A study published in the journal Cell Host & Microbe shows that SARS-CoV-2 is evolving in several genomic regions. Researchers from the United States discovered that adaptive evolution is predominantly driven by positively selected changes in the viral spike S1 subunit. This suggests that the virus may be susceptible to antigenic drift.
The original lineages of SARS-CoV-2 have almost totally been replaced by novel variations of concern (VOCs) and variants of interest as the coronavirus disease 2019 (COVID-19) pandemic has progressed (VOIs). These variations have developed with better fitness by gaining positively selected mutations across the viral genome, according to whole-genome sequencing studies. This is known as adaptive evolution, because the virus’s mutations make it more suited for its environment.
During the continuous viral evolutionary process, more than 80% of mutations occur just once, according to the research. The bulk of alterations that arose more than four times were found in the spike S1 subunit. Three of these mutations (Spike:95I, Spike:452R, and ORF1a:3675-3677deletion) had the most significant effect on viral growth rate.
ORF1a:3675-3677deletion, which is responsible for the deletion of three amino acids in Nsp6, has been discovered eight times. Further research revealed that ORF1a:3675-3677deletion is linked to the accumulation of mutations in the spike S1 subunit. These findings suggest that the ORF1a:3675-3677deletion is an adaptive mutation that aids in SARS-CoV-2 evolution.
During the current COVID-19 epidemic, the study reveals the development of SARS-CoV-2. The findings suggest that adaptive evolution, rather than neutral evolution, is linked to better fitness of developing viral strains. In addition, the accumulation of nonsynonymous mutations in the spike S1 subunit has been identified as the fundamental driving mechanism for viral evolution. These findings lead the researchers to believe that, like the influenza virus, SARS-CoV-2 may experience antigenic drift.