Virus Res. A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES

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Virus Res. 2020 Apr 12:197976. doi: 10.1016/j.virusres.2020.197976. [Epub ahead of print]
A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES.


Tort FL¹, Castells M¹, Cristina J².

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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.
Copyright ? 2020. Published by Elsevier B.V.



KEYWORDS:

2019-nCoV; Coronavirus; SARS-CoV-2; Wuhan; codon usage; evolution


PMID:32294518PMCID:PMC7152894DOI:10.1016/j.virusres.2020.197976
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