The global spread of 2019-nCoV: a molecular evolutionary analysis.
Identifieur interne : 000806 ( PubMed/Corpus ); précédent : 000805; suivant : 000807The global spread of 2019-nCoV: a molecular evolutionary analysis.
Auteurs : Domenico Benvenuto ; Marta Giovanetti ; Marco Salemi ; Mattia Prosperi ; Cecilia De Flora ; Luiz Carlos Junior Alcantara ; Silvia Angeletti ; Massimo CiccozziSource :
- Pathogens and global health [ 2047-7732 ] ; 2020.
English descriptors
- KwdEn :
- Animals, Bayes Theorem, Betacoronavirus (genetics), China (epidemiology), Chiroptera (virology), Coronavirus (genetics), Coronavirus (isolation & purification), Coronavirus Infections (epidemiology), Coronavirus Infections (genetics), Coronavirus Infections (virology), DNA, Viral (genetics), Disease Outbreaks, Disease Reservoirs (virology), Evolution, Molecular, Genome, Viral, Global Health, Humans, Pandemics, Phylogeny, Pneumonia, Viral (epidemiology), Pneumonia, Viral (genetics), Pneumonia, Viral (virology), Sequence Analysis, Protein, Zoonoses (epidemiology), Zoonoses (genetics).
- MESH :
- chemical , genetics : DNA, Viral.
- geographic , epidemiology : China.
- epidemiology : Coronavirus Infections, Pneumonia, Viral, Zoonoses.
- genetics : Betacoronavirus, Coronavirus, Coronavirus Infections, Pneumonia, Viral, Zoonoses.
- isolation & purification : Coronavirus.
- virology : Chiroptera, Coronavirus Infections, Disease Reservoirs, Pneumonia, Viral.
- Animals, Bayes Theorem, Disease Outbreaks, Evolution, Molecular, Genome, Viral, Global Health, Humans, Pandemics, Phylogeny, Sequence Analysis, Protein.
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 Rhinolophus 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 25th, 2019. These results, together with previously recorded epidemics, suggest a recurring pattern of periodical epizootic outbreaks due to Betacoronavirus. 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 Betacoronavirus among animals and Rhinolophus of the bat family.
DOI: 10.1080/20477724.2020.1725339
PubMed: 32048560
Links to Exploration step
pubmed:32048560Le document en format XML
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USA.</nlm:affiliation></affiliation></author><author><name sortKey="Prosperi, Mattia" sort="Prosperi, Mattia" uniqKey="Prosperi M" first="Mattia" last="Prosperi">Mattia Prosperi</name><affiliation><nlm:affiliation>Department of Epidemiology, University of Florida, Gainesville, FL, USA.</nlm:affiliation></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><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.</nlm:affiliation></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><nlm:affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.</nlm:affiliation></affiliation></author><author><name sortKey="Angeletti, Silvia" sort="Angeletti, Silvia" uniqKey="Angeletti S" first="Silvia" last="Angeletti">Silvia Angeletti</name><affiliation><nlm:affiliation>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><affiliation><nlm:affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32048560</idno><idno type="pmid">32048560</idno><idno type="doi">10.1080/20477724.2020.1725339</idno><idno type="wicri:Area/PubMed/Corpus">000806</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" 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University of Florida, Gainesville, FL, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Prosperi, Mattia" sort="Prosperi, Mattia" uniqKey="Prosperi M" first="Mattia" last="Prosperi">Mattia Prosperi</name><affiliation><nlm:affiliation>Department of Epidemiology, University of Florida, Gainesville, FL, USA.</nlm:affiliation></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><nlm:affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.</nlm:affiliation></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><nlm:affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.</nlm:affiliation></affiliation></author><author><name sortKey="Angeletti, Silvia" sort="Angeletti, Silvia" uniqKey="Angeletti S" first="Silvia" last="Angeletti">Silvia Angeletti</name><affiliation><nlm:affiliation>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Italy.</nlm:affiliation></affiliation></author><author><name sortKey="Ciccozzi, Massimo" sort="Ciccozzi, Massimo" uniqKey="Ciccozzi M" first="Massimo" last="Ciccozzi">Massimo Ciccozzi</name><affiliation><nlm:affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Pathogens and global health</title><idno type="eISSN">2047-7732</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Bayes Theorem</term><term>Betacoronavirus (genetics)</term><term>China (epidemiology)</term><term>Chiroptera (virology)</term><term>Coronavirus (genetics)</term><term>Coronavirus (isolation & purification)</term><term>Coronavirus Infections (epidemiology)</term><term>Coronavirus Infections (genetics)</term><term>Coronavirus Infections (virology)</term><term>DNA, Viral (genetics)</term><term>Disease Outbreaks</term><term>Disease Reservoirs (virology)</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Global Health</term><term>Humans</term><term>Pandemics</term><term>Phylogeny</term><term>Pneumonia, Viral (epidemiology)</term><term>Pneumonia, Viral (genetics)</term><term>Pneumonia, Viral (virology)</term><term>Sequence Analysis, Protein</term><term>Zoonoses (epidemiology)</term><term>Zoonoses (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Viral</term></keywords><keywords scheme="MESH" type="geographic" qualifier="epidemiology" xml:lang="en"><term>China</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term><term>Zoonoses</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term><term>Coronavirus</term><term>Coronavirus Infections</term><term>Pneumonia, Viral</term><term>Zoonoses</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chiroptera</term><term>Coronavirus Infections</term><term>Disease Reservoirs</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Bayes Theorem</term><term>Disease Outbreaks</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Global Health</term><term>Humans</term><term>Pandemics</term><term>Phylogeny</term><term>Sequence Analysis, Protein</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 <i>Rhinolophus</i> 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 <i>Betacoronavirus</i>. 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 <i>Betacoronavirus</i> among animals and <i>Rhinolophus</i> of the bat family.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32048560</PMID><DateCompleted><Year>2020</Year><Month>04</Month><Day>08</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">2047-7732</ISSN><JournalIssue CitedMedium="Internet"><Volume>114</Volume><Issue>2</Issue><PubDate><Year>2020</Year><Month>03</Month></PubDate></JournalIssue><Title>Pathogens and global health</Title><ISOAbbreviation>Pathog Glob Health</ISOAbbreviation></Journal><ArticleTitle>The global spread of 2019-nCoV: a molecular evolutionary analysis.</ArticleTitle><Pagination><MedlinePgn>64-67</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/20477724.2020.1725339</ELocationID><Abstract><AbstractText>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 <i>Rhinolophus</i> 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 <i>Betacoronavirus</i>. 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 <i>Betacoronavirus</i> among animals and <i>Rhinolophus</i> of the bat family.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Benvenuto</LastName><ForeName>Domenico</ForeName><Initials>D</Initials><Identifier Source="ORCID">0000-0003-3833-2927</Identifier><AffiliationInfo><Affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giovanetti</LastName><ForeName>Marta</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Salemi</LastName><ForeName>Marco</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Epidemiology, University of Florida, Gainesville, FL, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Prosperi</LastName><ForeName>Mattia</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Epidemiology, University of Florida, Gainesville, FL, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>De Flora</LastName><ForeName>Cecilia</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Junior Alcantara</LastName><ForeName>Luiz Carlos</ForeName><Initials>LC</Initials><AffiliationInfo><Affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Angeletti</LastName><ForeName>Silvia</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ciccozzi</LastName><ForeName>Massimo</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Pathog Glob Health</MedlineTA><NlmUniqueID>101583421</NlmUniqueID><ISSNLinking>2047-7724</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004279">DNA, Viral</NameOfSubstance></Chemical></ChemicalList><SupplMeshList><SupplMeshName Type="Disease" UI="C000657245">COVID-19</SupplMeshName><SupplMeshName Type="Organism" UI="C000656484">severe acute respiratory syndrome coronavirus 2</SupplMeshName></SupplMeshList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001499" MajorTopicYN="N">Bayes Theorem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000073640" MajorTopicYN="N">Betacoronavirus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002681" MajorTopicYN="N" Type="Geographic">China</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002685" MajorTopicYN="N">Chiroptera</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017934" MajorTopicYN="N">Coronavirus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004279" MajorTopicYN="N">DNA, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004196" MajorTopicYN="N">Disease Outbreaks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004197" MajorTopicYN="N">Disease Reservoirs</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="Y">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014943" MajorTopicYN="N">Global Health</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058873" MajorTopicYN="N">Pandemics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011024" MajorTopicYN="N">Pneumonia, Viral</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020539" MajorTopicYN="N">Sequence Analysis, Protein</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015047" MajorTopicYN="N">Zoonoses</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">2019-nCoV</Keyword><Keyword MajorTopicYN="Y">SARS</Keyword><Keyword MajorTopicYN="Y">molecular Epidemiology</Keyword><Keyword MajorTopicYN="Y">phylogeny</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32048560</ArticleId><ArticleId IdType="doi">10.1080/20477724.2020.1725339</ArticleId><ArticleId IdType="pmc">PMC7099638</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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