Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV
Identifieur interne : 000879 ( Pmc/Curation ); précédent : 000878; suivant : 000880Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV
Auteurs : Zhi-Gang Wang [République populaire de Chine] ; Zhi-Hua Zheng [République populaire de Chine] ; Lei Shang [République populaire de Chine] ; Lan-Juan Li [République populaire de Chine] ; Li-Ming Cong [République populaire de Chine] ; Ming-Guang Feng [République populaire de Chine] ; Yun Luo [République populaire de Chine] ; Su-Yun Cheng [République populaire de Chine] ; Yan-Jun Zhang [République populaire de Chine] ; Miao-Gui Ru [République populaire de Chine] ; Zan-Xin Wang [République populaire de Chine] ; Qi-Yu Bao [République populaire de Chine]Source :
- Febs Letters [ 0014-5793 ] ; 2005.
Abstract
In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. One hundred and seventy-four of these sites existed in two or more SARS-CoV genome sequences. According to the sequence polymorphism, all SARS-CoVs can be divided into three groups: (I) group 1, animal-origin viruses (such as SARS-CoV SZ1, SZ3, SZ13 and SZ16); (II) group 2, all viruses with clinical origin during first epidemic; and (III) group 3, SARS-CoV GD03T0013. According to 10 special loci, group 2 again can be divided into genotypes C and T, which can be further divided into sub-genotypes C1–C4 and T1–T4. Positive Darwinian selections were identified between any pair of these three groups. Genotype C gives neutral selection. Genotype T, however, shows negative selection. By comparing the death rates of SARS patients in the different regions, it was found that the death rate caused by the viruses of the genotype C was lower than that of the genotype T. SARS-CoVs might originate from an unknown ancestor.
Url:
DOI: 10.1016/j.febslet.2005.07.075
PubMed: 16112670
PubMed Central: 7118731
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Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008</wicri:regionArea></affiliation></author><author><name sortKey="Li, Lan Juan" sort="Li, Lan Juan" uniqKey="Li L" first="Lan-Juan" last="Li">Lan-Juan Li</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Cong, Li Ming" sort="Cong, Li Ming" uniqKey="Cong L" first="Li-Ming" last="Cong">Li-Ming Cong</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Feng, Ming Guang" sort="Feng, Ming Guang" uniqKey="Feng M" first="Ming-Guang" last="Feng">Ming-Guang Feng</name><affiliation wicri:level="1"><nlm:aff id="aff2">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008</wicri:regionArea></affiliation></author><author><name sortKey="Luo, Yun" sort="Luo, Yun" uniqKey="Luo Y" first="Yun" last="Luo">Yun Luo</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Cheng, Su Yun" sort="Cheng, Su Yun" uniqKey="Cheng S" first="Su-Yun" last="Cheng">Su-Yun Cheng</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Yan Jun" sort="Zhang, Yan Jun" uniqKey="Zhang Y" first="Yan-Jun" last="Zhang">Yan-Jun Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Ru, Miao Gui" sort="Ru, Miao Gui" uniqKey="Ru M" first="Miao-Gui" last="Ru">Miao-Gui Ru</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Zan Xin" sort="Wang, Zan Xin" uniqKey="Wang Z" first="Zan-Xin" last="Wang">Zan-Xin Wang</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Bao, Qi Yu" sort="Bao, Qi Yu" uniqKey="Bao Q" first="Qi-Yu" last="Bao">Qi-Yu Bao</name><affiliation wicri:level="1"><nlm:aff id="aff2">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3">Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">16112670</idno><idno type="pmc">7118731</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118731</idno><idno type="RBID">PMC:7118731</idno><idno type="doi">10.1016/j.febslet.2005.07.075</idno><date when="2005">2005</date><idno type="wicri:Area/Pmc/Corpus">000879</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000879</idno><idno type="wicri:Area/Pmc/Curation">000879</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000879</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV</title><author><name sortKey="Wang, Zhi Gang" sort="Wang, Zhi Gang" uniqKey="Wang Z" first="Zhi-Gang" last="Wang">Zhi-Gang Wang</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Zheng, Zhi Hua" sort="Zheng, Zhi Hua" uniqKey="Zheng Z" first="Zhi-Hua" last="Zheng">Zhi-Hua Zheng</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Shang, Lei" sort="Shang, Lei" uniqKey="Shang L" first="Lei" last="Shang">Lei Shang</name><affiliation wicri:level="1"><nlm:aff id="aff2">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008</wicri:regionArea></affiliation></author><author><name sortKey="Li, Lan Juan" sort="Li, Lan Juan" uniqKey="Li L" first="Lan-Juan" last="Li">Lan-Juan Li</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Cong, Li Ming" sort="Cong, Li Ming" uniqKey="Cong L" first="Li-Ming" last="Cong">Li-Ming Cong</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Feng, Ming Guang" sort="Feng, Ming Guang" uniqKey="Feng M" first="Ming-Guang" last="Feng">Ming-Guang Feng</name><affiliation wicri:level="1"><nlm:aff id="aff2">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008</wicri:regionArea></affiliation></author><author><name sortKey="Luo, Yun" sort="Luo, Yun" uniqKey="Luo Y" first="Yun" last="Luo">Yun Luo</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Cheng, Su Yun" sort="Cheng, Su Yun" uniqKey="Cheng S" first="Su-Yun" last="Cheng">Su-Yun Cheng</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Yan Jun" sort="Zhang, Yan Jun" uniqKey="Zhang Y" first="Yan-Jun" last="Zhang">Yan-Jun Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Ru, Miao Gui" sort="Ru, Miao Gui" uniqKey="Ru M" first="Miao-Gui" last="Ru">Miao-Gui Ru</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Zan Xin" sort="Wang, Zan Xin" uniqKey="Wang Z" first="Zan-Xin" last="Wang">Zan-Xin Wang</name><affiliation wicri:level="1"><nlm:aff id="aff1">Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009</wicri:regionArea></affiliation></author><author><name sortKey="Bao, Qi Yu" sort="Bao, Qi Yu" uniqKey="Bao Q" first="Qi-Yu" last="Bao">Qi-Yu Bao</name><affiliation wicri:level="1"><nlm:aff id="aff2">James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff3">Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000</wicri:regionArea></affiliation></author></analytic><series><title level="j">Febs Letters</title><idno type="ISSN">0014-5793</idno><idno type="eISSN">1873-3468</idno><imprint><date when="2005">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. One hundred and seventy-four of these sites existed in two or more SARS-CoV genome sequences. According to the sequence polymorphism, all SARS-CoVs can be divided into three groups: (I) group 1, animal-origin viruses (such as SARS-CoV SZ1, SZ3, SZ13 and SZ16); (II) group 2, all viruses with clinical origin during first epidemic; and (III) group 3, SARS-CoV GD03T0013. According to 10 special loci, group 2 again can be divided into genotypes C and T, which can be further divided into sub-genotypes C1–C4 and T1–T4. Positive Darwinian selections were identified between any pair of these three groups. Genotype C gives neutral selection. Genotype T, however, shows negative selection. By comparing the death rates of SARS patients in the different regions, it was found that the death rate caused by the viruses of the genotype C was lower than that of the genotype T. SARS-CoVs might originate from an unknown ancestor.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Groneberg, D A" uniqKey="Groneberg D">D.A. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">FEBS Lett</journal-id><journal-id journal-id-type="iso-abbrev">FEBS Lett</journal-id><journal-title-group><journal-title>Febs Letters</journal-title></journal-title-group><issn pub-type="ppub">0014-5793</issn><issn pub-type="epub">1873-3468</issn><publisher><publisher-name>Federation of European Biochemical Societies. Published by Elsevier B.V.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">16112670</article-id><article-id pub-id-type="pmc">7118731</article-id><article-id pub-id-type="publisher-id">S0014-5793(05)00943-9</article-id><article-id pub-id-type="doi">10.1016/j.febslet.2005.07.075</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Zhi-Gang</given-names></name><email>wzg188@sina.com.cn</email><xref rid="aff1" ref-type="aff">a</xref><xref rid="cor1" ref-type="corresp">⁎</xref></contrib><contrib contrib-type="author"><name><surname>Zheng</surname><given-names>Zhi-Hua</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Shang</surname><given-names>Lei</given-names></name><xref rid="aff2" ref-type="aff">b</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Lan-Juan</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Cong</surname><given-names>Li-Ming</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Feng</surname><given-names>Ming-Guang</given-names></name><xref rid="aff2" ref-type="aff">b</xref></contrib><contrib contrib-type="author"><name><surname>Luo</surname><given-names>Yun</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Cheng</surname><given-names>Su-Yun</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Yan-Jun</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Ru</surname><given-names>Miao-Gui</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Zan-Xin</given-names></name><xref rid="aff1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Bao</surname><given-names>Qi-Yu</given-names></name><email>baoqy@genomics.org.cn</email><xref rid="aff2" ref-type="aff">b</xref><xref rid="aff3" ref-type="aff">c</xref><xref rid="cor1" ref-type="corresp">⁎</xref></contrib></contrib-group><aff id="aff1"><label>a</label>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China</aff><aff id="aff2"><label>b</label>James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China</aff><aff id="aff3"><label>c</label>Institute of Biomedical Informatics, Wenzhou Medical College, Wenzhou 325000, China</aff><author-notes><corresp id="cor1"><label>⁎</label>Corresponding authors. Fax: +86 571 87235111 (Z.-G. Wang), +86 577 88892766 (Q.-Y. Bao). <email>wzg188@sina.com.cn</email><email>baoqy@genomics.org.cn</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>9</day><month>8</month><year>2005</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><day>12</day><month>9</month><year>2005</year></pub-date><pub-date pub-type="epub"><day>9</day><month>8</month><year>2005</year></pub-date><volume>579</volume><issue>22</issue><fpage>4928</fpage><lpage>4936</lpage><history><date date-type="received"><day>31</day><month>3</month><year>2005</year></date><date date-type="accepted"><day>15</day><month>7</month><year>2005</year></date></history><permissions><copyright-statement>Copyright © 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.</copyright-statement><copyright-year>2005</copyright-year><copyright-holder>Federation of European Biochemical Societies</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract><p>In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS-CoV available in the NCBI GenBank. One hundred and seventy-four of these sites existed in two or more SARS-CoV genome sequences. According to the sequence polymorphism, all SARS-CoVs can be divided into three groups: (I) group 1, animal-origin viruses (such as SARS-CoV SZ1, SZ3, SZ13 and SZ16); (II) group 2, all viruses with clinical origin during first epidemic; and (III) group 3, SARS-CoV GD03T0013. According to 10 special loci, group 2 again can be divided into genotypes C and T, which can be further divided into sub-genotypes C1–C4 and T1–T4. Positive Darwinian selections were identified between any pair of these three groups. Genotype C gives neutral selection. Genotype T, however, shows negative selection. By comparing the death rates of SARS patients in the different regions, it was found that the death rate caused by the viruses of the genotype C was lower than that of the genotype T. SARS-CoVs might originate from an unknown ancestor.</p></abstract><kwd-group><title>Keywords</title><kwd>Severe acute respiratory syndrome</kwd><kwd>SARS-CoV</kwd><kwd>Genotype</kwd><kwd>Phylogeny</kwd><kwd>Most recent common ancestor</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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