A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES.
Identifieur interne : 000108 ( PubMed/Corpus ); précédent : 000107; suivant : 000109A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES.
Auteurs : Fernando L. Tort ; Matías Castells ; Juan CristinaSource :
- Virus research [ 1872-7492 ] ; 2020.
Abstract
An outbreak of atypical pneumonia caused by a novel Betacoronavirus (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.
DOI: 10.1016/j.virusres.2020.197976
PubMed: 32294518
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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><affiliation><nlm:affiliation>Laboratorio de Virología Molecular, Sede Salto, Centro Universitario Regional, Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay.</nlm:affiliation></affiliation></author><author><name sortKey="Castells, Matias" sort="Castells, Matias" uniqKey="Castells M" first="Matías" last="Castells">Matías Castells</name><affiliation><nlm:affiliation>Laboratorio de Virología Molecular, Sede Salto, Centro Universitario Regional, Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay.</nlm:affiliation></affiliation></author><author><name sortKey="Cristina, Juan" sort="Cristina, Juan" uniqKey="Cristina J" first="Juan" last="Cristina">Juan Cristina</name><affiliation><nlm:affiliation>Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay. Electronic address: cristina@cin.edu.uy.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32294518</idno><idno type="pmid">32294518</idno><idno type="doi">10.1016/j.virusres.2020.197976</idno><idno type="wicri:Area/PubMed/Corpus">000108</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000108</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">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><affiliation><nlm:affiliation>Laboratorio de Virología Molecular, Sede Salto, Centro Universitario Regional, Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay.</nlm:affiliation></affiliation></author><author><name sortKey="Castells, Matias" sort="Castells, Matias" uniqKey="Castells M" first="Matías" last="Castells">Matías Castells</name><affiliation><nlm:affiliation>Laboratorio de Virología Molecular, Sede Salto, Centro Universitario Regional, Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay.</nlm:affiliation></affiliation></author><author><name sortKey="Cristina, Juan" sort="Cristina, Juan" uniqKey="Cristina J" first="Juan" last="Cristina">Juan Cristina</name><affiliation><nlm:affiliation>Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay. Electronic address: cristina@cin.edu.uy.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Virus research</title><idno type="eISSN">1872-7492</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">An outbreak of atypical pneumonia caused by a novel Betacoronavirus (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.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32294518</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>17</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1872-7492</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Apr</Month><Day>12</Day></PubDate></JournalIssue><Title>Virus research</Title><ISOAbbreviation>Virus Res.</ISOAbbreviation></Journal><ArticleTitle>A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES.</ArticleTitle><Pagination><MedlinePgn>197976</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0168-1702(20)30168-4</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.virusres.2020.197976</ELocationID><Abstract><AbstractText>An outbreak of atypical pneumonia caused by a novel Betacoronavirus (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.</AbstractText><CopyrightInformation>Copyright © 2020. Published by Elsevier B.V.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tort</LastName><ForeName>Fernando L</ForeName><Initials>FL</Initials><AffiliationInfo><Affiliation>Laboratorio de Virología Molecular, Sede Salto, Centro Universitario Regional, Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Castells</LastName><ForeName>Matías</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Laboratorio de Virología Molecular, Sede Salto, Centro Universitario Regional, Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cristina</LastName><ForeName>Juan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay. Electronic address: cristina@cin.edu.uy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Virus Res</MedlineTA><NlmUniqueID>8410979</NlmUniqueID><ISSNLinking>0168-1702</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">2019-nCoV</Keyword><Keyword MajorTopicYN="N">Coronavirus</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2</Keyword><Keyword MajorTopicYN="N">Wuhan</Keyword><Keyword MajorTopicYN="N">codon usage</Keyword><Keyword MajorTopicYN="N">evolution</Keyword></KeywordList><CoiStatement>Declaration of Competing Interest None.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate 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