Molecular epidemiology, evolution and phylogeny of SARS coronavirus
Identifieur interne : 001790 ( Pmc/Curation ); précédent : 001789; suivant : 001791Molecular epidemiology, evolution and phylogeny of SARS coronavirus
Auteurs : Hayes K. H. Luk [République populaire de Chine] ; Xin Li [République populaire de Chine] ; Joshua Fung [République populaire de Chine] ; Susanna K. P. Lau [République populaire de Chine] ; Patrick C. Y. Woo [République populaire de Chine]Source :
- Infection, Genetics and Evolution [ 1567-1348 ] ; 2019.
Abstract
Shortly after its emergence in southern China in 2002/2003, Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) was confirmed to be the cause of SARS. Subsequently, SARS-related CoVs (SARSr-CoVs) were found in palm civets from live animal markets in Guangdong and in various horseshoe bat species, which were believed to be the ultimate reservoir of SARSr-CoV. Till November 2018, 339 SARSr-CoV genomes have been sequenced, including 274 from human, 18 from civets and 47 from bats [mostly from Chinese horseshoe bats (
Url:
DOI: 10.1016/j.meegid.2019.03.001
PubMed: 30844511
PubMed Central: 7106202
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Luk</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Microbiology, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Li, Xin" sort="Li, Xin" uniqKey="Li X" first="Xin" last="Li">Xin Li</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Microbiology, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Fung, Joshua" sort="Fung, Joshua" uniqKey="Fung J" first="Joshua" last="Fung">Joshua Fung</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Microbiology, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. 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Lau</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Microbiology, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0010">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0015">Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0020">Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006</wicri:regionArea></affiliation></author><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. 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Woo</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Microbiology, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0010">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0015">Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0020">Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">30844511</idno><idno type="pmc">7106202</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106202</idno><idno type="RBID">PMC:7106202</idno><idno type="doi">10.1016/j.meegid.2019.03.001</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">001790</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001790</idno><idno type="wicri:Area/Pmc/Curation">001790</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001790</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular epidemiology, evolution and phylogeny of SARS coronavirus</title><author><name sortKey="Luk, Hayes K H" sort="Luk, Hayes K H" uniqKey="Luk H" first="Hayes K. H." last="Luk">Hayes K. H. Luk</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Microbiology, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Li, Xin" sort="Li, Xin" uniqKey="Li X" first="Xin" last="Li">Xin Li</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Microbiology, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Fung, Joshua" sort="Fung, Joshua" uniqKey="Fung J" first="Joshua" last="Fung">Joshua Fung</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Microbiology, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Microbiology, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0010">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0015">Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0020">Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006</wicri:regionArea></affiliation></author><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><affiliation wicri:level="1"><nlm:aff id="af0005">Department of Microbiology, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0010">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0015">Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="af0020">Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006</wicri:regionArea></affiliation></author></analytic><series><title level="j">Infection, Genetics and Evolution</title><idno type="ISSN">1567-1348</idno><idno type="eISSN">1567-7257</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Shortly after its emergence in southern China in 2002/2003, Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) was confirmed to be the cause of SARS. Subsequently, SARS-related CoVs (SARSr-CoVs) were found in palm civets from live animal markets in Guangdong and in various horseshoe bat species, which were believed to be the ultimate reservoir of SARSr-CoV. Till November 2018, 339 SARSr-CoV genomes have been sequenced, including 274 from human, 18 from civets and 47 from bats [mostly from Chinese horseshoe bats (<italic>Rhinolophus sinicus</italic>), n = 30; and greater horseshoe bats (<italic>Rhinolophus ferrumequinum</italic>), n = 9]. The human SARS-CoVs and civet SARSr-CoVs were collected in 2003/2004, while bat SARSr-CoVs were continuously isolated in the past 13 years even after the cessation of the SARS epidemic. SARSr-CoVs belong to the subgenus <italic>Sarbecovirus</italic> (previously lineage B) of genus <italic>Betacoronavirus</italic> and occupy a unique phylogenetic position. Overall, it is observed that the SARSr-CoV genomes from bats in Yunnan province of China possess the highest nucleotide identity to those from civets. It is evident from both multiple alignment and phylogenetic analyses that some genes of a particular SARSr-CoV from bats may possess higher while other genes possess much lower nucleotide identity to the corresponding genes of SARSr-CoV from human/civets, resulting in the shift of phylogenetic position in different phylogenetic trees. Our current model on the origin of SARS is that the human SARS-CoV that caused the epidemic in 2002/2003 was probably a result of multiple recombination events from a number of SARSr-CoV ancestors in different horseshoe bat species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Campanella, J J" uniqKey="Campanella J">J.J. Campanella</name></author><author><name sortKey="Bitincka, L" uniqKey="Bitincka L">L. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Infect Genet Evol</journal-id><journal-id journal-id-type="iso-abbrev">Infect. Genet. Evol</journal-id><journal-title-group><journal-title>Infection, Genetics and Evolution</journal-title></journal-title-group><issn pub-type="ppub">1567-1348</issn><issn pub-type="epub">1567-7257</issn><publisher><publisher-name>Published by Elsevier B.V.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">30844511</article-id><article-id pub-id-type="pmc">7106202</article-id><article-id pub-id-type="publisher-id">S1567-1348(19)30031-0</article-id><article-id pub-id-type="doi">10.1016/j.meegid.2019.03.001</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Molecular epidemiology, evolution and phylogeny of SARS coronavirus</article-title></title-group><contrib-group><contrib contrib-type="author" id="au0005"><name><surname>Luk</surname><given-names>Hayes K.H.</given-names></name><xref rid="af0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="au0010"><name><surname>Li</surname><given-names>Xin</given-names></name><xref rid="af0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="au0015"><name><surname>Fung</surname><given-names>Joshua</given-names></name><xref rid="af0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="au0020"><name><surname>Lau</surname><given-names>Susanna K.P.</given-names></name><email>skplau@hku.hk</email><xref rid="af0005" ref-type="aff">a</xref><xref rid="af0010" ref-type="aff">b</xref><xref rid="af0015" ref-type="aff">c</xref><xref rid="af0020" ref-type="aff">d</xref><xref rid="cr0005" ref-type="corresp">⁎</xref></contrib><contrib contrib-type="author" id="au0025"><name><surname>Woo</surname><given-names>Patrick C.Y.</given-names></name><email>pcywoo@hku.hk</email><xref rid="af0005" ref-type="aff">a</xref><xref rid="af0010" ref-type="aff">b</xref><xref rid="af0015" ref-type="aff">c</xref><xref rid="af0020" ref-type="aff">d</xref><xref rid="cr0005" ref-type="corresp">⁎</xref></contrib></contrib-group><aff id="af0005"><label>a</label>Department of Microbiology, The University of Hong Kong, Hong Kong, China</aff><aff id="af0010"><label>b</label>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China</aff><aff id="af0015"><label>c</label>Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China</aff><aff id="af0020"><label>d</label>Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310006, China</aff><author-notes><corresp id="cr0005"><label>⁎</label>Corresponding authors at: State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Block T, Queen Mary Hospital, Hong Kong, China. <email>skplau@hku.hk</email><email>pcywoo@hku.hk</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>4</day><month>3</month><year>2019</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>7</month><year>2019</year></pub-date><pub-date pub-type="epub"><day>4</day><month>3</month><year>2019</year></pub-date><volume>71</volume><fpage>21</fpage><lpage>30</lpage><history><date date-type="received"><day>11</day><month>12</month><year>2018</year></date><date date-type="rev-recd"><day>27</day><month>2</month><year>2019</year></date><date date-type="accepted"><day>1</day><month>3</month><year>2019</year></date></history><permissions><copyright-statement>© 2019 Published by Elsevier B.V.</copyright-statement><copyright-year>2019</copyright-year><copyright-holder></copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract id="ab0005"><p>Shortly after its emergence in southern China in 2002/2003, Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) was confirmed to be the cause of SARS. Subsequently, SARS-related CoVs (SARSr-CoVs) were found in palm civets from live animal markets in Guangdong and in various horseshoe bat species, which were believed to be the ultimate reservoir of SARSr-CoV. Till November 2018, 339 SARSr-CoV genomes have been sequenced, including 274 from human, 18 from civets and 47 from bats [mostly from Chinese horseshoe bats (<italic>Rhinolophus sinicus</italic>), n = 30; and greater horseshoe bats (<italic>Rhinolophus ferrumequinum</italic>), n = 9]. The human SARS-CoVs and civet SARSr-CoVs were collected in 2003/2004, while bat SARSr-CoVs were continuously isolated in the past 13 years even after the cessation of the SARS epidemic. SARSr-CoVs belong to the subgenus <italic>Sarbecovirus</italic> (previously lineage B) of genus <italic>Betacoronavirus</italic> and occupy a unique phylogenetic position. Overall, it is observed that the SARSr-CoV genomes from bats in Yunnan province of China possess the highest nucleotide identity to those from civets. It is evident from both multiple alignment and phylogenetic analyses that some genes of a particular SARSr-CoV from bats may possess higher while other genes possess much lower nucleotide identity to the corresponding genes of SARSr-CoV from human/civets, resulting in the shift of phylogenetic position in different phylogenetic trees. Our current model on the origin of SARS is that the human SARS-CoV that caused the epidemic in 2002/2003 was probably a result of multiple recombination events from a number of SARSr-CoV ancestors in different horseshoe bat species.</p></abstract><abstract abstract-type="author-highlights" id="ab0010"><title>Highlights</title><p><list list-type="simple" id="l0005"><list-item id="li0005"><label>•</label><p id="p0005">313 SARSr-CoV genomes have been sequenced (274 from human, 18 civets and 47 bats).</p></list-item><list-item id="li0010"><label>•</label><p id="p0010">SARSr-CoV genomes of bats in Yunnan possess highest nt identity to those from civets.</p></list-item><list-item id="li0015"><label>•</label><p id="p0015">The origin of human SARS-CoV was probably a result of multiple recombination events.</p></list-item><list-item id="li0020"><label>•</label><p id="p0020">Recombination from a number of SARSr-CoV ancestors in different horseshoe bat species.</p></list-item></list></p></abstract><kwd-group id="ks0005"><title>Keywords</title><kwd>SARS coronavirus</kwd><kwd>Molecular epidemiology</kwd><kwd>Evolution</kwd><kwd>Phylogeny</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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