Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic discordance in three genomic regions.
Identifieur interne : 002B52 ( PubMed/Corpus ); précédent : 002B51; suivant : 002B53Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic discordance in three genomic regions.
Auteurs : G. Magiorkinis ; E. Magiorkinis ; D. Paraskevis ; A M Vandamme ; M. Van Ranst ; V. Moulton ; A. HatzakisSource :
- Journal of medical virology [ 0146-6615 ] ; 2004.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Viral Proteins.
- classification : SARS Virus.
- genetics : SARS Virus.
- Evolution, Molecular, Genome, Viral, Humans, Phylogeny, Recombination, Genetic, Sequence Alignment.
Abstract
The origin of the severe acute respiratory syndrome-coronavirus (SARS-CoV) remains unclear. Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS-CoV, for the largest part of the genome ( approximately 80%), is more closely related to Group II coronaviruses sequences, whereas in three regions in the ORF1ab gene it shows no apparent similarity to any of the previously characterized groups of coronaviruses. There is discordant phylogenetic clustering of SARS-CoV and coronaviruses sequences, throughout the genome, compatible with either ancient recombination events or altered evolutionary rates in different lineages, or a combination of both.
DOI: 10.1002/jmv.20187
PubMed: 15368527
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pubmed:15368527Le document en format XML
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Paraskevis</name></author><author><name sortKey="Vandamme, A M" sort="Vandamme, A M" uniqKey="Vandamme A" first="A M" last="Vandamme">A M Vandamme</name></author><author><name sortKey="Van Ranst, M" sort="Van Ranst, M" uniqKey="Van Ranst M" first="M" last="Van Ranst">M. Van Ranst</name></author><author><name sortKey="Moulton, V" sort="Moulton, V" uniqKey="Moulton V" first="V" last="Moulton">V. Moulton</name></author><author><name sortKey="Hatzakis, A" sort="Hatzakis, A" uniqKey="Hatzakis A" first="A" last="Hatzakis">A. Hatzakis</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2004">2004</date><idno type="RBID">pubmed:15368527</idno><idno type="pmid">15368527</idno><idno type="doi">10.1002/jmv.20187</idno><idno type="wicri:Area/PubMed/Corpus">002B52</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002B52</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic discordance in three genomic regions.</title><author><name sortKey="Magiorkinis, G" sort="Magiorkinis, G" uniqKey="Magiorkinis G" first="G" last="Magiorkinis">G. 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Hatzakis</name></author></analytic><series><title level="j">Journal of medical virology</title><idno type="ISSN">0146-6615</idno><imprint><date when="2004" type="published">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Phylogeny</term><term>Recombination, Genetic</term><term>SARS Virus (classification)</term><term>SARS Virus (genetics)</term><term>Sequence Alignment</term><term>Viral Proteins (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Viral Proteins</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" xml:lang="en"><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Phylogeny</term><term>Recombination, Genetic</term><term>Sequence Alignment</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The origin of the severe acute respiratory syndrome-coronavirus (SARS-CoV) remains unclear. Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS-CoV, for the largest part of the genome ( approximately 80%), is more closely related to Group II coronaviruses sequences, whereas in three regions in the ORF1ab gene it shows no apparent similarity to any of the previously characterized groups of coronaviruses. There is discordant phylogenetic clustering of SARS-CoV and coronaviruses sequences, throughout the genome, compatible with either ancient recombination events or altered evolutionary rates in different lineages, or a combination of both.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15368527</PMID><DateCompleted><Year>2004</Year><Month>11</Month><Day>04</Day></DateCompleted><DateRevised><Year>2004</Year><Month>11</Month><Day>17</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0146-6615</ISSN><JournalIssue CitedMedium="Print"><Volume>74</Volume><Issue>3</Issue><PubDate><Year>2004</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Journal of medical virology</Title><ISOAbbreviation>J. Med. Virol.</ISOAbbreviation></Journal><ArticleTitle>Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic discordance in three genomic regions.</ArticleTitle><Pagination><MedlinePgn>369-72</MedlinePgn></Pagination><Abstract><AbstractText>The origin of the severe acute respiratory syndrome-coronavirus (SARS-CoV) remains unclear. Evidence based on Bayesian scanning plots and phylogenetic analysis using maximum likelihood (ML) and Bayesian methods indicates that SARS-CoV, for the largest part of the genome ( approximately 80%), is more closely related to Group II coronaviruses sequences, whereas in three regions in the ORF1ab gene it shows no apparent similarity to any of the previously characterized groups of coronaviruses. There is discordant phylogenetic clustering of SARS-CoV and coronaviruses sequences, throughout the genome, compatible with either ancient recombination events or altered evolutionary rates in different lineages, or a combination of both.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Magiorkinis</LastName><ForeName>G</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Magiorkinis</LastName><ForeName>E</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Paraskevis</LastName><ForeName>D</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Vandamme</LastName><ForeName>A M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>Van Ranst</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Moulton</LastName><ForeName>V</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Hatzakis</LastName><ForeName>A</ForeName><Initials>A</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Med Virol</MedlineTA><NlmUniqueID>7705876</NlmUniqueID><ISSNLinking>0146-6615</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014764">Viral Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</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" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014764" MajorTopicYN="N">Viral Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2004</Year><Month>9</Month><Day>16</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2004</Year><Month>11</Month><Day>5</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2004</Year><Month>9</Month><Day>16</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15368527</ArticleId><ArticleId IdType="doi">10.1002/jmv.20187</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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