Transmission dynamics and evolutionary history of 2019-nCoV.
Identifieur interne : 000082 ( new/Extraction ); précédent : 000081; suivant : 000083Transmission 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
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000B93
- to stream PubMed, to step Curation: 000B93
- to stream PubMed, to step Checkpoint: 000195
- to stream Ncbi, to step Merge: 000964
- to stream Ncbi, to step Curation: 000964
- to stream Ncbi, to step Checkpoint: 000964
- to stream Main, to step Merge: 000207
- to stream Main, to step Curation: 000205
- to stream Main, to step Exploration: 000205
Links to Exploration step
pubmed:32027035Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Transmission dynamics and evolutionary history of 2019-nCoV.</title>
<author><name sortKey="Li, Xingguang" sort="Li, Xingguang" uniqKey="Li X" first="Xingguang" last="Li">Xingguang Li</name>
<affiliation wicri:level="3"><nlm:affiliation>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wang, Wei" sort="Wang, Wei" uniqKey="Wang W" first="Wei" last="Wang">Wei Wang</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of 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>
<wicri:noRegion>Nanning</wicri:noRegion>
</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>
<wicri:noRegion>Nanning</wicri:noRegion>
</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>
<wicri:noRegion>Ningbo</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Zhao, Qiang" sort="Zhao, Qiang" uniqKey="Zhao Q" first="Qiang" last="Zhao">Qiang Zhao</name>
<affiliation wicri:level="3"><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>
<placeName><settlement type="city">Tianjin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Li, Yi" sort="Li, Yi" uniqKey="Li Y" first="Yi" last="Li">Yi Li</name>
<affiliation wicri:level="3"><nlm:affiliation>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Chaillon, Antoine" sort="Chaillon, Antoine" uniqKey="Chaillon A" first="Antoine" last="Chaillon">Antoine Chaillon</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Medicine, University of California San Diego, La Jolla, California.</nlm:affiliation>
<country>États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Department of Medicine, University of California San Diego, La Jolla</wicri:cityArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2020">2020</date>
<idno type="RBID">pubmed:32027035</idno>
<idno type="pmid">32027035</idno>
<idno type="doi">10.1002/jmv.25701</idno>
<idno type="wicri:Area/PubMed/Corpus">000B93</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000B93</idno>
<idno type="wicri:Area/PubMed/Curation">000B93</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000B93</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000195</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000195</idno>
<idno type="wicri:Area/Ncbi/Merge">000964</idno>
<idno type="wicri:Area/Ncbi/Curation">000964</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000964</idno>
<idno type="wicri:Area/Main/Merge">000207</idno>
<idno type="wicri:Area/Main/Curation">000205</idno>
<idno type="wicri:Area/Main/Exploration">000205</idno>
<idno type="wicri:Area/new/Extraction">000082</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Transmission dynamics and evolutionary history of 2019-nCoV.</title>
<author><name sortKey="Li, Xingguang" sort="Li, Xingguang" uniqKey="Li X" first="Xingguang" last="Li">Xingguang Li</name>
<affiliation wicri:level="3"><nlm:affiliation>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wang, Wei" sort="Wang, Wei" uniqKey="Wang W" first="Wei" last="Wang">Wei Wang</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of 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>
<wicri:noRegion>Nanning</wicri:noRegion>
</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>
<wicri:noRegion>Nanning</wicri:noRegion>
</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>
<wicri:noRegion>Ningbo</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Zhao, Qiang" sort="Zhao, Qiang" uniqKey="Zhao Q" first="Qiang" last="Zhao">Qiang Zhao</name>
<affiliation wicri:level="3"><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>
<placeName><settlement type="city">Tianjin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Li, Yi" sort="Li, Yi" uniqKey="Li Y" first="Yi" last="Li">Yi Li</name>
<affiliation wicri:level="3"><nlm:affiliation>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, China.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan</wicri:regionArea>
<placeName><settlement type="city">Wuhan</settlement>
<region type="région">Hubei</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Chaillon, Antoine" sort="Chaillon, Antoine" uniqKey="Chaillon A" first="Antoine" last="Chaillon">Antoine Chaillon</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Medicine, University of California San Diego, La Jolla, California.</nlm:affiliation>
<country>États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Department of Medicine, University of California San Diego, La Jolla</wicri:cityArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Journal of medical virology</title>
<idno type="eISSN">1096-9071</idno>
<imprint><date 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>
<affiliations><list><country><li>République populaire de Chine</li>
<li>États-Unis</li>
</country>
<region><li>Californie</li>
<li>Hubei</li>
</region>
<settlement><li>Tianjin</li>
<li>Wuhan</li>
</settlement>
</list>
<tree><country name="République populaire de Chine"><region name="Hubei"><name sortKey="Li, Xingguang" sort="Li, Xingguang" uniqKey="Li X" first="Xingguang" last="Li">Xingguang Li</name>
</region>
<name sortKey="Li, Yi" sort="Li, Yi" uniqKey="Li Y" first="Yi" last="Li">Yi Li</name>
<name sortKey="Wang, Wei" sort="Wang, Wei" uniqKey="Wang W" first="Wei" last="Wang">Wei Wang</name>
<name sortKey="Zai, Junjie" sort="Zai, Junjie" uniqKey="Zai J" first="Junjie" last="Zai">Junjie Zai</name>
<name sortKey="Zhao, Qiang" sort="Zhao, Qiang" uniqKey="Zhao Q" first="Qiang" last="Zhao">Qiang Zhao</name>
<name sortKey="Zhao, Xiaofang" sort="Zhao, Xiaofang" uniqKey="Zhao X" first="Xiaofang" last="Zhao">Xiaofang Zhao</name>
</country>
<country name="États-Unis"><region name="Californie"><name sortKey="Chaillon, Antoine" sort="Chaillon, Antoine" uniqKey="Chaillon A" first="Antoine" last="Chaillon">Antoine Chaillon</name>
</region>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV2/Data/new/Extraction
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000082 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/new/Extraction/biblio.hfd -nk 000082 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Sante |area= CovidV2 |flux= new |étape= Extraction |type= RBID |clé= pubmed:32027035 |texte= Transmission dynamics and evolutionary history of 2019-nCoV. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/new/Extraction/RBID.i -Sk "pubmed:32027035" \ | HfdSelect -Kh $EXPLOR_AREA/Data/new/Extraction/biblio.hfd \ | NlmPubMed2Wicri -a CovidV2
This area was generated with Dilib version V0.6.33. |