Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution

Abstract

Background and objectives To understand how organisms evolve, it is fundamental to study how mutations emerge and establish. Here, we estimated the rate of mutation accumulation of SARS-CoV-2 in vitro and investigated the repeatability of its evolution when facing a new cell type but no immune or drug pressures. Methodology We performed experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G). After 15 passages in Vero cells and whole genome sequencing, we characterized the spectrum and rate of the emerging mutations and looked for evidences of selection across the genomes of both strains. Results From the frequencies of the mutations accumulated, and excluding the genes with signals of selection, we estimate a spontaneous mutation rate of 1.3x1 0 −6 ± 0.2x1 0 −6 per-base per-infection cycle (mean across both lineages of SARS-CoV-2 ± 2SEM). We further show that mutation accumulation is larger in the CoV-2-D lineage and heterogeneous along the genome, consistent with the action of positive selection on the spike protein, which accumulated five times more mutations than the corresponding genomic average. We also observe the emergence of mutators in the CoV-2-G background, likely linked to mutations in the RNA-dependent RNA polymerase and/or in the error-correcting exonuclease protein. Conclusions and implications These results provide valuable information on how spontaneous mutations emerge in SARS-CoV-2 and on how selection can shape its genome towards adaptation to new environments. LAY SUMMARY Each time a virus replicates inside a cell, errors (mutations) occur. Here, via laboratory propagation in cells originally isolated from the kidney epithelium of African green monkeys, we estimated the rate at which the SARS-CoV-2 virus mutates—an important parameter for understanding how it can evolve within and across humans. We also confirm the potential of its Spike protein to adapt to a new environment and report the emergence of mutators—viral populations where mutations occur at a significantly faster rate.

Contributions of adaptation and purifying selection to SARS-CoV-2 evolution

“…Global epistasis of this nature can exist along side epistasis of specific amino acid changes as for example suggested for the S:N501Y mutation (Martin et al, 2021). Differences in diversification of SARS-CoV-2 with and without the S:D614G mutation where also observed in evolution experiments by Amicone et al (2022), who concluded that these differences were not due to a change in base line mutation rate but had selective origin.…”

“…An evolutionary rate of 6 synonymous changes per year at around 9700 positions corresponds to a per-site evolutionary rate of 6.2 × 10 −4 /site/year or 1.7 × 10 −6 /day, slightly higher than the estimated base-line mutation rate of 1.3 × 10 −6 /day (Amicone et al ., 2022). The total evolutionary rate within variants after mid 2020 (starting with 20E) is in the range of 9-16 changes per year, corresponding to a per site rate of 3 − 5 × 10 −4 /site/year, consistent with recent estimates by Hill et al .…”

COVID-19 Vaccine Booster Strategies in Light of Emerging Viral Variants: Frequency, Timing, and Target Groups

“…Should booster doses not be available or not be accepted particularly as more infectious and potentially more severe subvariants emerge, hospital admissions may once again overwhelm health systems. This compounded with the potential for double epidemics with influenza and respiratory syncytial virus (as has been reported in Australia [ 15 ]) escalates the need for stronger preparedness for such eventualities given the high mutation rate of SARS-CoV-2 [ 16 ]. Therefore, it is prudent for countries to continue targeting and supporting vaccination boosting campaigns for all.…”

Mutation informatics: SARS-CoV-2 receptor-binding domain of the spike protein

“… 10 Recent research showed that the rate of spontaneous mutation in SARS-CoV-2 is 1.3 × 10 –6 ± 0.2 × 10 –6 per base per infection cycle. 11 The repeatedly mutating residues can alter the transmissibility (viral spread) and virulence (viral ability to enter and replicate inside host cell) of SARS-CoV-2 and decrease the efficacy of vaccines/drugs, thus posing serious challenges to the discovery of drugs against multivariant strains of SARS-CoV-2.…”