Design of Epitope-Focused Vaccines via Epitope Cleavage

The design of epitope-focused immunogens that steer serum antibody responses toward epitopes targeted by broadly neutralizing antibodies (bnAbs) is a promising approach to develop broad-spectrum vaccines against pathogens with high genetic variability. Here, we introduce a strategy called epitope cleavage, which involves “cleaving” an epitope to steer antibodies away from it onto other regions of an antigen. We demonstrated the utility of epitope cleavage using two independent approaches: circular permutation and proteolytic cleavage. We first designed a sarbecovirus vaccine candidate by circularly permuting the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein; we next designed broad Ebolavirus immunogens by inserting the TEV protease cleavage site into the glycan cap of Ebola glycoprotein (GP) for site-specific epitope cleavage. By cleaving variable regions on each antigen, both the circular permuted RBD and cleaved GPs elicited antibodies with enhanced cross-reactivity to related viruses compared to unmodified antigen and exhibited a reduction in antibody responses toward the “cleaved” epitope. Our results present epitope cleavage as a vaccine design strategy that redirects antibody responses without compromising immunogenicity.