Evolutionary trajectory of SARS-CoV-2 genome shifts during widespread vaccination and emergence of Omicron variant

Abstract

Understanding the adaptation of SARS-CoV-2 is critical for the development of effective treatments against this exceptionally successful human pathogen. To predict the emergence of new variants that may escape host immunity or increase virulence, it is important to characterize the biological forces driving its evolution. We conducted a comprehensive population genetic study of over thirteen million SARS-CoV-2 genome sequences, collected over a timeframe of ~3 years, to investigate these forces. Our analysis revealed that during the first year of the pandemic (2020 to 2021), the SARS-CoV-2 genome was subject to strong conservation, with only 3.6% of sites under diversifying pressure in the receptor binding domain (RBD) of the Spike protein. However, we observed a sharp increase in the diversification of the RBD during 2021 (8.1% of sites under diversifying pressure up to 2022), indicating selective pressures that promote the accumulation of mutations. This period coincided with broad viral infection and adoption of vaccination worldwide, and we observed the acquisition of mutations that later defined the Omicron lineages in independent SARS-CoV-2 strains, suggesting that diversifying selection at these sites could have led to their fixation in Omicron lineages by convergent evolution. Since the emergence of Omicron, we observed a further decrease in the conservation of structural genes, including M, N, and the spike proteins (13.1% of RBD sites under diversifying pressure up to 2023), and identified new sites defining future potential emerging strains. Our results exhibit that ongoing rapid antigenic evolution continues to produce new high-frequency functional variants. Sites under selection are critical for virus fitness, and currently known T cell epitope sequences are highly conserved. Altogether, our study provides a comprehensive dynamic map of sites under selection and conservation across the entirety of the SARS-CoV-2 genome.