Mutation rates and selection on synonymous mutations in SARS-CoV-2

Abstract

The COVID-19 pandemic has seen an unprecedented response from the sequencing community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes, we study mutation rates and selective pressures affecting the virus. Understanding the processes and effects of mutation and selection has profound implications for the study of viral evolution, for vaccine design, and for the tracking of viral spread. We highlight and address some common genome sequence analysis pitfalls that can lead to inaccurate inference of mutation rates and selection, such as ignoring skews in the genetic code, not accounting for recurrent mutations, and assuming evolutionary equilibrium. We find that two particular mutation rates, G→U and C→U, are similarly elevated and considerably higher than all other mutation rates, causing the majority of mutations in the SARS-CoV-2 genome, and are possibly the result of APOBEC and ROS activity. These mutations also tend to occur many times at the same genome positions along the global SARS-CoV-2 phylogeny (i.e., they are very homoplasic). We observe an effect of genomic context on mutation rates, but the effect of the context is overall limited. While previous studies have suggested selection acting to decrease U content at synonymous sites, we bring forward evidence suggesting the opposite.

A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2

“…Consistent with previous observations 9,16 , a large fraction of the 1,552 homoplasies we detect (60%) derive from C→T changes likely caused by host anti-viral RNA editing machinery 14,15,17 (Supplementary Table S2, Supplementary Figure S2). We detect a significant genome-wide excess of synonymous recurrent mutations compared to non-synonymous changes (Wilcoxon p <1×10 −6 ), a trend largely driven by patterns over the largest open reading frame: ORF1ab (Supplementary Figure S3).…”

Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA

“…The oxoguanine bases formed are copied as adenine, creating G->T transversions. As ROSs may also target single-stranded RNA, the production of ROSs on viral infections [36] may potentially account for its previously described over-representation of G->U tranversions in SARS-CoV-2 sequences [15][16][17]. We found that higher frequencies of G->U compared to reverse (U->G) or complement (C->A) mutations were more widely found in coronaviruses but broadly absent in the other RNA viruses analysed in the study (S1 Fig) . The presence of ROS is not clearly associated with damage to other bases, such as modifications of cytidines that would template the observed excess of C->U transitions.…”

“…For example, APOBEC3G editing of the single stranded DNA generated by reverse transcription of retroviruses generates a damaged proviral copy unable to direct further retroviral replication [29,30,40]. There has been extensive discussion over whether the observed overrepresentation of C->U transitions in SARS-CoV-2 is driven by one or more of the APOBEC proteins [12][13][14][15][16][17][18]. The current study shows a similar over-representation of C->U changes in the subset of RNA viruses that possessed structured genomes, including other coronaviruses; these finding would therefore predict a strikingly wider breadth of the antiviral activity of this pathway than is currently recognised.…”

“…Of these, the best characterised are the interferon-inducible isoform of adenosine deaminase acting on RNA type 1 (ADAR1) [10] that targets RNA viruses during replication, and members of the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) family [11]. Although hitherto generally considered as an antiviral pathway primarily active against retroviruses and retroelements, there has been considerable discussion of whether the over-representation of C->U transitions observed in genomic sequences of SARS coronavirus 2 (SARS-CoV-2), rubella virus (RUBV) and potentially other mammalian RNA viruses might originate from a similar process for RNA editing by one or more APOBEC-related deaminases [12][13][14][15][16][17][18].…”

Small-Angle X-ray Scattering Models of APOBEC3B Catalytic Domain in a Complex with a Single-Stranded DNA Inhibitor

“…In humans there are seven A3 enzymes, APOBEC3A-APOBEC3H (A3A-A3H, excluding A3E), which have diverged and expanded from a single enzyme to provide protection against a range of exogenous retroviruses, DNA-based parasites, and endogenous retroelements [1,3,4]. However, misregulation of several A3 family members, in particular the mutagenic actions of A3A, A3B, and A3G, are exploited by viruses (including SARS-CoV-2) [5][6][7] and cancer cells to enhance their rate of evolution, leading to detrimental outcomes by their escaping adaptive immune responses and becoming drug resistant [8][9][10][11][12][13][14]. The A3 members exist as either single-domain enzymes (A3A, A3C, and A3H) or double-domain enzymes (A3B, A3G, A3D, and A3F) made up of two tandem homologous domains with a short flexible linker [15][16][17].…”