Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies

Syed Faraz Ahmed; Ahmed A. Quadeer; Matthew R. McKay

Population coverages for sets of T cell epitopes were computed using the tool provided by the Immune Epitope Database (IEDB) (http://tools.iedb.org/population/; accessed 9 February 2020) (Vita et al., 2019). This tool uses the distribution of MHC alleles (with at least 4-digit resolution, e.g., A*02:01) within a defined population (obtained from http://www.allelefrequencies.net/) to estimate the population coverage for a set of T cell epitopes. The estimated population coverage represents the percentage of individuals within the population that are likely to elicit an immune response to at least one T cell epitope from the set. To identify the set of epitopes associated with MHC alleles that would maximize the population coverage, we adopted a greedy approach: (i) we first identified the MHC allele with the highest individual population coverage and initialized the set with their associated epitopes, then (ii) we progressively added epitopes associated with other MHC alleles that resulted in the largest increase of the accumulated population coverage. We stopped when no increase in the accumulated population coverage was observed by adding epitopes associated with any of the remaining MHC alleles.