Causes and Consequences of Purifying Selection on SARS-CoV-2

Area of Science:

• Virology
• Evolutionary Biology
• Genomics

Background:

• Standard mutation rate estimation methods assume minimal mutation loss between generations.
• Previous SARS-CoV-2 studies suggested no significant within-host selection (Ka/Ks ratio ≈ 1.008).

Purpose of the Study:

• To investigate the extent and nature of intrahost selection in SARS-CoV-2.
• To re-evaluate mutation rate estimation in light of intrahost evolutionary pressures.

Main Methods:

• Analysis of single nucleotide polymorphisms (SNPs) at different genomic sites.
• Modeling of viral mutational and compositional biases.
• Estimation of selection pressures on nonsense, missense, and synonymous mutations.

Main Results:

• Observed SNPs at 4-fold degenerate sites are higher than expected, suggesting mutation rate is 49-67% underestimated.
• Selection against nonsense mutations accounts for only ~10% of "missing" mutations.
• Protein-level filters and codon usage bias significantly contribute to missing mutations, with evidence of selection against synonymous mutations altering human codon usage.

Conclusions:

• SARS-CoV-2 experiences substantial intrahost selection affecting nonsense, missense, and synonymous mutations.
• This selection impacts mutation rate estimations, divergence time calculations, and the potential for viral evolution, including vaccine escape.