Fig. 1

Visual summary of T and B cell epitope vaccine prediction and validation. (1) We explored the set of computationally predicted SARS-CoV-2 HLA-I and HLA-II ligands, examining source protein abundance, sequence conservation, coverage of high frequency HLA alleles, and predicted immunogenicity. (2) B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering for sequence conservation, surface accessibility, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. (3) Vaccine selection of 27mers peptides was performed by optimizing population HLA coverage of T cell epitopes, evaluating human/murine MHC ligand co-coverage, as well as examining peptides with optimal coverage of B cell, CD4⁺, and CD8⁺ epitopes. (4) Lastly, validation was performed through comparison against a curated dataset of ~ 1000 observed T cell epitopes from convalescent COVID-19 patients across eight studies, as well as murine ELISA/ELISpot studies using animals vaccinated with synthetic 27mer peptides with human/murine epitope co-coverage