The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

Lele Zhao*, Matthew Hall, Mariateresa de Cesare, George MacIntyre-Cockett, Katrina Lythgoe, Christophe Fraser, David Bonsall, Tanya Golubchik, Luca Ferretti*, The COVID-19 Genomics UK (COG-UK) Consortium, Matthew Bashton, Darren Smith, Andrew Nelson, Gregory R. Young, Clare McCann

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)
24 Downloads (Pure)


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.

Original languageEnglish
Article number20221747
Number of pages9
JournalProceedings of the Royal Society B: Biological Sciences
Issue number1987
Early online date16 Nov 2022
Publication statusPublished - 30 Nov 2022


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