Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody

Abstract

In this study, by characterizing several human monoclonal antibodies (mAbs) isolated from single B cells of the COVID-19–recovered individuals in India who experienced ancestral Wuhan strain (WA.1) of SARS-CoV-2 during early stages of the pandemic, we found a receptor binding domain (RBD)–specific mAb 002-S21F2 that has rare gene usage and potently neutralized live viral isolates of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron sublineages (BA.1, BA.2, BA.2.12.1, BA.4, and BA.5) with IC 50 ranging from 0.02 to 0.13 μg/ml. Structural studies of 002-S21F2 in complex with spike trimers of Omicron and WA.1 showed that it targets a conformationally conserved epitope on the outer face of RBD (class 3 surface) outside the ACE2-binding motif, thereby providing a mechanistic insights for its broad neutralization activity. The discovery of 002-S21F2 and the broadly neutralizing epitope it targets have timely implications for developing a broad range of therapeutic and vaccine interventions against SARS-CoV-2 variants including Omicron sublineages.

Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response

“…Next, we revealed that all three mAbs strongly bind spike protein with Kd values in low nM to pM range, by both BLI (Figure S2) and Mesoscale binding assay (Mesoscale Discovery) (Figure 2A). Additionally, in agreement with binding data they all potently neutralize the ancestral WA.1 live virus in a focus-reduction neutralization mNeonGreen (FRNT-mNG) assay (Figure 2B and 2C) (14,15). Taken together, these results confirm high binding affinity and potent neutralizing capacity of all three shared mAbs against the SARS-CoV-2 WA.1 strain.…”

“…Here, we focused on three mAbs that potently neutralize the ancestral WA.1 strain, but differentially neutralize SARS-CoV-2 variants for further characterization. The immunogenetic analysis confirms that all three mAbs were encoded by IGHV3-53/66 and IGHV3-30 genes and were publicly shared (14). While the Cryo-EM structure of all three mAbs showed bivalent spike binding, two mAbs (002-02 and 034-32) targeted the class-1 RBD epitope whereas mAb 002-13 targeted a relatively conserved class-4 epitope.…”

“…While there was no observable difference in the antibody functionality for variants containing mutations that lie outside the mapped epitope surface of a particular antibody, there was a remarkable drop in binding affinity, and neutralization of the antibody when the mutations mapped to the antibody footprint. Most broad neutralizing antibodies recognize all variants antigen that either carry no mutations within their epitopes or the mutations in epitope region are favored by mAb specific molecular interactions as we observed for class-3 mAb 002-S21F2 (14). Here, we show all three mAbs potently neutralized the ancestral WA.1 strain, but differentially neutralize other variants, primarily due to the presence of evading mutations present in their epitope antigenic sites, similar to the other well characterized mAbs recognizing the same epitope classes (Figure 5H) (7).…”

“…We recently reported the isolation of 92 SARS-CoV-2 RBD-specific mAbs from COVID-19 recovered individuals from India during the first wave of the pandemic and identified a broadly neutralizing class-3 antibody (002-S21F2), capable of neutralizing all omicron subvariants (14). Out of 92, three SARS-CoV-2 nAbs (002-13, 002-02 and 034 -32) characterized in this study, belong to shared public antibody responses.…”

“…The light chain of 002-13 contributes minimally to RBD binding, only the CDR2 loop of light chain comes into RBD proximity to make a hydrogen bond with the side chain of RBD residue T415 (Figure 3F). Although 002-13 binds outside the Receptor Binding Motif (RBM) surface, it can sterically block ACE2 binding through its light chain orientation as previously observed in ACE2 competition profiling (14).…”