3.2. Epitope map of SARS-CoV-2 neutralizing monoclonal antibodies
In order to understand the chances of antibody escape phenotype which is mediated by the naturally occurring mutations at the antibody binding epitopes, we selected 74 monoclonal antibodies capable of neutralizing SARS-CoV-2 and its variants. These mAbs have varying levels of neutralization efficacy ranging from modest to highly potent and their binding sites were characterized by structural studies. The antibody binding epitopes of these mAbs span the S1 domain of the spike and the details of the epitopes used in this study are shown in Figure 3 and Supplementary Table 1. We found 65 out of 74 mAbs having epitopes localized to the receptor-binding domain (RBD), whereas few (9 out of 74) are targeting the N-terminal domain (NTD) (Figure 4A). Moreover, most of the potent neutralizing antibodies were mapped to receptor binding motif (RBM), while the NTD targeting antibodies had less neutralizing efficacy than RBD [11].
Next, we analyzed the distribution of epitopes within the S1 domain and found that NTD or RBD neutralizing epitopes overlap with each other (Figure 4A). The NTD directed mAbs target the different loops within S1 (annotated as N1, N2, N3 and N4) and share the epitope sites at N1, N3 and N4. In contrast, one of the selected mAb 2-17 has an additional recognition site at N2 (Figure 4B). Similarly, majority of the RBD binding mAbs recognise spike RBM within the RBD (Figure 4B). These data suggest that both NTD and RBD binding mAbs share conserved recognition region/s independently within spike protein similar to other viruses including HIV, Influenza virus and Middle East respiratory syndrome (MERS) coronavirus, wherein the mAbs targets common conserved recognition sites [19–21].