SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting
Identifieur interne : 006361 ( Main/Merge ); précédent : 006360; suivant : 006362SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting
Auteurs : Joshua S. Rest ; David P. MindellSource :
- Infection, Genetics and Evolution [ 1567-1348 ] ; 2003.
Descripteurs français
- KwdFr :
- Animaux, Coronavirus (physiologie), Glycoprotéine de spicule des coronavirus, Glycoprotéines membranaires (génétique), Humains, Interactions hôte-parasite (physiologie), Nucléocapside (génétique), Phylogénie, Protéines de l'enveloppe virale (génétique), RNA replicase (génétique), Recombinaison génétique, Théorème de Bayes, Virus du SRAS (génétique), Virus du SRAS (physiologie).
- MESH :
- génétique : Glycoprotéines membranaires, Nucléocapside, Protéines de l'enveloppe virale, RNA replicase, Virus du SRAS.
- physiologie : Coronavirus, Interactions hôte-parasite, Virus du SRAS.
- Animaux, Glycoprotéine de spicule des coronavirus, Humains, Phylogénie, Recombinaison génétique, Théorème de Bayes.
English descriptors
- KwdEn :
- Animals, Bayes Theorem, Coronavirus (physiology), Host-Parasite Interactions (physiology), Humans, Membrane Glycoproteins (genetics), Nucleocapsid (genetics), Phylogeny, RNA Replicase (genetics), Recombination, Genetic, SARS Virus (genetics), SARS Virus (physiology), Spike Glycoprotein, Coronavirus, Viral Envelope Proteins (genetics).
- MESH :
- chemical , genetics : Membrane Glycoproteins, RNA Replicase, Viral Envelope Proteins.
- genetics : Nucleocapsid, SARS Virus.
- physiology : Coronavirus, Host-Parasite Interactions, SARS Virus.
- Animals, Bayes Theorem, Humans, Phylogeny, Recombination, Genetic, Spike Glycoprotein, Coronavirus.
Abstract
The sudden appearance and potential lethality of severe acute respiratory syndrome associated coronavirus (SARS-CoV) in humans has focused attention on understanding its origins. Here, we assess phylogenetic relationships for the SARS-CoV lineage as well as the history of host-species shifts for SARS-CoV and other coronaviruses. We used a Bayesian phylogenetic inference approach with sliding window analyses of three SARS-CoV proteins: RNA dependent RNA polymerase (RDRP), nucleocapsid (N) and spike (S). Conservation of RDRP allowed us to use a set of Arteriviridae taxa to root the Coronaviridae phylogeny. We found strong evidence for a recombination breakpoint within SARS-CoV RDRP, based on different, well supported trees for a 5′ fragment (supporting SARS-CoV as sister to a clade including all other coronaviruses) and a 3′ fragment (supporting SARS-CoV as sister to group three avian coronaviruses). These different topologies are statistically significant: the optimal 5′ tree could be rejected for the 3′ region, and the optimal 3′ tree could be rejected for the 5′ region. We did not find statistical evidence for recombination in analyses of N and S, as there is little signal to differentiate among alternative trees. Comparison of phylogenetic trees for 11 known host-species and 36 coronaviruses, representing coronavirus groups 1–3 and SARS-CoV, based on N showed statistical incongruence indicating multiple host-species shifts for coronaviruses. Inference of host-species associations is highly sensitive to sampling and must be considered cautiously. However, current sampling suggests host-species shifts between mouse and rat, chicken and turkey, mammals and manx shearwater, and humans and other mammals. The sister relationship between avian coronaviruses and the 3′ RDRP fragment of SARS-CoV suggests an additional host-species shift. Demonstration of recombination in the SARS-CoV lineage indicates its potential for rapid unpredictable change, a potentially important challenge for public health management and for drug and vaccine development.
Url:
DOI: 10.1016/j.meegid.2003.08.001
PubMed: 14522185
PubMed Central: 7129878
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PMC:7129878Le document en format XML
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Mindell</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">14522185</idno><idno type="pmc">7129878</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129878</idno><idno type="RBID">PMC:7129878</idno><idno type="doi">10.1016/j.meegid.2003.08.001</idno><date when="2003">2003</date><idno type="wicri:Area/Pmc/Corpus">001054</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001054</idno><idno type="wicri:Area/Pmc/Curation">001054</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001054</idno><idno type="wicri:Area/Pmc/Checkpoint">001849</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001849</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:14522185</idno><idno type="wicri:Area/PubMed/Corpus">003164</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003164</idno><idno type="wicri:Area/PubMed/Curation">003164</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">003164</idno><idno type="wicri:Area/PubMed/Checkpoint">003135</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">003135</idno><idno type="wicri:Area/Ncbi/Merge">000365</idno><idno type="wicri:Area/Ncbi/Curation">000365</idno><idno type="wicri:Area/Ncbi/Checkpoint">000365</idno><idno type="wicri:doubleKey">1567-1348:2003:Rest J:sars:associated:coronavirus</idno><idno type="wicri:Area/Main/Merge">006361</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting</title><author><name sortKey="Rest, Joshua S" sort="Rest, Joshua S" uniqKey="Rest J" first="Joshua S" last="Rest">Joshua S. Rest</name></author><author><name sortKey="Mindell, David P" sort="Mindell, David P" uniqKey="Mindell D" first="David P" last="Mindell">David P. Mindell</name></author></analytic><series><title level="j">Infection, Genetics and Evolution</title><idno type="ISSN">1567-1348</idno><idno type="eISSN">1567-7257</idno><imprint><date when="2003">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Bayes Theorem</term><term>Coronavirus (physiology)</term><term>Host-Parasite Interactions (physiology)</term><term>Humans</term><term>Membrane Glycoproteins (genetics)</term><term>Nucleocapsid (genetics)</term><term>Phylogeny</term><term>RNA Replicase (genetics)</term><term>Recombination, Genetic</term><term>SARS Virus (genetics)</term><term>SARS Virus (physiology)</term><term>Spike Glycoprotein, Coronavirus</term><term>Viral Envelope Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Coronavirus (physiologie)</term><term>Glycoprotéine de spicule des coronavirus</term><term>Glycoprotéines membranaires (génétique)</term><term>Humains</term><term>Interactions hôte-parasite (physiologie)</term><term>Nucléocapside (génétique)</term><term>Phylogénie</term><term>Protéines de l'enveloppe virale (génétique)</term><term>RNA replicase (génétique)</term><term>Recombinaison génétique</term><term>Théorème de Bayes</term><term>Virus du SRAS (génétique)</term><term>Virus du SRAS (physiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Membrane Glycoproteins</term><term>RNA Replicase</term><term>Viral Envelope Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Nucleocapsid</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Glycoprotéines membranaires</term><term>Nucléocapside</term><term>Protéines de l'enveloppe virale</term><term>RNA replicase</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Coronavirus</term><term>Interactions hôte-parasite</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Coronavirus</term><term>Host-Parasite Interactions</term><term>SARS Virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Bayes Theorem</term><term>Humans</term><term>Phylogeny</term><term>Recombination, Genetic</term><term>Spike Glycoprotein, Coronavirus</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Glycoprotéine de spicule des coronavirus</term><term>Humains</term><term>Phylogénie</term><term>Recombinaison génétique</term><term>Théorème de Bayes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The sudden appearance and potential lethality of severe acute respiratory syndrome associated coronavirus (SARS-CoV) in humans has focused attention on understanding its origins. Here, we assess phylogenetic relationships for the SARS-CoV lineage as well as the history of host-species shifts for SARS-CoV and other coronaviruses. We used a Bayesian phylogenetic inference approach with sliding window analyses of three SARS-CoV proteins: RNA dependent RNA polymerase (RDRP), nucleocapsid (N) and spike (S). Conservation of RDRP allowed us to use a set of Arteriviridae taxa to root the Coronaviridae phylogeny. We found strong evidence for a recombination breakpoint within SARS-CoV RDRP, based on different, well supported trees for a 5′ fragment (supporting SARS-CoV as sister to a clade including all other coronaviruses) and a 3′ fragment (supporting SARS-CoV as sister to group three avian coronaviruses). These different topologies are statistically significant: the optimal 5′ tree could be rejected for the 3′ region, and the optimal 3′ tree could be rejected for the 5′ region. We did not find statistical evidence for recombination in analyses of N and S, as there is little signal to differentiate among alternative trees. Comparison of phylogenetic trees for 11 known host-species and 36 coronaviruses, representing coronavirus groups 1–3 and SARS-CoV, based on N showed statistical incongruence indicating multiple host-species shifts for coronaviruses. Inference of host-species associations is highly sensitive to sampling and must be considered cautiously. However, current sampling suggests host-species shifts between mouse and rat, chicken and turkey, mammals and manx shearwater, and humans and other mammals. The sister relationship between avian coronaviruses and the 3′ RDRP fragment of SARS-CoV suggests an additional host-species shift. Demonstration of recombination in the SARS-CoV lineage indicates its potential for rapid unpredictable change, a potentially important challenge for public health management and for drug and vaccine development.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bateman, A" uniqKey="Bateman A">A Bateman</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author><author><name sortKey="Cerruti, L" uniqKey="Cerruti L">L Cerruti</name></author><author><name sortKey="Durbin, R" uniqKey="Durbin R">R Durbin</name></author><author><name sortKey="Etwiller, L" uniqKey="Etwiller L">L Etwiller</name></author><author><name sortKey="Eddy, S R" uniqKey="Eddy S">S.R Eddy</name></author><author><name sortKey="Griffiths Jones, S" uniqKey="Griffiths Jones S">S Griffiths-Jones</name></author><author><name sortKey="Howe, K L" uniqKey="Howe K">K.L Howe</name></author><author><name sortKey="Marshall, M" uniqKey="Marshall 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McCaustland</name></author><author><name sortKey="Olsen Rasmussen, M" uniqKey="Olsen Rasmussen M">M Olsen-Rasmussen</name></author><author><name sortKey="Fouchier, R" uniqKey="Fouchier R">R Fouchier</name></author><author><name sortKey="Gunther, S" uniqKey="Gunther S">S Gunther</name></author><author><name sortKey="Osterhaus, A D" uniqKey="Osterhaus A">A.D Osterhaus</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C Drosten</name></author><author><name sortKey="Pallansch, M A" uniqKey="Pallansch M">M.A Pallansch</name></author><author><name sortKey="Anderson, L J" uniqKey="Anderson L">L.J Anderson</name></author><author><name sortKey="Bellini, W J" uniqKey="Bellini W">W.J Bellini</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Salminen, M O" uniqKey="Salminen M">M.O Salminen</name></author><author><name sortKey="Carr, J K" uniqKey="Carr J">J.K Carr</name></author><author><name sortKey="Burke, D S" uniqKey="Burke D">D.S Burke</name></author><author><name sortKey="Mccutchan, F E" uniqKey="Mccutchan F">F.E McCutchan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shimodaira, H" uniqKey="Shimodaira H">H Shimodaira</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shimodaira, H" uniqKey="Shimodaira H">H Shimodaira</name></author><author><name sortKey="Hasegawa, M" uniqKey="Hasegawa M">M Hasegawa</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Sturman, L S" uniqKey="Sturman L">L.S Sturman</name></author><author><name sortKey="Holmes, K V" uniqKey="Holmes K">K.V Holmes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, L" uniqKey="Wang L">L Wang</name></author><author><name sortKey="Junker, D" uniqKey="Junker D">D Junker</name></author><author><name sortKey="Collisson, E W" uniqKey="Collisson E">E.W Collisson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Z H" uniqKey="Yang Z">Z.H Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Z H" uniqKey="Yang Z">Z.H Yang</name></author><author><name sortKey="Rannala, B" uniqKey="Rannala B">B Rannala</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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