Prefusion-stabilized SARS-CoV-2 spike reshapes antigenic hierarchy and antibody targeting against conserved and occluded epitopes

Receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike contains multiple classes of antibody epitopes that are associated with diverse neutralizing activities. Although both natural infection and vaccination robustly elicit RBD-reactive and neutralizing antibodies, the spike antigenic structures presented to the immune system may differ, leading to qualitative differences in the antibody responses. Using large and well-controlled cohorts, we show that the neutralizing potency index (NPI), calculated as the ratio of neutralizing titer to RBD IgG titer, is approximately fivefold lower in vaccine recipients than in convalescent individuals, independent of disease severity, comorbidities, or demographic factors. This reduction in NPI is associated with enhanced antibody targeting to non-neutralizing, yet conserved and structurally occluded RBD epitope. Molecular dynamics (MD) simulations together with the binding assay demonstrate that the occluded epitope is allosterically exposed by stabilizing mutations introduced into the vaccine spike antigen, a process mediated by a highly extended RBD-up conformation. Collectively, our findings demonstrate that RBD conformational modulation by stabilizing mutations shapes vaccine antigenicity and likely alters the epitope landscape of antibody responses.