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Article: Multivariate analyses of codon usage of SARS-CoV-2 and other betacoronaviruses

TitleMultivariate analyses of codon usage of SARS-CoV-2 and other betacoronaviruses
Authors
KeywordsCodon usage analysis
Coronavirus
SARS-CoV-2
WCA
Issue Date2020
Citation
Virus Evolution, 2020, v. 6, n. 1, article no. VEAA032 How to Cite?
AbstractCoronavirus disease 2019 (COVID-19) is a global health concern as it continues to spread within China and beyond. The causative agent of this disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the genus Betacoronavirus, which also includes severe acute respiratory syndrome-related coronavirus (SARSr-CoV) and Middle East respiratory syndrome-related coronavirus (MERSr-CoV). Codon usage of viral genes are believed to be subjected to different selection pressures in different host environments. Previous studies on codon usage of influenza A viruses helped identify viral host origins and evolution trends, however, similar studies on coronaviruses are lacking. In this study, we compared the codon usage bias using global correspondence analysis (CA), within-group CA and between-group CA. We found that the bat RaTG13 virus best matched the overall codon usage pattern of SARS-CoV-2 in orf1ab, spike and nucleocapsid genes, while the pangolin P1E virus had a more similar codon usage in membrane gene. The amino acid usage pattern of SARS-CoV-2 was generally found similar to bat and human SARSr-CoVs. However, we found greater synonymous codon usage differences between SARS-CoV-2 and its phylogenetic relatives on spike and membrane genes, suggesting these two genes of SARS-CoV-2 are subjected to different evolutionary pressures.
Persistent Identifierhttp://hdl.handle.net/10722/345012
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorGu, Haogao-
dc.contributor.authorChu, Daniel K.W.-
dc.contributor.authorPeiris, Malik-
dc.contributor.authorPoon, Leo L.M.-
dc.date.accessioned2024-08-15T09:24:39Z-
dc.date.available2024-08-15T09:24:39Z-
dc.date.issued2020-
dc.identifier.citationVirus Evolution, 2020, v. 6, n. 1, article no. VEAA032-
dc.identifier.urihttp://hdl.handle.net/10722/345012-
dc.description.abstractCoronavirus disease 2019 (COVID-19) is a global health concern as it continues to spread within China and beyond. The causative agent of this disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the genus Betacoronavirus, which also includes severe acute respiratory syndrome-related coronavirus (SARSr-CoV) and Middle East respiratory syndrome-related coronavirus (MERSr-CoV). Codon usage of viral genes are believed to be subjected to different selection pressures in different host environments. Previous studies on codon usage of influenza A viruses helped identify viral host origins and evolution trends, however, similar studies on coronaviruses are lacking. In this study, we compared the codon usage bias using global correspondence analysis (CA), within-group CA and between-group CA. We found that the bat RaTG13 virus best matched the overall codon usage pattern of SARS-CoV-2 in orf1ab, spike and nucleocapsid genes, while the pangolin P1E virus had a more similar codon usage in membrane gene. The amino acid usage pattern of SARS-CoV-2 was generally found similar to bat and human SARSr-CoVs. However, we found greater synonymous codon usage differences between SARS-CoV-2 and its phylogenetic relatives on spike and membrane genes, suggesting these two genes of SARS-CoV-2 are subjected to different evolutionary pressures.-
dc.languageeng-
dc.relation.ispartofVirus Evolution-
dc.subjectCodon usage analysis-
dc.subjectCoronavirus-
dc.subjectSARS-CoV-2-
dc.subjectWCA-
dc.titleMultivariate analyses of codon usage of SARS-CoV-2 and other betacoronaviruses-
dc.typeArticle-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/VE/VEAA032-
dc.identifier.scopuseid_2-s2.0-85091625518-
dc.identifier.volume6-
dc.identifier.issue1-
dc.identifier.spagearticle no. VEAA032-
dc.identifier.epagearticle no. VEAA032-
dc.identifier.eissn2057-1577-
dc.identifier.isiWOS:000546328400031-

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