Integrated Reiterative Pipeline for Rapid Epitope-Based Vaccine Design Against Alphaviruses

The known and unknown diverse virosphere demonstrated the importance of a rapid and adaptable vaccine development infrastructure in responding to any viral emergence and threat of a pandemic. Over the last century, public health authorities have raised concerns about the emergence or reemergence of arthropod-borne zoonotic agents – particularly of the genus Alphavirus, which significantly impact human and animal health. We demonstrate a rapid and responsive pipeline for B- and T-cell-specific multi-target vaccine development that leverages epitope identification through machine learning, protein modeling, and docking to render a collection of viral proteomes into a ranked list of peptide candidates scored for immunogenicity, allele coverage, solubility, and epitope stability in cleavage and processing. We evaluated epitope reactiveness by microarrays, and molecular dynamics simulations to assess the epitope's correct binding to the target host receptors. Finally, flow cytometry evaluated T-cell antigen-specific immunogenicity on mice and human peripheral blood mononuclear cells (PBMCs). Most epitopes elicited strong T-cell activation with secretion of IFN-ɣ, TNF-α, or IL-2 – varying by species and HLA allele and final candidates were selected by overall scores. Our data support the development of broadly protective pan-alphaviral vaccines and establishing efficient and tunable processes for vaccine development in a global setting.