3.4. Spike mutations and its role in emergence of antibody escape phenotypes
The mutations at the antibody binding sites and their conservation within the NTD or RBD raises the chances of escape from neutralizing antibodies through naturally occurring spike mutations. Here, we found several mutations in the antibody binding sites in either NTD or RBD with at least one variation in either of the analyzed lineages (Alpha, Beta, Gamma, Delta or Omicron). Notably, the Omicron variant (BA.1 and BA.2) showed the highest mutations (20 aa and-18 aa respectively) at different mAb binding epitopes (Figure 4A). These data are consistent with the recent experimental evidence which suggests the decreased neutralization efficacy of few monoclonal antibodies against the Omicron variant [22]. Similarly, majority of the antibody binding epitopes are highly mutated in different SARS-CoV-2 variants. The highest mutations were found in the epitopes of highly neutralizing mAbs (4-10 aa changes) whereas, less neutralizing antibodies were not affected by mutations in either of the variants. Interestingly, 5 out of 74 mAb binding sites had no mutations in the SARS-CoV-2 variants, but these mAbs have less neutralization potential, which predicts the chances of a natural selection based on antibody neutralization of SARS-CoV-2 (Figure 4A). In addi-tion, analysis of the Kd (dissociation constant) and IC50 values of the mAbs suggest a strong binding affinity to wildtype spike protein. However, the mAb binding affinity has decreased with respect to the spike variants of SARS-CoV-2 and the IC50 values have increased which shows the potential chances of escape from neutralizing anti-bodies (Supplementary Table 2). The decrease in affinity of mAbs towards the spike variants is clearly demonstrated by the increased Kd and IC50 values of mAbs including the well characterized REGN10933, LY-CoV555, LY-CoV016, and REGN10987. The data suggest that consequences in host adaptation along with other factors including im-mune pressure might trigger the chances of emergence of antibody escape variants with increased tropism and transmissibility.