Characterization of SARS-CoV-2 Mutational Signatures from 1.5+ Million Raw Sequencing Samples.
APOBEC
SARS-CoV-2
mutational signatures
variants
Journal
Viruses
ISSN: 1999-4915
Titre abrégé: Viruses
Pays: Switzerland
ID NLM: 101509722
Informations de publication
Date de publication:
20 12 2022
20 12 2022
Historique:
received:
07
10
2022
revised:
01
12
2022
accepted:
15
12
2022
entrez:
21
1
2023
pubmed:
22
1
2023
medline:
25
1
2023
Statut:
epublish
Résumé
We present a large-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) substitutions, considering 1,585,456 high-quality raw sequencing samples, aimed at investigating the existence and quantifying the effect of mutational processes causing mutations in SARS-CoV-2 genomes when interacting with the human host. As a result, we confirmed the presence of three well-differentiated mutational processes likely ruled by reactive oxygen species (ROS), apolipoprotein B editing complex (APOBEC), and adenosine deaminase acting on RNA (ADAR). We then evaluated the activity of these mutational processes in different continental groups, showing that some samples from Africa present a significantly higher number of substitutions, most likely due to higher APOBEC activity. We finally analyzed the activity of mutational processes across different SARS-CoV-2 variants, and we found a significantly lower number of mutations attributable to APOBEC activity in samples assigned to the Omicron variant.
Identifiants
pubmed: 36680048
pii: v15010007
doi: 10.3390/v15010007
pmc: PMC9864147
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Déclaration de conflit d'intérêts
Authors declare that they have no competing interest.
Références
PLoS Comput Biol. 2021 Jun 28;17(6):e1009119
pubmed: 34181655
Int J Infect Dis. 2022 Jan;114:268-272
pubmed: 34863925
Am J Trop Med Hyg. 2020 Aug;103(2):564-569
pubmed: 32484156
Viruses. 2015 Jun 11;7(6):2999-3018
pubmed: 26110583
Cell Chem Biol. 2018 Jan 18;25(1):36-49
pubmed: 29153851
Nat Rev Microbiol. 2019 Mar;17(3):181-192
pubmed: 30531947
Int J Infect Dis. 2020 Feb;91:264-266
pubmed: 31953166
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
Nat Med. 2021 Aug;27(8):1385-1394
pubmed: 34272499
Nat Biotechnol. 2008 Oct;26(10):1089-90
pubmed: 18846074
AIDS Rev. 2006 Jul-Sep;8(3):148-57
pubmed: 17078485
Nat Med. 2020 Jun;26(6):842-844
pubmed: 32398875
Virology. 2021 Apr;556:62-72
pubmed: 33545556
J Med Virol. 2022 May;94(5):1825-1832
pubmed: 35023191
Nat Med. 2021 Aug;27(8):1338-1339
pubmed: 34272500
Cell. 2022 Feb 3;185(3):467-484.e15
pubmed: 35081335
Vaccines (Basel). 2022 Mar 11;10(3):
pubmed: 35335059
Virus Evol. 2021 Jul 30;7(2):veab064
pubmed: 34527285
iScience. 2021 Feb 19;24(2):102116
pubmed: 33532709
BMC Med Genet. 2019 Jan 19;20(1):21
pubmed: 30660178
Patterns (N Y). 2021 Mar 12;2(3):100212
pubmed: 33728416
Nat Rev Microbiol. 2021 Mar;19(3):141-154
pubmed: 33024307
STAR Protoc. 2022 Sep 16;3(3):101513
pubmed: 35779264
Virus Evol. 2022 Mar 24;8(1):veac026
pubmed: 35371557