Assessing CD8⁺ T cell cross-reactivity to influenza A, B and C virus-derived peptides presented by HLA-B*18:01

Despite the availability of vaccines, influenza viruses still cause substantial morbidity and mortality. This highlights the need for improved vaccines and novel therapeutics. CD8⁺ T cells recognise conserved viral epitopes and can provide broad protection, making them attractive targets for next-generation vaccine design. A key step in this process is to identify T cell epitopes across influenza viruses. Here, we characterised three homologous influenza Polymerase Basic 1 (PB1)-derived peptides from influenza viruses (PB1-A₃₁₀, PB1-B₃₁₀ and PB1-C₃₁₂, respectively) presented by the common, but understudied, HLA-B*18:01 molecule.

We used a thermal melt assay and X-ray crystallography to assess the stability and structural features of each peptide. CD8⁺ T-cell responses were evaluated using intracellular cytokine staining with HLA-B*18:01⁺ samples.

The structures of HLA-B*18:01 presenting each peptide were solved, including the first structure of HLA-B*18:01 presenting a Gammainfluenzavirus (formerly influenza C virus) derived peptide. PB1-C₃₁₂ exhibited a higher thermal stability and a different conformation compared to PB1-A₃₁₀ and PB1-B₃₁₀. CD8⁺ T cell responses varied among samples, with PB1-A₃₁₀ eliciting the strongest activation. Minimal T cell cross-reactivity was observed and was mostly between PB1-A₃₁₀ and PB1-B₃₁₀ likely reflecting shared structural features.

These findings further expand knowledge on peptide presentation by the common HLA-B*18:01 molecule, and the limitations on CD8⁺ T cell cross-recognition of this PB1-derived epitope across influenza lineages. This highlights the importance of more research on cross-lineage T cell cross-reactivity that could inform the design of broadly protective T cell-based vaccines and therapeutics.