SARS-CoV Genome Polymorphism: A Bioinformatics Study
Identifieur interne : 001027 ( Pmc/Curation ); précédent : 001026; suivant : 001028SARS-CoV Genome Polymorphism: A Bioinformatics Study
Auteurs : Gordana M. Pavlovi Lažeti ; Nenad S. Miti ; Andrija M. Tomovi [Suisse] ; Mirjana D. Pavlovi ; Miloš V. BeljanskiSource :
- Genomics, Proteomics & Bioinformatics [ 1672-0229 ] ; 2005.
Abstract
A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of
Url:
DOI: 10.1016/S1672-0229(05)03004-4
PubMed: 16144519
PubMed Central: 5172477
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Gordana M. Pavlovi Lažeti<affiliation><nlm:aff id="aff0005">Faculty of Mathematics, University of Belgrade, 11001 Belgrade, Serbia and Montenegro</nlm:aff>
<wicri:noCountry code="subfield">Serbia and Montenegro</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="aff0005">Faculty of Mathematics, University of Belgrade, 11001 Belgrade, Serbia and Montenegro</nlm:aff>
<wicri:noCountry code="subfield">Serbia and Montenegro</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="aff0015">Institute of General and Physical Chemistry, 11001 Belgrade, Serbia and Montenegro</nlm:aff>
<wicri:noCountry code="subfield">Serbia and Montenegro</wicri:noCountry>
</affiliation>
<affiliation><nlm:aff id="aff0015">Institute of General and Physical Chemistry, 11001 Belgrade, Serbia and Montenegro</nlm:aff>
<wicri:noCountry code="subfield">Serbia and Montenegro</wicri:noCountry>
</affiliation>
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<front><div type="abstract" xml:lang="en"><p>A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of <bold>genome</bold>
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.</p>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genomics Proteomics Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">Genomics Proteomics Bioinformatics</journal-id>
<journal-title-group><journal-title>Genomics, Proteomics & Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="ppub">1672-0229</issn>
<issn pub-type="epub">2210-3244</issn>
<publisher><publisher-name>Beijing Institute of Genomics, the Chinese Academy of Sciences and the Genetics Society of China. Production and hosting by Elsevier B.V.</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">16144519</article-id>
<article-id pub-id-type="pmc">5172477</article-id>
<article-id pub-id-type="publisher-id">S1672-0229(05)03004-4</article-id>
<article-id pub-id-type="doi">10.1016/S1672-0229(05)03004-4</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>SARS-CoV Genome Polymorphism: A Bioinformatics Study</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="au0005"><name><surname>Pavlović-Lažetić</surname>
<given-names>Gordana M.</given-names>
</name>
<email>gordana@matf.bg.ac.yu</email>
<xref rid="aff0005" ref-type="aff">1</xref>
<xref rid="cor1" ref-type="corresp">*</xref>
</contrib>
<contrib contrib-type="author" id="au0010"><name><surname>Mitić</surname>
<given-names>Nenad S.</given-names>
</name>
<xref rid="aff0005" ref-type="aff">1</xref>
</contrib>
<contrib contrib-type="author" id="au0015"><name><surname>Tomović</surname>
<given-names>Andrija M.</given-names>
</name>
<xref rid="aff0010" ref-type="aff">2</xref>
</contrib>
<contrib contrib-type="author" id="au0020"><name><surname>Pavlović</surname>
<given-names>Mirjana D.</given-names>
</name>
<xref rid="aff0015" ref-type="aff">3</xref>
</contrib>
<contrib contrib-type="author" id="au0025"><name><surname>Beljanski</surname>
<given-names>Miloš V.</given-names>
</name>
<xref rid="aff0015" ref-type="aff">3</xref>
</contrib>
</contrib-group>
<aff id="aff0005"><label>1</label>
Faculty of Mathematics, University of Belgrade, 11001 Belgrade, Serbia and Montenegro</aff>
<aff id="aff0010"><label>2</label>
Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland</aff>
<aff id="aff0015"><label>3</label>
Institute of General and Physical Chemistry, 11001 Belgrade, Serbia and Montenegro</aff>
<author-notes><corresp id="cor1"><label>*</label>
Corresponding author. <email>gordana@matf.bg.ac.yu</email>
</corresp>
</author-notes>
<pub-date pub-type="pmc-release"><day>28</day>
<month>11</month>
<year>2016</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><year>2005</year>
</pub-date>
<pub-date pub-type="epub"><day>28</day>
<month>11</month>
<year>2016</year>
</pub-date>
<volume>3</volume>
<issue>1</issue>
<fpage>18</fpage>
<lpage>35</lpage>
<permissions><copyright-statement>Copyright © 2005 Beijing Institute of Genomics, the Chinese Academy of Sciences and the Genetics Society of China. Production and hosting by Elsevier B.V.</copyright-statement>
<copyright-year>2005</copyright-year>
<copyright-holder>Beijing Institute of Genomics, the Chinese Academy of Sciences and the Genetics Society of China</copyright-holder>
<license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p>
</license>
</permissions>
<abstract id="ab0005"><p>A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of <bold>genome</bold>
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.</p>
</abstract>
<kwd-group id="keys0005"><title>Key words</title>
<kwd>SARS Coronavirus</kwd>
<kwd>single nucleotide polymorphism</kwd>
<kwd>insertions</kwd>
<kwd>deletions</kwd>
<kwd>spike protein</kwd>
<kwd>phylogenesis</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>
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