Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions

Alba Grifoni; John Sidney; Yun Zhang; Richard H Scheuermann; Bjoern Peters; Alessandro Sette

To define potential B cell epitopes by an alternative method, we used the predictive tools provided with the IEDB Analysis Resource. B cell epitope predictions were carried out using the 2019-nCoV surface glycoprotein, nucleocapsid phosphoprotein, and membrane glycoprotein sequences, which, as described above, were found to be the main protein targets for B cell responses to other coronaviruses. In parallel, we performed predictions for linear B cell epitopes with Bepipred 2.0 (6), and for conformational epitopes with Discotope 2.0 (7 To predict CD4 T cell epitopes, we used the method described by Paul and co-authors (9) , as implemented in the Tepitool resource in IEDB (10) . This approach was designed and validated to predict dominant epitopes independently of ethnicity and HLA polymorphism, taking advantage of the extensive cross-reactivity and repertoire overlap between different HLA class II loci and allelic variants. Here, we selected peptides having a median consensus percentile ≤ 20, a threshold associated with epitope panels responsible for about 50% of target-specific responses. Using this threshold we identified 241 candidates in the 2019-nCoV sequence (see Table S3 ).