A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses.
Amino Acids
/ genetics
Animals
Betacoronavirus
/ classification
China
/ epidemiology
Chiroptera
/ virology
Codon Usage
/ genetics
Communicable Diseases, Emerging
/ virology
Coronavirus Infections
/ epidemiology
Evolution, Molecular
Ferrets
/ virology
Gene Expression Regulation, Viral
/ genetics
Genome, Viral
/ genetics
Genomics
Humans
Mutagenesis
/ genetics
Open Reading Frames
/ genetics
SARS-CoV-2
Viverridae
/ virology
2019-nCoV
Codon usage
Coronavirus
Evolution
SARS-CoV-2
Wuhan
Journal
Virus research
ISSN: 1872-7492
Titre abrégé: Virus Res
Pays: Netherlands
ID NLM: 8410979
Informations de publication
Date de publication:
02 07 2020
02 07 2020
Historique:
received:
29
02
2020
revised:
08
04
2020
accepted:
08
04
2020
pubmed:
16
4
2020
medline:
15
5
2020
entrez:
16
4
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32294518
pii: S0168-1702(20)30168-4
doi: 10.1016/j.virusres.2020.197976
pmc: PMC7152894
pii:
doi:
Substances chimiques
Amino Acids
0
Types de publication
Comparative Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
197976Informations de copyright
Copyright © 2020 Elsevier B.V. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Competing Interest None.
Références
Lancet. 2020 Feb 15;395(10223):514-523
pubmed: 31986261
Lancet. 2020 Feb 22;395(10224):565-574
pubmed: 32007145
J Med Virol. 2020 Mar 11;:
pubmed: 32159237
Curr Opin Microbiol. 2014 Aug;20:69-75
pubmed: 24908561
Virol J. 2004 Nov 17;1:7
pubmed: 15548333
PLoS One. 2012;7(4):e33502
pubmed: 22529893
Biol Direct. 2008 Sep 16;3:38
pubmed: 18796141
BMC Bioinformatics. 2008 Jan 29;9:65
pubmed: 18230160
Virus Res. 2003 Mar;92(1):1-7
pubmed: 12606071
Emerg Microbes Infect. 2020 Dec;9(1):221-236
pubmed: 31987001
Virol J. 2017 Jun 17;14(1):115
pubmed: 28623921
N Engl J Med. 2020 Feb 20;382(8):727-733
pubmed: 31978945
Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544
pubmed: 29790989
Nucleic Acids Res. 1987 Feb 11;15(3):1281-95
pubmed: 3547335
Nature. 2018 Apr;556(7700):255-258
pubmed: 29618817
N Engl J Med. 2012 Nov 8;367(19):1814-20
pubmed: 23075143
Virus Res. 2015 Apr 16;202:41-7
pubmed: 25656063
J Virol Methods. 2020 Mar;277:113806
pubmed: 31911390
Nucleic Acids Res. 2015 Jul 1;43(W1):W566-70
pubmed: 25969447
PLoS One. 2011;6(9):e22594
pubmed: 21949676
Gene. 1990 Mar 1;87(1):23-9
pubmed: 2110097
Virus Res. 2007 Jun;126(1-2):196-206
pubmed: 17434639
Trends Microbiol. 2016 Jun;24(6):490-502
pubmed: 27012512
J Med Virol. 2020 Apr;92(4):418-423
pubmed: 31967327
Virus Res. 2004 May;101(2):155-61
pubmed: 15041183
Nat Rev Microbiol. 2019 Mar;17(3):181-192
pubmed: 30531947
Virology. 2017 Jul;507:1-10
pubmed: 28384506
RNA Biol. 2013 Feb;10(2):211-5
pubmed: 23235488
Virus Res. 2013 Dec 26;178(2):264-71
pubmed: 24091362
Arch Virol. 2011 Jan;156(1):153-60
pubmed: 21069395
Biol Pharm Bull. 2017;40(8):1289-1298
pubmed: 28769010
Viruses. 2019 Feb 20;11(2):
pubmed: 30791586
J Mol Evol. 1986;24(1-2):28-38
pubmed: 3104616
Br Vet J. 1993 Jan-Feb;149(1):51-70
pubmed: 8382546
Nat Med. 2004 Dec;10(12 Suppl):S88-97
pubmed: 15577937
Oncotarget. 2017 Nov 27;8(66):110337-110349
pubmed: 29299151
Vet Res. 2007 Mar-Apr;38(2):281-97
pubmed: 17296157
Virus Res. 2014 Nov 26;193:16-23
pubmed: 24675274
Virology. 2007 Dec 20;369(2):431-42
pubmed: 17881030