The global spread of 2019-nCoV: a molecular evolutionary analysis
Identifieur interne : 000029 ( Pmc/Checkpoint ); précédent : 000028; suivant : 000030The global spread of 2019-nCoV: a molecular evolutionary analysis
Auteurs : Domenico Benvenuto [Italie] ; Marta Giovanetti [Brésil] ; Marco Salemi [États-Unis] ; Mattia Prosperi [États-Unis] ; Cecilia De Flora [Italie] ; Luiz Carlos Junior Alcantara [Brésil] ; Silvia Angeletti [Italie] ; Massimo Ciccozzi [Brésil]Source :
- Pathogens and Global Health [ 2047-7724 ] ; 2020.
Abstract
The global spread of the 2019-nCoV is continuing and is fast moving, as indicated by the WHO raising the risk assessment to high. In this article, we provide a preliminary phylodynamic and phylogeographic analysis of this new virus. A Maximum Clade Credibility tree has been built using the 29 available whole genome sequences of 2019-nCoV and two whole genome sequences that are highly similar sequences from Bat SARS-like Coronavirus available in GeneBank. We are able to clarify the mechanism of transmission among the countries which have provided the 2019-nCoV sequence isolates from their patients. The Bayesian phylogeographic reconstruction shows that the 2019–2020 nCoV most probably originated from the Bat SARS-like Coronavirus circulating in the
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DOI: 10.1080/20477724.2020.1725339
PubMed: 32048560
PubMed Central: 7099638
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Prosperi</name><affiliation wicri:level="1"><nlm:aff id="AFF0003"><institution>Department of Epidemiology, University of Florida</institution>, Gainesville, FL,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF0004"><institution>Emerging Pathogens Institute, University of Florida</institution>, Gainesville, FL,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="De Flora, Cecilia" sort="De Flora, Cecilia" uniqKey="De Flora C" first="Cecilia" last="De Flora">Cecilia De Flora</name><affiliation wicri:level="1"><nlm:aff id="AFF0001"><institution>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome</institution>,<country>Italy</country></nlm:aff><country 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xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><affiliation wicri:level="1"><nlm:aff id="AFF0002"><institution>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz</institution>, Rio de Janeiro,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">32048560</idno><idno type="pmc">7099638</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099638</idno><idno type="RBID">PMC:7099638</idno><idno type="doi">10.1080/20477724.2020.1725339</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">001420</idno><idno type="wicri:explorRef" 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strict</wicri:regionArea></affiliation></author><author><name sortKey="Giovanetti, Marta" sort="Giovanetti, Marta" uniqKey="Giovanetti M" first="Marta" last="Giovanetti">Marta Giovanetti</name><affiliation wicri:level="1"><nlm:aff id="AFF0002"><institution>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz</institution>, Rio de Janeiro,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Salemi, Marco" sort="Salemi, Marco" uniqKey="Salemi M" first="Marco" last="Salemi">Marco Salemi</name><affiliation wicri:level="1"><nlm:aff id="AFF0003"><institution>Department of Epidemiology, University of Florida</institution>, Gainesville, FL,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF0004"><institution>Emerging Pathogens Institute, University of Florida</institution>, Gainesville, FL,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Prosperi, Mattia" sort="Prosperi, Mattia" uniqKey="Prosperi M" first="Mattia" last="Prosperi">Mattia Prosperi</name><affiliation wicri:level="1"><nlm:aff id="AFF0003"><institution>Department of Epidemiology, University of Florida</institution>, Gainesville, FL,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF0004"><institution>Emerging Pathogens Institute, University of Florida</institution>, Gainesville, FL,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="De Flora, Cecilia" sort="De Flora, Cecilia" uniqKey="De Flora C" first="Cecilia" last="De Flora">Cecilia De Flora</name><affiliation wicri:level="1"><nlm:aff id="AFF0001"><institution>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome</institution>,<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Junior Alcantara, Luiz Carlos" sort="Junior Alcantara, Luiz Carlos" uniqKey="Junior Alcantara L" first="Luiz Carlos" last="Junior Alcantara">Luiz Carlos Junior Alcantara</name><affiliation wicri:level="1"><nlm:aff id="AFF0002"><institution>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz</institution>, Rio de Janeiro,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Angeletti, Silvia" sort="Angeletti, Silvia" uniqKey="Angeletti S" first="Silvia" last="Angeletti">Silvia Angeletti</name><affiliation wicri:level="1"><nlm:aff id="AFF0005"><institution>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome</institution>,<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><affiliation wicri:level="1"><nlm:aff id="AFF0002"><institution>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz</institution>, Rio de Janeiro,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Pathogens and Global Health</title><idno type="ISSN">2047-7724</idno><idno type="eISSN">2047-7732</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>ABSTRACT</title><p>The global spread of the 2019-nCoV is continuing and is fast moving, as indicated by the WHO raising the risk assessment to high. In this article, we provide a preliminary phylodynamic and phylogeographic analysis of this new virus. A Maximum Clade Credibility tree has been built using the 29 available whole genome sequences of 2019-nCoV and two whole genome sequences that are highly similar sequences from Bat SARS-like Coronavirus available in GeneBank. We are able to clarify the mechanism of transmission among the countries which have provided the 2019-nCoV sequence isolates from their patients. The Bayesian phylogeographic reconstruction shows that the 2019–2020 nCoV most probably originated from the Bat SARS-like Coronavirus circulating in the <italic>Rhinolophus</italic> bat family. In agreement with epidemiological observations, the most likely geographic origin of the new outbreak was the city of Wuhan, China, where 2019-nCoV time of the most recent common ancestor emerged, according to molecular clock analysis, around November 25<sup>th</sup>, 2019. These results, together with previously recorded epidemics, suggest a recurring pattern of periodical epizootic outbreaks due to <italic>Betacoronavirus</italic>. Moreover, our study describes the same population genetic dynamic underlying the SARS 2003 epidemic, and suggests the urgent need for the development of effective molecular surveillance strategies of <italic>Betacoronavirus</italic> among animals and <italic>Rhinolophus</italic> of the bat family.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Weiss, Sr" uniqKey="Weiss S">SR Weiss</name></author><author><name sortKey="Leibowitz, Jl" uniqKey="Leibowitz J">JL. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Pathog Glob Health</journal-id><journal-id journal-id-type="iso-abbrev">Pathog Glob Health</journal-id><journal-id journal-id-type="publisher-id">YPGH</journal-id><journal-id journal-id-type="publisher-id">ypgh20</journal-id><journal-title-group><journal-title>Pathogens and Global Health</journal-title></journal-title-group><issn pub-type="ppub">2047-7724</issn><issn pub-type="epub">2047-7732</issn><publisher><publisher-name>Taylor & Francis</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">32048560</article-id><article-id pub-id-type="pmc">7099638</article-id><article-id pub-id-type="publisher-id">1725339</article-id><article-id pub-id-type="doi">10.1080/20477724.2020.1725339</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>The global spread of 2019-nCoV: a molecular evolutionary analysis</article-title><alt-title alt-title-type="running-authors">D. BENVENUTO ET AL.</alt-title><alt-title alt-title-type="running-title">PATHOGENS AND GLOBAL HEALTH</alt-title></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-3833-2927</contrib-id><name><surname>Benvenuto</surname><given-names>Domenico</given-names></name><xref ref-type="aff" rid="AFF0001"><sup>a</sup></xref><xref ref-type="author-notes" rid="FT0001"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Giovanetti</surname><given-names>Marta</given-names></name><xref ref-type="aff" rid="AFF0002"><sup>b</sup></xref><xref ref-type="author-notes" rid="FT0001"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Salemi</surname><given-names>Marco</given-names></name><xref ref-type="aff" rid="AFF0003"><sup>c</sup></xref><xref ref-type="aff" rid="AFF0004"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Prosperi</surname><given-names>Mattia</given-names></name><xref ref-type="aff" rid="AFF0003"><sup>c</sup></xref><xref ref-type="aff" rid="AFF0004"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>De Flora</surname><given-names>Cecilia</given-names></name><xref ref-type="aff" rid="AFF0001"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Junior Alcantara</surname><given-names>Luiz Carlos</given-names></name><xref ref-type="aff" rid="AFF0002"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Angeletti</surname><given-names>Silvia</given-names></name><xref ref-type="corresp" rid="AN0001"></xref><xref ref-type="aff" rid="AFF0005"><sup>e</sup></xref><xref ref-type="author-notes" rid="FT0001"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ciccozzi</surname><given-names>Massimo</given-names></name><xref ref-type="aff" rid="AFF0002"><sup>b</sup></xref><xref ref-type="author-notes" rid="FT0001"><sup>*</sup></xref></contrib><aff id="AFF0001"><label>a</label><institution>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome</institution>,<country>Italy</country></aff><aff id="AFF0002"><label>b</label><institution>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz</institution>, Rio de Janeiro,<country>Brazil</country></aff><aff id="AFF0003"><label>c</label><institution>Department of Epidemiology, University of Florida</institution>, Gainesville, FL,<country>USA</country></aff><aff id="AFF0004"><label>d</label><institution>Emerging Pathogens Institute, University of Florida</institution>, Gainesville, FL,<country>USA</country></aff><aff id="AFF0005"><label>e</label><institution>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome</institution>,<country>Italy</country></aff></contrib-group><author-notes><corresp id="AN0001">CONTACT Silvia Angeletti <email xlink:href="s.angeletti@unicampus.it">s.angeletti@unicampus.it</email><institution>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome</institution>, <country>Italy</country></corresp><fn id="FT0001"><label>*</label><p>These authors contributed equally to this article</p></fn></author-notes><pub-date pub-type="collection"><year>2020</year></pub-date><pub-date pub-type="epub"><day>12</day><month>2</month><year>2020</year></pub-date><volume>0</volume><issue>0</issue><fpage seq="1">1</fpage><lpage>4</lpage><permissions><copyright-statement>© 2020 Informa UK Limited, trading as Taylor & Francis Group</copyright-statement><copyright-year>2020</copyright-year><copyright-holder>Informa UK Limited, trading as Taylor & Francis Group</copyright-holder><license><license-p>This article is made available via the PMC Open Access Subset for unrestricted re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the COVID-19 pandemic or until permissions are revoked in writing. Upon expiration of these permissions, PMC is granted a perpetual license to make this article available via PMC and Europe PMC, consistent with existing copyright protections.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="YPGH_0_1725339.pdf"></self-uri><abstract><title>ABSTRACT</title><p>The global spread of the 2019-nCoV is continuing and is fast moving, as indicated by the WHO raising the risk assessment to high. In this article, we provide a preliminary phylodynamic and phylogeographic analysis of this new virus. A Maximum Clade Credibility tree has been built using the 29 available whole genome sequences of 2019-nCoV and two whole genome sequences that are highly similar sequences from Bat SARS-like Coronavirus available in GeneBank. We are able to clarify the mechanism of transmission among the countries which have provided the 2019-nCoV sequence isolates from their patients. The Bayesian phylogeographic reconstruction shows that the 2019–2020 nCoV most probably originated from the Bat SARS-like Coronavirus circulating in the <italic>Rhinolophus</italic> bat family. In agreement with epidemiological observations, the most likely geographic origin of the new outbreak was the city of Wuhan, China, where 2019-nCoV time of the most recent common ancestor emerged, according to molecular clock analysis, around November 25<sup>th</sup>, 2019. These results, together with previously recorded epidemics, suggest a recurring pattern of periodical epizootic outbreaks due to <italic>Betacoronavirus</italic>. Moreover, our study describes the same population genetic dynamic underlying the SARS 2003 epidemic, and suggests the urgent need for the development of effective molecular surveillance strategies of <italic>Betacoronavirus</italic> among animals and <italic>Rhinolophus</italic> of the bat family.</p></abstract><kwd-group kwd-group-type="author"><title>KEYWORDS</title><kwd>2019-nCoV</kwd><kwd>molecular Epidemiology</kwd><kwd>phylogeny</kwd><kwd>SARS</kwd></kwd-group><counts><fig-count count="1"></fig-count><ref-count count="16"></ref-count><page-count count="4"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>Brésil</li><li>Italie</li><li>États-Unis</li></country></list><tree><country name="Italie"><noRegion><name sortKey="Benvenuto, Domenico" sort="Benvenuto, Domenico" uniqKey="Benvenuto D" first="Domenico" last="Benvenuto">Domenico Benvenuto</name></noRegion><name sortKey="Angeletti, Silvia" sort="Angeletti, Silvia" uniqKey="Angeletti S" first="Silvia" last="Angeletti">Silvia Angeletti</name><name sortKey="De Flora, Cecilia" sort="De Flora, Cecilia" uniqKey="De Flora C" first="Cecilia" last="De Flora">Cecilia De Flora</name></country><country name="Brésil"><noRegion><name sortKey="Giovanetti, Marta" sort="Giovanetti, Marta" uniqKey="Giovanetti M" first="Marta" last="Giovanetti">Marta Giovanetti</name></noRegion><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><name sortKey="Junior Alcantara, Luiz Carlos" sort="Junior Alcantara, Luiz Carlos" uniqKey="Junior Alcantara L" first="Luiz Carlos" last="Junior Alcantara">Luiz Carlos Junior Alcantara</name></country><country name="États-Unis"><noRegion><name sortKey="Salemi, Marco" sort="Salemi, Marco" uniqKey="Salemi M" first="Marco" last="Salemi">Marco Salemi</name></noRegion><name sortKey="Prosperi, Mattia" sort="Prosperi, Mattia" uniqKey="Prosperi M" first="Mattia" last="Prosperi">Mattia Prosperi</name><name sortKey="Prosperi, Mattia" sort="Prosperi, Mattia" uniqKey="Prosperi M" first="Mattia" last="Prosperi">Mattia Prosperi</name><name sortKey="Salemi, Marco" sort="Salemi, Marco" uniqKey="Salemi M" first="Marco" last="Salemi">Marco Salemi</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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