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

Ethan Fast; Russ B. Altman; Binbin Chen

Notably, the Cryo-EM solved structure has missing residues 178 in the RBD due to limited electron density. Using modeled 179 structures overcomes this issue. Fig. 6 ). We wanted to 204 explore whether these two linear epitopes are critical for viral 205 interaction with the human entry protein ACE2. After our 206 original analysis, two solved co-crystal structures of 2019-nCoV 207 S protein RBD and human ACE2 become available (19, 20). 208 We ran Discotope2 and obtained strikingly similar results 209 (Fig. 6C and D) . The main antibody binding site substantially 210 overlaps with the interacting surface where ACE2 (yellow) 211 binds to S protein, so an antibody binding to this surface is 212 likely to block viral entry into cells. Table 2 . Top potential epitopes for key 2019-nCoV proteins. We ranked epitopes based on their likely coverage of presentation by MHC-I and MHC-II alleles. S protein 494-508 is highly ranked based on MHC presentation and is also one of the predicted top B-cell epitopes, localized near the S protein receptor binding domain (Fig. 5) . MHC-I coverage is calculated by the 9mer with the highest MHC-I coverage for each epitope (highlighted in orange). All candidates are likely to be presented by both MHC-I and MHC-II. "SARS" under the antibody column indicates that one or more SARS homolog of this peptide is a known B-cell epitope. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.19.955484 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.19.955484 doi: bioRxiv preprint (Fig. 5D ). All mutations are distant from the S protein RBD, and one mutation (S247R) occurs near one of the predicted 218 minor antibody binding site (residue 246-257).