Evolution and Variation of the SARS-CoV Genome
Identifieur interne : 006011 ( Main/Exploration ); précédent : 006010; suivant : 006012Evolution and Variation of the SARS-CoV Genome
Auteurs : Jianfei Hu [République populaire de Chine] ; Jing Wang [République populaire de Chine] ; Jing Xu [République populaire de Chine] ; Wei Li [République populaire de Chine] ; Yujun Han [République populaire de Chine] ; Yan Li [République populaire de Chine] ; Jia Ji [République populaire de Chine] ; Jia Ye [République populaire de Chine] ; Zhao Xu [République populaire de Chine] ; Zizhang Zhang [République populaire de Chine] ; Wei Wei [République populaire de Chine] ; Songgang Li [République populaire de Chine] ; Jun Wang [République populaire de Chine] ; Jian Wang [République populaire de Chine] ; Jun Yu [République populaire de Chine] ; Huanming Yang [République populaire de Chine]Source :
- Genomics, Proteomics & Bioinformatics [ 1672-0229 ] ; 2003.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Codon.
- genetics : SARS Virus.
- Amino Acid Motifs, Amino Acid Substitution, Base Composition, Computational Biology, DNA Mutational Analysis, Evolution, Molecular, Gene Transfer, Horizontal, Genetic Variation, Genome, Viral, Phylogeny.
Abstract
Knowledge of the evolution of pathogens is of great medical and biological significance to the prevention, diagnosis, and therapy of infectious diseases. In order to understand the origin and evolution of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus), we collected complete genome sequences of all viruses available in GenBank, and made comparative analyses with the SARS-CoV. Genomic signature analysis demonstrates that the coronaviruses all take the TGTT as their richest tetranucleotide except the SARS-CoV. A detailed analysis of the forty-two complete SARS-CoV genome sequences revealed the existence of two distinct genotypes, and showed that these isolates could be classified into four groups. Our manual analysis of the BLASTN results demonstrates that the HE (hemagglutinin-esterase) gene exists in the SARS-CoV, and many mutations made it unfamiliar to us.
Url:
DOI: 10.1016/S1672-0229(03)01027-1
PubMed: 15629034
PubMed Central: 5172238
Affiliations:
- République populaire de Chine
- Pékin, Zhejiang
- Hangzhou, Pékin
- Université de Pékin, Université de Zhejiang
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Le document en format XML
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<affiliation wicri:level="4"><nlm:aff id="aff0020">College of Materials Science and Chemical Engineering, Yuquan Campus, Zhejiang University, Hangzhou 310027, China</nlm:aff>
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<wicri:regionArea>College of Materials Science and Chemical Engineering, Yuquan Campus, Zhejiang University, Hangzhou 310027</wicri:regionArea>
<placeName><settlement type="city">Hangzhou</settlement>
<region type="province">Zhejiang</region>
</placeName>
<orgName type="university">Université de Zhejiang</orgName>
<placeName><settlement type="city">Hangzhou</settlement>
<region type="province">Zhejiang</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wei, Wei" sort="Wei, Wei" uniqKey="Wei W" first="Wei" last="Wei">Wei Wei</name>
<affiliation wicri:level="1"><nlm:aff id="aff0015">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008</wicri:regionArea>
<placeName><settlement type="city">Hangzhou</settlement>
<region type="province">Zhejiang</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Li, Songgang" sort="Li, Songgang" uniqKey="Li S" first="Songgang" last="Li">Songgang Li</name>
<affiliation wicri:level="4"><nlm:aff id="aff0005">College of Life Sciences, Peking University, Beijing 100871, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>College of Life Sciences, Peking University, Beijing 100871</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
<orgName type="university">Université de Pékin</orgName>
<placeName><settlement type="city">Pékin</settlement>
<region type="capitale">Pékin</region>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff0010">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name>
<affiliation wicri:level="1"><nlm:aff id="aff0010">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wang, Jian" sort="Wang, Jian" uniqKey="Wang J" first="Jian" last="Wang">Jian Wang</name>
<affiliation wicri:level="1"><nlm:aff id="aff0010">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff0015">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008</wicri:regionArea>
<placeName><settlement type="city">Hangzhou</settlement>
<region type="province">Zhejiang</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Yu, Jun" sort="Yu, Jun" uniqKey="Yu J" first="Jun" last="Yu">Jun Yu</name>
<affiliation wicri:level="1"><nlm:aff id="aff0010">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff0015">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008</wicri:regionArea>
<placeName><settlement type="city">Hangzhou</settlement>
<region type="province">Zhejiang</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Yang, Huanming" sort="Yang, Huanming" uniqKey="Yang H" first="Huanming" last="Yang">Huanming Yang</name>
<affiliation wicri:level="1"><nlm:aff id="aff0010">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300</wicri:regionArea>
<placeName><settlement type="city">Pékin</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff0015">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff>
<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008</wicri:regionArea>
<placeName><settlement type="city">Hangzhou</settlement>
<region type="province">Zhejiang</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">Genomics, Proteomics & Bioinformatics</title>
<idno type="ISSN">1672-0229</idno>
<idno type="eISSN">2210-3244</idno>
<imprint><date when="2003">2003</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Motifs</term>
<term>Amino Acid Substitution</term>
<term>Base Composition</term>
<term>Codon (genetics)</term>
<term>Computational Biology</term>
<term>DNA Mutational Analysis</term>
<term>Evolution, Molecular</term>
<term>Gene Transfer, Horizontal</term>
<term>Genetic Variation</term>
<term>Genome, Viral</term>
<term>Phylogeny</term>
<term>SARS Virus (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de mutations d'ADN</term>
<term>Biologie informatique</term>
<term>Codon (génétique)</term>
<term>Composition en bases nucléiques</term>
<term>Génome viral</term>
<term>Motifs d'acides aminés</term>
<term>Phylogénie</term>
<term>Substitution d'acide aminé</term>
<term>Transfert horizontal de gène</term>
<term>Variation génétique</term>
<term>Virus du SRAS (génétique)</term>
<term>Évolution moléculaire</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Codon</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Codon</term>
<term>Virus du SRAS</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Motifs</term>
<term>Amino Acid Substitution</term>
<term>Base Composition</term>
<term>Computational Biology</term>
<term>DNA Mutational Analysis</term>
<term>Evolution, Molecular</term>
<term>Gene Transfer, Horizontal</term>
<term>Genetic Variation</term>
<term>Genome, Viral</term>
<term>Phylogeny</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de mutations d'ADN</term>
<term>Biologie informatique</term>
<term>Composition en bases nucléiques</term>
<term>Génome viral</term>
<term>Motifs d'acides aminés</term>
<term>Phylogénie</term>
<term>Substitution d'acide aminé</term>
<term>Transfert horizontal de gène</term>
<term>Variation génétique</term>
<term>Évolution moléculaire</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Knowledge of the evolution of pathogens is of great medical and biological significance to the prevention, diagnosis, and therapy of infectious diseases. In order to understand the origin and evolution of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus), we collected complete genome sequences of all viruses available in GenBank, and made comparative analyses with the SARS-CoV. Genomic signature analysis demonstrates that the coronaviruses all take the TGTT as their richest tetranucleotide except the SARS-CoV. A detailed analysis of the forty-two complete SARS-CoV genome sequences revealed the existence of two distinct genotypes, and showed that these isolates could be classified into four groups. Our manual analysis of the BLASTN results demonstrates that the HE (hemagglutinin-esterase) gene exists in the SARS-CoV, and many mutations made it unfamiliar to us.</p>
</div>
</front>
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</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ruan, Y" uniqKey="Ruan Y">Y. Ruan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rota, P A" uniqKey="Rota P">P.A. Rota</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Peiris, J S M" uniqKey="Peiris J">J.S.M. Peiris</name>
</author>
</analytic>
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<biblStruct><analytic><author><name sortKey="Grantham, R" uniqKey="Grantham R">R. Grantham</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Grantham, R" uniqKey="Grantham R">R. Grantham</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ikemura, T" uniqKey="Ikemura T">T. Ikemura</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Qin, E D" uniqKey="Qin E">E.D. Qin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yang, Z" uniqKey="Yang Z">Z. Yang</name>
</author>
<author><name sortKey="Yoder, A D" uniqKey="Yoder A">A.D. Yoder</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Qin, E D" uniqKey="Qin E">E.D. Qin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Aaziz, R" uniqKey="Aaziz R">R. Aaziz</name>
</author>
<author><name sortKey="Tepfer, M" uniqKey="Tepfer M">M. Tepfer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kirkegaard, K" uniqKey="Kirkegaard K">K. Kirkegaard</name>
</author>
<author><name sortKey="Baltimore, D" uniqKey="Baltimore D">D. Baltimore</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marra, M A" uniqKey="Marra M">M.A. Marra</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hao, B L" uniqKey="Hao B">B.L. Hao</name>
</author>
<author><name sortKey="Qi, J" uniqKey="Qi J">J. Qi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Deschavanne, P J" uniqKey="Deschavanne P">P.J. Deschavanne</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<affiliations><list><country><li>République populaire de Chine</li>
</country>
<region><li>Pékin</li>
<li>Zhejiang</li>
</region>
<settlement><li>Hangzhou</li>
<li>Pékin</li>
</settlement>
<orgName><li>Université de Pékin</li>
<li>Université de Zhejiang</li>
</orgName>
</list>
<tree><country name="République populaire de Chine"><noRegion><name sortKey="Hu, Jianfei" sort="Hu, Jianfei" uniqKey="Hu J" first="Jianfei" last="Hu">Jianfei Hu</name>
</noRegion>
<name sortKey="Han, Yujun" sort="Han, Yujun" uniqKey="Han Y" first="Yujun" last="Han">Yujun Han</name>
<name sortKey="Hu, Jianfei" sort="Hu, Jianfei" uniqKey="Hu J" first="Jianfei" last="Hu">Jianfei Hu</name>
<name sortKey="Ji, Jia" sort="Ji, Jia" uniqKey="Ji J" first="Jia" last="Ji">Jia Ji</name>
<name sortKey="Li, Songgang" sort="Li, Songgang" uniqKey="Li S" first="Songgang" last="Li">Songgang Li</name>
<name sortKey="Li, Songgang" sort="Li, Songgang" uniqKey="Li S" first="Songgang" last="Li">Songgang Li</name>
<name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name>
<name sortKey="Li, Yan" sort="Li, Yan" uniqKey="Li Y" first="Yan" last="Li">Yan Li</name>
<name sortKey="Wang, Jian" sort="Wang, Jian" uniqKey="Wang J" first="Jian" last="Wang">Jian Wang</name>
<name sortKey="Wang, Jian" sort="Wang, Jian" uniqKey="Wang J" first="Jian" last="Wang">Jian Wang</name>
<name sortKey="Wang, Jing" sort="Wang, Jing" uniqKey="Wang J" first="Jing" last="Wang">Jing Wang</name>
<name sortKey="Wang, Jing" sort="Wang, Jing" uniqKey="Wang J" first="Jing" last="Wang">Jing Wang</name>
<name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name>
<name sortKey="Wei, Wei" sort="Wei, Wei" uniqKey="Wei W" first="Wei" last="Wei">Wei Wei</name>
<name sortKey="Xu, Jing" sort="Xu, Jing" uniqKey="Xu J" first="Jing" last="Xu">Jing Xu</name>
<name sortKey="Xu, Zhao" sort="Xu, Zhao" uniqKey="Xu Z" first="Zhao" last="Xu">Zhao Xu</name>
<name sortKey="Yang, Huanming" sort="Yang, Huanming" uniqKey="Yang H" first="Huanming" last="Yang">Huanming Yang</name>
<name sortKey="Yang, Huanming" sort="Yang, Huanming" uniqKey="Yang H" first="Huanming" last="Yang">Huanming Yang</name>
<name sortKey="Ye, Jia" sort="Ye, Jia" uniqKey="Ye J" first="Jia" last="Ye">Jia Ye</name>
<name sortKey="Ye, Jia" sort="Ye, Jia" uniqKey="Ye J" first="Jia" last="Ye">Jia Ye</name>
<name sortKey="Yu, Jun" sort="Yu, Jun" uniqKey="Yu J" first="Jun" last="Yu">Jun Yu</name>
<name sortKey="Yu, Jun" sort="Yu, Jun" uniqKey="Yu J" first="Jun" last="Yu">Jun Yu</name>
<name sortKey="Zhang, Zizhang" sort="Zhang, Zizhang" uniqKey="Zhang Z" first="Zizhang" last="Zhang">Zizhang Zhang</name>
</country>
</tree>
</affiliations>
</record>
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