Epitopes prediction
The Immune Epitope Database and Analysis Resource (IEDB), NetMHC4.0 Server and NetMHCpan 4.1 Server are used to predict binding of peptides to MHC molecule of known sequence using artificial neural networks (ANNs). Specifically, nine-mer peptide as the peptide length option was selected. HLA-E*0101 or HLA-E*0103-restricted SARS-CoV-2 nine-mer peptide epitopes were predicted by inputting 1,273 amino acids of S protein sequence, 75 amino acids of E protein sequence, 222 amino acids of M protein sequence and 419 amino acids of N protein sequence of SARS-CoV-2 prototype strain Wuhan-Hu-1 (GenBank accession number: NC_045512.2) into the databases, respectively.
There is only HLA-E*0101 allele option could be selected in NetMHC4.0 Server database, while both HLA-E*0101 and E*0103 alleles could be selected in NetMHCpan 4.1 Server database under the loci or species option with HLA-E. Both the two methods specified if a sequence is a strong MHC binder (SB) or a weak MHC binder (WB) based on a %Rank score. By default, %Rank < 0.5% and %Rank < 2% thresholds are considered for detecting as SB and WB for HLA-E molecule.