Potential T-cell and B-cell Epitopes of 2019-nCoV

Ethan Fast; Russ B. Altman; Binbin Chen

is the main trans-membrane glycoprotein expressed on the 66 surface of 2019-nCoV and is responsible for receptor binding 67 and virion entry to cells (1, 18 NetMHCpan4 predicts that a larger number of 2019-nCoV 102 protein sequences can be presented by HLA-C alleles across all 103 genes (Fisher's exact test, p = 4.2e −59 ) compared to HLA-A 104 or HLA-B (Table 1) . Specifically, ORF1ab (p = 6.7e −54 ), S 105 (p = 1.4e −9 ), ORF3a (p = 0.01), and M (p = 0.025) can be 106 better presented by HLA-C alleles after Bonferroni correction. 107 T-cell epitope validation. To estimate the ability of antigen 108 presentation scores to identify 2019-nCoV T-cell epitopes, we 109 performed a validation study with known SARS-CoV CD8 and 110 CD4 T-cell epitopes (Fig. 3) . From 4 independent experimen-111 tal studies (23-26), we identified known CD8 T-cell epitopes 112 (MHC-I, n=17) and known CD4 T-cell epitopes (MHC-II, 113 n=3). We also obtained known non-epitopes (n=1236 and 114 246) for CD4, while for CD8 we include all 9mer sliding win-115 dows of S protein without a known epitope as non-epitopes. 116 MHC-I presentation (with recommended cut-off 98% (17)) has 117 a sensitivity of 82.3%, specificity of 97.0% and an AUC of 0.98 118 (Fig. 3A) . MHC-II presentation (recommended cut-off 95% 119 (15)) has a sensitivity of 66.6%, specificity of 91.1% and an 120 AUC of 0.83 (Fig. 3B ).