least one of the four fecal pathogens E. coli K99, bovine rotavirus and coronavirus, and C. parvum .", "Microbiological cure was defined as a negative fecal ELISA test at resolution of clinical diarrhea for calves with a positive ELISA test on the first day of diarrhea for at least one of the four fecal pathogens E. coli K99, bovine rotavirus and coronavirus, and C. parvum . Models were generated for each fecal pathogen individually and an overall model, which evaluated microbiological cure at clinical diarrhea resolution for calves that tested positive for any single pathogen on the first day of diarrhea. Serum total protein and calf age at first diarrhea were included in all final models to control for potential confounding by passive transfer status and age.", "Serum total protein and calf age at first diarrhea were included in all final models to control for potential confounding by passive transfer status and age. Mean daily weight change. Linear regression was used to evaluate associations between ADG kg and treatment group during the treatment and pre-weaning periods separately.", "Linear regression was used to evaluate associations between ADG kg and treatment group during the treatment and pre-weaning periods separately. Other predictor variables of interest included sex, birth weight kg , serum total protein, number of days having diarrhea, age, and volume L of milk, Calva, and NuLife electrolytes fed at either end of treatment or hutch exit. For each calf, ADG during the treatment and pre-weaning period was calculated as the difference between birth and end treatment or hutch exit weight, respectively, divided by the number of days between these time points.", "For each calf, ADG during the treatment and pre-weaning period was calculated as the difference between birth and end treatment or hutch exit weight, respectively, divided by the number of days between these time points. To explore the possibility of an interaction between treatment group, sex, and birth weight, the final linear regression model for ADG during the pre-weaning period was stratified by sex. Age at the end of treatment or hutch exit and number of days with diarrhea were dropped from all final models in favor of improved Akaike information criterion AIC .", "Age at the end of treatment or hutch exit and number of days with diarrhea were dropped from all final models in favor of improved Akaike information criterion AIC . Onset of diarrhea and clinical cure. For all survival analyses, diarrhea was defined as a fecal score greater than 1 while diarrhea cure was defined as the second consecutive day of normal feces fecal score of 1 following the first diarrhea episode.", "For all survival analyses, diarrhea was defined as a fecal score greater than 1 while diarrhea cure was defined as the second consecutive day of normal feces fecal score of 1 following the first diarrhea episode. Subsequent episodes of diarrhea were not included in the analysis. Calves that died or did not experience diarrhea or cure from diarrhea were censored.", "Calves that died or did not experience diarrhea or cure from diarrhea were censored. If fresh feces were not observed on daily calf hutch assessment, a fecal score was not recorded for that day and not included in the analyses. Kaplan-Meier analysis was used to determine median days to first diarrhea event and, for those calves that developed diarrhea during the assessment period, median days to clinical diarrhea cure.", "Kaplan-Meier analysis was used to determine median days to first diarrhea event and, for those calves that developed diarrhea during the assessment period, median days to clinical diarrhea cure. A Log Rank test of equality was used to compare survivor functions between treatments. Cox Proportional Hazards regression analysis was used to estimate and compare the hazard of diarrhea and diarrhea cure between treatment groups.", "Cox Proportional Hazards regression analysis was used to estimate and compare the hazard of diarrhea and diarrhea cure between treatment groups. Sex, age, serum total protein at enrollment, birth weight kg , antimicrobial therapy, and application of fresh straw to the hutches were evaluated as predictor variables and potential confounders. When modeling the hazard of diarrhea cure, a binary variable termed therapeutic supplementation indicating whether calves were treated with either ZM, ZS or placebo for all or at least the first 5 days of diarrhea was evaluated as an additional covariate.", "When modeling the hazard of diarrhea cure, a binary variable termed therapeutic supplementation indicating whether calves were treated with either ZM, ZS or placebo for all or at least the first 5 days of diarrhea was evaluated as an additional covariate. A five-day period was selected by the authors based on clinical experience, as five days represents a reasonable duration over which most therapeutic treatments for calf diarrhea should be applied and be expected to alleviate disease. The proportional hazards assumption that the hazard of diarrhea is independent of time was assessed using analysis of Schoenfeld residuals and testing whether the log hazard-ratio function is constant over time.", "The proportional hazards assumption that the hazard of diarrhea is independent of time was assessed using analysis of Schoenfeld residuals and testing whether the log hazard-ratio function is constant over time. Any variable found to violate the proportional hazards assumption was included in the final regression model as a time varying covariate. A total of 1,513 calves were enrolled in the trial.", "A total of 1,513 calves were enrolled in the trial. However, due to failure to immediately recognize exclusion criteria, 23 calves were excluded shortly after enrollment. In addition, 8 calves were excluded due to treatment errors.", "In addition, 8 calves were excluded due to treatment errors. Therefore, a total of 1,482 calves placebo = 500, ZM = 491, ZS = 491 were included in the final analyses. A total of 242 calves 16.3% had minimal fecal output at the time of enrollment while 125 calves 8.4% had abnormal fecal scores of 2 or 3 that were described as meconium.", "A total of 242 calves 16.3% had minimal fecal output at the time of enrollment while 125 calves 8.4% had abnormal fecal scores of 2 or 3 that were described as meconium. All enrolled calves appeared healthy on visual assessment and hence were assumed to have a normal fecal score at the time of enrollment. The three treatment groups at enrollment did not differ significantly in mean birth weight kg P = 0.244 , mean serum total protein g/dL P = 0.541 , mean attitude score P = 0.845 , mean fecal score P = 0.522 , as shown in Table 1 , or distribution of calf sex P = 0.472 .", "The three treatment groups at enrollment did not differ significantly in mean birth weight kg P = 0.244 , mean serum total protein g/dL P = 0.541 , mean attitude score P = 0.845 , mean fecal score P = 0.522 , as shown in Table 1 , or distribution of calf sex P = 0.472 . Of the 1,482 study calves, 21 1.4% died during the trial: 5 calves in the placebo group 1.0% , 11 calves in the ZM group 2.2% , and 5 calves in the ZS group 1.0% . Of these 21 calves that died, 14 66.7% were bulls and 7 33.3% were heifers.", "Of these 21 calves that died, 14 66.7% were bulls and 7 33.3% were heifers. Eighteen of the 21 calves 85.7% were found dead, rather than euthanized, due to acute and spontaneous death without previous obvious clinical signs of disease. The remaining 3 calves were euthanized prior to death due to severe and/or prolonged morbidity.", "The remaining 3 calves were euthanized prior to death due to severe and/or prolonged morbidity. Characteristics and causes of death based on field necropsy of these calves can be found in S4 Table. There was no significant difference in the proportion of calves that died between treatment groups P = 0.168 , though mortality was significantly higher in bulls compared to heifer calves P = 0.049 .", "There was no significant difference in the proportion of calves that died between treatment groups P = 0.168 , though mortality was significantly higher in bulls compared to heifer calves P = 0.049 . Birth weight data were available for all 1,482 calves. Due to calf mortality between enrollment and completion of treatment n = 4 , end treatment weight data were available for 1,478 calves.", "Due to calf mortality between enrollment and completion of treatment n = 4 , end treatment weight data were available for 1,478 calves. Similarly, due to calf mortality n = 21 or missing data for body weight at hutch exit from the dairy's records n = 40 , hutch exit weight data were available for 1,421 calves. A summary of body weight data stratified by treatment group and sex is presented in Table 2 .", "A summary of body weight data stratified by treatment group and sex is presented in Table 2 . Within each treatment group, bull calves showed consistently higher birth weight P < 0.001 , end treatment weight P < 0.001 , and exit hutch weight P < 0.001 compared to heifer calves. However, at birth, end of treatment, or hutch exit there were no differences in body weight between treatment groups for bulls P > 0.1 or heifers P > 0.1 .", "However, at birth, end of treatment, or hutch exit there were no differences in body weight between treatment groups for bulls P > 0.1 or heifers P > 0.1 . The mean attitude scores during the study period were 1.2 across the three treatment groups P = 0.208 . Of 1,482 calves included in the final analysis, A total of 629 treated milk samples were obtained throughout the 107-day study period and pooled by treatment group and week, yielding a total of 16 pooled samples per treatment group.", "Of 1,482 calves included in the final analysis, A total of 629 treated milk samples were obtained throughout the 107-day study period and pooled by treatment group and week, yielding a total of 16 pooled samples per treatment group. Zinc concentrations ppm were significantly higher in pooled milk samples treated with ZM P < 0.001 and ZS P < 0.001 compared to placebo-treated samples, and there were no significant differences between ZM and ZS-treated samples P = 1.000 , as shown in S5 Table. Within zinc treatment groups, oral zinc dose at the start and end of treatment is summarized by sex in S6 Table.", "Within zinc treatment groups, oral zinc dose at the start and end of treatment is summarized by sex in S6 Table. For both ZM-and ZS-treated calves, oral zinc dose at the start P < 0.001 and end P < 0.001 of treatment was significantly higher in heifer versus bull calves. Serum zinc concentrations before and after treatment were obtained from 36 calves n = 12 for each treatment group and are summarized in S7 Table.", "Serum zinc concentrations before and after treatment were obtained from 36 calves n = 12 for each treatment group and are summarized in S7 Table. Overall, there were no significant differences in mean pre-treatment serum zinc concentrations between treatment groups P = 0.233 . Mean post-treatment serum zinc concentrations were significantly higher in calves treated with ZM P < 0.001 and ZS P = 0.002 compared to placebo-treated calves, and there were no significant differences among calves treated with ZM and ZS P = 0.406 .", "Mean post-treatment serum zinc concentrations were significantly higher in calves treated with ZM P < 0.001 and ZS P = 0.002 compared to placebo-treated calves, and there were no significant differences among calves treated with ZM and ZS P = 0.406 . Stratification of serum zinc data by treatment group and sex demonstrated that for ZM-treated calves, heifers had a numerically higher post-treatment serum zinc concentration compared to bulls, though the difference was not statistically significant P = 0.199 . In contrast, in ZStreated calves, heifers had a numerically lower post-treatment serum zinc concentration compared to bulls, though the difference was also not statistically significant P = 0.538 .", "In contrast, in ZStreated calves, heifers had a numerically lower post-treatment serum zinc concentration compared to bulls, though the difference was also not statistically significant P = 0.538 . Fecal analysis data were analyzed for 92 of the 127 randomly-selected calves. The remaining 35 calves were not included in the analysis due to not acquiring diarrhea during the assessment period n = 10 , death prior to final sampling n = 1 , exclusion due to improper treatment regimen n = 1 , or incorrect sampling day n = 23 .The 92 calves had a mean age at onset of diarrhea of 13.3, 11.0 and 11.3 days for ZM, ZS and placebo-treated groups, respectively; and a mean age at resolution of diarrhea of 18.8, 16.1 and 15.7 days for ZM, ZS and placebo-treated groups, respectively.", "The remaining 35 calves were not included in the analysis due to not acquiring diarrhea during the assessment period n = 10 , death prior to final sampling n = 1 , exclusion due to improper treatment regimen n = 1 , or incorrect sampling day n = 23 .The 92 calves had a mean age at onset of diarrhea of 13.3, 11.0 and 11.3 days for ZM, ZS and placebo-treated groups, respectively; and a mean age at resolution of diarrhea of 18.8, 16.1 and 15.7 days for ZM, ZS and placebo-treated groups, respectively. There were no significant differences in the prevalence of E. coli K99 P = 0.694 , rotavirus P = 0.331 , coronavirus P = 0.819 , or C. parvum P = 0.719 fecal shedding on the first day of diarrhea between treatment groups S8 Table . There were no significant differences in the prevalence of E. coli K99 P = 0.256 , rotavirus P = 0.344 , or coronavirus P = 1.000 fecal shedding at resolution of diarrhea between treatment groups, though there was a difference in C. parvum P = 0.006 fecal shedding between treatment groups S9 Table .", "There were no significant differences in the prevalence of E. coli K99 P = 0.256 , rotavirus P = 0.344 , or coronavirus P = 1.000 fecal shedding at resolution of diarrhea between treatment groups, though there was a difference in C. parvum P = 0.006 fecal shedding between treatment groups S9 Table . The prevalence of C. parvum fecal shedding at resolution of diarrhea was significantly higher in calves treated with ZM P = 0.009 and ZS P = 0.023 compared to placebo-treated calves, and there were no significant differences among calves treated with ZM and ZS P = 1.000 . Results of logistic regression models for overall and pathogen-specific microbiological cure are presented in Tables 3-5 .", "Results of logistic regression models for overall and pathogen-specific microbiological cure are presented in Tables 3-5 . For pathogen-specific cure, all calves that tested positive on the first day of diarrhea for coronavirus n = 4 tested negative at clinical diarrhea resolution. For calves that tested positive on the first day of diarrhea for E. coli K99 n = 9 , all placebo-treated calves n = 2 tested negative at clinical diarrhea resolution while half n = 2 of all ZS-treated calves tested either positive or negative at clinical diarrhea resolution, resulting in omission of ZS treatment variable from the model due to collinearity.", "For calves that tested positive on the first day of diarrhea for E. coli K99 n = 9 , all placebo-treated calves n = 2 tested negative at clinical diarrhea resolution while half n = 2 of all ZS-treated calves tested either positive or negative at clinical diarrhea resolution, resulting in omission of ZS treatment variable from the model due to collinearity. Hence, logistic regression analyses for microbiological cure in calves that tested positive for coronavirus and E. coli K99 were not possible. For 59 calves that tested positive for rotavirus on the first day of diarrhea Table 3 , calves treated with ZM had a 50% increased odds of testing negative at diarrhea resolution compared to placebo-treated calves, though this difference was not significant P = 0.549 .", "For 59 calves that tested positive for rotavirus on the first day of diarrhea Table 3 , calves treated with ZM had a 50% increased odds of testing negative at diarrhea resolution compared to placebo-treated calves, though this difference was not significant P = 0.549 . Likewise, calves treated with ZS had 100% increased odds 2 times the odds of testing negative for rotavirus at diarrhea resolution compared to placebo-treated calves, though this difference was also not significant P = 0.314 . However, this model demonstrated a significant main effect of serum total protein, such that for every 1 unit g/dL increase in serum total protein at enrollment, the odds of microbiological cure of rotavirus decreased by 79% P = 0.026 .", "However, this model demonstrated a significant main effect of serum total protein, such that for every 1 unit g/dL increase in serum total protein at enrollment, the odds of microbiological cure of rotavirus decreased by 79% P = 0.026 . For 40 calves that tested positive for Cryptosporidium parvum on the first day of diarrhea Table 4 , calves treated with ZM had an 87% reduced odds of testing negative at diarrhea resolution Effect of zinc on diarrhea in calves compared to placebo-treated calves, though this difference was not significant P = 0.119 . Likewise, calves treated with ZS had a 74% reduced odds of testing negative for Cryptosporidium parvum at diarrhea resolution compared to placebo-treated calves, though this difference was also not significant P = 0.183 .", "Likewise, calves treated with ZS had a 74% reduced odds of testing negative for Cryptosporidium parvum at diarrhea resolution compared to placebo-treated calves, though this difference was also not significant P = 0.183 . For 55 calves that tested positive for any one of the four fecal pathogens E. coli K99, rotavirus, coronavirus, Cryptosporidium parvum on the first day of diarrhea Table 5 , calves treated with ZM had a 25% increased odds of testing negative at diarrhea resolution compared to placebo-treated calves, though this difference was not significant P = 0.769 . Likewise, calves treated with ZS had a 52% increased odds of testing negative for Cryptosporidium parvum at diarrhea resolution compared to placebo-treated calves, though this difference was also not significant P = 0.633 .", "Likewise, calves treated with ZS had a 52% increased odds of testing negative for Cryptosporidium parvum at diarrhea resolution compared to placebo-treated calves, though this difference was also not significant P = 0.633 . However, this model demonstrated that heifer calves had 71% lower odds of microbiological cure of any single fecal pathogen compared to bull calves P = 0.076 . A total of 1,482 calves were included in the linear regression model results for ADG during the treatment period, which are presented in Table 6 .", "A total of 1,482 calves were included in the linear regression model results for ADG during the treatment period, which are presented in Table 6 . There was no significant difference in ADG for ZM-or ZS-treated calves compared to placebo-treated calves, though there were significant main effects of sex, birth weight, and milk volume. Specifically, heifer calves gained 70 g bodyweight per day less compared to bull calves P < 0.001 .", "Specifically, heifer calves gained 70 g bodyweight per day less compared to bull calves P < 0.001 . For every 1 kg increase in birth weight, calves gained 16 g per day less than their herd mates P < 0.001 . For every 1 L increase in milk volume per day during the treatment period, calves gained an additional 13 g per day P < 0.001 .", "For every 1 L increase in milk volume per day during the treatment period, calves gained an additional 13 g per day P < 0.001 . Table 7 summarizes the linear regression analysis of ADG during the pre-weaning period for 1,421 calves which showed a significant difference in ADG for ZM-treated calves compared to placebo-treated calves and in bull versus heifer calves. Milk volume had a significant effect on ADG, such that for every 1 L increase in milk volume per day during the treatment period, calves gained an additional 2 g bodyweight per day P = 0.001 .", "Milk volume had a significant effect on ADG, such that for every 1 L increase in milk volume per day during the treatment period, calves gained an additional 2 g bodyweight per day P = 0.001 . Results of the final model showed a significant main effect for ZM-treated bull calves and a significant interaction term for ZM treatment by sex. After controlling for milk volume received during the treatment Table 6 calves n = 1,482 Effect of zinc on diarrhea in calves period, ZM-treated bulls gained 22 g body weight per day on average more than placebotreated bull calves P = 0.042 and ZM-treated heifers gained 12 g less body weight per day on average compared to placebo-treated heifers P = 0.019 .", "After controlling for milk volume received during the treatment Table 6 calves n = 1,482 Effect of zinc on diarrhea in calves period, ZM-treated bulls gained 22 g body weight per day on average more than placebotreated bull calves P = 0.042 and ZM-treated heifers gained 12 g less body weight per day on average compared to placebo-treated heifers P = 0.019 . When considering the model coefficients for treatment group, sex, and their interaction, bull calves treated with ZM gained 454 g per day 0.432 + 0.022 while female calves treated with ZM gained 0.404 g per day 0.432 + 0.022-0.016-0.034 , hence 50 g per day more gain in male calves compared to heifers treated with ZM P = 0.019 . For ZS-treated calves, there was a numerical decrease in weight gain of 5 g per day in bulls and 11 g per day in heifers compared to placebo-treated calves, though the differences were not significant P = 0.673 bulls; P = 0.681 heifers .", "For ZS-treated calves, there was a numerical decrease in weight gain of 5 g per day in bulls and 11 g per day in heifers compared to placebo-treated calves, though the differences were not significant P = 0.673 bulls; P = 0.681 heifers . Linear regression models of ADG during the pre-weaning period were stratified by sex in order to avoid interpreting a three-way interaction between treatment group, sex, and birth weight. In the heifer model S10 Table , the interaction between ZM treatment and birth weight was significant which implied that birth weight modified the effect of ZM treatment on ADG.", "In the heifer model S10 Table , the interaction between ZM treatment and birth weight was significant which implied that birth weight modified the effect of ZM treatment on ADG. At a 29 kg birth weight two standard deviations below the mean , ZM-treated heifers gained 49 g body weight per day on average less than placebo-treated heifers P = 0.037 . However, at a 49 kg birth weight two standard deviations above the mean , ZM-treated heifers gained 30 g body weight per day on average more than placebo-treated heifers P = 0.037 .", "However, at a 49 kg birth weight two standard deviations above the mean , ZM-treated heifers gained 30 g body weight per day on average more than placebo-treated heifers P = 0.037 . In the bull calves model S11 Table there was no significant interaction between treatment group and birth weight. A total of 1,482 calves were included in the Kaplan-Meier survival analysis of time to first diarrhea event Fig 1 .", "A total of 1,482 calves were included in the Kaplan-Meier survival analysis of time to first diarrhea event Fig 1 . There were no significant differences in median age at onset of diarrhea, specifically, 8, 8 and 7 days for the ZM, ZS and placebo-treated calves, respectively P = 0.402 . Cox proportional hazard regression model for diarrhea hazard are presented in Table 8 .", "Cox proportional hazard regression model for diarrhea hazard are presented in Table 8 . After controlling for age, calves treated with ZM had a 14.7% reduced hazard of diarrhea compared to placebo-treated calves P = 0.015 . Calves treated with ZS had 13.9% reduced hazard of diarrhea compared to placebo-treated calves P = 0.022 .", "Calves treated with ZS had 13.9% reduced hazard of diarrhea compared to placebo-treated calves P = 0.022 . calves n = 1,421 A total of 1,394 calves were included in the Kaplan-Meier survival analysis of time to clinical diarrhea cure Fig 2 , as 88 calves failed to acquire diarrhea during the assessment period. There were no significant differences in the median days to diarrhea cure which was 7 days across all 3 treatment groups P = 0.264 .", "There were no significant differences in the median days to diarrhea cure which was 7 days across all 3 treatment groups P = 0.264 . Cox proportional hazard regression model for diarrhea cure hazard are presented in Table 9 . Results of the final model showed a significant interaction term between treatment and therapeutic supplementation as well as the need for age as a time varying covariate.", "Results of the final model showed a significant interaction term between treatment and therapeutic supplementation as well as the need for age as a time varying covariate. When considering calves that did not receive supplementation, respective to each of the 3 groups, for at least the first five days of diarrhea there was no significant difference between either ZM-and ZS-treated calves compared to placebo-treated calves P = 0.223 ZM, P = 0.134 ZS . However, when considering calves that were supplemented for at least the first five days of diarrhea, ZM-treated calves experienced a 21.4% higher hazard of cure from diarrhea compared to placebo-treated calves P = 0.027 .", "However, when considering calves that were supplemented for at least the first five days of diarrhea, ZM-treated calves experienced a 21.4% higher hazard of cure from diarrhea compared to placebo-treated calves P = 0.027 . Likewise, ZS-treated calves experienced a 13.0% higher hazard of cure from diarrhea compared to placebo-treated calves P = 0.040 . The current trial demonstrated evidence for the beneficial effect of ZM on ADG and neonatal diarrhea as well as an effect of ZS on diarrhea in dairy calves during the pre-weaning period.", "The current trial demonstrated evidence for the beneficial effect of ZM on ADG and neonatal diarrhea as well as an effect of ZS on diarrhea in dairy calves during the pre-weaning period. It is important to consider these results in the context of the entire pre-weaning and hutch period. On average, after 90 days from birth to hutch exit, placebo-treated bull calves gained 38.88 kg body weight while ZM-treated bull calves gained an additional 1.98 kg 40.86 kg .", "On average, after 90 days from birth to hutch exit, placebo-treated bull calves gained 38.88 kg body weight while ZM-treated bull calves gained an additional 1.98 kg 40.86 kg . In contrast, the effect of zinc on weight gain in treated heifers depended on birth weight. Low birth weight heifers treated with ZM gained on average less than a placebo-treated heifer of the same birth weight.", "Low birth weight heifers treated with ZM gained on average less than a placebo-treated heifer of the same birth weight. In contrast, high birth weight heifers treated with ZM gained more than placebo-treated heifers of the same birth weight. The switch in direction of the association between ZM treatment and ADG in heifer calves depending on birth weight suggests a doseresponse effect rather than a true sex-specific effect of ZM on ADG.", "The switch in direction of the association between ZM treatment and ADG in heifer calves depending on birth weight suggests a doseresponse effect rather than a true sex-specific effect of ZM on ADG. Hence, low birth weight calves including heifers may require a lower dose of ZM to mitigate any negative effect of what is otherwise a suitable dose for higher birth weight calves. These findings are in agreement with a previous randomized clinical trial testing the effect of daily oral zinc in diarrheic neonatal Holstein calves which, showed that ZM-treated calves had a numerically, though not significantly increased ADG compared to calves treated with zinc oxide or placebo due to small sample size .", "These findings are in agreement with a previous randomized clinical trial testing the effect of daily oral zinc in diarrheic neonatal Holstein calves which, showed that ZM-treated calves had a numerically, though not significantly increased ADG compared to calves treated with zinc oxide or placebo due to small sample size . In general, our trial findings are in agreement with the large body of human literature supporting the use of oral zinc for the prevention and treatment of diarrhea and impaired growth in children . Zinc supplementation is widely accepted by global health organizations as a vital component of therapy for childhood diarrhea , however, recent reviews of the literature demonstrated heterogeneity in study results on the basis of age, baseline zinc status, geographic location, and supplementation regimen .", "Zinc supplementation is widely accepted by global health organizations as a vital component of therapy for childhood diarrhea , however, recent reviews of the literature demonstrated heterogeneity in study results on the basis of age, baseline zinc status, geographic location, and supplementation regimen . Similar to our findings, a sex-specific response to zinc supplementation has been demonstrated in several human studies. Zinc gluconate administered for diarrhea prevention reduced the incidence of dysentery in treated boys but not girls ; when given therapeutically, it reduced diarrhea duration and frequency more dramatically in boys compared to girls .", "Zinc gluconate administered for diarrhea prevention reduced the incidence of dysentery in treated boys but not girls ; when given therapeutically, it reduced diarrhea duration and frequency more dramatically in boys compared to girls . Similarly, zinc sulfate was shown to improve Effect of zinc on diarrhea in calves diarrhea outcomes in boys but improved growth rates in girls . Broadly, these differences between male and female responses to zinc supplementation are not understood, though theories regarding differences in immune function and response , diarrhea etiology , and nutrient requirements have been proposed.", "Broadly, these differences between male and female responses to zinc supplementation are not understood, though theories regarding differences in immune function and response , diarrhea etiology , and nutrient requirements have been proposed. In the current study, ZM-treated bulls demonstrated increased ADG compared to placebo-treated bulls while ZM-treated heifers demonstrated decreased ADG compared to placebo-treated heifers. However, due to a significant interaction between ZM treatment and birth weight, this reduction in ADG in ZMtreated heifers was overcome with increasing birth weight, such that ZM-treated heifers with birth weights above 42 kg experienced increased ADG during the pre-weaning period, compared to placebo-treated heifers with birth weights above 42 kg.", "However, due to a significant interaction between ZM treatment and birth weight, this reduction in ADG in ZMtreated heifers was overcome with increasing birth weight, such that ZM-treated heifers with birth weights above 42 kg experienced increased ADG during the pre-weaning period, compared to placebo-treated heifers with birth weights above 42 kg. Differences in the growth response to ZM supplementation between bull and heifer calves may have been related to its effect on feed intake. Previous research on the effects of feeding various doses of oral zinc oxide to pre-ruminant dairy calves demonstrated that high levels of oral zinc supplementation resulted in reduced feed intake .", "Previous research on the effects of feeding various doses of oral zinc oxide to pre-ruminant dairy calves demonstrated that high levels of oral zinc supplementation resulted in reduced feed intake . In the current trial, oral ZM dose was estimated to be significantly higher in heifers compared to bulls due to the significantly lower birth weight of heifers. Additionally, serum zinc concentrations in ZM-treated heifers were numerically higher than that of bulls, though this difference was not significant, likely due to the small sample size.", "Additionally, serum zinc concentrations in ZM-treated heifers were numerically higher than that of bulls, though this difference was not significant, likely due to the small sample size. Perhaps the higher zinc dose in heifers was associated with reduced feed intake, leading to reduced growth, and that this effect was more pronounced for ZM compared to ZS. The fact that ZM-treated heifers with birth weights approaching those of average bull calves and, therefore, a similar zinc dose to that in bulls experienced an increase in ADG over placebo-treated heifers similar to that of bull calves partially supports this theory.", "The fact that ZM-treated heifers with birth weights approaching those of average bull calves and, therefore, a similar zinc dose to that in bulls experienced an increase in ADG over placebo-treated heifers similar to that of bull calves partially supports this theory. Although management practices on the study dairy were designed to be identical for both bulls and heifers, it is possible that subtle, unrecognized differences in nutritional and health management may also have contributed to sex-specific differences in weight gain. Nevertheless, future trials are warranted to investigate the potential differences in the dose-response to zinc supplementation between bulls and heifers.", "Nevertheless, future trials are warranted to investigate the potential differences in the dose-response to zinc supplementation between bulls and heifers. We hypothesized that ADG would be increased in zinc-supplemented calves compared to placebo-supplemented calves due to the potential preventive and therapeutic effects of zinc supplementation on neonatal diarrhea. In other words, calf diarrhea is mitigated by zinc supplementation and, therefore, on the causal pathway between zinc and ADG.", "In other words, calf diarrhea is mitigated by zinc supplementation and, therefore, on the causal pathway between zinc and ADG. However, considering the similarly-reduced hazard of diarrhea and increased hazard of cure from diarrhea in both ZM and ZS treatment groups but a lack of effect of ZS on ADG, it is likely that the effect of ZM on ADG is not solely mediated through its effects on diarrhea. Differences in effectiveness between organic and inorganic formulations also may exist.", "Differences in effectiveness between organic and inorganic formulations also may exist. In fact, the underlying mechanism of action of oral zinc remains unknown . Several theories of the mechanisms of action of zinc in the prevention and treatment of childhood diarrhea exist, including a mucosal-protective role, a diarrhea-induced zinc deficiency, an essential element in cell-mediated immunity, and a modifier of intra-luminal electrolyte secretion and absorption 6, .", "Several theories of the mechanisms of action of zinc in the prevention and treatment of childhood diarrhea exist, including a mucosal-protective role, a diarrhea-induced zinc deficiency, an essential element in cell-mediated immunity, and a modifier of intra-luminal electrolyte secretion and absorption 6, . The clinical and practical implications of effects of ZM supplementation on ADG and diarrhea must be considered. Pre-weaned calf diarrhea remains an ongoing issue for the dairy industry.", "Pre-weaned calf diarrhea remains an ongoing issue for the dairy industry. The deleterious effects on calf health and performance and the resulting economic burden create a strong incentive to treat and prevent diarrhea in pre-weaned calves. On large dairy operations like those in California's Central Valley, small changes in disease incidence and duration as well as animal growth and performance can have profound economic consequences.", "On large dairy operations like those in California's Central Valley, small changes in disease incidence and duration as well as animal growth and performance can have profound economic consequences. As a non-antimicrobial product, zinc may become increasingly attractive as antimicrobials in livestock feed are under increased scrutiny and regulation due to concerns about antimicrobial resistance . Prevalence of C. parvum fecal shedding in a random sample of 92 study calves at onset and resolution of diarrhea was significantly higher in calves treated with zinc compared to Placebo-treated calves.", "Prevalence of C. parvum fecal shedding in a random sample of 92 study calves at onset and resolution of diarrhea was significantly higher in calves treated with zinc compared to Placebo-treated calves. In contrast, a previous study where calves that tested positive for C. parvum at the start of diarrhea and were treated with ZM had 16 times higher odds of being fecal ELISA negative at exit compared to the Placebo group P = 0.08; power = 72.3% . The difference in findings may be due to the differences in the timing of diarrhea across treatment groups.", "The difference in findings may be due to the differences in the timing of diarrhea across treatment groups. For the current study's random sample of calves that acquired, survived, and were sampled on the correct days, the mean age of calves on both onset and resolution of diarrhea was higher for ZM and ZS calves compared to placebo-treated calves. Although C. parvum oocyst shedding in infected calves can occur as early as 3 days of age, peak shedding occurs at about 14 days of age .", "Although C. parvum oocyst shedding in infected calves can occur as early as 3 days of age, peak shedding occurs at about 14 days of age . It is possible that the increase in prevalence of C. parvum shedding in ZM and ZS treated groups was due to the increased age of zinc-treated calves compared to placebo-treated calves at resolution of diarrhea. The latter explanation is also supported by our findings that the odds of microbiological cure from C. parvum significantly decreased in older calves, with no significant differences in the odds of cure between treatment groups.", "The latter explanation is also supported by our findings that the odds of microbiological cure from C. parvum significantly decreased in older calves, with no significant differences in the odds of cure between treatment groups. In addition, the current testing did not estimate the concentration of C. parvum shedding which may still differ between treatment groups. Despite the large sample size, the current trial was limited to a single California dairy, which may represent other large dairies but does not reflect all the dairy management systems in California or elsewhere.", "Despite the large sample size, the current trial was limited to a single California dairy, which may represent other large dairies but does not reflect all the dairy management systems in California or elsewhere. Additionally, our results show that calves respond to zinc supplementation for diarrhea prevention differently depending on chemical formulation and calf sex. The latter could be due to differences in body weight between bulls and heifers and may point towards the need for sex-specific dosing.", "The latter could be due to differences in body weight between bulls and heifers and may point towards the need for sex-specific dosing. Furthermore, the current research did not evaluate the potential economic utility of zinc supplementation. Future studies on more accurate dosing of zinc by calf sex, the practical feasibility of weight-based dosing, and the expected cost-effectiveness of zinc administration as part of the management of pre-weaned dairy calves are warranted.", "Future studies on more accurate dosing of zinc by calf sex, the practical feasibility of weight-based dosing, and the expected cost-effectiveness of zinc administration as part of the management of pre-weaned dairy calves are warranted. Finally, our clinical trial was performed on a single, large, predominately Holstein, California dairy over a six-month period, which precluded our ability to evaluate differences due to season or breed. Hence, future studies to assess any modifying effect of breed and seasonal differences on the effect of zinc on calf health and weight gain are also needed.", "Hence, future studies to assess any modifying effect of breed and seasonal differences on the effect of zinc on calf health and weight gain are also needed. The current double blind, block-randomized placebo controlled clinical trial tested the effect of a prophylactic daily oral zinc supplementation in neonatal Holstein calves. Bull calves treated with ZM had a significantly increased ADG 22 g per day during the pre-weaning period compared to placebo-treated bulls.", "Bull calves treated with ZM had a significantly increased ADG 22 g per day during the pre-weaning period compared to placebo-treated bulls. In comparison, ZM-treated heifers had significantly lower average daily gain 9 g per day compared to placebo-treated heifers, although higher ZM doses in low birthweight heifers may explain the lower ADG. Calves treated with either ZM or ZS had significantly lower risks of diarrhea and significantly higher risk of cure from diarrhea over the first 30 days of life compared to placebo-treated calves and hence the current trial demonstrated that zinc supplementation delayed diarrhea and expedited diarrhea recovery in pre-weaned calves.", "Calves treated with either ZM or ZS had significantly lower risks of diarrhea and significantly higher risk of cure from diarrhea over the first 30 days of life compared to placebo-treated calves and hence the current trial demonstrated that zinc supplementation delayed diarrhea and expedited diarrhea recovery in pre-weaned calves. Additionally, zinc improved weight gain differentially in bulls compared to heifers, indicating the need for further research to investigate zinc dosing in calves. Supporting information S1 DOCX S1 Dataset.", "Supporting information S1 DOCX S1 Dataset. Raw data collected from trial, organized as separate excel sheets for enrollment, daily assessment, serum total protein, birth weight, exit treatment weight, exit trial weight, serum zinc testing, fecal samples, fecal testing, milk testing, and dead calves. XLSX" ]

[ "The objective of this clinical trial was to evaluate the effectiveness of zinc supplementation on diarrhea and average daily weight gain ADG in pre-weaned dairy calves. A total of 1,482 healthy Holstein heifer and bull calves from a large California dairy were enrolled at 24 to 48 hours of age until hutch exit at approximately 90 days of age. Calves were block-randomized by time to one of three treatments: 1 placebo, 2 zinc methionine ZM , or 3 zinc sulfate ZS administered in milk once daily for 14 days.", "Calves were block-randomized by time to one of three treatments: 1 placebo, 2 zinc methionine ZM , or 3 zinc sulfate ZS administered in milk once daily for 14 days. Serum total protein at enrollment and body weight at birth, treatment end, and hutch exit were measured. Fecal consistency was assessed daily for 28 days post-enrollment.", "Fecal consistency was assessed daily for 28 days post-enrollment. For a random sample of 127 calves, serum zinc concentrations before and after treatment and a fecal antigen ELISA at diarrhea start and resolution for Escherichia coli K99, rotavirus, coronavirus, and Cryptosporidium parvum were performed. Linear regression showed that ZM-treated bull calves had 22 g increased ADG compared to placebo-treated bulls P = 0.042 .", "Linear regression showed that ZM-treated bull calves had 22 g increased ADG compared to placebo-treated bulls P = 0.042 . ZM-treated heifers had 9 g decreased ADG compared to placebo-treated heifers P = 0.037 , after adjusting for average birth weight. Sex-stratified models showed that high birth weight heifers treated with ZM gained more than placebo-treated heifers of the same birth weight, which suggests a dose-response effect rather than a true sex-specific effect of ZM on ADG.", "Sex-stratified models showed that high birth weight heifers treated with ZM gained more than placebo-treated heifers of the same birth weight, which suggests a dose-response effect rather than a true sex-specific effect of ZM on ADG. Cox regression showed that ZM and ZS-treated calves had a 14.7% P = 0.015 and 13.9% P = 0.022 reduced hazard of diarrhea, respectively, compared to placebo-treated calves. Calves supplemented for at least the first five days of diarrhea with ZM and ZS had a 21.4% P = 0.027 and 13.0% P = 0.040 increased hazard of cure from diarrhea, respectively, compared to placebo-treated calves.", "Calves supplemented for at least the first five days of diarrhea with ZM and ZS had a 21.4% P = 0.027 and 13.0% P = 0.040 increased hazard of cure from diarrhea, respectively, compared to placebo-treated calves. Logistic regression showed that the odds of microbiological cure at diarrhea resolution for rotavirus, C. parvum, or any single fecal pathogen was not different between treatment groups. Zinc supplementation delayed diarrhea and expedited diarrhea recovery in pre-weaned calves.", "Zinc supplementation delayed diarrhea and expedited diarrhea recovery in pre-weaned calves. Additionally, zinc improved weight gain differentially in bulls compared to heifers, indicating a research need for sex-specific dosing. Text: Introduction Diarrhea is the leading cause of morbidity and mortality and the most common reason for antimicrobial drug treatments in pre-weaned dairy heifers .", "Text: Introduction Diarrhea is the leading cause of morbidity and mortality and the most common reason for antimicrobial drug treatments in pre-weaned dairy heifers . A USDA survey of preweaned dairy heifers reported that 24% experienced diarrhea and 18% received antimicrobial treatment for it . Diarrhea is also a leading cause of morbidity and the second foremost cause of mortality in children with over 1 billion cases and a half a million deaths annually .", "Diarrhea is also a leading cause of morbidity and the second foremost cause of mortality in children with over 1 billion cases and a half a million deaths annually . Zinc supplementation in children decreases the incidence, duration, and severity of diarrhea, increases recovery rates, decreases the use of antibiotics and antidiarrheal medications, and reduces mortality . In a clinical trial that established a non-toxic zinc dose and investigated its therapeutic use for diarrhea in neonatal dairy calves, zinc-treated calves had numerically quicker clinical recovery, increased weight gain, and higher odds of fecal clearance of Cryptosporidium parvum between diarrhea onset and recovery compared with placebotreated calves .", "In a clinical trial that established a non-toxic zinc dose and investigated its therapeutic use for diarrhea in neonatal dairy calves, zinc-treated calves had numerically quicker clinical recovery, increased weight gain, and higher odds of fecal clearance of Cryptosporidium parvum between diarrhea onset and recovery compared with placebotreated calves . As a result, zinc supplementation may be beneficial for prevention of diarrhea in dairy calves and, thus, minimize antimicrobial use. However, studies investigating zinc's potential effectiveness are lacking.", "However, studies investigating zinc's potential effectiveness are lacking. In children, both organic zinc acetate, zinc gluconate, and zinc methionine and inorganic zinc sulfate and zinc oxide zinc formulations are beneficial in the prevention and treatment of childhood diarrhea . However, differing bioavailability was observed in several animal studies .", "However, differing bioavailability was observed in several animal studies . In addition, the underlying mechanism of action of oral zinc is unknown . Hence, contrasting the effect, if any, of organic compared to inorganic zinc formulations in pre-weaned calves may help identify differences in mode of action.", "Hence, contrasting the effect, if any, of organic compared to inorganic zinc formulations in pre-weaned calves may help identify differences in mode of action. The objective of this clinical trial was to compare average daily weight gain ADG and the incidence and duration of diarrhea in pre-weaned dairy calves randomly assigned to receive either organic zinc methionine ZM , inorganic zinc sulfate ZS , or a placebo in milk once daily for 14 days. By elucidating the potential role of zinc supplementation in prevention of diarrhea in preweaned dairy calves, calf morbidity, mortality, and antimicrobial usage may be mitigated.", "By elucidating the potential role of zinc supplementation in prevention of diarrhea in preweaned dairy calves, calf morbidity, mortality, and antimicrobial usage may be mitigated. A double-blind, block randomized, placebo-controlled clinical trial was conducted between December 14, 2015 and June 15, 2016 on a large dairy in California's San Joaquin Valley. The dairy was selected based on the owner and calf manager's willingness to participate in the study.", "The dairy was selected based on the owner and calf manager's willingness to participate in the study. The dairy herd was composed of 5,500 lactating cows, predominantly Holsteins, and housed approximately 1,600 pre-weaned calves. Approximately 75% of the calves were born on the participating dairy and 25% were born on an affiliated dairy located approximately 10 miles away.", "Approximately 75% of the calves were born on the participating dairy and 25% were born on an affiliated dairy located approximately 10 miles away. Calves enrolled in the trial included healthy Holstein heifer or bull calves 24 to 48 hours of age. Calves were determined to be healthy via visual examination by a veterinarian HF or a trained researcher.", "Calves were determined to be healthy via visual examination by a veterinarian HF or a trained researcher. Calves were excluded if they had obvious morbidities or congenital defects, were non-Holstein, born on the affiliated dairy, younger than 24 hours of age or older than 48 hours of age at the time of enrollment. Calves from the affiliated dairy were excluded due to differences in physical location and management practices of pre-partum cows.", "Calves from the affiliated dairy were excluded due to differences in physical location and management practices of pre-partum cows. All procedures were approved by the University of California Davis Institutional Animal Care and Use Committee protocol number 18067 Approved: March 6, 2014 . 107 g between treatment groups Stata, College Station, TX .", "107 g between treatment groups Stata, College Station, TX . After allowing for 15% attrition and assuming 50% incidence of diarrhea based on study authors expert opinion, and a difference in ADG of 107g , a sample size of 500 calves per treatment group n = 1500 total was deemed required. Newborn calves were removed from the dam within an hour of birth and placed in a strawbedded, group calf pen where their navels were dipped in an iodine-based solution.", "Newborn calves were removed from the dam within an hour of birth and placed in a strawbedded, group calf pen where their navels were dipped in an iodine-based solution. Each calf received 4 liters of colostrum within 1 hour of birth and a second colostrum feeding 2 liters 6-10 hours after birth. Colostrum was refrigerated for < 48 hours and heated in a hot water bath prior to feeding using an esophageal tube feeder.", "Colostrum was refrigerated for < 48 hours and heated in a hot water bath prior to feeding using an esophageal tube feeder. Within 18 hours of birth, pre-weaned calves were transported to individual metal hutches initially bedded with almond shells. Straw hay was later added to wet and muddy hutches throughout the pre-weaning period.", "Straw hay was later added to wet and muddy hutches throughout the pre-weaning period. For the first 14 days of life, pre-weaned calves were bottle-fed 1.9 liters of milk twice daily and 1.9 liters of a commercial oral electrolyte solution Calva Lyte; Calva Products, Inc., Acampo, CA once daily between milk feedings. Milk consisted of a combination of pasteurized waste milk, rehydrated commercial milk replacer powder Strauss Feeds LLC, Watertown, WI , tetracycline and neomycin powder, and additional supplements S1 Table .", "Milk consisted of a combination of pasteurized waste milk, rehydrated commercial milk replacer powder Strauss Feeds LLC, Watertown, WI , tetracycline and neomycin powder, and additional supplements S1 Table . The proportion of pasteurized waste milk to milk replacer varied with each feeding, as the volume of waste milk varied with changes in the number and production of cows contributing to the waste milk tank. After 14 days of age, calves were bottle-fed 2.8 liters of milk twice daily.", "After 14 days of age, calves were bottle-fed 2.8 liters of milk twice daily. Calves with clinical diarrhea received 1.9 liters of a commercial oral electrolyte solution NuLife; Genex Cooperative, Inc., Shawano, WI once daily between milk feedings. A list of ingredients that make up the two oral electrolyte solutions can be found in S2 Table.", "A list of ingredients that make up the two oral electrolyte solutions can be found in S2 Table. All pre-weaned calves had free choice access to water and a calf starter grain mix. Calves were gradually weaned over a 10-day period, starting at approximately 60 days of age after which calves received a grower grain mix until 90 days of age when they were moved to group pens.", "Calves were gradually weaned over a 10-day period, starting at approximately 60 days of age after which calves received a grower grain mix until 90 days of age when they were moved to group pens. Each calf received 1 mL of a selenium supplement MU-SE; Merck Animal Health, Boxmeer, Netherlands intramuscularly within 24 hours of age and an intranasal vaccine Inforce 3, Zoetis, Inc., Florham Park, NJ within 48 hours of age and again near the time of weaning. Approximately 8.3% n = 126 of all enrolled calves were also vaccinated using an autogenous Moraxella bovis/bovoculi bacterin vaccine Newport Laboratories, Inc., Worthington, MN for the prevention of pinkeye at 5 and 7 weeks of age.", "Approximately 8.3% n = 126 of all enrolled calves were also vaccinated using an autogenous Moraxella bovis/bovoculi bacterin vaccine Newport Laboratories, Inc., Worthington, MN for the prevention of pinkeye at 5 and 7 weeks of age. All pre-weaned calves were evaluated daily by dairy personnel for calfhood diseases and treated according to standard on-farm treatment protocols. With regard to diarrhea therapy, calves less than two weeks of age with clinical diarrhea received an oral mixture of 118.5 mL 2.08 g bismuth subsalicylate Bismusal Suspension, Durvet, Inc., Blue Springs, MO and 31.5 mL 1575 mg spectinomycin SpectoGard, Bimeda, Inc., Le Sueur, MN once daily for two days.", "With regard to diarrhea therapy, calves less than two weeks of age with clinical diarrhea received an oral mixture of 118.5 mL 2.08 g bismuth subsalicylate Bismusal Suspension, Durvet, Inc., Blue Springs, MO and 31.5 mL 1575 mg spectinomycin SpectoGard, Bimeda, Inc., Le Sueur, MN once daily for two days. Calves older than two weeks of age with clinical diarrhea received oral sulfamethoxazole 1600 mg /trimethoprim 320 mg Amneal Pharmaceuticls of NY, Hauppauge, NY once daily for 2 to 3 days. Repeated treatment was at the discretion of the calf manager.", "Repeated treatment was at the discretion of the calf manager. inductively coupled plasma mass spectrometry . Financial limitations restricted the ability to test more than two samples of each dietary component.", "Financial limitations restricted the ability to test more than two samples of each dietary component. Due to variation of zinc content in duplicate samples, the maximum concentration was used to estimate the daily zinc intake during the first 14 days of life S3 Table . In blocks of 36, enrolled calves were randomized using a random number generator Microsoft Corporation, Redmond, WA to one of three treatment groups: 1 placebo, 2 ZM, or 3 ZS to be administered in the morning milk feeding once daily for 14 days, starting on the day after enrollment.", "In blocks of 36, enrolled calves were randomized using a random number generator Microsoft Corporation, Redmond, WA to one of three treatment groups: 1 placebo, 2 ZM, or 3 ZS to be administered in the morning milk feeding once daily for 14 days, starting on the day after enrollment. During the 14-day zinc treatment period, study calves that did not drink the entire milk bottle were tube-fed the remaining milk by trained technicians using an esophageal feeder disinfected between uses. The ZM treatment group received 0.45 g zinc methionine complex equivalent to 80 mg of elemental zinc as the product Zinpro180 Zinpro Corporation, Eden Prairie, MN combined with 0.44 g milk replacer powder.", "The ZM treatment group received 0.45 g zinc methionine complex equivalent to 80 mg of elemental zinc as the product Zinpro180 Zinpro Corporation, Eden Prairie, MN combined with 0.44 g milk replacer powder. The ZS treatment group received 0.22 g zinc sulfate monohydrate equivalent to 80 mg of elemental zinc Sigma-Aldrich Company, St. Louis, MO combined with 0.44 g milk replacer powder. The placebo treatment group received approximately 0.44 g fresh milk replacer powder.", "The placebo treatment group received approximately 0.44 g fresh milk replacer powder. Zinc supplementation was based on a previously published clinical trial, toxicological studies, and nutritional guidelines 11, . The milk replacer powder used in treatment preparation was the same product used in the pre-weaned calf milk ration.", "The milk replacer powder used in treatment preparation was the same product used in the pre-weaned calf milk ration. Treatments were weighed GX-2000 precision scale; A&D Co Ltd., San Jose, CA at the Dairy Epidemiology Laboratory at the University of California, Davis Veterinary Medicine Teaching and Research Center VMTRC; Aly Lab in Tulare, CA and placed in 2.0 mL microcentrifuge tubes with polypropylene snap caps Fisher Scientific, Pittsburgh, PA . Prior to study commencement, a color was randomly and permanently assigned to each treatment group, after which treatment tubes, calf milk bottles and calf hutches were marked with either pink, orange, or yellow ink.", "Prior to study commencement, a color was randomly and permanently assigned to each treatment group, after which treatment tubes, calf milk bottles and calf hutches were marked with either pink, orange, or yellow ink. The study investigators and technicians responsible for treatment preparation, allocation, administration and data collection were blinded to the color assignment until completion of the trial. For each calf, the study period started at enrollment 24 to 48 hours of age and ended when the calf exited the hutch approximately 90 days of age and from here onwards will be referred to as the \"pre-weaning period.\"", "For each calf, the study period started at enrollment 24 to 48 hours of age and ended when the calf exited the hutch approximately 90 days of age and from here onwards will be referred to as the \"pre-weaning period.\" Calf enrollment and study procedures were performed daily at the time of morning feeding. At enrollment, calf characteristics, including sex, birth date, time of first colostrum feeding, and treatment color were recorded.", "At enrollment, calf characteristics, including sex, birth date, time of first colostrum feeding, and treatment color were recorded. Attitude and feces were assessed daily until 28 days post-enrollment using previously published methods by two study investigators, a veterinarian and a trained researcher. Attitude scoring was based on a threepoint scale.", "Attitude scoring was based on a threepoint scale. A calf with an attitude score of 1 was bright, alert, and readily stood with stimulation; a calf with a score of 2 was quiet, alert, and stood only with moderate stimulation; a calf with a score of 3 exhibited a dull mentation and remained recumbent in response to stimulation. Fecal scoring was performed only on fresh feces and was also based on a three-point scale, as 1 solid , 2 semi-formed/loose , or 3 watery .", "Fecal scoring was performed only on fresh feces and was also based on a three-point scale, as 1 solid , 2 semi-formed/loose , or 3 watery . If no fresh feces were observed in the hutch, \"none seen\" NS was recorded. Body weight was measured using a digital scale at birth, end of treatment, and hutch exit by farm employees with the exception of end of treatment weights, which were recorded by study investigators.", "Body weight was measured using a digital scale at birth, end of treatment, and hutch exit by farm employees with the exception of end of treatment weights, which were recorded by study investigators. Treatments for farm-diagnosed illnesses were performed and recorded on hutch cards by the calf manager. Study investigators regularly recorded this information from cards in addition to extracting treatment event reports from DairyComp 305 Valley Agricultural Software, Tulare, CA .", "Study investigators regularly recorded this information from cards in addition to extracting treatment event reports from DairyComp 305 Valley Agricultural Software, Tulare, CA . Though daily diagnosis and treatment of study calves was performed and recorded by the calf manager, a veterinarian was responsible for examining and determining whether study calves met specific criteria for euthanasia. A calf was euthanized if morbidity was severe enough to significantly depress appetite, hydration status, attitude, mentation, and/or ambulatory capability and the calf showed limited to no immediate response to therapy or supportive care.", "A calf was euthanized if morbidity was severe enough to significantly depress appetite, hydration status, attitude, mentation, and/or ambulatory capability and the calf showed limited to no immediate response to therapy or supportive care. Study calves were euthanized by the calf manager using an on-farm captive bolt protocol established by the herd veterinarian within 3 hours of the decision to euthanize. Enrolled calves that died prior to hutch exit were necropsied within 24 hours of death by a veterinarian.", "Enrolled calves that died prior to hutch exit were necropsied within 24 hours of death by a veterinarian. All calves were monitored throughout the study period for evidence of zinc toxicity. At the end of the study period, calves were cared for at the dairy in accordance with standard commercial operations.", "At the end of the study period, calves were cared for at the dairy in accordance with standard commercial operations. Using the same random number generator, a random sample of 127 calves was selected for additional biologic sampling. Approximately 8 to 10% of the study population was selected due to the financial constraints of additional laboratory testing.", "Approximately 8 to 10% of the study population was selected due to the financial constraints of additional laboratory testing. Serum zinc concentration at baseline and in response to treatment were evaluated for the three treatment groups. Feces collected on the first day of diarrhea and at diarrhea resolution were evaluated for four fecal pathogens Escherichia.", "Feces collected on the first day of diarrhea and at diarrhea resolution were evaluated for four fecal pathogens Escherichia. coli K99, bovine rotavirus and coronavirus, and Cryptosporidium parvum oocysts . Serum total protein.", "Serum total protein. At enrollment, blood from each calf was collected from the jugular vein using a 20 gauge 1-inch multi-sample needle Exelint International Co., Redondo Beach, CA and placed into a 10 mL red top serum tube BD Vacutainer, Franklin Lakes, NJ for determination of total protein. Samples remained at room temperature for up to 12 hours until clotting and were then centrifuged International Equipment Company, CRU-5000, Needham Heights, MA for 15 minutes.", "Samples remained at room temperature for up to 12 hours until clotting and were then centrifuged International Equipment Company, CRU-5000, Needham Heights, MA for 15 minutes. Total protein g/dL was measured by a single investigator HF on decanted serum using a handheld refractometer Sper Scientific, Model 300005, Scottsdale, AZ . Serum zinc.", "Serum zinc. For the 127 randomly-sampled calves, additional blood was collected at enrollment and on the last day of treatment, as described above, and placed into 6.0 mL trace element tubes BD Vacutainer, Franklin Lakes, NJ . Serum was extracted, as described above, and placed in a 2.0 mL microcentrifuge tube with a polypropylene snap cap Fisher Scientific, Pittsburgh, PA and stored at −20˚C until analysis.", "Serum was extracted, as described above, and placed in a 2.0 mL microcentrifuge tube with a polypropylene snap cap Fisher Scientific, Pittsburgh, PA and stored at −20˚C until analysis. Using the same random number generator, 36 of the 127 sampled calves were randomly selected for analysis due to limited financial resources. The pre-and post-zinc supplementation serum samples from each calf n = 72 were analyzed for zinc concentration ppm by ICP-OES inductively coupled plasma-optical emission spectroscopy at the CAHFS Laboratory.", "The pre-and post-zinc supplementation serum samples from each calf n = 72 were analyzed for zinc concentration ppm by ICP-OES inductively coupled plasma-optical emission spectroscopy at the CAHFS Laboratory. Quality control samples, including method blanks, laboratory control spikes, and reference Sigma serum, were run with each set of study samples. Fecal analysis.", "Fecal analysis. For 127 randomly-sampled calves at the first diarrhea episode, fecal samples were collected at two time points, the first day of diarrhea fecal score > 1 and the day diarrhea resolved second day of fecal score = 1 . Using new gloves and sterile lubricant, fresh feces was collected by digital rectal stimulation into 20 mL polypropylene twist-top jars The Cary Company, Addison, IL and stored at -20˚C until analysis.", "Using new gloves and sterile lubricant, fresh feces was collected by digital rectal stimulation into 20 mL polypropylene twist-top jars The Cary Company, Addison, IL and stored at -20˚C until analysis. Fecal samples were tested at the Dairy Epidemiology Laboratory, VMTRC by a veterinarian for E. coli K99, bovine rotavirus and coronavirus, and C. parvum oocysts using a commercial kit Pathasure Enteritis 4; Biovet, Quebec, Canada that is highly specific > 90% and sensitive E. coli K99, 93%; rotavirus, 100%; coronavirus, 77% . For calves with a first-day diarrhea sample on or before 7 days of age, both fecal samples were tested for all four pathogens.", "For calves with a first-day diarrhea sample on or before 7 days of age, both fecal samples were tested for all four pathogens. For calves with a first-day diarrhea sample after 7 days of age, both fecal samples were tested for three pathogens C. parvum, bovine rotavirus and coronavirus . Samples from calves older than 7 days of age were not tested for E. coli K99 based on calves' susceptibility .", "Samples from calves older than 7 days of age were not tested for E. coli K99 based on calves' susceptibility . Testing was performed according to kit manufacturer guidelines, and a low-temperature incubator Fisher Scientific, Model 146, Pittsburgh, PA was used during incubation periods. Test results were recorded as positive or negative using control wells for color comparison.", "Test results were recorded as positive or negative using control wells for color comparison. If the color change was darker than the negative control, the sample was considered positive. Milk zinc.", "Milk zinc. For each of the 107 study days December 15, 2015 to March 31, 2016 of zinc supplementation, approximately 1.5 mL of treated milk from two bottles of each treatment group were randomly collected into 2.0 mL microcentrifuge tubes with polypropylene snap caps Fisher Scientific, Pittsburgh, PA , and stored at −20˚C until analysis. At the time of analysis, milk samples were thawed at 4˚C, vortexed, pooled by week and treatment group, and analyzed for zinc concentration ppm by ICP-MS inductively coupled plasma mass spectrometry at the CAHFS Laboratory.", "At the time of analysis, milk samples were thawed at 4˚C, vortexed, pooled by week and treatment group, and analyzed for zinc concentration ppm by ICP-MS inductively coupled plasma mass spectrometry at the CAHFS Laboratory. Quality control samples, including method blanks, laboratory control spikes, National Institute of Standards and Technology NIST reference materials NIST 1640 , and a spiked milk sample, were run with each set of study samples. Data analysis was performed using R Statistic Software version 3.3.1 and Stata IC 14.2 College Station, TX .", "Data analysis was performed using R Statistic Software version 3.3.1 and Stata IC 14.2 College Station, TX . Statistical differences were determined at the 5% level of significance using per protocol analysis. An ANOVA was used to compare calves in each treatment group at enrollment with respect to birth weight kg , serum total protein g/dL , attitude score, and fecal score.", "An ANOVA was used to compare calves in each treatment group at enrollment with respect to birth weight kg , serum total protein g/dL , attitude score, and fecal score. Oral zinc dose at the start and end of treatment was calculated as the zinc supplementation dose 80 mg divided by calf body weight kg at birth and on the last day of treatment, respectively. An ANOVA was used to compare oral zinc dose mg/kg at treatment start and end as well as mean body weight kg at birth, end of treatment, and hutch exit between treatment groups and between bulls and heifers.", "An ANOVA was used to compare oral zinc dose mg/kg at treatment start and end as well as mean body weight kg at birth, end of treatment, and hutch exit between treatment groups and between bulls and heifers. A Chi-Square test of Independence was used to compare the proportions of calves by sex as well as mortality between treatment groups. For all analyses, Tukey's Honest Significant Difference method was used to generate pairwise comparisons to further characterize significant differences identified by ANOVA.", "For all analyses, Tukey's Honest Significant Difference method was used to generate pairwise comparisons to further characterize significant differences identified by ANOVA. Residual diagnostics, including Residuals vs. Fitted, Scale-Location, Normal Q-Q, and Cook's distances plots, were used to validate all ANOVA model assumptions. The non-parametric Kruskal-Wallis Rank Sum test was used when assumptions were violated.", "The non-parametric Kruskal-Wallis Rank Sum test was used when assumptions were violated. For the randomly-sampled calves, Fisher exact tests were used to compare fecal pathogen prevalence on the first day of diarrhea and at diarrhea resolution between treatment groups. Pairwise comparisons with Bonferroni adjustment were used to identify specific differences in pathogen prevalence.", "Pairwise comparisons with Bonferroni adjustment were used to identify specific differences in pathogen prevalence. An ANOVA was used to compare serum zinc concentration before and after treatment between treatment groups and between bulls and heifers. A Kruskal-Wallis Rank Sum test was used to compare rank sums of zinc concentrations in pooled milk samples from different treatment groups.", "A Kruskal-Wallis Rank Sum test was used to compare rank sums of zinc concentrations in pooled milk samples from different treatment groups. Post-hoc Nemenyi-tests for pairwise multiple comparisons of ranked data were used to identify specific differences in zinc concentrations between groups. For all regression models in this study, univariate regression was first used to evaluate associations between individual predictor variables and outcomes.", "For all regression models in this study, univariate regression was first used to evaluate associations between individual predictor variables and outcomes. All variables with statistical and/or biological significance were initially included in multivariate regression models. The final models were built using a manual backwards elimination procedure, with a significance level of P > 0.05 as the removal criterion.", "The final models were built using a manual backwards elimination procedure, with a significance level of P > 0.05 as the removal criterion. Confounding was assessed using the method of change of estimates, where a 10% or greater change in the estimate of the treatment group regression coefficient between the models with and without the confounder variable was used as evidence of confounding . Variables identified as confounders were included in the final model.", "Variables identified as confounders were included in the final model. All possible interactions between treatment group and predictor variables were explored and retained in the final model if statistically significant. Microbiological cure. For the randomly-sampled calves, logistic regression was used to evaluate associations between microbiological cure and treatment group.", "For the randomly-sampled calves, logistic regression was used to evaluate associations between microbiological cure and treatment group. Other predictor variables of interest included sex, serum total protein, and age on the first day of diarrhea. Microbiological cure was defined as a negative fecal ELISA test at resolution of clinical diarrhea for calves with a positive ELISA test on the first day of diarrhea for at least one of the four fecal pathogens E. coli K99, bovine rotavirus and coronavirus, and C. parvum .", "Microbiological cure was defined as a negative fecal ELISA test at resolution of clinical diarrhea for calves with a positive ELISA test on the first day of diarrhea for at least one of the four fecal pathogens E. coli K99, bovine rotavirus and coronavirus, and C. parvum . Models were generated for each fecal pathogen individually and an overall model, which evaluated microbiological cure at clinical diarrhea resolution for calves that tested positive for any single pathogen on the first day of diarrhea. Serum total protein and calf age at first diarrhea were included in all final models to control for potential confounding by passive transfer status and age.", "Serum total protein and calf age at first diarrhea were included in all final models to control for potential confounding by passive transfer status and age. Mean daily weight change. Linear regression was used to evaluate associations between ADG kg and treatment group during the treatment and pre-weaning periods separately.", "Linear regression was used to evaluate associations between ADG kg and treatment group during the treatment and pre-weaning periods separately. Other predictor variables of interest included sex, birth weight kg , serum total protein, number of days having diarrhea, age, and volume L of milk, Calva, and NuLife electrolytes fed at either end of treatment or hutch exit. For each calf, ADG during the treatment and pre-weaning period was calculated as the difference between birth and end treatment or hutch exit weight, respectively, divided by the number of days between these time points.", "For each calf, ADG during the treatment and pre-weaning period was calculated as the difference between birth and end treatment or hutch exit weight, respectively, divided by the number of days between these time points. To explore the possibility of an interaction between treatment group, sex, and birth weight, the final linear regression model for ADG during the pre-weaning period was stratified by sex. Age at the end of treatment or hutch exit and number of days with diarrhea were dropped from all final models in favor of improved Akaike information criterion AIC .", "Age at the end of treatment or hutch exit and number of days with diarrhea were dropped from all final models in favor of improved Akaike information criterion AIC . Onset of diarrhea and clinical cure. For all survival analyses, diarrhea was defined as a fecal score greater than 1 while diarrhea cure was defined as the second consecutive day of normal feces fecal score of 1 following the first diarrhea episode.", "For all survival analyses, diarrhea was defined as a fecal score greater than 1 while diarrhea cure was defined as the second consecutive day of normal feces fecal score of 1 following the first diarrhea episode. Subsequent episodes of diarrhea were not included in the analysis. Calves that died or did not experience diarrhea or cure from diarrhea were censored.", "Calves that died or did not experience diarrhea or cure from diarrhea were censored. If fresh feces were not observed on daily calf hutch assessment, a fecal score was not recorded for that day and not included in the analyses. Kaplan-Meier analysis was used to determine median days to first diarrhea event and, for those calves that developed diarrhea during the assessment period, median days to clinical diarrhea cure.", "Kaplan-Meier analysis was used to determine median days to first diarrhea event and, for those calves that developed diarrhea during the assessment period, median days to clinical diarrhea cure. A Log Rank test of equality was used to compare survivor functions between treatments. Cox Proportional Hazards regression analysis was used to estimate and compare the hazard of diarrhea and diarrhea cure between treatment groups.", "Cox Proportional Hazards regression analysis was used to estimate and compare the hazard of diarrhea and diarrhea cure between treatment groups. Sex, age, serum total protein at enrollment, birth weight kg , antimicrobial therapy, and application of fresh straw to the hutches were evaluated as predictor variables and potential confounders. When modeling the hazard of diarrhea cure, a binary variable termed therapeutic supplementation indicating whether calves were treated with either ZM, ZS or placebo for all or at least the first 5 days of diarrhea was evaluated as an additional covariate.", "When modeling the hazard of diarrhea cure, a binary variable termed therapeutic supplementation indicating whether calves were treated with either ZM, ZS or placebo for all or at least the first 5 days of diarrhea was evaluated as an additional covariate. A five-day period was selected by the authors based on clinical experience, as five days represents a reasonable duration over which most therapeutic treatments for calf diarrhea should be applied and be expected to alleviate disease. The proportional hazards assumption that the hazard of diarrhea is independent of time was assessed using analysis of Schoenfeld residuals and testing whether the log hazard-ratio function is constant over time.", "The proportional hazards assumption that the hazard of diarrhea is independent of time was assessed using analysis of Schoenfeld residuals and testing whether the log hazard-ratio function is constant over time. Any variable found to violate the proportional hazards assumption was included in the final regression model as a time varying covariate. A total of 1,513 calves were enrolled in the trial.", "A total of 1,513 calves were enrolled in the trial. However, due to failure to immediately recognize exclusion criteria, 23 calves were excluded shortly after enrollment. In addition, 8 calves were excluded due to treatment errors.", "In addition, 8 calves were excluded due to treatment errors. Therefore, a total of 1,482 calves placebo = 500, ZM = 491, ZS = 491 were included in the final analyses. A total of 242 calves 16.3% had minimal fecal output at the time of enrollment while 125 calves 8.4% had abnormal fecal scores of 2 or 3 that were described as meconium.", "A total of 242 calves 16.3% had minimal fecal output at the time of enrollment while 125 calves 8.4% had abnormal fecal scores of 2 or 3 that were described as meconium. All enrolled calves appeared healthy on visual assessment and hence were assumed to have a normal fecal score at the time of enrollment. The three treatment groups at enrollment did not differ significantly in mean birth weight kg P = 0.244 , mean serum total protein g/dL P = 0.541 , mean attitude score P = 0.845 , mean fecal score P = 0.522 , as shown in Table 1 , or distribution of calf sex P = 0.472 .", "The three treatment groups at enrollment did not differ significantly in mean birth weight kg P = 0.244 , mean serum total protein g/dL P = 0.541 , mean attitude score P = 0.845 , mean fecal score P = 0.522 , as shown in Table 1 , or distribution of calf sex P = 0.472 . Of the 1,482 study calves, 21 1.4% died during the trial: 5 calves in the placebo group 1.0% , 11 calves in the ZM group 2.2% , and 5 calves in the ZS group 1.0% . Of these 21 calves that died, 14 66.7% were bulls and 7 33.3% were heifers.", "Of these 21 calves that died, 14 66.7% were bulls and 7 33.3% were heifers. Eighteen of the 21 calves 85.7% were found dead, rather than euthanized, due to acute and spontaneous death without previous obvious clinical signs of disease. The remaining 3 calves were euthanized prior to death due to severe and/or prolonged morbidity.", "The remaining 3 calves were euthanized prior to death due to severe and/or prolonged morbidity. Characteristics and causes of death based on field necropsy of these calves can be found in S4 Table. There was no significant difference in the proportion of calves that died between treatment groups P = 0.168 , though mortality was significantly higher in bulls compared to heifer calves P = 0.049 .", "There was no significant difference in the proportion of calves that died between treatment groups P = 0.168 , though mortality was significantly higher in bulls compared to heifer calves P = 0.049 . Birth weight data were available for all 1,482 calves. Due to calf mortality between enrollment and completion of treatment n = 4 , end treatment weight data were available for 1,478 calves.", "Due to calf mortality between enrollment and completion of treatment n = 4 , end treatment weight data were available for 1,478 calves. Similarly, due to calf mortality n = 21 or missing data for body weight at hutch exit from the dairy's records n = 40 , hutch exit weight data were available for 1,421 calves. A summary of body weight data stratified by treatment group and sex is presented in Table 2 .", "A summary of body weight data stratified by treatment group and sex is presented in Table 2 . Within each treatment group, bull calves showed consistently higher birth weight P < 0.001 , end treatment weight P < 0.001 , and exit hutch weight P < 0.001 compared to heifer calves. However, at birth, end of treatment, or hutch exit there were no differences in body weight between treatment groups for bulls P > 0.1 or heifers P > 0.1 .", "However, at birth, end of treatment, or hutch exit there were no differences in body weight between treatment groups for bulls P > 0.1 or heifers P > 0.1 . The mean attitude scores during the study period were 1.2 across the three treatment groups P = 0.208 . Of 1,482 calves included in the final analysis, A total of 629 treated milk samples were obtained throughout the 107-day study period and pooled by treatment group and week, yielding a total of 16 pooled samples per treatment group.", "Of 1,482 calves included in the final analysis, A total of 629 treated milk samples were obtained throughout the 107-day study period and pooled by treatment group and week, yielding a total of 16 pooled samples per treatment group. Zinc concentrations ppm were significantly higher in pooled milk samples treated with ZM P < 0.001 and ZS P < 0.001 compared to placebo-treated samples, and there were no significant differences between ZM and ZS-treated samples P = 1.000 , as shown in S5 Table. Within zinc treatment groups, oral zinc dose at the start and end of treatment is summarized by sex in S6 Table.", "Within zinc treatment groups, oral zinc dose at the start and end of treatment is summarized by sex in S6 Table. For both ZM-and ZS-treated calves, oral zinc dose at the start P < 0.001 and end P < 0.001 of treatment was significantly higher in heifer versus bull calves. Serum zinc concentrations before and after treatment were obtained from 36 calves n = 12 for each treatment group and are summarized in S7 Table.", "Serum zinc concentrations before and after treatment were obtained from 36 calves n = 12 for each treatment group and are summarized in S7 Table. Overall, there were no significant differences in mean pre-treatment serum zinc concentrations between treatment groups P = 0.233 . Mean post-treatment serum zinc concentrations were significantly higher in calves treated with ZM P < 0.001 and ZS P = 0.002 compared to placebo-treated calves, and there were no significant differences among calves treated with ZM and ZS P = 0.406 .", "Mean post-treatment serum zinc concentrations were significantly higher in calves treated with ZM P < 0.001 and ZS P = 0.002 compared to placebo-treated calves, and there were no significant differences among calves treated with ZM and ZS P = 0.406 . Stratification of serum zinc data by treatment group and sex demonstrated that for ZM-treated calves, heifers had a numerically higher post-treatment serum zinc concentration compared to bulls, though the difference was not statistically significant P = 0.199 . In contrast, in ZStreated calves, heifers had a numerically lower post-treatment serum zinc concentration compared to bulls, though the difference was also not statistically significant P = 0.538 .", "In contrast, in ZStreated calves, heifers had a numerically lower post-treatment serum zinc concentration compared to bulls, though the difference was also not statistically significant P = 0.538 . Fecal analysis data were analyzed for 92 of the 127 randomly-selected calves. The remaining 35 calves were not included in the analysis due to not acquiring diarrhea during the assessment period n = 10 , death prior to final sampling n = 1 , exclusion due to improper treatment regimen n = 1 , or incorrect sampling day n = 23 .The 92 calves had a mean age at onset of diarrhea of 13.3, 11.0 and 11.3 days for ZM, ZS and placebo-treated groups, respectively; and a mean age at resolution of diarrhea of 18.8, 16.1 and 15.7 days for ZM, ZS and placebo-treated groups, respectively.", "The remaining 35 calves were not included in the analysis due to not acquiring diarrhea during the assessment period n = 10 , death prior to final sampling n = 1 , exclusion due to improper treatment regimen n = 1 , or incorrect sampling day n = 23 .The 92 calves had a mean age at onset of diarrhea of 13.3, 11.0 and 11.3 days for ZM, ZS and placebo-treated groups, respectively; and a mean age at resolution of diarrhea of 18.8, 16.1 and 15.7 days for ZM, ZS and placebo-treated groups, respectively. There were no significant differences in the prevalence of E. coli K99 P = 0.694 , rotavirus P = 0.331 , coronavirus P = 0.819 , or C. parvum P = 0.719 fecal shedding on the first day of diarrhea between treatment groups S8 Table . There were no significant differences in the prevalence of E. coli K99 P = 0.256 , rotavirus P = 0.344 , or coronavirus P = 1.000 fecal shedding at resolution of diarrhea between treatment groups, though there was a difference in C. parvum P = 0.006 fecal shedding between treatment groups S9 Table .", "There were no significant differences in the prevalence of E. coli K99 P = 0.256 , rotavirus P = 0.344 , or coronavirus P = 1.000 fecal shedding at resolution of diarrhea between treatment groups, though there was a difference in C. parvum P = 0.006 fecal shedding between treatment groups S9 Table . The prevalence of C. parvum fecal shedding at resolution of diarrhea was significantly higher in calves treated with ZM P = 0.009 and ZS P = 0.023 compared to placebo-treated calves, and there were no significant differences among calves treated with ZM and ZS P = 1.000 . Results of logistic regression models for overall and pathogen-specific microbiological cure are presented in Tables 3-5 .", "Results of logistic regression models for overall and pathogen-specific microbiological cure are presented in Tables 3-5 . For pathogen-specific cure, all calves that tested positive on the first day of diarrhea for coronavirus n = 4 tested negative at clinical diarrhea resolution. For calves that tested positive on the first day of diarrhea for E. coli K99 n = 9 , all placebo-treated calves n = 2 tested negative at clinical diarrhea resolution while half n = 2 of all ZS-treated calves tested either positive or negative at clinical diarrhea resolution, resulting in omission of ZS treatment variable from the model due to collinearity.", "For calves that tested positive on the first day of diarrhea for E. coli K99 n = 9 , all placebo-treated calves n = 2 tested negative at clinical diarrhea resolution while half n = 2 of all ZS-treated calves tested either positive or negative at clinical diarrhea resolution, resulting in omission of ZS treatment variable from the model due to collinearity. Hence, logistic regression analyses for microbiological cure in calves that tested positive for coronavirus and E. coli K99 were not possible. For 59 calves that tested positive for rotavirus on the first day of diarrhea Table 3 , calves treated with ZM had a 50% increased odds of testing negative at diarrhea resolution compared to placebo-treated calves, though this difference was not significant P = 0.549 .", "For 59 calves that tested positive for rotavirus on the first day of diarrhea Table 3 , calves treated with ZM had a 50% increased odds of testing negative at diarrhea resolution compared to placebo-treated calves, though this difference was not significant P = 0.549 . Likewise, calves treated with ZS had 100% increased odds 2 times the odds of testing negative for rotavirus at diarrhea resolution compared to placebo-treated calves, though this difference was also not significant P = 0.314 . However, this model demonstrated a significant main effect of serum total protein, such that for every 1 unit g/dL increase in serum total protein at enrollment, the odds of microbiological cure of rotavirus decreased by 79% P = 0.026 .", "However, this model demonstrated a significant main effect of serum total protein, such that for every 1 unit g/dL increase in serum total protein at enrollment, the odds of microbiological cure of rotavirus decreased by 79% P = 0.026 . For 40 calves that tested positive for Cryptosporidium parvum on the first day of diarrhea Table 4 , calves treated with ZM had an 87% reduced odds of testing negative at diarrhea resolution Effect of zinc on diarrhea in calves compared to placebo-treated calves, though this difference was not significant P = 0.119 . Likewise, calves treated with ZS had a 74% reduced odds of testing negative for Cryptosporidium parvum at diarrhea resolution compared to placebo-treated calves, though this difference was also not significant P = 0.183 .", "Likewise, calves treated with ZS had a 74% reduced odds of testing negative for Cryptosporidium parvum at diarrhea resolution compared to placebo-treated calves, though this difference was also not significant P = 0.183 . For 55 calves that tested positive for any one of the four fecal pathogens E. coli K99, rotavirus, coronavirus, Cryptosporidium parvum on the first day of diarrhea Table 5 , calves treated with ZM had a 25% increased odds of testing negative at diarrhea resolution compared to placebo-treated calves, though this difference was not significant P = 0.769 . Likewise, calves treated with ZS had a 52% increased odds of testing negative for Cryptosporidium parvum at diarrhea resolution compared to placebo-treated calves, though this difference was also not significant P = 0.633 .", "Likewise, calves treated with ZS had a 52% increased odds of testing negative for Cryptosporidium parvum at diarrhea resolution compared to placebo-treated calves, though this difference was also not significant P = 0.633 . However, this model demonstrated that heifer calves had 71% lower odds of microbiological cure of any single fecal pathogen compared to bull calves P = 0.076 . A total of 1,482 calves were included in the linear regression model results for ADG during the treatment period, which are presented in Table 6 .", "A total of 1,482 calves were included in the linear regression model results for ADG during the treatment period, which are presented in Table 6 . There was no significant difference in ADG for ZM-or ZS-treated calves compared to placebo-treated calves, though there were significant main effects of sex, birth weight, and milk volume. Specifically, heifer calves gained 70 g bodyweight per day less compared to bull calves P < 0.001 .", "Specifically, heifer calves gained 70 g bodyweight per day less compared to bull calves P < 0.001 . For every 1 kg increase in birth weight, calves gained 16 g per day less than their herd mates P < 0.001 . For every 1 L increase in milk volume per day during the treatment period, calves gained an additional 13 g per day P < 0.001 .", "For every 1 L increase in milk volume per day during the treatment period, calves gained an additional 13 g per day P < 0.001 . Table 7 summarizes the linear regression analysis of ADG during the pre-weaning period for 1,421 calves which showed a significant difference in ADG for ZM-treated calves compared to placebo-treated calves and in bull versus heifer calves. Milk volume had a significant effect on ADG, such that for every 1 L increase in milk volume per day during the treatment period, calves gained an additional 2 g bodyweight per day P = 0.001 .", "Milk volume had a significant effect on ADG, such that for every 1 L increase in milk volume per day during the treatment period, calves gained an additional 2 g bodyweight per day P = 0.001 . Results of the final model showed a significant main effect for ZM-treated bull calves and a significant interaction term for ZM treatment by sex. After controlling for milk volume received during the treatment Table 6 calves n = 1,482 Effect of zinc on diarrhea in calves period, ZM-treated bulls gained 22 g body weight per day on average more than placebotreated bull calves P = 0.042 and ZM-treated heifers gained 12 g less body weight per day on average compared to placebo-treated heifers P = 0.019 .", "After controlling for milk volume received during the treatment Table 6 calves n = 1,482 Effect of zinc on diarrhea in calves period, ZM-treated bulls gained 22 g body weight per day on average more than placebotreated bull calves P = 0.042 and ZM-treated heifers gained 12 g less body weight per day on average compared to placebo-treated heifers P = 0.019 . When considering the model coefficients for treatment group, sex, and their interaction, bull calves treated with ZM gained 454 g per day 0.432 + 0.022 while female calves treated with ZM gained 0.404 g per day 0.432 + 0.022-0.016-0.034 , hence 50 g per day more gain in male calves compared to heifers treated with ZM P = 0.019 . For ZS-treated calves, there was a numerical decrease in weight gain of 5 g per day in bulls and 11 g per day in heifers compared to placebo-treated calves, though the differences were not significant P = 0.673 bulls; P = 0.681 heifers .", "For ZS-treated calves, there was a numerical decrease in weight gain of 5 g per day in bulls and 11 g per day in heifers compared to placebo-treated calves, though the differences were not significant P = 0.673 bulls; P = 0.681 heifers . Linear regression models of ADG during the pre-weaning period were stratified by sex in order to avoid interpreting a three-way interaction between treatment group, sex, and birth weight. In the heifer model S10 Table , the interaction between ZM treatment and birth weight was significant which implied that birth weight modified the effect of ZM treatment on ADG.", "In the heifer model S10 Table , the interaction between ZM treatment and birth weight was significant which implied that birth weight modified the effect of ZM treatment on ADG. At a 29 kg birth weight two standard deviations below the mean , ZM-treated heifers gained 49 g body weight per day on average less than placebo-treated heifers P = 0.037 . However, at a 49 kg birth weight two standard deviations above the mean , ZM-treated heifers gained 30 g body weight per day on average more than placebo-treated heifers P = 0.037 .", "However, at a 49 kg birth weight two standard deviations above the mean , ZM-treated heifers gained 30 g body weight per day on average more than placebo-treated heifers P = 0.037 . In the bull calves model S11 Table there was no significant interaction between treatment group and birth weight. A total of 1,482 calves were included in the Kaplan-Meier survival analysis of time to first diarrhea event Fig 1 .", "A total of 1,482 calves were included in the Kaplan-Meier survival analysis of time to first diarrhea event Fig 1 . There were no significant differences in median age at onset of diarrhea, specifically, 8, 8 and 7 days for the ZM, ZS and placebo-treated calves, respectively P = 0.402 . Cox proportional hazard regression model for diarrhea hazard are presented in Table 8 .", "Cox proportional hazard regression model for diarrhea hazard are presented in Table 8 . After controlling for age, calves treated with ZM had a 14.7% reduced hazard of diarrhea compared to placebo-treated calves P = 0.015 . Calves treated with ZS had 13.9% reduced hazard of diarrhea compared to placebo-treated calves P = 0.022 .", "Calves treated with ZS had 13.9% reduced hazard of diarrhea compared to placebo-treated calves P = 0.022 . calves n = 1,421 A total of 1,394 calves were included in the Kaplan-Meier survival analysis of time to clinical diarrhea cure Fig 2 , as 88 calves failed to acquire diarrhea during the assessment period. There were no significant differences in the median days to diarrhea cure which was 7 days across all 3 treatment groups P = 0.264 .", "There were no significant differences in the median days to diarrhea cure which was 7 days across all 3 treatment groups P = 0.264 . Cox proportional hazard regression model for diarrhea cure hazard are presented in Table 9 . Results of the final model showed a significant interaction term between treatment and therapeutic supplementation as well as the need for age as a time varying covariate.", "Results of the final model showed a significant interaction term between treatment and therapeutic supplementation as well as the need for age as a time varying covariate. When considering calves that did not receive supplementation, respective to each of the 3 groups, for at least the first five days of diarrhea there was no significant difference between either ZM-and ZS-treated calves compared to placebo-treated calves P = 0.223 ZM, P = 0.134 ZS . However, when considering calves that were supplemented for at least the first five days of diarrhea, ZM-treated calves experienced a 21.4% higher hazard of cure from diarrhea compared to placebo-treated calves P = 0.027 .", "However, when considering calves that were supplemented for at least the first five days of diarrhea, ZM-treated calves experienced a 21.4% higher hazard of cure from diarrhea compared to placebo-treated calves P = 0.027 . Likewise, ZS-treated calves experienced a 13.0% higher hazard of cure from diarrhea compared to placebo-treated calves P = 0.040 . The current trial demonstrated evidence for the beneficial effect of ZM on ADG and neonatal diarrhea as well as an effect of ZS on diarrhea in dairy calves during the pre-weaning period.", "The current trial demonstrated evidence for the beneficial effect of ZM on ADG and neonatal diarrhea as well as an effect of ZS on diarrhea in dairy calves during the pre-weaning period. It is important to consider these results in the context of the entire pre-weaning and hutch period. On average, after 90 days from birth to hutch exit, placebo-treated bull calves gained 38.88 kg body weight while ZM-treated bull calves gained an additional 1.98 kg 40.86 kg .", "On average, after 90 days from birth to hutch exit, placebo-treated bull calves gained 38.88 kg body weight while ZM-treated bull calves gained an additional 1.98 kg 40.86 kg . In contrast, the effect of zinc on weight gain in treated heifers depended on birth weight. Low birth weight heifers treated with ZM gained on average less than a placebo-treated heifer of the same birth weight.", "Low birth weight heifers treated with ZM gained on average less than a placebo-treated heifer of the same birth weight. In contrast, high birth weight heifers treated with ZM gained more than placebo-treated heifers of the same birth weight. The switch in direction of the association between ZM treatment and ADG in heifer calves depending on birth weight suggests a doseresponse effect rather than a true sex-specific effect of ZM on ADG.", "The switch in direction of the association between ZM treatment and ADG in heifer calves depending on birth weight suggests a doseresponse effect rather than a true sex-specific effect of ZM on ADG. Hence, low birth weight calves including heifers may require a lower dose of ZM to mitigate any negative effect of what is otherwise a suitable dose for higher birth weight calves. These findings are in agreement with a previous randomized clinical trial testing the effect of daily oral zinc in diarrheic neonatal Holstein calves which, showed that ZM-treated calves had a numerically, though not significantly increased ADG compared to calves treated with zinc oxide or placebo due to small sample size .", "These findings are in agreement with a previous randomized clinical trial testing the effect of daily oral zinc in diarrheic neonatal Holstein calves which, showed that ZM-treated calves had a numerically, though not significantly increased ADG compared to calves treated with zinc oxide or placebo due to small sample size . In general, our trial findings are in agreement with the large body of human literature supporting the use of oral zinc for the prevention and treatment of diarrhea and impaired growth in children . Zinc supplementation is widely accepted by global health organizations as a vital component of therapy for childhood diarrhea , however, recent reviews of the literature demonstrated heterogeneity in study results on the basis of age, baseline zinc status, geographic location, and supplementation regimen .", "Zinc supplementation is widely accepted by global health organizations as a vital component of therapy for childhood diarrhea , however, recent reviews of the literature demonstrated heterogeneity in study results on the basis of age, baseline zinc status, geographic location, and supplementation regimen . Similar to our findings, a sex-specific response to zinc supplementation has been demonstrated in several human studies. Zinc gluconate administered for diarrhea prevention reduced the incidence of dysentery in treated boys but not girls ; when given therapeutically, it reduced diarrhea duration and frequency more dramatically in boys compared to girls .", "Zinc gluconate administered for diarrhea prevention reduced the incidence of dysentery in treated boys but not girls ; when given therapeutically, it reduced diarrhea duration and frequency more dramatically in boys compared to girls . Similarly, zinc sulfate was shown to improve Effect of zinc on diarrhea in calves diarrhea outcomes in boys but improved growth rates in girls . Broadly, these differences between male and female responses to zinc supplementation are not understood, though theories regarding differences in immune function and response , diarrhea etiology , and nutrient requirements have been proposed.", "Broadly, these differences between male and female responses to zinc supplementation are not understood, though theories regarding differences in immune function and response , diarrhea etiology , and nutrient requirements have been proposed. In the current study, ZM-treated bulls demonstrated increased ADG compared to placebo-treated bulls while ZM-treated heifers demonstrated decreased ADG compared to placebo-treated heifers. However, due to a significant interaction between ZM treatment and birth weight, this reduction in ADG in ZMtreated heifers was overcome with increasing birth weight, such that ZM-treated heifers with birth weights above 42 kg experienced increased ADG during the pre-weaning period, compared to placebo-treated heifers with birth weights above 42 kg.", "However, due to a significant interaction between ZM treatment and birth weight, this reduction in ADG in ZMtreated heifers was overcome with increasing birth weight, such that ZM-treated heifers with birth weights above 42 kg experienced increased ADG during the pre-weaning period, compared to placebo-treated heifers with birth weights above 42 kg. Differences in the growth response to ZM supplementation between bull and heifer calves may have been related to its effect on feed intake. Previous research on the effects of feeding various doses of oral zinc oxide to pre-ruminant dairy calves demonstrated that high levels of oral zinc supplementation resulted in reduced feed intake .", "Previous research on the effects of feeding various doses of oral zinc oxide to pre-ruminant dairy calves demonstrated that high levels of oral zinc supplementation resulted in reduced feed intake . In the current trial, oral ZM dose was estimated to be significantly higher in heifers compared to bulls due to the significantly lower birth weight of heifers. Additionally, serum zinc concentrations in ZM-treated heifers were numerically higher than that of bulls, though this difference was not significant, likely due to the small sample size.", "Additionally, serum zinc concentrations in ZM-treated heifers were numerically higher than that of bulls, though this difference was not significant, likely due to the small sample size. Perhaps the higher zinc dose in heifers was associated with reduced feed intake, leading to reduced growth, and that this effect was more pronounced for ZM compared to ZS. The fact that ZM-treated heifers with birth weights approaching those of average bull calves and, therefore, a similar zinc dose to that in bulls experienced an increase in ADG over placebo-treated heifers similar to that of bull calves partially supports this theory.", "The fact that ZM-treated heifers with birth weights approaching those of average bull calves and, therefore, a similar zinc dose to that in bulls experienced an increase in ADG over placebo-treated heifers similar to that of bull calves partially supports this theory. Although management practices on the study dairy were designed to be identical for both bulls and heifers, it is possible that subtle, unrecognized differences in nutritional and health management may also have contributed to sex-specific differences in weight gain. Nevertheless, future trials are warranted to investigate the potential differences in the dose-response to zinc supplementation between bulls and heifers.", "Nevertheless, future trials are warranted to investigate the potential differences in the dose-response to zinc supplementation between bulls and heifers. We hypothesized that ADG would be increased in zinc-supplemented calves compared to placebo-supplemented calves due to the potential preventive and therapeutic effects of zinc supplementation on neonatal diarrhea. In other words, calf diarrhea is mitigated by zinc supplementation and, therefore, on the causal pathway between zinc and ADG.", "In other words, calf diarrhea is mitigated by zinc supplementation and, therefore, on the causal pathway between zinc and ADG. However, considering the similarly-reduced hazard of diarrhea and increased hazard of cure from diarrhea in both ZM and ZS treatment groups but a lack of effect of ZS on ADG, it is likely that the effect of ZM on ADG is not solely mediated through its effects on diarrhea. Differences in effectiveness between organic and inorganic formulations also may exist.", "Differences in effectiveness between organic and inorganic formulations also may exist. In fact, the underlying mechanism of action of oral zinc remains unknown . Several theories of the mechanisms of action of zinc in the prevention and treatment of childhood diarrhea exist, including a mucosal-protective role, a diarrhea-induced zinc deficiency, an essential element in cell-mediated immunity, and a modifier of intra-luminal electrolyte secretion and absorption 6, .", "Several theories of the mechanisms of action of zinc in the prevention and treatment of childhood diarrhea exist, including a mucosal-protective role, a diarrhea-induced zinc deficiency, an essential element in cell-mediated immunity, and a modifier of intra-luminal electrolyte secretion and absorption 6, . The clinical and practical implications of effects of ZM supplementation on ADG and diarrhea must be considered. Pre-weaned calf diarrhea remains an ongoing issue for the dairy industry.", "Pre-weaned calf diarrhea remains an ongoing issue for the dairy industry. The deleterious effects on calf health and performance and the resulting economic burden create a strong incentive to treat and prevent diarrhea in pre-weaned calves. On large dairy operations like those in California's Central Valley, small changes in disease incidence and duration as well as animal growth and performance can have profound economic consequences.", "On large dairy operations like those in California's Central Valley, small changes in disease incidence and duration as well as animal growth and performance can have profound economic consequences. As a non-antimicrobial product, zinc may become increasingly attractive as antimicrobials in livestock feed are under increased scrutiny and regulation due to concerns about antimicrobial resistance . Prevalence of C. parvum fecal shedding in a random sample of 92 study calves at onset and resolution of diarrhea was significantly higher in calves treated with zinc compared to Placebo-treated calves.", "Prevalence of C. parvum fecal shedding in a random sample of 92 study calves at onset and resolution of diarrhea was significantly higher in calves treated with zinc compared to Placebo-treated calves. In contrast, a previous study where calves that tested positive for C. parvum at the start of diarrhea and were treated with ZM had 16 times higher odds of being fecal ELISA negative at exit compared to the Placebo group P = 0.08; power = 72.3% . The difference in findings may be due to the differences in the timing of diarrhea across treatment groups.", "The difference in findings may be due to the differences in the timing of diarrhea across treatment groups. For the current study's random sample of calves that acquired, survived, and were sampled on the correct days, the mean age of calves on both onset and resolution of diarrhea was higher for ZM and ZS calves compared to placebo-treated calves. Although C. parvum oocyst shedding in infected calves can occur as early as 3 days of age, peak shedding occurs at about 14 days of age .", "Although C. parvum oocyst shedding in infected calves can occur as early as 3 days of age, peak shedding occurs at about 14 days of age . It is possible that the increase in prevalence of C. parvum shedding in ZM and ZS treated groups was due to the increased age of zinc-treated calves compared to placebo-treated calves at resolution of diarrhea. The latter explanation is also supported by our findings that the odds of microbiological cure from C. parvum significantly decreased in older calves, with no significant differences in the odds of cure between treatment groups.", "The latter explanation is also supported by our findings that the odds of microbiological cure from C. parvum significantly decreased in older calves, with no significant differences in the odds of cure between treatment groups. In addition, the current testing did not estimate the concentration of C. parvum shedding which may still differ between treatment groups. Despite the large sample size, the current trial was limited to a single California dairy, which may represent other large dairies but does not reflect all the dairy management systems in California or elsewhere.", "Despite the large sample size, the current trial was limited to a single California dairy, which may represent other large dairies but does not reflect all the dairy management systems in California or elsewhere. Additionally, our results show that calves respond to zinc supplementation for diarrhea prevention differently depending on chemical formulation and calf sex. The latter could be due to differences in body weight between bulls and heifers and may point towards the need for sex-specific dosing.", "The latter could be due to differences in body weight between bulls and heifers and may point towards the need for sex-specific dosing. Furthermore, the current research did not evaluate the potential economic utility of zinc supplementation. Future studies on more accurate dosing of zinc by calf sex, the practical feasibility of weight-based dosing, and the expected cost-effectiveness of zinc administration as part of the management of pre-weaned dairy calves are warranted.", "Future studies on more accurate dosing of zinc by calf sex, the practical feasibility of weight-based dosing, and the expected cost-effectiveness of zinc administration as part of the management of pre-weaned dairy calves are warranted. Finally, our clinical trial was performed on a single, large, predominately Holstein, California dairy over a six-month period, which precluded our ability to evaluate differences due to season or breed. Hence, future studies to assess any modifying effect of breed and seasonal differences on the effect of zinc on calf health and weight gain are also needed.", "Hence, future studies to assess any modifying effect of breed and seasonal differences on the effect of zinc on calf health and weight gain are also needed. The current double blind, block-randomized placebo controlled clinical trial tested the effect of a prophylactic daily oral zinc supplementation in neonatal Holstein calves. Bull calves treated with ZM had a significantly increased ADG 22 g per day during the pre-weaning period compared to placebo-treated bulls.", "Bull calves treated with ZM had a significantly increased ADG 22 g per day during the pre-weaning period compared to placebo-treated bulls. In comparison, ZM-treated heifers had significantly lower average daily gain 9 g per day compared to placebo-treated heifers, although higher ZM doses in low birthweight heifers may explain the lower ADG. Calves treated with either ZM or ZS had significantly lower risks of diarrhea and significantly higher risk of cure from diarrhea over the first 30 days of life compared to placebo-treated calves and hence the current trial demonstrated that zinc supplementation delayed diarrhea and expedited diarrhea recovery in pre-weaned calves.", "Calves treated with either ZM or ZS had significantly lower risks of diarrhea and significantly higher risk of cure from diarrhea over the first 30 days of life compared to placebo-treated calves and hence the current trial demonstrated that zinc supplementation delayed diarrhea and expedited diarrhea recovery in pre-weaned calves. Additionally, zinc improved weight gain differentially in bulls compared to heifers, indicating the need for further research to investigate zinc dosing in calves. Supporting information S1 DOCX S1 Dataset.", "Supporting information S1 DOCX S1 Dataset. Raw data collected from trial, organized as separate excel sheets for enrollment, daily assessment, serum total protein, birth weight, exit treatment weight, exit trial weight, serum zinc testing, fecal samples, fecal testing, milk testing, and dead calves. XLSX" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]

[ "Rapid diagnostics, vaccines and therapeutics are important interventions for the management of the 2019 novel coronavirus 2019-nCoV outbreak. It is timely to systematically review the potential of these interventions, including those for Middle East respiratory syndrome-Coronavirus MERS-CoV and severe acute respiratory syndrome SARS -CoV, to guide policymakers globally on their prioritization of resources for research and development. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines.", "A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. Supplementary strategies through Google Search and personal communications were used. A total of 27 studies fulfilled the criteria for review.", "A total of 27 studies fulfilled the criteria for review. Several laboratory protocols for confirmation of suspected 2019-nCoV cases using real-time reverse transcription polymerase chain reaction RT-PCR have been published. A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia.", "A commercial RT-PCR kit developed by the Beijing Genomic Institute is currently widely used in China and likely in Asia. However, serological assays as well as point-of-care testing kits have not been developed but are likely in the near future. Several vaccine candidates are in the pipeline.", "Several vaccine candidates are in the pipeline. The likely earliest Phase 1 vaccine trial is a synthetic DNA-based candidate. A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV.", "A number of novel compounds as well as therapeutics licensed for other conditions appear to have in vitro efficacy against the 2019-nCoV. Some are being tested in clinical trials against MERS-CoV and SARS-CoV, while others have been listed for clinical trials against 2019-nCoV. However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence.", "However, there are currently no effective specific antivirals or drug combinations supported by high-level evidence. Text: Since mid-December 2019 and as of early February 2020, the 2019 novel coronavirus 2019-nCoV originating from Wuhan Hubei Province, China has infected over 25,000 laboratory-confirmed cases across 28 countries with about 500 deaths a case-fatality rate of about 2% . More than 90% of the cases and deaths were in China .", "More than 90% of the cases and deaths were in China . Based on the initial reported surge of cases in Wuhan, the majority were males with a median age of 55 years and linked to the Huanan Seafood Wholesale Market . Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue.", "Most of the reported cases had similar symptoms at the onset of illness such as fever, cough, and myalgia or fatigue. Most cases developed pneumonia and some severe and even fatal respiratory diseases such as acute respiratory distress syndrome . The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily .", "The 2019 novel coronavirus 2019-nCoV , a betacoronavirus, forms a clade within the subgenus sarbecovirus of the Orthocoronavirinae subfamily . The severe acute respiratory syndrome coronavirus SARS-CoV and Middle East respiratory syndrome coronavirus MERS-CoV are also betacoronaviruses that are zoonotic in origin and have been linked to potential fatal illness during the outbreaks in 2003 and 2012, respectively . Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% .", "Based on current evidence, pathogenicity for 2019-nCoV is about 3%, which is significantly lower than SARS-CoV 10% and MERS-CoV 40% . However, 2019-nCoV has potentially higher transmissibility R0: 1.4-5.5 than both SARS-CoV R0: and MERS-CoV R0: <1 . With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly.", "With the possible expansion of 2019-nCoV globally and the declaration of the 2019-nCoV outbreak as a Public Health Emergency of International Concern by the World Health Organization, there is an urgent need for rapid diagnostics, vaccines and therapeutics to detect, prevent and contain 2019-nCoV promptly. There is however currently a lack of understanding of what is available in the early phase of 2019-nCoV outbreak. The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV.", "The systematic review describes and assesses the potential rapid diagnostics, vaccines and therapeutics for 2019-nCoV, based in part on the developments for MERS-CoV and SARS-CoV. A systematic search was carried out in three major electronic databases PubMed, Embase and Cochrane Library to identify published studies examining the diagnosis, therapeutic drugs and vaccines for Severe Acute Respiratory Syndrome SARS , Middle East Respiratory Syndrome MERS and the 2019 novel coronavirus 2019-nCoV , in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses PRISMA guidelines. There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively.", "There were two independent reviewers each focusing on SARS, MERS, and 2019-nCoV, respectively. A third independent reviewer was engaged to resolve any conflicting article of interest. We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy.", "We used the key words \"SARS\", \"coronavirus\", \"MERS\", \"2019 Novel coronavirus\", \"Wuhan virus\" to identify the diseases in the search strategy. The systematic searches for diagnosis, therapeutic drugs and vaccines were carried out independently and the key words \"drug\", \"therapy\", \"vaccine\", \"diagnosis\", \"point of care testing\" and \"rapid diagnostic test\" were used in conjunction with the disease key words for the respective searches. Examples of search strings can be found in Table S1 .", "Examples of search strings can be found in Table S1 . We searched for randomized controlled trials RCTs and validation trials for diagnostics test published in English, that measured a the sensitivity and/or specificity of a rapid diagnostic test or a point-of-care testing kit, b the impact of drug therapy or c vaccine efficacy against either of these diseases with no date restriction applied. For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest.", "For the 2019-nCoV, we searched for all in vitro, animal, or human studies published in English between 1 December 2019 and 6 February 2020, on the same outcomes of interest. In addition, we reviewed the references of retrieved articles in order to identify additional studies or reports not retrieved by the initial searches. Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded.", "Studies that examined the mechanisms of diagnostic tests, drug therapy or vaccine efficacy against SARS, MERS and 2019-nCoV were excluded. A Google search for 2019-nCoV diagnostics as of 6 February 2020; Table S2 yielded five webpage links from government and international bodies with official information and guidelines WHO, Europe CDC, US CDC, US FDA , three webpage links on diagnostic protocols and scientific commentaries, and five webpage links on market news and press releases. Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website .", "Six protocols for diagnostics using reverse transcriptase polymerase chain reaction RT-PCR from six countries were published on WHO's website . Google search for 2019-nCoV vaccines yielded 19 relevant articles. With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 .", "With the emergence of 2019-nCoV, real time RT-PCR remains the primary means for diagnosing the new virus strain among the many diagnostic platforms available ; Table S3 . Among the 16 diagnostics studies selected, one study discussed the use of RT-PCR in diagnosing patients with 2019-nCoV Table 1 . The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV.", "The period and type of specimen collected for RT-PCR play an important role in the diagnosis of 2019-nCoV. It was found that the respiratory specimens were positive for the virus while serum was negative in the early period. It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms.", "It has also suggested that in the early days of illness, patients have high levels of virus despite the mild symptoms. Apart from the commonly used RT-PCR in diagnosing MERS-CoV, four studies identified various diagnostic methods such as reverse transcription loop-mediated isothermal amplification RT-LAMP , RT-insulated isothermal PCR RT-iiPCR and a one-step rRT-PCR assay based on specific TaqMan probes. RT-LAMP has similar sensitivity as real time RT-PCR.", "RT-LAMP has similar sensitivity as real time RT-PCR. It is also highly specific and is used to detect MERS-CoV. It is comparable to the usual diagnostic tests and is rapid, simple and convenient. Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV.", "Likewise, RT-iiPCR and a one-step rRT-PCR assay have also shown similar sensitivity and high specificity for MER-CoV. Lastly, one study focused on the validation of the six commercial real RT-PCR kits, with high accuracy. Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 .", "Although real time RT-PCR is a primary method for diagnosing MERS-CoV, high levels of PCR inhibition may hinder PCR sensitivity Table 1 . There are eleven studies that focus on SARS-CoV diagnostic testing Table 1 . These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis.", "These papers described diagnostic methods to detect the virus with the majority of them using molecular testing for diagnosis. Comparison between the molecular test i.e RT-PCR and serological test i.e., ELISA showed that the molecular test has better sensitivity and specificity. Hence, enhancements to the current molecular test were conducted to improve the diagnosis.", "Hence, enhancements to the current molecular test were conducted to improve the diagnosis. Studies looked at using nested PCR to include a pre-amplification step or incorporating N gene as an additional sensitive molecular marker to improve on the sensitivity Table 1 . In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV.", "In addition, there are seven potential rapid diagnostic kits as of 24 January 2020; Table 2 available on the market for 2019-nCoV. Six of these are only for research purposes. Only one kit from Beijing Genome Institute BGI is approved for use in the clinical setting for rapid diagnosis. Most of the kits are for RT-PCR.", "Most of the kits are for RT-PCR. There were two kits BGI, China and Veredus, Singapore with the capability to detect multiple pathogens using sequencing and microarray technologies, respectively. The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%.", "The limit of detection of the enhanced realtime PCR method was 10 2 -fold higher than the standard real-time PCR assay and 10 7fold higher than conventional PCR methods In the clinical aspect, the enhanced realtime PCR method was able to detect 6 cases of SARS-CoV positive samples that were not confirmed by any other assay • The real time PCR has a threshold sensitivity of 10 genome equivalents per reaction and it has a good reproducibility with the inter-assay coefficients of variation of 1.73 to 2.72%. • 13 specimens from 6 patients were positive with viral load range from 362 to 36,240,000 genome equivalents/mL. The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control.", "The real-time RT-PCR reaction was more sensitive than the nested PCR reaction, as the detection limit for the nested PCR reaction was about 10 3 genome equivalents in the standard cDNA control. Real-time reverse-transcription PCR rRT-PCR ; RNA-dependent RNA polymerase RdRp ; open reading frame 1a ORF1a ; Loop-mediated isothermal amplification LAMP ; enzyme-linked immunosorbent assay ELISA ; immunofluorescent assay IFA ; immunochromatographic test ICT ; nasopharyngeal aspirate NPA . With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied.", "With the emergence of 2019-nCoV, there are about 15 potential vaccine candidates in the pipeline globally Table 3 , in which a wide range of technology such as messenger RNA, DNA-based, nanoparticle, synthetic and modified virus-like particle was applied. It will likely take about a year for most candidates to start phase 1 clinical trials except for those funded by Coalition for Epidemic Preparedness Innovations CEPI . However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China .", "However, the kit developed by the BGI have passed emergency approval procedure of the National Medical Products Administration, and are currently used in clinical and surveillance centers of China . Of the total of 570 unique studies on 2019-nCoV, SARS CoV or MERS-CoV vaccines screened, only four were eventually included in the review. Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 .", "Most studies on SARS and MERS vaccines were excluded as they were performed in cell or animal models Figure 1 . The four studies included in this review were Phase I clinical trials on SARS or MERS vaccines Table 4 . There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening.", "There were no studies of any population type cell, animal, human on the 2019-nCoV at the point of screening. The published clinical trials were mostly done in United States except for one on the SARS vaccine done in China . All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants.", "All vaccine candidates for SARS and MERS were reported to be safe, well-tolerated and able to trigger the relevant and appropriate immune responses in the participants. In addition, we highlight six ongoing Phase I clinical trials identified in the ClinicalTrials.gov register ; Table S4 . These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet.", "These trials are all testing the safety and immunogenicity of their respective MERS-CoV vaccine candidates but were excluded as there are no results published yet. The trials are projected to complete in December 2020 two studies in Russia and December 2021 in Germany . Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing.", "Existing literature search did not return any results on completed 2019-nCoV trials at the time of writing. Among 23 trials found from the systematic review Table 5 , there are nine clinical trials registered under the clinical trials registry ClinicalTrials.gov for 2019-nCoV therapeutics . Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment.", "Of which five studies on hydroxychloroquine, lopinavir plus ritonavir and arbidol, mesenchymal stem cells, traditional Chinese medicine and glucocorticoid therapy usage have commenced recruitment. The remaining four studies encompass investigation of antivirals, interferon atomization, darunavir and cobicistat, arbidol, and remdesivir usage for 2019-nCoV patients Table 5 . Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60.", "Seroconversion measured by S1-ELISA occurred in 86% and 94% participants after 2 and 3 doses, respectively, and was maintained in 79% participants up to study end at week 60. Neutralising antibodies were detected in 50% participants at one or more time points during the study, but only 3% maintained neutralisation activity to end of study. T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively.", "T-cell responses were detected in 71% and 76% participants after 2 and 3 doses, respectively. There were no differences in immune responses between dose groups after 6 weeks and vaccine-induced humoral and cellular responses were respectively detected in 77% and 64% participants at week 60. Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication.", "Molecules developed by the university scientists inhibit two coronavirus enzymes and prevent its replication. The discovered drug targets are said to be more than 95% similar to enzyme targets found on the SARS virus. Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks.", "Researchers note that identified drugs may not be available to address the ongoing outbreak but they hope to make it accessible for future outbreaks. Besides the six completed randomized controlled trials RCT selected from the systematic review Table 6 , there is only one ongoing randomized controlled trial targeted at SARS therapeutics . The studies found from ClinicalTrials.gov have not been updated since 2013.", "The studies found from ClinicalTrials.gov have not been updated since 2013. While many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir or ribavirin only, there has yet to be well-designed clinical trials investigating their usage. Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong .", "Three completed randomized controlled trials were conducted during the SARS epidemic-3 in China, 1 in Taiwan and 2 in Hong Kong . The studies respectively investigated antibiotic usage involving 190 participants, combination of western and Chinese treatment vs. Chinese treatment in 123 participants, integrative Chinese and Western treatment in 49 patients, usage of a specific Chinese medicine in four participants and early use of corticosteroid in 16 participants. Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants .", "Another notable study was an open non-randomized study investigating ribavirin/lopinavir/ritonavir usage in 152 participants . One randomized controlled trial investigating integrative western and Chinese treatment during the SARS epidemic was excluded as it was a Chinese article . There is only one ongoing randomized controlled trial targeted at MERS therapeutics . It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B.", "It investigates the usage of Lopinavir/Ritonavir and Interferon Beta 1B. Likewise, many prospective and retrospective cohort studies conducted during the epidemic centered on usage of ribavirin with lopinavir/ritonavir/ribavirin, interferon, and convalescent plasma usage. To date, only one trial has been completed.", "To date, only one trial has been completed. One phase 1 clinical trial investigating the safety and tolerability of a fully human polyclonal IgG immunoglobulin SAB-301 was found in available literature . The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses.", "The trial conducted in the United States in 2017 demonstrated SAB-301 to be safe and well-tolerated at single doses. Another trial on MERS therapeutics was found on ClinicalTrials.gov-a phase 2/3 trial in the United States evaluating the safety, tolerability, pharmacokinetics PK , and immunogenicity on coadministered MERS-CoV antibodies REGN3048 & REGN3051 . Rapid diagnostics plays an important role in disease and outbreak management.", "Rapid diagnostics plays an important role in disease and outbreak management. The fast and accurate diagnosis of a specific viral infection enables prompt and accurate public health surveillance, prevention and control measures. Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home.", "Local transmission and clusters can be prevented or delayed by isolation of laboratory-confirmed cases and their close contacts quarantined and monitored at home. Rapid diagnostic also facilitates other specific public health interventions such as closure of high-risk facilities and areas associated with the confirmed cases for prompt infection control and environmental decontamination . Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles.", "Laboratory diagnosis can be performed by: a detecting the genetic material of the virus, b detecting the antibodies that neutralize the viral particles of interest, c detecting the viral epitopes of interest with antibodies serological testing , or d culture and isolation of viable virus particles. The key limitations of genetic material detection are the lack of knowledge of the presence of viable virus, the potential cross-reactivity with non-specific genetic regions and the short timeframe for accurate detection during the acute infection phase. The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses.", "The key limitations of serological testing is the need to collect paired serum samples in the acute and convalescent phases from cases under investigation for confirmation to eliminate potential cross-reactivity from non-specific antibodies from past exposure and/or infection by other coronaviruses. The limitation of virus culture and isolation is the long duration and the highly specialized skills required of the technicians to process the samples. All patients recovered.", "All patients recovered. Significantly shorted time from the disease onset to the symptom improvement in treatment 5.10 ± 2.83 days compared to control group 7.62 ± 2.27 days p < 0.05 No significant difference in blood routine improvement, pulmonary chest shadow in chest film improvement and corticosteroid usgae between the 2 groups. However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone.", "However, particularly in the respect of improving clinical symptoms, elevating quality of life, promoting immune function recovery, promoting absorption of pulmonary inflammation, reducing the dosage of cortisteroid and shortening the therapeutic course, treatment with integrative chinese and western medicine treatment had obvious superiority compared with using control treatment alone. Single infusions of SAB-301 up to 50 mg/kg appear to be safe and well-tolerated in healthy participants. Where the biological samples are taken from also play a role in the sensitivity of these tests.", "Where the biological samples are taken from also play a role in the sensitivity of these tests. For SARS-CoV and MERS-CoV, specimens collected from the lower respiratory tract such as sputum and tracheal aspirates have higher and more prolonged levels of viral RNA because of the tropism of the virus. MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases.", "MERS-CoV viral loads are also higher for severe cases and have longer viral shedding compared to mild cases. Although upper respiratory tract specimens such as nasopharyngeal or oropharyngeal swabs can be used, they have potentially lower viral loads and may have higher risk of false-negatives among the mild MERS and SARS cases , and likely among the 2019-nCoV cases. The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP .", "The existing practices in detecting genetic material of coronaviruses such as SARS-CoV and MERS-CoV include a reverse transcription-polymerase chain reaction RT-PCR , b real-time RT-PCR rRT-PCR , c reverse transcription loop-mediated isothermal amplification RT-LAMP and d real-time RT-LAMP . Nucleic amplification tests NAAT are usually preferred as in the case of MERS-CoV diagnosis as it has the highest sensitivity at the earliest time point in the acute phase of infection . Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus .", "Chinese health authorities have recently posted the full genome of 2019-nCoV in the GenBank and in GISAID portal to facilitate in the detection of the virus . Several laboratory assays have been developed to detect the novel coronavirus in Wuhan, as highlighted in WHO's interim guidance on nCoV laboratory testing of suspected cases. These include protocols from other countries such as Thailand, Japan and China .", "These include protocols from other countries such as Thailand, Japan and China . The first validated diagnostic test was designed in Germany. Corman et al. had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like.", "had initially designed a candidate diagnostic RT-PCR assay based on the SARS or SARS-related coronavirus as it was suggested that circulating virus was SARS-like. Upon the release of the sequence, assays were selected based on the match against 2019-nCoV upon inspection of the sequence alignment. Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing.", "Two assays were used for the RNA dependent RNA polymerase RdRP gene and E gene where E gene assay acts as the first-line screening tool and RdRp gene assay as the confirmatory testing. All assays were highly sensitive and specific in that they did not cross-react with other coronavirus and also human clinical samples that contained respiratory viruses . The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus .", "The Hong Kong University used two monoplex assays which were reactive with coronaviruses under the subgenus Sarbecovirus consisting of 2019-nCoV, SARS-CoV and SARS-like coronavirus . Viral RNA extracted from SARS-CoV can be used as the positive control for the suggested protocol assuming that SARS has been eradicated. It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test.", "It is proposed that the N gene RT-PCR can be used as a screening assay while the Orf1b assay acts as a confirmatory test. However, this protocol has only been evaluated with a panel of controls with the only positive control SARS-CoV RNA. Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested .", "Synthetic oligonucleotide positive control or 2019-nCoV have yet to be tested . The US CDC shared the protocol on the real time RT-PCR assay for the detection of the 2019-nCoV with the primers and probes designed for the universal detection of SARS-like coronavirus and the specific detection of 2019-nCoV. However, the protocol has not been validated on other platforms or chemistries apart from the protocol described.", "However, the protocol has not been validated on other platforms or chemistries apart from the protocol described. There are some limitations for the assay. Analysts engaged have to be trained and familiar with the testing procedure and result interpretation.", "Analysts engaged have to be trained and familiar with the testing procedure and result interpretation. False negative results may occur due to insufficient organisms in the specimen resulting from improper collection, transportation or handling. Also, RNA viruses may show substantial genetic variability.", "Also, RNA viruses may show substantial genetic variability. This could result in mismatch between the primer and probes with the target sequence which can diminish the assay performance or result in false negative results . Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months.", "Point-of-care test kit can potentially minimize these limitations, which should be highly prioritized for research and development in the next few months. Serological testing such as ELISA, IIFT and neutralization tests are effective in determining the extent of infection, including estimating asymptomatic and attack rate. Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens.", "Compared to the detection of viral genome through molecular methods, serological testing detects antibodies and antigens. There would be a lag period as antibodies specifically targeting the virus would normally appear between 14 and 28 days after the illness onset . Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load.", "Furthermore, studies suggest that low antibody titers in the second week or delayed antibody production could be associated with mortality with a high viral load. Hence, serological diagnoses are likely used when nucleic amplification tests NAAT are not available or accessible . Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes.", "Vaccines can prevent and protect against infection and disease occurrence when exposed to the specific pathogen of interest, especially in vulnerable populations who are more prone to severe outcomes. In the context of the current 2019-nCoV outbreak, vaccines will help control and reduce disease transmission by creating herd immunity in addition to protecting healthy individuals from infection. This decreases the effective R0 value of the disease.", "This decreases the effective R0 value of the disease. Nonetheless, there are social, clinical and economic hurdles for vaccine and vaccination programmes, including a the willingness of the public to undergo vaccination with a novel vaccine, b the side effects and severe adverse reactions of vaccination, c the potential difference and/or low efficacy of the vaccine in populations different from the clinical trials' populations and d the accessibility of the vaccines to a given population including the cost and availability of the vaccine . Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing .", "Vaccines against the 2019-nCoV are currently in development and none are in testing at the time of writing . On 23 January 2020, the Coalition for Epidemic Preparedness Innovations CEPI announced that they will fund vaccine development programmes with Inovio, The University of Queensland and Moderna, Inc respectively, with the aim to test the experimental vaccines clinically in 16 weeks By June 2020 . The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations .", "The vaccine candidates will be developed by the DNA, recombinant and mRNA vaccine platforms from these organizations . Based on the most recent MERS-CoV outbreak, there are already a number of vaccine candidates being developed but most are still in the preclinical testing stage. The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine.", "The vaccines in development include viral vector-based vaccine, DNA vaccine, subunit vaccine, virus-like particles VLPs -based vaccine, inactivated whole-virus IWV vaccine and live attenuated vaccine. The latest findings for these vaccines arebased on the review by Yong et al. . in August 2019 .", ". in August 2019 . As of the date of reporting, there is only one published clinical study on the MERS-CoV vaccine by GeneOne Life Science & Inovio Pharmaceuticals . There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases.", "There was one SARS vaccine trial conducted by the US National Institute of Allergy and Infectious Diseases. Both Phase I clinical trials reported positive results, but only one has announced plans to proceed to Phase 2 trial . Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine.", "Due to the close genetic relatedness of SARS-CoV 79% with 2019-nCoV , there may be potential cross-protective effect of using a safe SARS-CoV vaccine while awaiting the 2019-nCoV vaccine. However, this would require small scale phase-by-phase implementation and close monitoring of vaccinees before any large scale implementation. Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered.", "Apart from the timely diagnosis of cases, the achievement of favorable clinical outcomes depends on the timely treatment administered. ACE2 has been reported to be the same cell entry receptor used by 2019-nCoV to infect humans as SARS-CoV . Hence, clinical similarity between the two viruses is expected, particularly in severe cases.", "Hence, clinical similarity between the two viruses is expected, particularly in severe cases. In addition, most of those who have died from MERS-CoV, SARS-CoV and 2019-nCoV were advance in age and had underlying health conditions such as hypertension, diabetes or cardiovascular disease that compromised their immune systems . Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events.", "Coronaviruses have error-prone RNA-dependent RNA polymerases RdRP , which result in frequent mutations and recombination events. This results in quasispecies diversity that is closely associated with adaptive evolution and the capacity to enhance viral-cell entry to cause disease over time in a specific population at-risk . Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV.", "Since ACE2 is abundantly present in humans in the epithelia of the lung and small intestine, coronaviruses are likely to infect the upper respiratory and gastrointestinal tract and this may influence the type of therapeutics against 2019-nCoV, similarly to SAR-CoV. However, in the years following two major coronavirus outbreaks SARS-CoV in 2003 and MERS-CoV in 2012, there remains no consensus on the optimal therapy for either disease . Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce.", "Well-designed clinical trials that provide the gold standard for assessing the therapeutic measures are scarce. No coronavirus protease inhibitors have successfully completed a preclinical development program despite large efforts exploring SARS-CoV inhibitors. The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle.", "The bulk of potential therapeutic strategies remain in the experimental phase, with only a handful crossing the in vitro hurdle. Stronger efforts are required in the research for treatment options for major coronaviruses given their pandemic potential. Effective treatment options are essential to maximize the restoration of affected populations to good health following infections.", "Effective treatment options are essential to maximize the restoration of affected populations to good health following infections. Clinical trials have commenced in China to identify effective treatments for 2019-nCoV based on the treatment evidence from SARS and MERS. There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial.", "There is currently no effective specific antiviral with high-level evidence; any specific antiviral therapy should be provided in the context of a clinical study/trial. Few treatments have shown real curative action against SARS and MERS and the literature generally describes isolated cases or small case series. Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models.", "Many interferons from the three classes have been tested for their antiviral activities against SARS-CoV both in vitro and in animal models. Interferon β has consistently been shown to be the most active, followed by interferon α. The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls.", "The use of corticosteroids with interferon alfacon-1 synthetic interferon α appeared to have improved oxygenation and faster resolution of chest radiograph abnormalities in observational studies with untreated controls. Interferon has been used in multiple observational studies to treat SARS-CoV and MERS-CoV patients . Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV.", "Interferons, with or without ribavirin, and lopinavir/ritonavir are most likely to be beneficial and are being trialed in China for 2019-nCoV. This drug treatment appears to be the most advanced. Timing of treatment is likely an important factor in effectiveness.", "Timing of treatment is likely an important factor in effectiveness. A combination of ribavirin and lopinavir/ritonavir was used as a post-exposure prophylaxis in health care workers and may have reduced the risk of infection. Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages.", "Ribavirin alone is unlikely to have substantial antiviral activities at clinically used dosages. Hence, ribavirin with or without corticosteroids and with lopinavir and ritonavir are among the combinations employed. This was the most common agent reported in the available literature.", "This was the most common agent reported in the available literature. Its efficacy has been assessed in observational studies, retrospective case series, retrospective cohort study, a prospective observational study, a prospective cohort study and randomized controlled trial ranging from seven to 229 participants . Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV.", "Lopinavir/ritonavir Kaletra was the earliest protease inhibitor combination introduced for the treatment of SARS-CoV. Its efficacy was documented in several studies, causing notably lower incidence of adverse outcomes than with ribavirin alone. Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes.", "Combined usage with ribavirin was also associated with lower incidence of acute respiratory distress syndrome, nosocomial infection and death, amongst other favorable outcomes. Recent in vitro studies have shown another HIV protease inhibitor, nelfinavir, to have antiviral capacity against SARS-CoV, although it has yet to show favorable outcomes in animal studies . Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs.", "Remdesivir Gilead Sciences, GS-5734 nucleoside analogue in vitro and in vivo data support GS-5734 development as a potential pan-coronavirus antiviral based on results against several coronaviruses CoVs , including highly pathogenic CoVs and potentially emergent BatCoVs. The use of remdesivir may be a good candidate as an investigational treatment. Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology.", "Improved mortality following receipt of convalescent plasma in various doses was consistently reported in several observational studies involving cases with severe acute respiratory infections SARIs of viral etiology. A significant reduction in the pooled odds of mortality following treatment of 0.25 compared to placebo or no therapy was observed . Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma.", "Studies were however at moderate to high risk of bias given their small sample sizes, allocation of treatment based on the physician's discretion, and the availability of plasma. Factors like concomitant treatment may have also confounded the results. Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature.", "Associations between convalescent plasma and hospital length of stay, viral antibody levels, and viral load respectively were similarly inconsistent across available literature. Convalescent plasma, while promising, is likely not yet feasible, given the limited pool of potential donors and issues of scalability. Monoclonal antibody treatment is progressing.", "Monoclonal antibody treatment is progressing. SARS-CoV enters host cells through the binding of their spike S protein to angiotensin converting enzyme 2 ACE2 and CD209L . Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection .", "Human monoclonal antibodies to the S protein have been shown to significantly reduce the severity of lung pathology in non-human primates following MERS-CoV infection . Such neutralizing antibodies can be elicited by active or passive immunization using vaccines or convalescent plasma respectively. While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies.", "While such neutralizing antibodies can theoretically be harvested from individuals immunized with vaccines, there is uncertainty over the achievement of therapeutic levels of antibodies. Other therapeutic agents have also been reported. A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E.", "A known antimalarial agent, chloroquine, elicits antiviral effects against multiple viruses including HIV type 1, hepatitis B and HCoV-229E. Chloroquine is also immunomodulatory, capable of suppressing the production and release of factors which mediate the inflammatory complications of viral diseases tumor necrosis factor and interleukin 6 . It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH.", "It is postulated that chloroquine works by altering ACE2 glycosylation and endosomal pH. Its anti-inflammatory properties may be beneficial for the treatment of SARS. Niclosamide as a known drug used in antihelminthic treatment. The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays.", "The efficacy of niclosamide as an inhibitor of virus replication was proven in several assays. In both immunoblot analysis and immunofluorescence assays, niclosamide treatment was observed to completely inhibit viral antigen synthesis. Reduction of virus yield in infected cells was dose dependent.", "Reduction of virus yield in infected cells was dose dependent. Niclosamide likely does not interfere in the early stages of virus attachment and entry into cells, nor does it function as a protease inhibitor. Mechanisms of niclosamide activity warrant further investigation . Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication.", "Glycyrrhizin also reportedly inhibits virus adsorption and penetration in the early steps of virus replication. Glycyrrhizin was a significantly potent inhibitor with a low selectivity index when tested against several pathogenic flaviviruses. While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear.", "While preliminary results suggest production of nitrous oxide which inhibits virus replication through induction of nitrous oxide synthase, the mechanism of Glycyrrhizin against SARS-CoV remains unclear. The compound also has relatively lower toxicity compared to protease inhibitors like ribavirin . Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong.", "Inhibitory activity was also detected in baicalin , extracted from another herb used in the treatment of SARS in China and Hong Kong. Findings on these compounds are limited to in vitro studies . Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review.", "Due to the rapidly evolving situation of the 2019-nCoV, there will be potential limitations to the systematic review. The systematic review is likely to have publication bias as some developments have yet to be reported while for other developments there is no intention to report publicly or in scientific platforms due to confidentiality concerns. However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder.", "However, this may be limited to only a few developments for review as publicity does help in branding to some extent for the company and/or the funder. Furthermore, due to the rapid need to share the status of these developments, there may be reporting bias in some details provided by authors of the scientific articles or commentary articles in traditional media. Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak.", "Lastly, while it is not viable for any form of quality assessment and metaanalysis of the selected articles due to the limited data provided and the heterogeneous style of reporting by different articles, this paper has provided a comprehensive overview of the potential developments of these pharmaceutical interventions during the early phase of the outbreak. This systematic review would be useful for cross-check when the quality assessment and meta-analysis of these developments are performed as a follow-up study. Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases.", "Rapid diagnostics, vaccines and therapeutics are key pharmaceutical interventions to limit transmission of respiratory infectious diseases. Many potential developments on these pharmaceutical interventions for 2019-nCoV are ongoing in the containment phase of this outbreak, potentially due to better pandemic preparedness than before. However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead.", "However, lessons from MERS-CoV and SARS-CoV have shown that the journeys for these developments can still be challenging moving ahead. Supplementary Materials: The following are available online at .com/xxx/s1, Table S1 : Example of full search strategy in Pubmed, Table S2 : Google Search: 2019-nCoV diagnostics, Table S3 : Summary of diagnostic assays developed for 2019-nCoV, Table S4" ]