Transmission dynamics and evolutionary history of 2019-nCoV.
Identifieur interne : 000B93 ( PubMed/Curation ); précédent : 000B92; suivant : 000B94Transmission dynamics and evolutionary history of 2019-nCoV.
Auteurs : Xingguang Li [République populaire de Chine] ; Wei Wang [République populaire de Chine] ; Xiaofang Zhao [République populaire de Chine] ; Junjie Zai [République populaire de Chine] ; Qiang Zhao [République populaire de Chine] ; Yi Li [République populaire de Chine] ; Antoine Chaillon [États-Unis]Source :
- Journal of medical virology [ 1096-9071 ] ; 2020.
Descripteurs français
- KwdFr :
- Chine, Flambées de maladies, Fonctions de vraisemblance, Génome viral, Humains, Infections à coronavirus (transmission), Infections à coronavirus (épidémiologie), Modèles génétiques, Phylogénie, Pneumopathie virale (transmission), Pneumopathie virale (épidémiologie), Taux de mutation, Thaïlande, Théorème de Bayes, États-Unis d'Amérique.
- MESH :
- Wicri :
- geographic : République populaire de Chine, Thaïlande, États-Unis.
English descriptors
- KwdEn :
- Bayes Theorem, Betacoronavirus (genetics), China, Coronavirus Infections (epidemiology), Coronavirus Infections (transmission), Disease Outbreaks, Genome, Viral, Humans, Likelihood Functions, Models, Genetic, Mutation Rate, Phylogeny, Pneumonia, Viral (epidemiology), Pneumonia, Viral (transmission), Thailand, United States.
- MESH :
- geographic : China, Thailand, United States.
- epidemiology : Coronavirus Infections, Pneumonia, Viral.
- genetics : Betacoronavirus.
- transmission : Coronavirus Infections, Pneumonia, Viral.
- Bayes Theorem, Disease Outbreaks, Genome, Viral, Humans, Likelihood Functions, Models, Genetic, Mutation Rate, Phylogeny.
Abstract
To investigate the time origin, genetic diversity, and transmission dynamics of the recent 2019-nCoV outbreak in China and beyond, a total of 32 genomes of virus strains sampled from China, Thailand, and the USA with sampling dates between 24 December 2019 and 23 January 2020 were analyzed. Phylogenetic, transmission network, and likelihood-mapping analyses of the genome sequences were performed. On the basis of the likelihood-mapping analysis, the increasing tree-like signals (from 0% to 8.2%, 18.2%, and 25.4%) over time may be indicative of increasing genetic diversity of 2019-nCoV in human hosts. We identified three phylogenetic clusters using the Bayesian inference framework and three transmission clusters using transmission network analysis, with only one cluster identified by both methods using the above genome sequences of 2019-nCoV strains. The estimated mean evolutionary rate for 2019-nCoV ranged from 1.7926 × 10-3 to 1.8266 × 10-3 substitutions per site per year. On the basis of our study, undertaking epidemiological investigations and genomic data surveillance could positively impact public health in terms of guiding prevention efforts to reduce 2019-nCOV transmission in real-time.
DOI: 10.1002/jmv.25701
PubMed: 32027035
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Spleen and Stomach Diseases, First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Spleen and Stomach Diseases, First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning</wicri:regionArea></affiliation></author><author><name sortKey="Zhao, Xiaofang" sort="Zhao, Xiaofang" uniqKey="Zhao X" first="Xiaofang" last="Zhao">Xiaofang Zhao</name><affiliation wicri:level="1"><nlm:affiliation>Department of Science and Technology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Science and Technology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning</wicri:regionArea></affiliation></author><author><name sortKey="Zai, Junjie" sort="Zai, Junjie" uniqKey="Zai J" first="Junjie" last="Zai">Junjie Zai</name><affiliation wicri:level="1"><nlm:affiliation>Immunology Innovation Team, School of Medicine, Ningbo University, Ningbo, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Immunology Innovation Team, School of Medicine, Ningbo University, Ningbo</wicri:regionArea></affiliation></author><author><name sortKey="Zhao, Qiang" sort="Zhao, Qiang" uniqKey="Zhao Q" first="Qiang" last="Zhao">Qiang Zhao</name><affiliation wicri:level="1"><nlm:affiliation>Precision Cancer Center Airport Center, Tianjin Cancer Hospital Airport Hospital, Tianjin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Precision Cancer Center Airport Center, Tianjin Cancer Hospital Airport Hospital, Tianjin</wicri:regionArea></affiliation></author><author><name sortKey="Li, Yi" sort="Li, Yi" uniqKey="Li Y" first="Yi" last="Li">Yi Li</name><affiliation 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when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bayes Theorem</term><term>Betacoronavirus (genetics)</term><term>China</term><term>Coronavirus Infections (epidemiology)</term><term>Coronavirus Infections (transmission)</term><term>Disease Outbreaks</term><term>Genome, Viral</term><term>Humans</term><term>Likelihood Functions</term><term>Models, Genetic</term><term>Mutation Rate</term><term>Phylogeny</term><term>Pneumonia, Viral (epidemiology)</term><term>Pneumonia, Viral (transmission)</term><term>Thailand</term><term>United States</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Chine</term><term>Flambées de maladies</term><term>Fonctions de vraisemblance</term><term>Génome viral</term><term>Humains</term><term>Infections à coronavirus (transmission)</term><term>Infections à coronavirus (épidémiologie)</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Pneumopathie virale (transmission)</term><term>Pneumopathie virale (épidémiologie)</term><term>Taux de mutation</term><term>Thaïlande</term><term>Théorème de Bayes</term><term>États-Unis d'Amérique</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term><term>Thailand</term><term>United States</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="transmission" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Infections à coronavirus</term><term>Pneumopathie virale</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Bayes Theorem</term><term>Disease Outbreaks</term><term>Genome, Viral</term><term>Humans</term><term>Likelihood Functions</term><term>Models, Genetic</term><term>Mutation Rate</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Chine</term><term>Flambées de maladies</term><term>Fonctions de vraisemblance</term><term>Génome viral</term><term>Humains</term><term>Modèles génétiques</term><term>Phylogénie</term><term>Taux de mutation</term><term>Thaïlande</term><term>Théorème de Bayes</term><term>États-Unis d'Amérique</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term><term>Thaïlande</term><term>États-Unis</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">To investigate the time origin, genetic diversity, and transmission dynamics of the recent 2019-nCoV outbreak in China and beyond, a total of 32 genomes of virus strains sampled from China, Thailand, and the USA with sampling dates between 24 December 2019 and 23 January 2020 were analyzed. Phylogenetic, transmission network, and likelihood-mapping analyses of the genome sequences were performed. On the basis of the likelihood-mapping analysis, the increasing tree-like signals (from 0% to 8.2%, 18.2%, and 25.4%) over time may be indicative of increasing genetic diversity of 2019-nCoV in human hosts. We identified three phylogenetic clusters using the Bayesian inference framework and three transmission clusters using transmission network analysis, with only one cluster identified by both methods using the above genome sequences of 2019-nCoV strains. The estimated mean evolutionary rate for 2019-nCoV ranged from 1.7926 × 10<sup>-3</sup> to 1.8266 × 10<sup>-3</sup> substitutions per site per year. On the basis of our study, undertaking epidemiological investigations and genomic data surveillance could positively impact public health in terms of guiding prevention efforts to reduce 2019-nCOV transmission in real-time.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32027035</PMID><DateCompleted><Year>2020</Year><Month>03</Month><Day>18</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-9071</ISSN><JournalIssue CitedMedium="Internet"><Volume>92</Volume><Issue>5</Issue><PubDate><Year>2020</Year><Month>05</Month></PubDate></JournalIssue><Title>Journal of medical virology</Title><ISOAbbreviation>J. Med. Virol.</ISOAbbreviation></Journal><ArticleTitle>Transmission dynamics and evolutionary history of 2019-nCoV.</ArticleTitle><Pagination><MedlinePgn>501-511</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/jmv.25701</ELocationID><Abstract><AbstractText>To investigate the time origin, genetic diversity, and transmission dynamics of the recent 2019-nCoV outbreak in China and beyond, a total of 32 genomes of virus strains sampled from China, Thailand, and the USA with sampling dates between 24 December 2019 and 23 January 2020 were analyzed. Phylogenetic, transmission network, and likelihood-mapping analyses of the genome sequences were performed. On the basis of the likelihood-mapping analysis, the increasing tree-like signals (from 0% to 8.2%, 18.2%, and 25.4%) over time may be indicative of increasing genetic diversity of 2019-nCoV in human hosts. We identified three phylogenetic clusters using the Bayesian inference framework and three transmission clusters using transmission network analysis, with only one cluster identified by both methods using the above genome sequences of 2019-nCoV strains. The estimated mean evolutionary rate for 2019-nCoV ranged from 1.7926 × 10<sup>-3</sup> to 1.8266 × 10<sup>-3</sup> substitutions per site per year. On the basis of our study, undertaking epidemiological investigations and genomic data surveillance could positively impact public health in terms of guiding prevention efforts to reduce 2019-nCOV transmission in real-time.</AbstractText><CopyrightInformation>© 2020 Wiley Periodicals, Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Xingguang</ForeName><Initials>X</Initials><Identifier Source="ORCID">0000-0002-3470-2196</Identifier><AffiliationInfo><Affiliation>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Wei</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Department of Spleen and Stomach Diseases, First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Xiaofang</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Department of Science and Technology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zai</LastName><ForeName>Junjie</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Immunology Innovation Team, School of Medicine, Ningbo University, Ningbo, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Qiang</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Precision Cancer Center Airport Center, Tianjin Cancer Hospital Airport Hospital, Tianjin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Yi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chaillon</LastName><ForeName>Antoine</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Medicine, University of California San Diego, La Jolla, California.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>31470268</GrantID><Agency>National Natural Science Foundation of China</Agency><Country>International</Country></Grant><Grant><GrantID>Z20191111</GrantID><Agency>Project of Guangxi Health Committee</Agency><Country>International</Country></Grant><Grant><GrantID>2017GXNSFAA198080</GrantID><Agency>Natural Science Foundation of Guangxi Province of China</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Med Virol</MedlineTA><NlmUniqueID>7705876</NlmUniqueID><ISSNLinking>0146-6615</ISSNLinking></MedlineJournalInfo><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="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></MeshHeading><MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000635" MajorTopicYN="Y">transmission</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004196" MajorTopicYN="N">Disease Outbreaks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="Y">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016013" MajorTopicYN="N">Likelihood Functions</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059645" MajorTopicYN="N">Mutation Rate</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011024" MajorTopicYN="N">Pneumonia, Viral</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName><QualifierName UI="Q000635" MajorTopicYN="Y">transmission</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013785" MajorTopicYN="N" Type="Geographic">Thailand</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014481" MajorTopicYN="N" Type="Geographic">United States</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">2019-nCoV</Keyword><Keyword MajorTopicYN="Y">TMRCA</Keyword><Keyword MajorTopicYN="Y">evolutionary rate</Keyword><Keyword MajorTopicYN="Y">phylogenetic cluster</Keyword><Keyword MajorTopicYN="Y">time to most recent common ancestor</Keyword><Keyword MajorTopicYN="Y">transmission cluster</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>02</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>02</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>3</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32027035</ArticleId><ArticleId IdType="doi">10.1002/jmv.25701</ArticleId></ArticleIdList><ReferenceList><Title>REFERENCES</Title><Reference><Citation>Chan JFW, Yuan S, Kok KH, et al. 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