In silico conservation and HLA-binding profiles of HMPV F and G protein epitopes: implications for universal vaccine development

BACKGROUND: Human metapneumovirus (HMPV) is a significant cause of respiratory infection, yet no licensed vaccine exists. Variability across viral subgroups, particularly in the attachment (G) protein, can complicate universal design. We assessed the immunogenetic regions in the fusion (F) and G proteins to identify stable vaccine targets. METHODS: We analyzed N = 324 Pittsburgh and N = 655 global HMPV genomes (2017-2022) for genome diversity per viral subgroup. Previously identified epitope sequences were obtained from the Immune Epitope DataBase (IEDB) for F and G proteins and sequence similarity was determined. Using NetMHCpan-4.1, we identified and computed inferred human leukocyte antigen (HLA) binding affinities for 15 epitope variants (1 or 2 substitutions) against universally common human alleles. RESULTS: The F protein was highly conserved across all subgroups (>96% amino acid sequence identity). In the G protein, we identified a conserved epitope cluster (G3-G7) where epitope G7 was present in 91% of A2 genomes. Functional modeling of the G-protein epitope variants revealed that the majority of HLA alleles maintained or gained binding affinity, a subset exhibited diminished binding (escape), suggesting these regions are subject to ongoing antigenic drift. B-genotypes showed fewer retained binders and were notably underrepresented in the current epitope databases. CONCLUSION: The conserved F protein remains an optimal target for neutralization, while the G3-G7 cluster provides a robust secondary target for T-cell mediated immunity. A bivalent vaccine strategy could pair the stable F protein with these high-frequency G-protein epitopes to elicit an immune response. This approach addresses the A2 subgroup, and incorporating B-genotypes through ongoing surveillance and epitope mapping will be essential to achieve comprehensive, multi-antigen coverage across circulating HMPV strains.