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

Ethan Fast; Russ B. Altman; Binbin Chen

Given the high similarity between SARS-CoV and 2019-122 nCoV proteins, we expect our analysis on 2019-nCoV to per-123 form similarly against future experimentally validated T-cell 124 epitopes. The detailed scores and sequences of this analysis 125 can be found in SI Appendix, Supplementary Tables 7 and 8. 126 Viral mutation and antigen presentation. Human immune se-127 lection pressure has been shown to drive viral mutations which 128 evade immune surveillance (e.g. low MHC presentation). We 129 hypothesize that a similar phenomenon can occur in 2019-130 nCoV. We curated a cohort of 68 viral genomes across four 131 continents and identified 93 point mutations, 2 nonsense mu-132 tation and 1 deletion mutation compared to the published 133 reference genome (5). We plot point mutations against regions 134 of MHC-I or MHC-II presentation in Fig. 4 . The full pro-135 tein sequence and mutation information can be found in SI 136 Appendix, Dataset S2 and S3. We plot results at both medium (A) and high (B) cut-offs for presentation. The X-axis indicates the position of each viral protein, and the y-axis indicates each human HLA gene family. Each blue stripe indicates the fraction of HLA alleles that can present a 9mer or 15mer viral peptide starting from a given position. A peptide being presented by more than one third of common alleles (red) is considered to be high coverage. Fig. S1 ).