Coronavirus phylogeny based on a geometric approach
Identifieur interne : 004B92 ( Main/Merge ); précédent : 004B91; suivant : 004B93Coronavirus phylogeny based on a geometric approach
Auteurs : Wen-Xin Zheng [République populaire de Chine] ; Ling-Ling Chen [République populaire de Chine] ; Hong-Yu Ou [République populaire de Chine] ; Feng Gao [République populaire de Chine] ; Chun-Ting Zhang [République populaire de Chine]Source :
- Molecular Phylogenetics and Evolution [ 1055-7903 ] ; 2005.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Coronavirus, Virus du SRAS.
- Algorithmes, Animaux, Coronavirus, Génome viral, Humains, Phylogénie, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- classification : Coronavirus.
- genetics : Coronavirus, SARS Virus.
- Algorithms, Animals, Evolution, Molecular, Genome, Viral, Humans, Phylogeny.
Abstract
A novel coronavirus has been identified as the cause of the outbreak of severe acute respiratory syndrome (SARS). Previous phylogenetic analyses based on sequence alignments show that SARS-CoVs form a new group distantly related to the other three groups of previously characterized coronaviruses. In this paper, a geometric approach based on the
Url:
DOI: 10.1016/j.ympev.2005.03.030
PubMed: 15890535
PubMed Central: 7111192
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PMC:7111192Le document en format XML
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Zheng</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author><author><name sortKey="Chen, Ling Ling" sort="Chen, Ling Ling" uniqKey="Chen L" first="Ling-Ling" last="Chen">Ling-Ling Chen</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2">Laboratory for Computational Biology, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo 255049, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory for Computational Biology, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology, Zibo 255049</wicri:regionArea><wicri:noRegion>Zibo 255049</wicri:noRegion></affiliation></author><author><name sortKey="Ou, Hong Yu" sort="Ou, Hong Yu" uniqKey="Ou H" first="Hong-Yu" last="Ou">Hong-Yu Ou</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author><author><name sortKey="Gao, Feng" sort="Gao, Feng" uniqKey="Gao F" first="Feng" last="Gao">Feng Gao</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author><author><name sortKey="Zhang, Chun Ting" sort="Zhang, Chun Ting" uniqKey="Zhang C" first="Chun-Ting" last="Zhang">Chun-Ting Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Physics, Tianjin University, Tianjin 300072, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea><placeName><settlement type="city">Tianjin</settlement></placeName></affiliation></author></analytic><series><title level="j">Molecular Phylogenetics and Evolution</title><idno type="ISSN">1055-7903</idno><idno type="eISSN">1095-9513</idno><imprint><date when="2005">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Coronavirus (classification)</term><term>Coronavirus (genetics)</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Phylogeny</term><term>SARS Virus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Coronavirus ()</term><term>Coronavirus (génétique)</term><term>Génome viral</term><term>Humains</term><term>Phylogénie</term><term>Virus du SRAS (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Coronavirus</term><term>Génome viral</term><term>Humains</term><term>Phylogénie</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>A novel coronavirus has been identified as the cause of the outbreak of severe acute respiratory syndrome (SARS). Previous phylogenetic analyses based on sequence alignments show that SARS-CoVs form a new group distantly related to the other three groups of previously characterized coronaviruses. In this paper, a geometric approach based on the <italic>Z</italic>-curve representation of the whole genome sequence is proposed to analyze the phylogenetic relationships of coronaviruses. The evolutionary distances are obtained through measuring the differences among the three-dimensional <italic>Z</italic>-curves. The <italic>Z</italic>-curve is approximately described by its geometric center and the associated three eigenvectors, which indicate the center position and the trend of the <italic>Z</italic>-curve, respectively. Although some information is lost due to the approximate description of the <italic>Z</italic>-curve, the phylogenetic tree constructed based on these parameters is consistent with those of previous analyses. The present method has the merits of simplicity and intuitiveness, but it is still in its premature stage. Because the phylogenetic relationships are inferred from the whole genome, instead of some individual genes, the present method represents a new direction of phylogeny study in the post-genome era.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chen, L L" uniqKey="Chen L">L.L. Chen</name></author><author><name sortKey="Ou, H Y" uniqKey="Ou H">H.Y. Ou</name></author><author><name sortKey="Zhang, R" uniqKey="Zhang R">R. Zhang</name></author><author><name sortKey="Zhang, C T" uniqKey="Zhang C">C.-T. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cork, D J" uniqKey="Cork D">D.J. Cork</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Cornish Bowden, A" uniqKey="Cornish Bowden A">A. 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