A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES
Identifieur interne : 003C75 ( Ncbi/Merge ); précédent : 003C74; suivant : 003C76A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES
Auteurs : Fernando L. Tort [Uruguay] ; Matías Castells [Uruguay] ; Juan Cristina [Uruguay]Source :
- Virus Research [ 0168-1702 ] ; 2020.
Abstract
A comprehensive genome and codon usage analysis of SARS-CoV-2 was performed. SARS-CoV-2 has a distinct genome composition in relation to other βCoV strains. The overall codon usage in SARS-CoV-2 is slightly biased. Most of the highly frequent codons are A- and U-ending codons. Different codon preferences in SARS-CoV-2 genes in relation to human ones were found. These differences are due to codon usage preferences.
Url:
DOI: 10.1016/j.virusres.2020.197976
PubMed: NONE
PubMed Central: 7152894
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PMC:7152894Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES</title>
<author><name sortKey="Tort, Fernando L" sort="Tort, Fernando L" uniqKey="Tort F" first="Fernando L." last="Tort">Fernando L. Tort</name>
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<author><name sortKey="Castells, Matias" sort="Castells, Matias" uniqKey="Castells M" first="Matías" last="Castells">Matías Castells</name>
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<author><name sortKey="Cristina, Juan" sort="Cristina, Juan" uniqKey="Cristina J" first="Juan" last="Cristina">Juan Cristina</name>
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<series><title level="j">Virus Research</title>
<idno type="ISSN">0168-1702</idno>
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<front><div type="abstract" xml:lang="en"><title>Highlights</title>
<p><list list-type="simple" id="lis0005"><list-item id="lsti0005"><label>•</label>
<p id="par0005">A comprehensive genome and codon usage analysis of SARS-CoV-2 was performed.</p>
</list-item>
<list-item id="lsti0010"><label>•</label>
<p id="par0010">SARS-CoV-2 has a distinct genome composition in relation to other βCoV strains.</p>
</list-item>
<list-item id="lsti0015"><label>•</label>
<p id="par0015">The overall codon usage in SARS-CoV-2 is slightly biased.</p>
</list-item>
<list-item id="lsti0020"><label>•</label>
<p id="par0020">Most of the highly frequent codons are A- and U-ending codons.</p>
</list-item>
<list-item id="lsti0025"><label>•</label>
<p id="par0025">Different codon preferences in SARS-CoV-2 genes in relation to human ones were found.</p>
</list-item>
<list-item id="lsti0030"><label>•</label>
<p id="par0030">These differences are due to codon usage preferences.</p>
</list-item>
</list>
</p>
</div>
</front>
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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">Virus Res</journal-id>
<journal-id journal-id-type="iso-abbrev">Virus Res</journal-id>
<journal-title-group><journal-title>Virus Research</journal-title>
</journal-title-group>
<issn pub-type="ppub">0168-1702</issn>
<issn pub-type="epub">1872-7492</issn>
<publisher><publisher-name>Elsevier B.V.</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmc">7152894</article-id>
<article-id pub-id-type="publisher-id">S0168-1702(20)30168-4</article-id>
<article-id pub-id-type="doi">10.1016/j.virusres.2020.197976</article-id>
<article-id pub-id-type="publisher-id">197976</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="aut0005"><name><surname>Tort</surname>
<given-names>Fernando L.</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
<xref rid="fn0005" ref-type="fn">1</xref>
</contrib>
<contrib contrib-type="author" id="aut0010"><name><surname>Castells</surname>
<given-names>Matías</given-names>
</name>
<xref rid="aff0005" ref-type="aff">a</xref>
<xref rid="fn0005" ref-type="fn">1</xref>
</contrib>
<contrib contrib-type="author" id="aut0015"><name><surname>Cristina</surname>
<given-names>Juan</given-names>
</name>
<email>cristina@cin.edu.uy</email>
<xref rid="aff0010" ref-type="aff">b</xref>
<xref rid="cor0005" ref-type="corresp">⁎</xref>
</contrib>
</contrib-group>
<aff id="aff0005"><label>a</label>
Laboratorio de Virología Molecular, Sede Salto, Centro Universitario Regional, Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay</aff>
<aff id="aff0010"><label>b</label>
Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay</aff>
<author-notes><corresp id="cor0005"><label>⁎</label>
Corresponding author. <email>cristina@cin.edu.uy</email>
</corresp>
<fn id="fn0005"><label>1</label>
<p id="npar0015">These authors contributed equally to this work.</p>
</fn>
</author-notes>
<pub-date pub-type="pmc-release"><day>12</day>
<month>4</month>
<year>2020</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="epub"><day>12</day>
<month>4</month>
<year>2020</year>
</pub-date>
<elocation-id>197976</elocation-id>
<history><date date-type="received"><day>29</day>
<month>2</month>
<year>2020</year>
</date>
<date date-type="rev-recd"><day>8</day>
<month>4</month>
<year>2020</year>
</date>
<date date-type="accepted"><day>8</day>
<month>4</month>
<year>2020</year>
</date>
</history>
<permissions><copyright-statement>© 2020 Elsevier B.V. All rights reserved.</copyright-statement>
<copyright-year>2020</copyright-year>
<copyright-holder></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 abstract-type="author-highlights" id="abs0005"><title>Highlights</title>
<p><list list-type="simple" id="lis0005"><list-item id="lsti0005"><label>•</label>
<p id="par0005">A comprehensive genome and codon usage analysis of SARS-CoV-2 was performed.</p>
</list-item>
<list-item id="lsti0010"><label>•</label>
<p id="par0010">SARS-CoV-2 has a distinct genome composition in relation to other βCoV strains.</p>
</list-item>
<list-item id="lsti0015"><label>•</label>
<p id="par0015">The overall codon usage in SARS-CoV-2 is slightly biased.</p>
</list-item>
<list-item id="lsti0020"><label>•</label>
<p id="par0020">Most of the highly frequent codons are A- and U-ending codons.</p>
</list-item>
<list-item id="lsti0025"><label>•</label>
<p id="par0025">Different codon preferences in SARS-CoV-2 genes in relation to human ones were found.</p>
</list-item>
<list-item id="lsti0030"><label>•</label>
<p id="par0030">These differences are due to codon usage preferences.</p>
</list-item>
</list>
</p>
</abstract>
<abstract id="abs0010"><p>An outbreak of atypical pneumonia caused by a novel <italic>Betacoronavirus</italic>
(βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences.</p>
</abstract>
<kwd-group id="kwd0005"><title>Keywords</title>
<kwd>Coronavirus</kwd>
<kwd>evolution</kwd>
<kwd>codon usage</kwd>
<kwd>Wuhan</kwd>
<kwd>2019-nCoV</kwd>
<kwd>SARS-CoV-2</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Uruguay</li>
</country>
</list>
<tree><country name="Uruguay"><noRegion><name sortKey="Tort, Fernando L" sort="Tort, Fernando L" uniqKey="Tort F" first="Fernando L." last="Tort">Fernando L. Tort</name>
</noRegion>
<name sortKey="Castells, Matias" sort="Castells, Matias" uniqKey="Castells M" first="Matías" last="Castells">Matías Castells</name>
<name sortKey="Cristina, Juan" sort="Cristina, Juan" uniqKey="Cristina J" first="Juan" last="Cristina">Juan Cristina</name>
</country>
</tree>
</affiliations>
</record>
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