Insight into SNPs and epitopes of E protein of newly emerged genotype-I isolates of JEV from Midnapur, West Bengal, India

Table 4 Prediction of MHC class I specific peptide epitopes

Start	Peptide	MHC-I binding score^a	Proteosomal Cleavage score^b	Allele (Human Leukocyte Antigen [HLA] specific)	Antigenic Score^c
59	YYYHASVTD	1.3–17.0	0.82	HLA-A24:02,HLA-A23:01,HLA-A29:02,HLA-B18:01,HLA-B39:01, HLA-B48:01,HLA-B51:01,HLA-C01:02,HLA-C03:03,HLA-C06:02, HLA-C07:01,HLA-C07:02,HLA-C07:04,HLA-C12:02,HLA-C14:02, HLA-C16:01,HLA-G01:01,HLA-G01:02,HLA-G01:03,HLA-G01:04, HLA-G*01:06	0.9572
95	GFTDRGWGK	4.4–15.5	0.85	HLA-A03:01,HLA-A11:01,HLA-A29:02,HLA-A30:01,HLA-A33:03, HLA-A31:01,HLA-A68:01,HLA-A74:01,HLA-C*04:01	1.4597
382	YIVVGRKDK	6.4–6.6	0.92	HLA-A03:01; HLA-A11:01;HLA-A*68:01	2.5185
394	HHRHKAGST	8.9–13.7	0.70	HLA-B07:02, HLA-B14:02	0.5088

^aPercentile score vary in allele specific manner. The lower the score better is the binding specificity [46]. The range of scores was obtained by setting cut off. ^bProteosomal cleavage score is the average of two kinds of scores: constitutively expressed type and INF-γ induced type. ^cAntigenic score was computed using Doytchinova and Flower's (2007) method [47]
Three score criteria were followed to screen the epitopes: MHC class I binding score, proteosomal cleavage score and antigenicity score. Association of HLA alleles for each epitope was determined by a cut off for percentile rank value ≤ 20.0. Epitopes were further checked for their efficacy in interactions at the peptide binding groove (see below)

ISSN: 1471-2172