A Multi-Antigen Broad-Spectrum Coronavirus Vaccine Induces Potent and Durable Cross- Protection Against Infection and Disease Caused by Multiple SARS-CoV-2 Variants

The first generation of Spike-based COVID-19 vaccines has reduced the risk of hospitalization, serious illness, and death caused by SARS-CoV-2 infections. However, waning immunity induced by these vaccines has failed to prevent immune escape, resulting in the emergence of multiple variants of concern (VOCs) and the prolongation of the COVID-19 pandemic. We hypothesize that a next-generation Coronavirus (CoV) vaccine incorporating highly conserved SARS-CoV-2 T cell antigens would confer potent, broad, and long-lasting cross-protective immunity against multiple VOCs. In the present study, we identified ten non-Spike antigens that are common and highly conserved among 8.7 million SARS-CoV-2 strains, twenty-one VOCs, SARS-CoV-1, MERS-CoV, seasonal human common cold CoVs, and animal CoVs. Seven of the ten antigens were preferentially recognized by CD8 ⁺ and CD4 ⁺ T cells from unvaccinated asymptomatic COVID-19 patients, irrespective of VOC infection. Three out of the seven conserved T cell antigens (NSP2, NSP14, and Nucleocapsid), when administered to golden Syrian hamsters: ( i ) Induced high frequencies of lung-resident polyfunctional antigen-specific CXCR5 ⁺ CD4 ⁺ T follicular helper (T _FH ) cells, GzmB ⁺ CD4 ⁺ and GzmB ⁺ CD8 ⁺ cytotoxic T cells (T _CYT ), and CD69 ⁺ IFN-g ⁺ TNFa ⁺ CD4 ⁺ and CD8 ⁺ effector T cells (T _EFF ); ( ii ) Reduced morbidity, viral load, lung pathology, and COVID-19-like symptoms caused by various VOCs, including the highly pathogenic B.1.617.2 Delta variant and the recently circulating KP.3 Omicron variant; ( iii ) Improved protection conferred by spike-alone mRNA, and (iv) Conferred protection that last for more than one year post-vaccination. This multi-antigen CoV vaccine could be adapted for clinical use to confer potent, broad-spectrum, and durable cross-protective immunity against current and future variants of concern.