RBD-down stabilization of SARS-CoV-2 spike enhances cross-neutralizing antibody responses by redirecting immunodominance toward conserved epitopes

Abstract

The continuous emergence of SARS-CoV-2 variants has enabled partial escape from neutralizing antibodies, necessitating frequent updates of vaccine antigens. These observations motivate vaccine strategies that can redirect antibody responses toward conserved regions of the spike (S) protein. Here, we engineered a SARS-CoV-2 S protein that exclusively maintains its trimeric conformation while concealing the receptor-binding motif (RBM), designated S-cred. In mice, S-cred elicited antibody responses targeting the conserved regions, particularly the subdomain 1 (SD1) and S2 subunits. Neutralizing antibody titers against closely related variants were modestly increased, whereas neutralizing antibody titers against antigenically distant strains remained limited. Additionally, antibodies targeting the receptor-binding domain showed increased recognition of conserved non-RBM regions. Immunization with BA.2-based S-cred improved survival following lethal challenge with a mouse-adapted ancestral SARS-CoV-2 strain. These findings demonstrate that conformational control of the S protein can reproducibly bias immunodominance toward conserved epitopes, providing a framework for next-generation coronavirus vaccine design.