SARS-CoV genome polymorphism: a bioinformatics study.
Identifieur interne : 002553 ( PubMed/Curation ); précédent : 002552; suivant : 002554SARS-CoV genome polymorphism: a bioinformatics study.
Auteurs : Gordana M. Pavlovi Lazeti ; Nenad S. Miti ; Andrija M. Tomovi ; Mirjana D. Pavlovi ; Milos V. BeljanskiSource :
- Genomics, proteomics & bioinformatics [ 1672-0229 ] ; 2005.
Descripteurs français
- KwdFr :
- Animaux, Biologie informatique, Données de séquences moléculaires, Délétion de séquence, Génome, Humains, Mutation, Phylogénie, Polymorphisme génétique (génétique), Similitude de séquences d'acides aminés, Syndrome respiratoire aigu sévère (génétique), Séquence d'acides aminés, Taïwan, Variation génétique, Virus du SRAS (génétique), Viverridae (génétique).
- MESH :
- génétique : Polymorphisme génétique, Syndrome respiratoire aigu sévère, Virus du SRAS, Viverridae.
- Animaux, Biologie informatique, Données de séquences moléculaires, Délétion de séquence, Génome, Humains, Mutation, Phylogénie, Similitude de séquences d'acides aminés, Séquence d'acides aminés, Taïwan, Variation génétique.
- Wicri :
- geographic : Taïwan.
English descriptors
- KwdEn :
- Amino Acid Sequence, Animals, Computational Biology, Genetic Variation, Genome, Humans, Molecular Sequence Data, Mutation, Phylogeny, Polymorphism, Genetic (genetics), SARS Virus (genetics), Sequence Deletion, Sequence Homology, Amino Acid, Severe Acute Respiratory Syndrome (genetics), Taiwan, Viverridae (genetics).
- MESH :
Abstract
A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a "profile", were determined and discussed ("profile" being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.
DOI: 10.1016/s1672-0229(05)03004-4
PubMed: 16144519
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Gordana M. Pavlovi Lazeti<affiliation><nlm:affiliation>Faculty of Mathematics, University of Belgrade, 11001 Belgrade, Serbia and Montenegro. gordana@matf.bg.ac.yu</nlm:affiliation><wicri:noCountry code="subField">Serbia and Montenegro</wicri:noCountry></affiliation>Le document en format XML
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Pavlovi</name></author><author><name sortKey="Beljanski, Milos V" sort="Beljanski, Milos V" uniqKey="Beljanski M" first="Milos V" last="Beljanski">Milos V. Beljanski</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:16144519</idno><idno type="pmid">16144519</idno><idno type="doi">10.1016/s1672-0229(05)03004-4</idno><idno type="wicri:Area/PubMed/Corpus">002553</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002553</idno><idno type="wicri:Area/PubMed/Curation">002553</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002553</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">SARS-CoV genome polymorphism: a bioinformatics study.</title><author><name sortKey="Pavlovi Lazeti, Gordana M" sort="Pavlovi Lazeti, Gordana M" uniqKey="Pavlovi Lazeti G" first="Gordana M" last="Pavlovi Lazeti">Gordana M. Pavlovi Lazeti</name><affiliation><nlm:affiliation>Faculty of Mathematics, University of Belgrade, 11001 Belgrade, Serbia and Montenegro. gordana@matf.bg.ac.yu</nlm:affiliation><wicri:noCountry code="subField">Serbia and Montenegro</wicri:noCountry></affiliation></author><author><name sortKey="Miti, Nenad S" sort="Miti, Nenad S" uniqKey="Miti N" first="Nenad S" last="Miti">Nenad S. Miti</name></author><author><name sortKey="Tomovi, Andrija M" sort="Tomovi, Andrija M" uniqKey="Tomovi A" first="Andrija M" last="Tomovi">Andrija M. Tomovi</name></author><author><name sortKey="Pavlovi, Mirjana D" sort="Pavlovi, Mirjana D" uniqKey="Pavlovi M" first="Mirjana D" last="Pavlovi">Mirjana D. Pavlovi</name></author><author><name sortKey="Beljanski, Milos V" sort="Beljanski, Milos V" uniqKey="Beljanski M" first="Milos V" last="Beljanski">Milos V. Beljanski</name></author></analytic><series><title level="j">Genomics, proteomics & bioinformatics</title><idno type="ISSN">1672-0229</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Computational Biology</term><term>Genetic Variation</term><term>Genome</term><term>Humans</term><term>Molecular Sequence Data</term><term>Mutation</term><term>Phylogeny</term><term>Polymorphism, Genetic (genetics)</term><term>SARS Virus (genetics)</term><term>Sequence Deletion</term><term>Sequence Homology, Amino Acid</term><term>Severe Acute Respiratory Syndrome (genetics)</term><term>Taiwan</term><term>Viverridae (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Biologie informatique</term><term>Données de séquences moléculaires</term><term>Délétion de séquence</term><term>Génome</term><term>Humains</term><term>Mutation</term><term>Phylogénie</term><term>Polymorphisme génétique (génétique)</term><term>Similitude de séquences d'acides aminés</term><term>Syndrome respiratoire aigu sévère (génétique)</term><term>Séquence d'acides aminés</term><term>Taïwan</term><term>Variation génétique</term><term>Virus du SRAS (génétique)</term><term>Viverridae (génétique)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Taiwan</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Polymorphism, Genetic</term><term>SARS Virus</term><term>Severe Acute Respiratory Syndrome</term><term>Viverridae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Polymorphisme génétique</term><term>Syndrome respiratoire aigu sévère</term><term>Virus du SRAS</term><term>Viverridae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Computational Biology</term><term>Genetic Variation</term><term>Genome</term><term>Humans</term><term>Molecular Sequence Data</term><term>Mutation</term><term>Phylogeny</term><term>Sequence Deletion</term><term>Sequence Homology, Amino Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Biologie informatique</term><term>Données de séquences moléculaires</term><term>Délétion de séquence</term><term>Génome</term><term>Humains</term><term>Mutation</term><term>Phylogénie</term><term>Similitude de séquences d'acides aminés</term><term>Séquence d'acides aminés</term><term>Taïwan</term><term>Variation génétique</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Taïwan</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a "profile", were determined and discussed ("profile" being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16144519</PMID><DateCompleted><Year>2005</Year><Month>11</Month><Day>01</Day></DateCompleted><DateRevised><Year>2019</Year><Month>05</Month><Day>16</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1672-0229</ISSN><JournalIssue CitedMedium="Print"><Volume>3</Volume><Issue>1</Issue><PubDate><Year>2005</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Genomics, proteomics & bioinformatics</Title><ISOAbbreviation>Genomics Proteomics Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>SARS-CoV genome polymorphism: a bioinformatics study.</ArticleTitle><Pagination><MedlinePgn>18-35</MedlinePgn></Pagination><Abstract><AbstractText>A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a "profile", were determined and discussed ("profile" being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pavlović-Lazetić</LastName><ForeName>Gordana M</ForeName><Initials>GM</Initials><AffiliationInfo><Affiliation>Faculty of Mathematics, University of Belgrade, 11001 Belgrade, Serbia and Montenegro. gordana@matf.bg.ac.yu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mitić</LastName><ForeName>Nenad S</ForeName><Initials>NS</Initials></Author><Author ValidYN="Y"><LastName>Tomović</LastName><ForeName>Andrija M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>Pavlović</LastName><ForeName>Mirjana D</ForeName><Initials>MD</Initials></Author><Author ValidYN="Y"><LastName>Beljanski</LastName><ForeName>Milos V</ForeName><Initials>MV</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>China</Country><MedlineTA>Genomics Proteomics Bioinformatics</MedlineTA><NlmUniqueID>101197608</NlmUniqueID><ISSNLinking>1672-0229</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="Y">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="Y">Genome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="N">Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011110" MajorTopicYN="N">Polymorphism, Genetic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017384" MajorTopicYN="N">Sequence Deletion</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017386" MajorTopicYN="N">Sequence Homology, Amino 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