A Simple Method for the Design and Development of Flavivirus NS1 Recombinant Proteins Using an In Silico Approach

Table 3

Prediction of MHC class II binding peptides in JEV NS1 by the T-cell epitope prediction tool at IEDB.

Genotype	Amino acid position^a (epitope ID)^d	Human allele	Mean percentile rank^b	Core peptide^c
Genotype 1 & 3	14–32	HLA-DRB	0.568	RCGSGIFVH; FVHNDVEAW; VHNDVEAWV
	91–109	HLA-DRB	0.474	RYRSAPKRL; YRSAPKRLS
	143–159	HLA-DQA/DQB	0.687	CPDEHRAWN; EHRAWNSMQ; AWNSMQIED; WNSMQIEDF; NSMQIEDFG
	148–168	HLA-DRB	0.317	WNSMQIEDF; QIEDFGFGI; FGITSTRVW
	192–211 (539105, 540128)	HLA-DQA/DQB	0.502	DLSYWIESR; LSYWIESRY
	267–287	HLA-DRB, HLA-DQA/DQB	0.116	WDENGIVLD; ENGIVLDFD; IVLDFDYCP
	317–335	HLA-DRB	0.698	SLPPLRFRT; RFRTENGCW; FRTENGCWY
	332–350	HLA-DRB	0.316	GMEIRPVRH; VRHDETTLV
Genotype 5	14–32	HLA-DRB	0.568	RCGSGIFVH; FVHNDVEAW; VHNDVEAWV
	144–158	HLA-DQA/DQB	0.95	AWNSMQIED; WNSMQIEDF
	148–168	HLA-DRB	0.284	WNSMQIEDF; QIEDFGFGI; FGITSTRVW
	192–211 (539105, 540128)	HLA-DQA/DQB	0.195	DLSYWIESH; LSYWIESHL
	267–287	HLA-DRB	0.171	DENEITLDF; ITLDFDYCP; FDYCPGTTV
	332–349	HLA-DRB	0.458	GMEIRPMKH; IRPMKHDES; MKHDESTLV

These data were extracted by filtering at below 1.0 percentile rank. Bold letters indicate the same core peptide among JEV genotypes. ^aNS1 amino acid sequence number. ^bMean of percentile ranks of the predicted peptides in this region. ^cValues predicted by the combinatorial peptide library, SMM-align, and NN-align methods. ^dThese represent epitopes associated with the positive result of T-cell response (T-cell assay such as ELISPOT, ICS assay, and MHC ligand assay), previously reported at some reference. Epitope ID is assigned at IEDB. These epitopes include all or part of the core peptides in the table.