Multi-antigen coronavirus vaccine induces potent and durable cross-protection against multiple SARS-CoV-2 variants

The first-generation Spike-based COVID-19 vaccines reduced the risk of hospitalization, serious illness, and death from SARS-CoV-2 infections. However, waning immunity failed to prevent immune escape, resulting in multiple variants of concern (VOCs) and prolonging the pandemic. We hypothesize that next-generation CoV vaccines incorporating highly conserved SARS-CoV-2 T cell antigens would confer potent, broad, long-lasting cross-protective immunity against multiple VOCs. In this study, we identified 10 non-Spike antigens common and highly conserved across 8.7 million SARS-CoV-2 strains, prior VOCs, SARS-CoV-1, MERS-CoV, seasonal human cold CoVs, and animal CoVs. Seven antigens were preferentially recognized by CD8⁺ and CD4⁺ T cells from unvaccinated asymptomatic COVID-19 patients, irrespective of VOC. Three conserved antigens (NSP2, NSP14, Nucleoprotein) administered to golden Syrian hamsters: (i) induced high frequencies of lung-resident polyfunctional CXCR5⁺CD4⁺ T_FH cells, GzmB⁺CD4⁺/CD8⁺ cytotoxic T cells, and CD69⁺IFN-γ⁺TNFα⁺CD4⁺/CD8⁺ effector T cells; (ii) reduced morbidity, viral load, lung pathology, and COVID-19-like symptoms from various VOCs, including the pathogenic B.1.617.2 Delta and the recent KP.3 Omicron variants; (iii) improved protection conferred by spike-alone mRNA; and (iv) conferred protection that lasted for more than 1 year. This multi-antigen CoV vaccine could provide potent, broad-spectrum, and durable cross-protective immunity against current and future variants of concern in the clinic.