Sequence-based prediction of vaccine targets for inducing T cell responses to SARS-CoV-2 utilizing the bioinformatics predictor RECON

Asaf Poran; Dewi Harjanto; Matthew Malloy; Michael S. Rooney; Lakshmi Srinivasan; Richard B. Gaynor

2 Assays of T cell reactivity (e.g., interferon-gamma ELISpots, tetramers), which are stricter 3 measures for T cell immunogenicity to epitopes, were performed in significantly lower numbers 4 compared with MHC-binding assays. For HLA-I, the overlap between peptide-MHC allele pairs 5 for which we had a prediction (supported alleles) and pairs with a reported T cell assay consisted 6 of only 32 pairs, of which 23 had a positive result. We did not detect differences in the percent 7 ranks across the positive and negative groups, however sample sizes are extremely small (data not 8 shown). In addition, for HLA-I epitopes, the validation dataset only contained T cell assay results 9 for peptide-MHC allele pairs that had a positive result in a binding assay, suggesting a biased pool 10 of epitopes selected for testing. Table 9 ). There were 259 unique peptide-MHC allele pairs assayed by MHC-binding assays in the 18 ViPR validation dataset for HLA-II. As before, we compared their percent rank with their reported 19 'best' (in the case of multiple measurements) MHC-binding assay result. This comparison could 20 not be performed with the "Negative" pairs as an independent group since there was only one 21 negative result in the validation dataset for HLA-II. The low negative counts may be due to under-22 reporting of negative assay results or biased selection of the peptides to be assayed. Therefore, we 23 author/funder. All rights reserved. No reuse allowed without permission.