The Spike protein of SARS-coV2 19B (S) clade mirrors critical features of viral adaptation and coevolution

Abstract

Pathogens including viruses evolve in tandem with diversity in their animal and human hosts. For SARS-coV2, the focus is generally for understanding such coevolution on the virus spike protein since it demonstrates high mutation rates compared to other genome regions, particularly in the receptor-binding domain (RBD). Viral sequences of the SARS-coV2 19B (S) clade and variants of concern from different continents, were investigated, with a focus on the A.29 lineage which presented with different mutational patterns within the 19B (S) lineages in order to learn more about how SARS-coV2 may have evolved and adapted to widely diverse populations globally. Results indicated that SARS-coV2 went through evolutionary constrains and intense selective pressure, particularly in Africa. This was manifested in a departure from neutrality with excess nonsynonymous mutations and a negative Tajima D consistent with rapid expansion and directional selection as well as deletion and deletion-frameshifts in the N-terminal domain (NTD region) of the spike protein. In conclusion, viral transmission during epidemics through population of diverse genomic structure and marked complexity may be a significant factor for the virus to acquire distinct patterns of mutations within these populations in order to ensure its survival and fitness, hence in the emergence of novel variants and strains. ImportanceIn this study, we justify the fact that the viruss evolution varies across continents, with each continent showing different amounts and patterns of mutations and deletions, which was manifested in the 19B (S) clade of SARS-coV2, particularly in areas with high population complexity, such as Africa, despite the low rate of sampling and data sharing. The findings show that SARS-coV2 was subject to evolutionary constraints and intense selective pressure. This study will contribute to the scanty amount of research on the SARS-coV2 coevolution and adaptation, in which the host variation is of great significance in understanding the intricacies of viral host coevolution.