Origin and Possible Genetic Recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence Analysis
Identifieur interne : 001637 ( Main/Exploration ); précédent : 001636; suivant : 001638Origin and Possible Genetic Recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence Analysis
Auteurs : Yanqun Wang [République populaire de Chine] ; Di Liu [République populaire de Chine] ; Weifeng Shi [République populaire de Chine] ; Roujian Lu [République populaire de Chine] ; Wenling Wang [République populaire de Chine] ; Yanjie Zhao [République populaire de Chine] ; Yao Deng [République populaire de Chine] ; Weimin Zhou [République populaire de Chine] ; Hongguang Ren [République populaire de Chine] ; Jun Wu [République populaire de Chine] ; Yu Wang [République populaire de Chine] ; Guizhen Wu [République populaire de Chine] ; George F. Gao [République populaire de Chine] ; Wenjie Tan [République populaire de Chine]Source :
- mBio [ 2150-7511 ] ; 2015.
Descripteurs français
- KwdFr :
- ARN viral (génétique), Analyse de regroupements, Analyse de séquence d'ADN, Chine, Coronavirus du syndrome respiratoire du Moyen-Orient (), Coronavirus du syndrome respiratoire du Moyen-Orient (génétique), Coronavirus du syndrome respiratoire du Moyen-Orient (isolement et purification), Données de séquences moléculaires, Génome viral, Humains, Infections à coronavirus (virologie), Phylogénie, Recombinaison génétique, Similitude de séquences, Évolution moléculaire.
- MESH :
- génétique : ARN viral, Coronavirus du syndrome respiratoire du Moyen-Orient.
- isolement et purification : Coronavirus du syndrome respiratoire du Moyen-Orient.
- virologie : Infections à coronavirus.
- Analyse de regroupements, Analyse de séquence d'ADN, Chine, Coronavirus du syndrome respiratoire du Moyen-Orient, Données de séquences moléculaires, Génome viral, Humains, Phylogénie, Recombinaison génétique, Similitude de séquences, Évolution moléculaire.
- Wicri :
- geographic : République populaire de Chine.
English descriptors
- KwdEn :
- China, Cluster Analysis, Coronavirus Infections (virology), Evolution, Molecular, Genome, Viral, Humans, Middle East Respiratory Syndrome Coronavirus (classification), Middle East Respiratory Syndrome Coronavirus (genetics), Middle East Respiratory Syndrome Coronavirus (isolation & purification), Molecular Sequence Data, Phylogeny, RNA, Viral (genetics), Recombination, Genetic, Sequence Analysis, DNA, Sequence Homology.
- MESH :
- chemical , genetics : RNA, Viral.
- geographic : China.
- classification : Middle East Respiratory Syndrome Coronavirus.
- genetics : Middle East Respiratory Syndrome Coronavirus.
- isolation & purification : Middle East Respiratory Syndrome Coronavirus.
- virology : Coronavirus Infections.
- Cluster Analysis, Evolution, Molecular, Genome, Viral, Humans, Molecular Sequence Data, Phylogeny, Recombination, Genetic, Sequence Analysis, DNA, Sequence Homology.
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus.
Url:
DOI: 10.1128/mBio.01280-15
PubMed: 26350969
PubMed Central: 4600111
Affiliations:
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Le document en format XML
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type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Liu, Di" sort="Liu, Di" uniqKey="Liu D" first="Di" last="Liu">Di Liu</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Network Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Shi, Weifeng" sort="Shi, Weifeng" uniqKey="Shi W" first="Weifeng" last="Shi">Weifeng Shi</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Institute of Pathogen Biology, Taishan Medical College, Taian, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Pathogen Biology, Taishan Medical College, Taian</wicri:regionArea><wicri:noRegion>Taian</wicri:noRegion></affiliation></author><author><name sortKey="Lu, Roujian" sort="Lu, Roujian" uniqKey="Lu R" first="Roujian" last="Lu">Roujian Lu</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Wenling" sort="Wang, Wenling" uniqKey="Wang W" first="Wenling" last="Wang">Wenling Wang</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhao, Yanjie" sort="Zhao, Yanjie" uniqKey="Zhao Y" first="Yanjie" last="Zhao">Yanjie Zhao</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Deng, Yao" sort="Deng, Yao" uniqKey="Deng Y" first="Yao" last="Deng">Yao Deng</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhou, Weimin" sort="Zhou, Weimin" uniqKey="Zhou W" first="Weimin" last="Zhou">Weimin Zhou</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Ren, Hongguang" sort="Ren, Hongguang" uniqKey="Ren H" first="Hongguang" last="Ren">Hongguang Ren</name><affiliation wicri:level="3"><nlm:aff id="aff5"><addr-line>State Key Laboratory of Pathogen and Biosecurity, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Pathogen and Biosecurity, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wu, Jun" sort="Wu, Jun" uniqKey="Wu J" first="Jun" last="Wu">Jun Wu</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Yu" sort="Wang, Yu" uniqKey="Wang Y" first="Yu" last="Wang">Yu Wang</name><affiliation wicri:level="3"><nlm:aff id="aff6"><addr-line>Office of Director-General, Chinese Center for Disease Control and Prevention, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Office of Director-General, Chinese Center for Disease Control and Prevention, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wu, Guizhen" sort="Wu, Guizhen" uniqKey="Wu G" first="Guizhen" last="Wu">Guizhen Wu</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Gao, George F" sort="Gao, George F" uniqKey="Gao G" first="George F." last="Gao">George F. Gao</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="aff6"><addr-line>Office of Director-General, Chinese Center for Disease Control and Prevention, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Office of Director-General, Chinese Center for Disease Control and Prevention, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Tan, Wenjie" sort="Tan, Wenjie" uniqKey="Tan W" first="Wenjie" last="Tan">Wenjie Tan</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">mBio</title><idno type="eISSN">2150-7511</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>China</term><term>Cluster Analysis</term><term>Coronavirus Infections (virology)</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Middle East Respiratory Syndrome Coronavirus (classification)</term><term>Middle East Respiratory Syndrome Coronavirus (genetics)</term><term>Middle East Respiratory Syndrome Coronavirus (isolation & purification)</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>RNA, Viral (genetics)</term><term>Recombination, Genetic</term><term>Sequence Analysis, DNA</term><term>Sequence Homology</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Chine</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient ()</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient (génétique)</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient (isolement et purification)</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Humains</term><term>Infections à coronavirus (virologie)</term><term>Phylogénie</term><term>Recombinaison génétique</term><term>Similitude de séquences</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à coronavirus</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Recombination, Genetic</term><term>Sequence Analysis, DNA</term><term>Sequence Homology</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Chine</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Humains</term><term>Phylogénie</term><term>Recombinaison génétique</term><term>Similitude de séquences</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>ABSTRACT</title><p>The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zumla, A" uniqKey="Zumla A">A Zumla</name></author><author><name sortKey="Hui, Ds" uniqKey="Hui D">DS Hui</name></author><author><name sortKey="Perlman, S" uniqKey="Perlman S">S Perlman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guery, B" uniqKey="Guery B">B Guery</name></author><author><name sortKey="Poissy, J" uniqKey="Poissy J">J Poissy</name></author><author><name sortKey="El Mansouf, L" uniqKey="El Mansouf L">L el Mansouf</name></author><author><name sortKey="Sejourne, C" uniqKey="Sejourne C">C Séjourné</name></author><author><name sortKey="Ettahar, N" uniqKey="Ettahar N">N Ettahar</name></author><author><name sortKey="Lemaire, X" uniqKey="Lemaire X">X Lemaire</name></author><author><name sortKey="Vuotto, F" 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sortKey="Kulkarni, Ss" uniqKey="Kulkarni S">SS Kulkarni</name></author><author><name sortKey="Novak, Ng" uniqKey="Novak N">NG Novak</name></author><author><name sortKey="Ingersoll, R" uniqKey="Ingersoll R">R Ingersoll</name></author><author><name sortKey="Sheppard, Hw" uniqKey="Sheppard H">HW Sheppard</name></author><author><name sortKey="Ray, Sc" uniqKey="Ray S">SC Ray</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Pékin</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Wang, Yanqun" sort="Wang, Yanqun" uniqKey="Wang Y" first="Yanqun" last="Wang">Yanqun Wang</name></noRegion><name sortKey="Deng, Yao" sort="Deng, Yao" uniqKey="Deng Y" first="Yao" last="Deng">Yao Deng</name><name sortKey="Gao, George F" sort="Gao, George F" uniqKey="Gao G" first="George F." last="Gao">George F. Gao</name><name sortKey="Gao, George F" sort="Gao, George F" uniqKey="Gao G" first="George F." last="Gao">George F. Gao</name><name sortKey="Gao, George F" sort="Gao, George F" uniqKey="Gao G" first="George F." last="Gao">George F. Gao</name><name sortKey="Liu, Di" sort="Liu, Di" uniqKey="Liu D" first="Di" last="Liu">Di Liu</name><name sortKey="Liu, Di" sort="Liu, Di" uniqKey="Liu D" first="Di" last="Liu">Di Liu</name><name sortKey="Lu, Roujian" sort="Lu, Roujian" uniqKey="Lu R" first="Roujian" last="Lu">Roujian Lu</name><name sortKey="Ren, Hongguang" sort="Ren, Hongguang" uniqKey="Ren H" first="Hongguang" last="Ren">Hongguang Ren</name><name sortKey="Shi, Weifeng" sort="Shi, Weifeng" uniqKey="Shi W" first="Weifeng" last="Shi">Weifeng Shi</name><name sortKey="Tan, Wenjie" sort="Tan, Wenjie" uniqKey="Tan W" first="Wenjie" last="Tan">Wenjie Tan</name><name sortKey="Wang, Wenling" sort="Wang, Wenling" uniqKey="Wang W" first="Wenling" last="Wang">Wenling Wang</name><name sortKey="Wang, Yu" sort="Wang, Yu" uniqKey="Wang Y" first="Yu" last="Wang">Yu Wang</name><name sortKey="Wu, Guizhen" sort="Wu, Guizhen" uniqKey="Wu G" first="Guizhen" last="Wu">Guizhen Wu</name><name sortKey="Wu, Jun" sort="Wu, Jun" uniqKey="Wu J" first="Jun" last="Wu">Jun Wu</name><name sortKey="Zhao, Yanjie" sort="Zhao, Yanjie" uniqKey="Zhao Y" first="Yanjie" last="Zhao">Yanjie Zhao</name><name sortKey="Zhou, Weimin" sort="Zhou, Weimin" uniqKey="Zhou W" first="Weimin" last="Zhou">Weimin Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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