Characterizing 56 complete SARS-CoV S-gene sequences from Hong Kong
Identifieur interne : 003F55 ( Main/Exploration ); précédent : 003F54; suivant : 003F56Characterizing 56 complete SARS-CoV S-gene sequences from Hong Kong
Auteurs : Julian W. Tang [République populaire de Chine] ; Jo L. K. Cheung [République populaire de Chine] ; Ida M. T. Chu [République populaire de Chine] ; Margaret Ip [République populaire de Chine] ; Mamie Hui [République populaire de Chine] ; Malik Peiris [République populaire de Chine] ; Paul K. S. Chan [République populaire de Chine]Source :
- Journal of Clinical Virology [ 1386-6532 ] ; 2006.
Descripteurs français
- KwdFr :
- Données de séquences moléculaires, Famille multigénique, Femelle, Flambées de maladies, Glycoprotéine de spicule des coronavirus, Glycoprotéines membranaires (génétique), Gènes viraux (génétique), Hong Kong (épidémiologie), Humains, Mâle, Protéines de l'enveloppe virale (génétique), Syndrome respiratoire aigu sévère (épidémiologie), Variation génétique, Virus du SRAS (génétique), Épidémiologie moléculaire, Évolution moléculaire.
- MESH :
- génétique : Glycoprotéines membranaires, Gènes viraux, Protéines de l'enveloppe virale, Virus du SRAS.
- épidémiologie : Hong Kong, Syndrome respiratoire aigu sévère.
- Données de séquences moléculaires, Famille multigénique, Femelle, Flambées de maladies, Glycoprotéine de spicule des coronavirus, Humains, Mâle, Variation génétique, Épidémiologie moléculaire, Évolution moléculaire.
- Wicri :
- geographic : Hong Kong.
English descriptors
- KwdEn :
- Disease Outbreaks, Evolution, Molecular, Female, Genes, Viral (genetics), Genetic Variation, Hong Kong (epidemiology), Humans, Male, Membrane Glycoproteins (genetics), Molecular Epidemiology, Molecular Sequence Data, Multigene Family, SARS Virus (genetics), Severe Acute Respiratory Syndrome (epidemiology), Spike Glycoprotein, Coronavirus, Viral Envelope Proteins (genetics).
- MESH :
- chemical , genetics : Membrane Glycoproteins, Viral Envelope Proteins.
- geographic , epidemiology : Hong Kong.
- epidemiology : Severe Acute Respiratory Syndrome.
- genetics : Genes, Viral, SARS Virus.
- Disease Outbreaks, Evolution, Molecular, Female, Genetic Variation, Humans, Male, Molecular Epidemiology, Molecular Sequence Data, Multigene Family, Spike Glycoprotein, Coronavirus.
Abstract
The spike glycoprotein (S) gene of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) has been useful in analyzing the molecular epidemiology of the 2003 SARS outbreaks.
To characterize complete SARS-CoV S-gene sequences from Hong Kong.
Fifty-six SARS-CoV S-gene sequences, obtained from patients who presented with SARS to the Prince of Wales Hospital during March–May 2003, were analysed using a maximum likelihood (ML) approach, together with 138 other (both human and animal) S-gene sequences downloaded from GenBank.
The maximum-likelihood (ML) trees showed little evolution occurring within these 56 sequences. Analysis with the other sequences, showed three distinct SARS clusters, closely correlated to previously defined early, middle and late phases of the 2003 international SARS outbreaks. In addition, two new single nucleotide variations (SNVs), T21615A and T21901A, were discovered, not previously reported elsewhere.
The ML approach to the reconstruction of tree phylogenies is known to be superior to the more popular, less computationally and time-demanding neighbour-joining (NJ) approach. The ML analysis in this study confirms the previously reported SARS epidemiology analysed mostly using the NJ approach. The two new SNVs reported here are most likely due to the tissue-culture passaging of the clinical samples.
Url:
DOI: 10.1016/j.jcv.2006.10.001
PubMed: 17112780
PubMed Central: 7108452
Affiliations:
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Le document en format XML
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Chan</name><affiliation wicri:level="4"><nlm:aff id="aff1">Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff3">Centre for Emerging Infectious Diseases, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Centre for Emerging Infectious Diseases, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">17112780</idno><idno type="pmc">7108452</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108452</idno><idno type="RBID">PMC:7108452</idno><idno type="doi">10.1016/j.jcv.2006.10.001</idno><date when="2006">2006</date><idno type="wicri:Area/Pmc/Corpus">001121</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001121</idno><idno type="wicri:Area/Pmc/Curation">001121</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001121</idno><idno type="wicri:Area/Pmc/Checkpoint">001158</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001158</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:17112780</idno><idno type="wicri:Area/PubMed/Corpus">001F82</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001F82</idno><idno type="wicri:Area/PubMed/Curation">001F82</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001F82</idno><idno type="wicri:Area/PubMed/Checkpoint">001E58</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001E58</idno><idno type="wicri:Area/Ncbi/Merge">001772</idno><idno type="wicri:Area/Ncbi/Curation">001772</idno><idno type="wicri:Area/Ncbi/Checkpoint">001772</idno><idno type="wicri:doubleKey">1386-6532:2006:Tang J:characterizing:complete:sars</idno><idno type="wicri:Area/Main/Merge">004164</idno><idno type="wicri:Area/Main/Curation">003F55</idno><idno type="wicri:Area/Main/Exploration">003F55</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Characterizing 56 complete SARS-CoV S-gene sequences from Hong Kong</title><author><name sortKey="Tang, Julian W" sort="Tang, Julian W" uniqKey="Tang J" first="Julian W." last="Tang">Julian W. Tang</name><affiliation wicri:level="4"><nlm:aff id="aff1">Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation></author><author><name sortKey="Cheung, Jo L K" sort="Cheung, Jo L K" uniqKey="Cheung J" first="Jo L. K." last="Cheung">Jo L. K. Cheung</name><affiliation wicri:level="4"><nlm:aff id="aff1">Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation></author><author><name sortKey="Chu, Ida M T" sort="Chu, Ida M T" uniqKey="Chu I" first="Ida M. T." last="Chu">Ida M. T. Chu</name><affiliation wicri:level="4"><nlm:aff id="aff1">Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation></author><author><name sortKey="Ip, Margaret" sort="Ip, Margaret" uniqKey="Ip M" first="Margaret" last="Ip">Margaret Ip</name><affiliation wicri:level="4"><nlm:aff id="aff1">Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation></author><author><name sortKey="Hui, Mamie" sort="Hui, Mamie" uniqKey="Hui M" first="Mamie" last="Hui">Mamie Hui</name><affiliation wicri:level="4"><nlm:aff id="aff1">Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation></author><author><name sortKey="Peiris, Malik" sort="Peiris, Malik" uniqKey="Peiris M" first="Malik" last="Peiris">Malik Peiris</name><affiliation wicri:level="1"><nlm:aff id="aff2">Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China.</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR</wicri:regionArea><wicri:noRegion>Hong Kong SAR</wicri:noRegion></affiliation></author><author><name sortKey="Chan, Paul K S" sort="Chan, Paul K S" uniqKey="Chan P" first="Paul K. S." last="Chan">Paul K. S. Chan</name><affiliation wicri:level="4"><nlm:aff id="aff1">Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff3">Centre for Emerging Infectious Diseases, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Centre for Emerging Infectious Diseases, School of Public Health, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR</wicri:regionArea><orgName type="university">Université chinoise de Hong Kong</orgName><placeName><settlement type="city">Sha Tin</settlement></placeName></affiliation></author></analytic><series><title level="j">Journal of Clinical Virology</title><idno type="ISSN">1386-6532</idno><idno type="eISSN">1873-5967</idno><imprint><date when="2006">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Disease Outbreaks</term><term>Evolution, Molecular</term><term>Female</term><term>Genes, Viral (genetics)</term><term>Genetic Variation</term><term>Hong Kong (epidemiology)</term><term>Humans</term><term>Male</term><term>Membrane Glycoproteins (genetics)</term><term>Molecular Epidemiology</term><term>Molecular Sequence Data</term><term>Multigene Family</term><term>SARS Virus (genetics)</term><term>Severe Acute Respiratory Syndrome (epidemiology)</term><term>Spike Glycoprotein, Coronavirus</term><term>Viral Envelope Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Données de séquences moléculaires</term><term>Famille multigénique</term><term>Femelle</term><term>Flambées de maladies</term><term>Glycoprotéine de spicule des coronavirus</term><term>Glycoprotéines membranaires (génétique)</term><term>Gènes viraux (génétique)</term><term>Hong Kong (épidémiologie)</term><term>Humains</term><term>Mâle</term><term>Protéines de l'enveloppe virale (génétique)</term><term>Syndrome respiratoire aigu sévère (épidémiologie)</term><term>Variation génétique</term><term>Virus du SRAS (génétique)</term><term>Épidémiologie moléculaire</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Membrane Glycoproteins</term><term>Viral Envelope Proteins</term></keywords><keywords scheme="MESH" type="geographic" qualifier="epidemiology" xml:lang="en"><term>Hong Kong</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genes, Viral</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Glycoprotéines membranaires</term><term>Gènes viraux</term><term>Protéines de l'enveloppe virale</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Hong Kong</term><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Disease Outbreaks</term><term>Evolution, Molecular</term><term>Female</term><term>Genetic Variation</term><term>Humans</term><term>Male</term><term>Molecular Epidemiology</term><term>Molecular Sequence Data</term><term>Multigene Family</term><term>Spike Glycoprotein, Coronavirus</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Données de séquences moléculaires</term><term>Famille multigénique</term><term>Femelle</term><term>Flambées de maladies</term><term>Glycoprotéine de spicule des coronavirus</term><term>Humains</term><term>Mâle</term><term>Variation génétique</term><term>Épidémiologie moléculaire</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Hong Kong</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The spike glycoprotein (S) gene of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) has been useful in analyzing the molecular epidemiology of the 2003 SARS outbreaks.</p></sec><sec><title>Objectives</title><p>To characterize complete SARS-CoV S-gene sequences from Hong Kong.</p></sec><sec><title>Study design</title><p>Fifty-six SARS-CoV S-gene sequences, obtained from patients who presented with SARS to the Prince of Wales Hospital during March–May 2003, were analysed using a maximum likelihood (ML) approach, together with 138 other (both human and animal) S-gene sequences downloaded from GenBank.</p></sec><sec><title>Results</title><p>The maximum-likelihood (ML) trees showed little evolution occurring within these 56 sequences. Analysis with the other sequences, showed three distinct SARS clusters, closely correlated to previously defined early, middle and late phases of the 2003 international SARS outbreaks. In addition, two new single nucleotide variations (SNVs), T21615A and T21901A, were discovered, not previously reported elsewhere.</p></sec><sec><title>Conclusions</title><p>The ML approach to the reconstruction of tree phylogenies is known to be superior to the more popular, less computationally and time-demanding neighbour-joining (NJ) approach. The ML analysis in this study confirms the previously reported SARS epidemiology analysed mostly using the NJ approach. The two new SNVs reported here are most likely due to the tissue-culture passaging of the clinical samples.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chan, P K" uniqKey="Chan P">P.K. Chan</name></author><author><name sortKey="To, W K" uniqKey="To W">W.K. 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Wu</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Sha Tin</li></settlement><orgName><li>Université chinoise de Hong Kong</li></orgName></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Tang, Julian W" sort="Tang, Julian W" uniqKey="Tang J" first="Julian W." last="Tang">Julian W. Tang</name></noRegion><name sortKey="Chan, Paul K S" sort="Chan, Paul K S" uniqKey="Chan P" first="Paul K. S." last="Chan">Paul K. S. Chan</name><name sortKey="Chan, Paul K S" sort="Chan, Paul K S" uniqKey="Chan P" first="Paul K. S." last="Chan">Paul K. S. Chan</name><name sortKey="Cheung, Jo L K" sort="Cheung, Jo L K" uniqKey="Cheung J" first="Jo L. K." last="Cheung">Jo L. K. Cheung</name><name sortKey="Chu, Ida M T" sort="Chu, Ida M T" uniqKey="Chu I" first="Ida M. T." last="Chu">Ida M. T. Chu</name><name sortKey="Hui, Mamie" sort="Hui, Mamie" uniqKey="Hui M" first="Mamie" last="Hui">Mamie Hui</name><name sortKey="Ip, Margaret" sort="Ip, Margaret" uniqKey="Ip M" first="Margaret" last="Ip">Margaret Ip</name><name sortKey="Peiris, Malik" sort="Peiris, Malik" uniqKey="Peiris M" first="Malik" last="Peiris">Malik Peiris</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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