Global patterns in coronavirus diversity.
Identifieur interne : 000C54 ( PubMed/Curation ); précédent : 000C53; suivant : 000C55Global patterns in coronavirus diversity.
Auteurs : Simon J. Anthony [États-Unis] ; Christine K. Johnson [États-Unis] ; Denise J. Greig [États-Unis] ; Sarah Kramer [États-Unis] ; Xiaoyu Che [États-Unis] ; Heather Wells [États-Unis] ; Allison L. Hicks [États-Unis] ; Damien O. Joly [États-Unis] ; Nathan D. Wolfe [États-Unis] ; Peter Daszak [États-Unis] ; William Karesh [États-Unis] ; W I Lipkin [États-Unis] ; Stephen S. Morse [États-Unis] ; Jonna A K. Mazet [États-Unis] ; Tracey Goldstein [États-Unis]Source :
- Virus evolution [ 2057-1577 ] ; 2017.
Abstract
Since the emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrom Coronavirus (MERS-CoV) it has become increasingly clear that bats are important reservoirs of CoVs. Despite this, only 6% of all CoV sequences in GenBank are from bats. The remaining 94% largely consist of known pathogens of public health or agricultural significance, indicating that current research effort is heavily biased towards describing known diseases rather than the 'pre-emergent' diversity in bats. Our study addresses this critical gap, and focuses on resource poor countries where the risk of zoonotic emergence is believed to be highest. We surveyed the diversity of CoVs in multiple host taxa from twenty countries to explore the factors driving viral diversity at a global scale. We identified sequences representing 100 discrete phylogenetic clusters, ninety-one of which were found in bats, and used ecological and epidemiologic analyses to show that patterns of CoV diversity correlate with those of bat diversity. This cements bats as the major evolutionary reservoirs and ecological drivers of CoV diversity. Co-phylogenetic reconciliation analysis was also used to show that host switching has contributed to CoV evolution, and a preliminary analysis suggests that regional variation exists in the dynamics of this process. Overall our study represents a model for exploring global viral diversity and advances our fundamental understanding of CoV biodiversity and the potential risk factors associated with zoonotic emergence.
DOI: 10.1093/ve/vex012
PubMed: 28630747
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Johnson</name><affiliation wicri:level="1"><nlm:affiliation>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616</wicri:regionArea></affiliation></author><author><name sortKey="Greig, Denise J" sort="Greig, Denise J" uniqKey="Greig D" first="Denise J" last="Greig">Denise J. 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One Sutter, Suite 600, San Francisco, CA 94104</wicri:regionArea></affiliation></author><author><name sortKey="Daszak, Peter" sort="Daszak, Peter" uniqKey="Daszak P" first="Peter" last="Daszak">Peter Daszak</name><affiliation wicri:level="1"><nlm:affiliation>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001</wicri:regionArea></affiliation></author><author><name sortKey="Karesh, William" sort="Karesh, William" uniqKey="Karesh W" first="William" last="Karesh">William Karesh</name><affiliation wicri:level="1"><nlm:affiliation>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001</wicri:regionArea></affiliation></author><author><name sortKey="Lipkin, W I" sort="Lipkin, W I" uniqKey="Lipkin W" first="W I" last="Lipkin">W I Lipkin</name><affiliation wicri:level="1"><nlm:affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032</wicri:regionArea></affiliation></author><author><name sortKey="Morse, Stephen S" sort="Morse, Stephen S" uniqKey="Morse S" first="Stephen S" last="Morse">Stephen S. 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Anthony</name><affiliation wicri:level="1"><nlm:affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032</wicri:regionArea></affiliation></author><author><name sortKey="Johnson, Christine K" sort="Johnson, Christine K" uniqKey="Johnson C" first="Christine K" last="Johnson">Christine K. Johnson</name><affiliation wicri:level="1"><nlm:affiliation>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616</wicri:regionArea></affiliation></author><author><name sortKey="Greig, Denise J" sort="Greig, Denise J" uniqKey="Greig D" first="Denise J" last="Greig">Denise J. Greig</name><affiliation wicri:level="1"><nlm:affiliation>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616</wicri:regionArea></affiliation></author><author><name sortKey="Kramer, Sarah" sort="Kramer, Sarah" uniqKey="Kramer S" first="Sarah" last="Kramer">Sarah Kramer</name><affiliation wicri:level="1"><nlm:affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032</wicri:regionArea></affiliation></author><author><name sortKey="Che, Xiaoyu" sort="Che, Xiaoyu" uniqKey="Che X" first="Xiaoyu" last="Che">Xiaoyu Che</name><affiliation wicri:level="1"><nlm:affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032</wicri:regionArea></affiliation></author><author><name sortKey="Wells, Heather" sort="Wells, Heather" uniqKey="Wells H" first="Heather" last="Wells">Heather Wells</name><affiliation wicri:level="1"><nlm:affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032</wicri:regionArea></affiliation></author><author><name sortKey="Hicks, Allison L" sort="Hicks, Allison L" uniqKey="Hicks A" first="Allison L" last="Hicks">Allison L. Hicks</name><affiliation wicri:level="1"><nlm:affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032</wicri:regionArea></affiliation></author><author><name sortKey="Joly, Damien O" sort="Joly, Damien O" uniqKey="Joly D" first="Damien O" last="Joly">Damien O. Joly</name><affiliation wicri:level="1"><nlm:affiliation>Metabiota, Inc. One Sutter, Suite 600, San Francisco, CA 94104, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Metabiota, Inc. One Sutter, Suite 600, San Francisco, CA 94104</wicri:regionArea></affiliation></author><author><name sortKey="Wolfe, Nathan D" sort="Wolfe, Nathan D" uniqKey="Wolfe N" first="Nathan D" last="Wolfe">Nathan D. Wolfe</name><affiliation wicri:level="1"><nlm:affiliation>Metabiota, Inc. One Sutter, Suite 600, San Francisco, CA 94104, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Metabiota, Inc. One Sutter, Suite 600, San Francisco, CA 94104</wicri:regionArea></affiliation></author><author><name sortKey="Daszak, Peter" sort="Daszak, Peter" uniqKey="Daszak P" first="Peter" last="Daszak">Peter Daszak</name><affiliation wicri:level="1"><nlm:affiliation>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001</wicri:regionArea></affiliation></author><author><name sortKey="Karesh, William" sort="Karesh, William" uniqKey="Karesh W" first="William" last="Karesh">William Karesh</name><affiliation wicri:level="1"><nlm:affiliation>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001</wicri:regionArea></affiliation></author><author><name sortKey="Lipkin, W I" sort="Lipkin, W I" uniqKey="Lipkin W" first="W I" last="Lipkin">W I Lipkin</name><affiliation wicri:level="1"><nlm:affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032</wicri:regionArea></affiliation></author><author><name sortKey="Morse, Stephen S" sort="Morse, Stephen S" uniqKey="Morse S" first="Stephen S" last="Morse">Stephen S. Morse</name><affiliation wicri:level="1"><nlm:affiliation>Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032</wicri:regionArea></affiliation></author><author><name sortKey="Mazet, Jonna A K" sort="Mazet, Jonna A K" uniqKey="Mazet J" first="Jonna A K" last="Mazet">Jonna A K. Mazet</name><affiliation wicri:level="1"><nlm:affiliation>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616</wicri:regionArea></affiliation></author><author><name sortKey="Goldstein, Tracey" sort="Goldstein, Tracey" uniqKey="Goldstein T" first="Tracey" last="Goldstein">Tracey Goldstein</name><affiliation wicri:level="1"><nlm:affiliation>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616</wicri:regionArea></affiliation></author></analytic><series><title level="j">Virus evolution</title><idno type="ISSN">2057-1577</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Since the emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrom Coronavirus (MERS-CoV) it has become increasingly clear that bats are important reservoirs of CoVs. Despite this, only 6% of all CoV sequences in GenBank are from bats. The remaining 94% largely consist of known pathogens of public health or agricultural significance, indicating that current research effort is heavily biased towards describing known diseases rather than the 'pre-emergent' diversity in bats. Our study addresses this critical gap, and focuses on resource poor countries where the risk of zoonotic emergence is believed to be highest. We surveyed the diversity of CoVs in multiple host taxa from twenty countries to explore the factors driving viral diversity at a global scale. We identified sequences representing 100 discrete phylogenetic clusters, ninety-one of which were found in bats, and used ecological and epidemiologic analyses to show that patterns of CoV diversity correlate with those of bat diversity. This cements bats as the major evolutionary reservoirs and ecological drivers of CoV diversity. Co-phylogenetic reconciliation analysis was also used to show that host switching has contributed to CoV evolution, and a preliminary analysis suggests that regional variation exists in the dynamics of this process. Overall our study represents a model for exploring global viral diversity and advances our fundamental understanding of CoV biodiversity and the potential risk factors associated with zoonotic emergence.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">28630747</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2057-1577</ISSN><JournalIssue CitedMedium="Print"><Volume>3</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>Jan</Month></PubDate></JournalIssue><Title>Virus evolution</Title><ISOAbbreviation>Virus Evol</ISOAbbreviation></Journal><ArticleTitle>Global patterns in coronavirus diversity.</ArticleTitle><Pagination><MedlinePgn>vex012</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/ve/vex012</ELocationID><Abstract><AbstractText>Since the emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrom Coronavirus (MERS-CoV) it has become increasingly clear that bats are important reservoirs of CoVs. Despite this, only 6% of all CoV sequences in GenBank are from bats. The remaining 94% largely consist of known pathogens of public health or agricultural significance, indicating that current research effort is heavily biased towards describing known diseases rather than the 'pre-emergent' diversity in bats. Our study addresses this critical gap, and focuses on resource poor countries where the risk of zoonotic emergence is believed to be highest. We surveyed the diversity of CoVs in multiple host taxa from twenty countries to explore the factors driving viral diversity at a global scale. We identified sequences representing 100 discrete phylogenetic clusters, ninety-one of which were found in bats, and used ecological and epidemiologic analyses to show that patterns of CoV diversity correlate with those of bat diversity. This cements bats as the major evolutionary reservoirs and ecological drivers of CoV diversity. Co-phylogenetic reconciliation analysis was also used to show that host switching has contributed to CoV evolution, and a preliminary analysis suggests that regional variation exists in the dynamics of this process. Overall our study represents a model for exploring global viral diversity and advances our fundamental understanding of CoV biodiversity and the potential risk factors associated with zoonotic emergence.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Anthony</LastName><ForeName>Simon J</ForeName><Initials>SJ</Initials><AffiliationInfo><Affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Johnson</LastName><ForeName>Christine K</ForeName><Initials>CK</Initials><AffiliationInfo><Affiliation>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Greig</LastName><ForeName>Denise J</ForeName><Initials>DJ</Initials><AffiliationInfo><Affiliation>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kramer</LastName><ForeName>Sarah</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Che</LastName><ForeName>Xiaoyu</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wells</LastName><ForeName>Heather</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hicks</LastName><ForeName>Allison L</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Joly</LastName><ForeName>Damien O</ForeName><Initials>DO</Initials><AffiliationInfo><Affiliation>Metabiota, Inc. One Sutter, Suite 600, San Francisco, CA 94104, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Wildlife Conservation Society, New York, NY 10460, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wolfe</LastName><ForeName>Nathan D</ForeName><Initials>ND</Initials><AffiliationInfo><Affiliation>Metabiota, Inc. One Sutter, Suite 600, San Francisco, CA 94104, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Daszak</LastName><ForeName>Peter</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Karesh</LastName><ForeName>William</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lipkin</LastName><ForeName>W I</ForeName><Initials>WI</Initials><AffiliationInfo><Affiliation>Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Morse</LastName><ForeName>Stephen S</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><CollectiveName>PREDICT Consortium</CollectiveName></Author><Author ValidYN="Y"><LastName>Mazet</LastName><ForeName>Jonna A K</ForeName><Initials>JAK</Initials><AffiliationInfo><Affiliation>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Goldstein</LastName><ForeName>Tracey</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>06</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Virus Evol</MedlineTA><NlmUniqueID>101664675</NlmUniqueID><ISSNLinking>2057-1577</ISSNLinking></MedlineJournalInfo><CommentsCorrectionsList><CommentsCorrections RefType="CommentIn"><RefSource>Nature. 2017 Jun 12;546(7658):340</RefSource><PMID Version="1">28617480</PMID></CommentsCorrections></CommentsCorrectionsList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">bat</Keyword><Keyword MajorTopicYN="N">coronavirus</Keyword><Keyword MajorTopicYN="N">evolution</Keyword><Keyword MajorTopicYN="N">viral ecology</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate 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