Bivalent vaccination fails to enhance conserved spike T cell responses across BetaCoronaviruses

Introduction/Rationale: The COVID-19 pandemic highlighted the need for vaccines strategies that elicit broad T cell-mediated immunity against emerging viral families. BetaCoronaviruses - including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome (MERS) and SARS-CoV-2 – pose significant pandemic risks due to their zoonotic potential and genetic diversity. In previous work, we identified conserved Spike T cell epitope regions (S-CTERs) within the ancestral Wuhan S protein sequence that demonstrated strong cross-reactive potential across diverse BetaCoronaviruses.

Methods: Here, we investigated whether bivalent vaccination (Beta + Omicron) preferentially enhances T cell responses targeting CTERs and improves cross-reactivity across Betacoronavirus subgenera. PBMC samples were collected at baseline (day 0) and post-vaccination (day 90) from a cohort of 60 adults receiving either the Pfizer or Moderna bivalent vaccine. Antigen-specific CD4+ and CD8+ T cell responses were assessed using a combined activation-induced marker (AIM) and intracellular cytokine (ICS) assay in a 25-colour-flow cytometry panel.

Results: Overall, bivalent vaccination did not increase the response magnitude to spike or the relative fraction of S-CTER responses within total spike responses. A trend toward increased cytokine polyfunctionality was observed post-vaccination, but no significant differences were observed between pre- and post-vaccination samples across CTER pools derived from multiple BetaCoV isolates.

Conclusion: These findings suggest that spike-based bivalent vaccination alone cannot direct a T-cell focused response to achieve broad immunity across the BetaCoronaviruses family. Incorporation of additional protein sequences will likely be required to shift response toward the CTER approach. Understanding how bivalent vaccinations shape T cell recognition of CTER pools will be critical for advancing universal BetaCoronavirus vaccine design.