mRNA Vaccines Targeting the Conserved SARS-CoV-2 Fusion Machinery Elicit Cross-Variant and Robust Immunity

Despite the gradual waning of global interest in SARS-CoV-2, the continued evolution and emergence of viral variants underscore the need for broadly protective vaccines. Vaccines targeting the highly mutable S1 subunit of the spike protein have shown limited breadth of protection, whereas conserved regions within the S2 fusion machinery remain critical targets for the development of vaccines effective against future variants. This study evaluated two mRNA-lipid nanoparticle (mRNA-LNP) vaccines encoding HR121, a conserved HR1-HR2-HR1 fusion-intermediate immunogen, in comparison with a recombinant HR121 protein vaccine.

Two mRNA vaccine candidates, TM-HR121 and Fc-HR121, were designed to present HR121 through distinct antigen presentation strategies by incorporating a transmembrane anchor or an IgG Fc domain, respectively. Immunogenicity and protective efficacy were assessed in New Zealand White rabbits, BALB/c mice, and Golden Syrian hamsters.

Both mRNA vaccines elicited robust HR121-specific binding antibody responses and broad neutralizing activity against seven SARS-CoV-2 pseudoviruses in rabbits. In mice, the mRNA vaccines induced higher peak IgG titers, a more balanced IgG1/IgG2a profile, stronger antigen-specific IFN-γ responses, and enhanced T-cell responses compared with the recombinant protein vaccine, while maintaining detectable IL-4 responses. In hamsters, immunization with the HR121 mRNA vaccines significantly reduced lung viral RNA levels and attenuated pulmonary pathology and nucleocapsid antigen expression following authentic SARS-CoV-2 challenge.

HR121-based mRNA-LNP vaccines successfully elicited cross-variant humoral and cellular immune responses and conferred protective efficacy in small-animal models. These findings support HR121 mRNA-LNP vaccines as a promising strategy for the development of broadly protective coronavirus vaccines targeting conserved S2 fusion epitopes.