A Broad-Spectrum Multi-Antigen mRNA/LNP-Based Pan-Coronavirus Vaccine Induced Potent Cross-Protective Immunity Against Infection and Disease Caused by Highly Pathogenic and Heavily Spike-Mutated SARS-CoV-2 Variants of Concern in the Syrian Hamster Model
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The first-generation Spike-alone-based COVID-19 vaccines have successfully contributed to reducing the risk of hospitalization, serious illness, and death caused by SARS-CoV-2 infections. However, waning immunity induced by these vaccines failed to prevent immune escape by many variants of concern (VOCs) that emerged from 2020 to 2024, resulting in a prolonged COVID-19 pandemic. We hypothesize that a next-generation Coronavirus (CoV) vaccine incorporating highly conserved non-Spike SARS-CoV-2 antigens would confer stronger and broader cross-protective immunity against multiple VOCs. In the present study, we identified ten non-Spike antigens that are highly conserved in 8.7 million SARS-CoV-2 strains, twenty-one VOCs, SARS-CoV, MERS-CoV, Common Cold CoVs, and animal CoVs. Seven of the 10 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 non-Spike T cell antigens belong to the early expressed Replication and Transcription Complex (RTC) region, when administered to the golden Syrian hamsters, in combination with Spike, as nucleoside-modified mRNA encapsulated in lipid nanoparticles (LNP) (i.e., combined mRNA/LNP-based pan-CoV vaccine): ( i ) Induced high frequencies of lung-resident antigen-specific CXCR5 + CD4 + T follicular helper (T FH ) cells, GzmB + CD4 + and GzmB + CD8 + cytotoxic T cells (T CYT ), and CD69 + IFN-γ + TNFα + CD4 + and CD69 + IFN-γ + TNFα + CD8 + effector T cells (T EFF ); and ( ii ) Reduced viral load and COVID-19-like symptoms caused by various VOCs, including the highly pathogenic B.1.617.2 Delta variant and the highly transmittable heavily Spike-mutated XBB1.5 Omicron sub-variant. The combined mRNA/LNP-based pan-CoV vaccine could be rapidly adapted for clinical use to confer broader cross-protective immunity against emerging highly mutated and pathogenic VOCs.
IMPORTANCE
As of January 2024, over 1500 individuals in the United States alone are still dying from COVID-19 each week despite the implementation of first-generation Spike-alone-based COVID-19 vaccines. The emergence of highly transmissible SARS-CoV-2 variants of concern (VOCs), such as the currently circulating highly mutated BA.2.86 and JN.1 Omicron sub-variants, constantly overrode immunity induced by the first-generation Spike-alone-based COVID-19 vaccines. Here we report a next generation broad spectrum combined multi-antigen mRNA/LNP-based pan-CoV vaccine that consists of nucleoside-modified mRNA encapsulated in lipid nanoparticles (LNP) that delivers three highly conserved non-Spike viral T cell protein antigens together with the Spike protein B-cell antigen. Compared side-by-side to the clinically proven first-generation Spike-alone mRNA/LNP-based vaccine, the combined multi-antigen mRNA/LNP-based pan-CoV vaccine-induced higher frequencies of lung-resident non-Spike antigen-specific T follicular helper (T FH ) cells, cytotoxic T cells (T CYT ), effector T cells (T EFF ) and Spike specific-neutralizing antibodies. This was associated to a potent cross-reactive protection against various VOCs, including the highly pathogenic Delta variant and the highly transmittable heavily Spike-mutated Omicron sub-variants. Our findings suggest an alternative broad-spectrum pan-Coronavirus vaccine capable of ( i ) disrupting the current COVID-19 booster paradigm; ( ii ) outpacing the bivalent variant-adapted COVID-19 vaccines; and ( iii ) ending an apparent prolonged COVID-19 pandemic.
