Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus.
Identifieur interne : 001C60 ( PubMed/Corpus ); précédent : 001C59; suivant : 001C61Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus.
Auteurs : Chung-Chau Hon ; Tsan-Yuk Lam ; Zheng-Li Shi ; Alexei J. Drummond ; Chi-Wai Yip ; Fanya Zeng ; Pui-Yi Lam ; Frederick Chi-Ching LeungSource :
- Journal of virology [ 1098-5514 ] ; 2008.
English descriptors
- KwdEn :
- MESH :
- classification : SARS Virus.
- genetics : Genome, Viral, SARS Virus.
- isolation & purification : SARS Virus.
- virology : Chiroptera.
- Animals, Base Sequence, Bayes Theorem, Models, Genetic, Molecular Sequence Data, Phylogeny, Recombination, Genetic.
Abstract
Bats have been identified as the natural reservoir of severe acute respiratory syndrome (SARS)-like and SARS coronaviruses (SLCoV and SCoV). However, previous studies suggested that none of the currently sampled bat SLCoVs is the descendant of the direct ancestor of SCoV, based on their relatively distant phylogenetic relationship. In this study, evidence of the recombinant origin of the genome of a bat SLCoV is demonstrated. We identified a potential recombination breakpoint immediately after the consensus intergenic sequence between open reading frame 1 and the S coding region, suggesting the replication intermediates may participate in the recombination event, as previously speculated for other CoVs. Phylogenetic analysis of its parental regions suggests the presence of an uncharacterized SLCoV lineage that is phylogenetically closer to SCoVs than any of the currently sampled bat SLCoVs. Using various Bayesian molecular-clock models, interspecies transfer of this SLCoV lineage from bats to the amplifying host (e.g., civets) was estimated to have happened a median of 4.08 years before the SARS outbreak. Based on this relatively short window period, we speculate that this uncharacterized SLCoV lineage may contain the direct ancestor of SCoV. This study sheds light on the possible host bat species of the direct ancestor of SCoV, providing valuable information on the scope and focus of surveillance for the origin of SCoV.
DOI: 10.1128/JVI.01926-07
PubMed: 18057240
Links to Exploration step
pubmed:18057240Le document en format XML
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Drummond</name></author><author><name sortKey="Yip, Chi Wai" sort="Yip, Chi Wai" uniqKey="Yip C" first="Chi-Wai" last="Yip">Chi-Wai Yip</name></author><author><name sortKey="Zeng, Fanya" sort="Zeng, Fanya" uniqKey="Zeng F" first="Fanya" last="Zeng">Fanya Zeng</name></author><author><name sortKey="Lam, Pui Yi" sort="Lam, Pui Yi" uniqKey="Lam P" first="Pui-Yi" last="Lam">Pui-Yi Lam</name></author><author><name sortKey="Leung, Frederick Chi Ching" sort="Leung, Frederick Chi Ching" uniqKey="Leung F" first="Frederick Chi-Ching" last="Leung">Frederick Chi-Ching Leung</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18057240</idno><idno type="pmid">18057240</idno><idno type="doi">10.1128/JVI.01926-07</idno><idno type="wicri:Area/PubMed/Corpus">001C60</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001C60</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus.</title><author><name sortKey="Hon, Chung Chau" sort="Hon, Chung Chau" uniqKey="Hon C" first="Chung-Chau" last="Hon">Chung-Chau Hon</name><affiliation><nlm:affiliation>5N-12, Kadoorie Biological Science Building, The University of Hong Kong, Hong Kong, China.</nlm:affiliation></affiliation></author><author><name sortKey="Lam, Tsan Yuk" sort="Lam, Tsan Yuk" uniqKey="Lam T" first="Tsan-Yuk" last="Lam">Tsan-Yuk Lam</name></author><author><name sortKey="Shi, Zheng Li" sort="Shi, Zheng Li" uniqKey="Shi Z" first="Zheng-Li" last="Shi">Zheng-Li Shi</name></author><author><name sortKey="Drummond, Alexei J" sort="Drummond, Alexei J" uniqKey="Drummond A" first="Alexei J" last="Drummond">Alexei J. Drummond</name></author><author><name sortKey="Yip, Chi Wai" sort="Yip, Chi Wai" uniqKey="Yip C" first="Chi-Wai" last="Yip">Chi-Wai Yip</name></author><author><name sortKey="Zeng, Fanya" sort="Zeng, Fanya" uniqKey="Zeng F" first="Fanya" last="Zeng">Fanya Zeng</name></author><author><name sortKey="Lam, Pui Yi" sort="Lam, Pui Yi" uniqKey="Lam P" first="Pui-Yi" last="Lam">Pui-Yi Lam</name></author><author><name sortKey="Leung, Frederick Chi Ching" sort="Leung, Frederick Chi Ching" uniqKey="Leung F" first="Frederick Chi-Ching" last="Leung">Frederick Chi-Ching Leung</name></author></analytic><series><title level="j">Journal of virology</title><idno type="eISSN">1098-5514</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Bayes Theorem</term><term>Chiroptera (virology)</term><term>Genome, Viral (genetics)</term><term>Models, Genetic</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Recombination, Genetic</term><term>SARS Virus (classification)</term><term>SARS Virus (genetics)</term><term>SARS Virus (isolation & purification)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Viral</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chiroptera</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Bayes Theorem</term><term>Models, Genetic</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Recombination, Genetic</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Bats have been identified as the natural reservoir of severe acute respiratory syndrome (SARS)-like and SARS coronaviruses (SLCoV and SCoV). However, previous studies suggested that none of the currently sampled bat SLCoVs is the descendant of the direct ancestor of SCoV, based on their relatively distant phylogenetic relationship. In this study, evidence of the recombinant origin of the genome of a bat SLCoV is demonstrated. We identified a potential recombination breakpoint immediately after the consensus intergenic sequence between open reading frame 1 and the S coding region, suggesting the replication intermediates may participate in the recombination event, as previously speculated for other CoVs. Phylogenetic analysis of its parental regions suggests the presence of an uncharacterized SLCoV lineage that is phylogenetically closer to SCoVs than any of the currently sampled bat SLCoVs. Using various Bayesian molecular-clock models, interspecies transfer of this SLCoV lineage from bats to the amplifying host (e.g., civets) was estimated to have happened a median of 4.08 years before the SARS outbreak. Based on this relatively short window period, we speculate that this uncharacterized SLCoV lineage may contain the direct ancestor of SCoV. This study sheds light on the possible host bat species of the direct ancestor of SCoV, providing valuable information on the scope and focus of surveillance for the origin of SCoV.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18057240</PMID><DateCompleted><Year>2008</Year><Month>03</Month><Day>05</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1098-5514</ISSN><JournalIssue CitedMedium="Internet"><Volume>82</Volume><Issue>4</Issue><PubDate><Year>2008</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Journal of virology</Title><ISOAbbreviation>J. Virol.</ISOAbbreviation></Journal><ArticleTitle>Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus.</ArticleTitle><Pagination><MedlinePgn>1819-26</MedlinePgn></Pagination><Abstract><AbstractText>Bats have been identified as the natural reservoir of severe acute respiratory syndrome (SARS)-like and SARS coronaviruses (SLCoV and SCoV). However, previous studies suggested that none of the currently sampled bat SLCoVs is the descendant of the direct ancestor of SCoV, based on their relatively distant phylogenetic relationship. In this study, evidence of the recombinant origin of the genome of a bat SLCoV is demonstrated. We identified a potential recombination breakpoint immediately after the consensus intergenic sequence between open reading frame 1 and the S coding region, suggesting the replication intermediates may participate in the recombination event, as previously speculated for other CoVs. Phylogenetic analysis of its parental regions suggests the presence of an uncharacterized SLCoV lineage that is phylogenetically closer to SCoVs than any of the currently sampled bat SLCoVs. Using various Bayesian molecular-clock models, interspecies transfer of this SLCoV lineage from bats to the amplifying host (e.g., civets) was estimated to have happened a median of 4.08 years before the SARS outbreak. Based on this relatively short window period, we speculate that this uncharacterized SLCoV lineage may contain the direct ancestor of SCoV. This study sheds light on the possible host bat species of the direct ancestor of SCoV, providing valuable information on the scope and focus of surveillance for the origin of SCoV.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hon</LastName><ForeName>Chung-Chau</ForeName><Initials>CC</Initials><AffiliationInfo><Affiliation>5N-12, Kadoorie Biological Science Building, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lam</LastName><ForeName>Tsan-Yuk</ForeName><Initials>TY</Initials></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Zheng-Li</ForeName><Initials>ZL</Initials></Author><Author ValidYN="Y"><LastName>Drummond</LastName><ForeName>Alexei J</ForeName><Initials>AJ</Initials></Author><Author ValidYN="Y"><LastName>Yip</LastName><ForeName>Chi-Wai</ForeName><Initials>CW</Initials></Author><Author ValidYN="Y"><LastName>Zeng</LastName><ForeName>Fanya</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Lam</LastName><ForeName>Pui-Yi</ForeName><Initials>PY</Initials></Author><Author ValidYN="Y"><LastName>Leung</LastName><ForeName>Frederick Chi-Ching</ForeName><Initials>FC</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2007</Year><Month>12</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Virol</MedlineTA><NlmUniqueID>0113724</NlmUniqueID><ISSNLinking>0022-538X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001499" MajorTopicYN="N">Bayes Theorem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002685" MajorTopicYN="N">Chiroptera</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="Y">Models, Genetic</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="D011995" MajorTopicYN="N">Recombination, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D045473" 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