Background There is an urgent need for a vaccine with efficacy against SARS-CoV-2. We hypothesize that peptide vaccines containing epitope regions optimized for concurrent B cell, CD4+ T cell, and CD8+ T cell stimulation would drive both humoral and cellular immunity with high specificity, potentially avoiding undesired effects such as antibody-dependent enhancement (ADE) (figure 1). Leveraging methods initially developed for prediction of tumor-specific antigen targets, we combine computational prediction of T cell epitopes, recently published B cell epitope mapping studies, and epitope accessibility to select candidate peptide vaccines for SARS-CoV-2 (figure 2).
Methods SARS-CoV-2 HLA-I and HLA-II ligands were predicted using multiple MHC binding prediction software. T cell vaccine candidates were further refined by predicted immunogenicity, viral source protein abundance, sequence conservation, coverage of high frequency HLA alleles, and co-localization of CD4+/CD8+ T cell epitopes. B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, filtering to select regions with surface accessibility, high sequence conservation, spatial localization near functional domains of the spike glycoprotein, and avoidance of glycosylation sites. Using murine compatible T/B cell epitopes, vaccine studies were performed with downstream ELISA/ELISpot to monitor immunogenicity.
Results We observed distribution of HLA-I (n = 2486) and -II (n = 3138) ligands evenly across the SARS-CoV-2 proteome, with significant overlap between predicted human and murine ligands (figure 3). Applying a multivariable immunogenicity model trained from IEDB viral tetramer data (AUC 0.7 and 0.9 for HLA-I and -II, respectively), alongside filters for entropy and protein expression resulted in 292 CD8+ and 616 CD4+ epitopes (figure 4). From an initial pool of 58 B cell epitope candidates, three epitope regions were identified (figure 5). Combining B cell and T cell analyses, alongside manufacturability heuristic, we propose a set of SARS-CoV-2 vaccine peptides for use in subsequent murine studies and clinical trials (figure 6). Preliminary murine studies demonstrate evidence of T and B cell activation (figure 7).
Conclusions A peptide vaccine targeting B cells, CD4+ T cells, and CD8+ T cells in parallel may prove an important part of a multifaceted response to the COVID-19 pandemic. Adapting methods for predicting tumor-specific antigens, we presented a set of peptide candidates with high overlap for T and B cell epitopes and broad haplotype population coverage, with validation of immunogenicity in murine vaccine studies.
Acknowledgements The authors appreciate funding support from University of North Carolina University Cancer Research Fund (AR and BGV), the Susan G. Komen Foundation (BGV), the V Foundation for Cancer Research (BGV), and the National Institutes of Health (CCS, 1F30CA225136). We would like to thank members of the #DownWithTheCrown Slack channel for helpful discussion and feedback.
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