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

Table 4

Prediction of MHC class II binding peptide in NS1 from WNV, YFV, and ZIKV by the T-cell epitope prediction tool at IEDB.

Amino acid position^a (epitope ID)^d	Human allele	Mean^b	Core peptide^c
WNV
14–32	HLA-DRB	0.642	RCGSGVFIH; FIHNDVEAW; IHNDVEAWM
91–109	HLA-DRB	0.102	MYKSAPKRL; YKSAPKRLT
144–158	HLA-DQA/DQB	0.96	QNRAWNSLE; AWNSLEVED
154–174 (21175)	HLA-DRB, HLA-DPA/DPB	0.611	EVEDFGFGL; FGLTSTRMF; GLTSTRMFL; LTSTRMFLK; TSTRMFLKV
188–211 (159026)	HLA-DRB, HLA-DQA/DQB	0.244	AIHSDLSYW; IHSDLSYWI; DLSYWIESR; LSYWIESRL
317–336 (57994)	HLA-DRB	0.293	YQTDSGCWY; TLPPLRYQT
YFV
15–31 (10088)	HLA-DQA/DQB	0.91	IFIFRDSDD; IFRDSDDWL
64–78 (113828)	HLA-DRB, HLA-DQA/DQB	0.162	EHEMWRSRA; SRADEINAI; ADEINAIFE; DEINAIFEE
71–95 (113319, 137424)	HLA-DQA/DQB	0.633	DEINAIFEE; NAIFEENEV; AIFEENEVD; FEENEVDIS; EENEVDISV; EVDISVVVQ; VDISVVVQD; DISVVVQDP
144–158 (181115]	HLA-DPA/DPB, HLA-DQA/DQB	0.804	NRVWNSFQI; RVWNSFQIE; SFQIEEFGT; FQIEEFGTG; RVYMDAVFE; VYMDAVFEY
169–183 (137404, 232424]	HLA-DRB	0.01	MDAVFEYTI; YTIDCDGSI
207–221	HLA-DQA/DQB	0.7	WMIHTLEAL
222–237 (231830152485)	HLA-DRB	0.675	KECEWPLTH; LTHTIGTSV
ZIKV
14–31 (569047, 863166, 871319)	HLA-DRB	0.89	RCGTGVFVY; FVYNDVEAW; YNDVEAWRD
28–46 (862875, 862438)	HLA-DRB	0.69	WRDRYKYHP; RDRYKYHPD; YHPDSPRRL
67–86 (862872, 862852)	HLA-DQA/DQB	0.57	SVEGELNAI; VEGELNAIL; EGELNAILE; GELNAILEE; ELNAILEEN; NAILEENGV
142–160 (862457, 862672, 863124]	HLA-DPA/DPB	0.321	HRAWNSFLV; RAWNSFLVE
157–160 (862889, 862596]	HLA-DPA/DPB	0.819	GVFHTSVWL; VFHTSVWLK; FHTSVWLKV; HTSVWLKVR
193–201 (862673]	HLA-DQA/DQB	0.668	DLGYWIESE

These data were extracted by filtering at below 1.0 percentile rank. Bold letters indicate the same core peptide as that of JEV. ^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.