Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.
Identifieur interne : 002577 ( PubMed/Corpus ); précédent : 002576; suivant : 002578Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.
Auteurs : Zhi-Gang Wang ; Zhi-Hua Zheng ; Lei Shang ; Lan-Juan Li ; Li-Ming Cong ; Ming-Guang Feng ; Yun Luo ; Su-Yun Cheng ; Yan-Jun Zhang ; Miao-Gui Ru ; Zan-Xin Wang ; Qi-Yu BaoSource :
- FEBS letters [ 0014-5793 ] ; 2005.
English descriptors
- KwdEn :
- MESH :
- classification : SARS Virus.
- genetics : SARS Virus.
- pathogenicity : SARS Virus.
- Base Sequence, Databases, Nucleic Acid, Evolution, Molecular, Genotype, Humans, Molecular Sequence Data, Phylogeny, Polymorphism, Genetic, Selection, Genetic, Sequence Analysis, DNA.
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.
DOI: 10.1016/j.febslet.2005.07.075
PubMed: 16112670
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Ming Guang" sort="Feng, Ming Guang" uniqKey="Feng M" first="Ming-Guang" last="Feng">Ming-Guang Feng</name></author><author><name sortKey="Luo, Yun" sort="Luo, Yun" uniqKey="Luo Y" first="Yun" last="Luo">Yun Luo</name></author><author><name sortKey="Cheng, Su Yun" sort="Cheng, Su Yun" uniqKey="Cheng S" first="Su-Yun" last="Cheng">Su-Yun Cheng</name></author><author><name sortKey="Zhang, Yan Jun" sort="Zhang, Yan Jun" uniqKey="Zhang Y" first="Yan-Jun" last="Zhang">Yan-Jun Zhang</name></author><author><name sortKey="Ru, Miao Gui" sort="Ru, Miao Gui" uniqKey="Ru M" first="Miao-Gui" last="Ru">Miao-Gui Ru</name></author><author><name sortKey="Wang, Zan Xin" sort="Wang, Zan Xin" uniqKey="Wang Z" first="Zan-Xin" last="Wang">Zan-Xin Wang</name></author><author><name sortKey="Bao, Qi Yu" sort="Bao, Qi Yu" uniqKey="Bao Q" first="Qi-Yu" last="Bao">Qi-Yu Bao</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno 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Shang</name></author><author><name sortKey="Li, Lan Juan" sort="Li, Lan Juan" uniqKey="Li L" first="Lan-Juan" last="Li">Lan-Juan Li</name></author><author><name sortKey="Cong, Li Ming" sort="Cong, Li Ming" uniqKey="Cong L" first="Li-Ming" last="Cong">Li-Ming Cong</name></author><author><name sortKey="Feng, Ming Guang" sort="Feng, Ming Guang" uniqKey="Feng M" first="Ming-Guang" last="Feng">Ming-Guang Feng</name></author><author><name sortKey="Luo, Yun" sort="Luo, Yun" uniqKey="Luo Y" first="Yun" last="Luo">Yun Luo</name></author><author><name sortKey="Cheng, Su Yun" sort="Cheng, Su Yun" uniqKey="Cheng S" first="Su-Yun" last="Cheng">Su-Yun Cheng</name></author><author><name sortKey="Zhang, Yan Jun" sort="Zhang, Yan Jun" uniqKey="Zhang Y" first="Yan-Jun" last="Zhang">Yan-Jun Zhang</name></author><author><name sortKey="Ru, Miao Gui" sort="Ru, Miao Gui" uniqKey="Ru M" first="Miao-Gui" last="Ru">Miao-Gui Ru</name></author><author><name sortKey="Wang, Zan Xin" sort="Wang, Zan Xin" uniqKey="Wang Z" first="Zan-Xin" last="Wang">Zan-Xin Wang</name></author><author><name sortKey="Bao, Qi Yu" sort="Bao, Qi Yu" uniqKey="Bao Q" first="Qi-Yu" last="Bao">Qi-Yu Bao</name></author></analytic><series><title level="j">FEBS letters</title><idno type="ISSN">0014-5793</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Databases, Nucleic Acid</term><term>Evolution, Molecular</term><term>Genotype</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Polymorphism, Genetic</term><term>SARS Virus (classification)</term><term>SARS Virus (genetics)</term><term>SARS Virus (pathogenicity)</term><term>Selection, Genetic</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Databases, Nucleic Acid</term><term>Evolution, Molecular</term><term>Genotype</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Polymorphism, Genetic</term><term>Selection, Genetic</term><term>Sequence Analysis, DNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16112670</PMID><DateCompleted><Year>2005</Year><Month>10</Month><Day>25</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>04</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0014-5793</ISSN><JournalIssue CitedMedium="Print"><Volume>579</Volume><Issue>22</Issue><PubDate><Year>2005</Year><Month>Sep</Month><Day>12</Day></PubDate></JournalIssue><Title>FEBS letters</Title><ISOAbbreviation>FEBS Lett.</ISOAbbreviation></Journal><ArticleTitle>Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.</ArticleTitle><Pagination><MedlinePgn>4928-36</MedlinePgn></Pagination><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Zhi-Gang</ForeName><Initials>ZG</Initials><AffiliationInfo><Affiliation>Zhejiang Provincial Center for Disease Prevention and Control, Hangzhou 310009, China. wzg188@sina.com.cn</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Zhi-Hua</ForeName><Initials>ZH</Initials></Author><Author ValidYN="Y"><LastName>Shang</LastName><ForeName>Lei</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Lan-Juan</ForeName><Initials>LJ</Initials></Author><Author ValidYN="Y"><LastName>Cong</LastName><ForeName>Li-Ming</ForeName><Initials>LM</Initials></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Ming-Guang</ForeName><Initials>MG</Initials></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Yun</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Su-Yun</ForeName><Initials>SY</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yan-Jun</ForeName><Initials>YJ</Initials></Author><Author ValidYN="Y"><LastName>Ru</LastName><ForeName>Miao-Gui</ForeName><Initials>MG</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Zan-Xin</ForeName><Initials>ZX</Initials></Author><Author ValidYN="Y"><LastName>Bao</LastName><ForeName>Qi-Yu</ForeName><Initials>QY</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>FEBS Lett</MedlineTA><NlmUniqueID>0155157</NlmUniqueID><ISSNLinking>0014-5793</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="N">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011110" MajorTopicYN="Y">Polymorphism, 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