Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology

Abstract

Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms

“…Three out of eight S2M11 heavy chain residues that are mutated relative to germline contribute to epitope recognition (Ile54, Thr77 and Phe102) whereas none of the two light chain mutated residues participate in RBD binding. The observation that all particle images correspond to closed S trimers when bound to S2M11 contrasts with our previous finding of ~50%/50% of trimers closed or with one RBD open in the absence of bound mAb (6) or in complex with S309 (21) or S2H13 (28), which do not select for any specific RBD conformation. Based on these data, we conclude that S2M11 stabilizes the closed conformation of the S trimer by interacting with a composite epitope including two neighboring RBDs (from two distinct protomers) that are close to each other in the closed state but spread apart upon RBD opening (6) ( fig.…”

“…We recently described that the magnitude of Ab responses to SARS-CoV-2 S and nucleoprotein and neutralizing Ab titers correlate with clinical scores (28). The SARS-CoV-2 RBD is the main target of potent neutralizing S-specific Abs in COVID-19 patient sera or plasma samples, thereby focusing most of the selective pressure imposed by the humoral immune response on this domain (23,28).…”

“…The concave S2E12 paratope recognizes the convex RBM tip through electrostatic and van der Waals interactions (Fig. 2, C (22,28,37).…”

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

“…Blue data points represent 501 human antibodies complexed with protein antigens. IMGT-numbered structures (resolutions of 3.5 Å or better) were downloaded from the Structural Antibody Database (SAbDab) [68][69][70][71] and BSAs were calculated using PDBePISA 66 . BSAs from antibody structures with identical or nearidentical heavy chain sequences were averaged to give a single point on the graph.…”

Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be

“…Through the determination of the structure of six mABs, Piccoli et al, were able to map sites within the RBD that are predominantly recognized by the analyzed neutralizing antibodies. The study found that the dominant neutralizing strategy adopted by these antibodies includes binding to the receptor binding motif (RBM) which is only exposed in the S trimer open state or binding to a second site, which is also exposed in the closed state (Piccoli et al, 2020). Epitopes targeted by the isolated antibodies have been precisely identified through determination of the structure of the S protein-candidate antibody complex with cryo-EM and X-ray crystallography.…”