期刊
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
卷 289, 期 1987, 页码 -出版社
ROYAL SOC
DOI: 10.1098/rspb.2022.1747
关键词
SARS-CoV-2; antigenomes; mutational spectrum; RNA editing
资金
- Medical Research Council (MRC) part of UK Research & Innovation (UKRI)
- National Institute of Health Research (NIHR) [MC_PC_19027]
- Genome Research Limited
- Li Ka Shing Foundation
- Wellcome Trust [203141/Z/16/Z]
- NIHR Oxford BRC
The raw material for viral evolution comes from intra-host mutations during replication, transcription, or post-transcription. This study explores the mutational spectrum of SARS-CoV-2 and reveals differences in mutation patterns between the negative and positive strands, potentially influenced by host factors.
The raw material for viral evolution is provided by intra-host mutations occurring during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense 'antigenomes' acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the mutational spectrum of SARS-CoV-2 (sub)genomic and anti(sub)genomic RNA. We use a high-quality deep sequencing dataset produced using a quantitative strand-aware sequencing method, controlled for artefacts and sequencing errors, and scrutinized for accurate detection of within-host diversity. The nucleotide differences between negative- and positive-sense strand consensus vary between patients and do not show dependence on age or sex. Similarities and differences in mutational patterns between within-host minor variants on the two RNA strands suggested strand-specific mutations or editing by host deaminases and oxidative damage. We observe generally neutral and slight negative selection on the negative strand, contrasting with purifying selection in ORF1a, ORF1b and S genes of the positive strand of the genome.
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