A dimeric mRNA vaccine based on key-mutant and KP.3 RBDs induces broad-spectrum immunity and protects mice against JN.1 and XDV challenges

The continued antigenic evolution of SARS-CoV-2 Omicron subvariants has progressively eroded vaccine-elicited protective immunity, driving demand for next-generation candidates that confer broad-spectrum protection against phylogenetically divergent strains. Here we report the design and preclinical evaluation of SV, an mRNA vaccine encoding a heterodimeric receptor-binding domain (RBD) antigen. In this construct, a previously optimized monomeric RBD (BSCOV06) is tandemly linked to the KP.3 RBD, presenting two antigenically distinct RBDs within a single immunogen. A two-dose SV regimen in BALB/c mice elicited high-titer neutralizing antibodies with potent cross-reactivity against BA.1, XBB.1.5, JN.1, KP.3, and the phylogenetically distant XDV variant. Integrated B cell receptor (BCR) and T cell receptor (TCR) repertoire profiling revealed that SV drives qualitatively distinct adaptive immune remodeling relative to BSCOV06. Key features included elevated class-switched somatic hypermutation, sustained naive B cell engagement, broad polyclonal T cell expansion, and extensive VJ gene-usage reprogramming across both lymphocyte compartments. In BALB/c and K18-hACE2 transgenic mice, SV conferred robust protection against JN.1 and XDV challenge, substantially reducing pulmonary viral loads and attenuating histopathological injury. Notably, SV achieved immunogenicity and cross-protective efficacy comparable to or exceeding those of the three-dose BSCOV06 schedule, supporting the potential of heterodimeric antigen design. These findings support SV as a promising broad-spectrum COVID-19 vaccine candidate. More broadly, they suggest that heterodimeric RBD architectures incorporating antigenically divergent variants may represent a generalizable platform for countering viral immune evasion, with implications for future SARS-CoV-2 variants and other rapidly evolving viral pathogens.