Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic discordance in three genomic regions.
Identifieur interne : 000A75 ( Ncbi/Checkpoint ); précédent : 000A74; suivant : 000A76Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic discordance in three genomic regions.
Auteurs : G. Magiorkinis [Grèce] ; E. Magiorkinis ; D. Paraskevis ; A M Vandamme ; M. Van Ranst ; V. Moulton ; A. HatzakisSource :
- Journal of medical virology [ 0146-6615 ] ; 2004.
Descripteurs français
- KwdFr :
- MESH :
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
Affiliations:
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Magiorkinis</name><affiliation wicri:level="3"><nlm:affiliation>National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens, Greece.</nlm:affiliation><country xml:lang="fr">Grèce</country><wicri:regionArea>National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Magiorkinis, E" sort="Magiorkinis, E" uniqKey="Magiorkinis E" first="E" last="Magiorkinis">E. Magiorkinis</name></author><author><name sortKey="Paraskevis, D" sort="Paraskevis, D" uniqKey="Paraskevis D" first="D" last="Paraskevis">D. 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></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="KwdFr" xml:lang="fr"><term>Alignement de séquences</term><term>Génome viral</term><term>Humains</term><term>Phylogénie</term><term>Protéines virales (génétique)</term><term>Recombinaison génétique</term><term>Virus du SRAS ()</term><term>Virus du SRAS (génétique)</term><term>Évolution moléculaire</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" qualifier="génétique" xml:lang="fr"><term>Protéines virales</term><term>Virus du SRAS</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><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Génome viral</term><term>Humains</term><term>Phylogénie</term><term>Recombinaison génétique</term><term>Virus du SRAS</term><term>Évolution moléculaire</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><affiliations><list><country><li>Grèce</li></country><region><li>Attique (région)</li></region><settlement><li>Athènes</li></settlement></list><tree><noCountry><name sortKey="Hatzakis, A" sort="Hatzakis, A" uniqKey="Hatzakis A" first="A" last="Hatzakis">A. Hatzakis</name><name sortKey="Magiorkinis, E" sort="Magiorkinis, E" uniqKey="Magiorkinis E" first="E" last="Magiorkinis">E. Magiorkinis</name><name sortKey="Moulton, V" sort="Moulton, V" uniqKey="Moulton V" first="V" last="Moulton">V. Moulton</name><name sortKey="Paraskevis, D" sort="Paraskevis, D" uniqKey="Paraskevis D" first="D" last="Paraskevis">D. Paraskevis</name><name sortKey="Van Ranst, M" sort="Van Ranst, M" uniqKey="Van Ranst M" first="M" last="Van Ranst">M. Van Ranst</name><name sortKey="Vandamme, A M" sort="Vandamme, A M" uniqKey="Vandamme A" first="A M" last="Vandamme">A M Vandamme</name></noCountry><country name="Grèce"><region name="Attique (région)"><name sortKey="Magiorkinis, G" sort="Magiorkinis, G" uniqKey="Magiorkinis G" first="G" last="Magiorkinis">G. Magiorkinis</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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