The 2019/20 SARS-Cov2 pandemic is a modern-day reminder of the impact that novel viral strains can have on a population without pre-existing immunity. The influenza A virus (IAV) has caused five pandemics in the last 150 years and is particularly prone to mutations in the surface glycoprotein haemagglutinin (HA) which is the primary target of the CD4+ T cell and antibody responses.
CD4+ T cells recognise peptide presented by human leukocyte antigen class II (HLA-II) molecules with their T cell receptor (TCR). Although the pHLA-II-TCR interaction is extremely specific, it may cross-recognise similar peptides leading to a cross-reactive response, providing broad protection against different IAV strains. The ability of CD4+ T cells to cross-react with variants of a HA peptide from different IAV strains, especially those not in circulation, is not well understood. Furthermore, individuals expressing certain HLA-II molecules are known to be more susceptible to severe viral infections. In the context of IAV, HLA-DRB1*07:01 has been associated with poor response to the influenza vaccine whereas HLA-DRB1*11:01 has been associated with protection from viruses such as HIV and HCV. An investigation into the molecular basis underlying this association is warranted.
We expanded CD4+ T-cells from healthy donors expressing HLA-DRB1*07:01 or HLA-DRB1*11:01, against a haemagglutinin-peptide and its variants from different IAV strains. Using intracellular cytokine staining and HLA-II tetramer staining combined with multiparameter flow cytometry, we compared the responses of CD4+ T cells in regard to their polyfunctionality, cross-reactivity and memory phenotype. We then used fluorescence polarisation to identify the relative affinity of peptide binding for each of the HA peptide variants to HLA-DRB1*07:01 and HLA-DRB1*11:01. The molecular basis of peptide presentation was then determined using X-ray crystallography. HLA-DRB1*11:01+ individuals were found to have more cross-reactive responses towards HA peptides derived from different IAV strains than HLA-DRB1*07:01+ individuals, and the cross-reacting CD4+ T cells generally had lower polyfunctionality than specific CD4+ T cells. Each of the HA peptides were found to have different relative affinities for HLA-DRB1*07:01 and HLA-DRB1*11:01. Moreover, we provide the first insight into the molecular and functional basis of IAV epitope presentation by different HLA-II molecules.