A comprehensive analysis of predicted HLA binding peptides of JE viral proteins specific to north Indian isolates

Japanese encephalitis (JE), a viral disease has significantly increased worldwide especially, in the developing region due to challenges in immunization, vector control and lack of appropriate treatment methods. An effective, yet an expensive heat-killed vaccine is available for the disease. Therefore, the design and development of short peptide vaccine candidate is promising. We used immune-informatics methods to perform a comprehensive analysis of the entire JEV proteome of north Indian isolate to identify the conserved peptides binding known specific HLA alleles among the documented JEV genotypes 1, 2, 3, 4 and 5. The prediction analysis identified 102 class I (using propred I) and 118 class II (using propred) binding peptides at 4% threshold value. These predicted HLA allele binding peptides were further analyzed for potential conserved region using IEDB (an immune epitope database and analysis resource). This analysis shows that 78.81% of class II (in genotype 2) and 76.47% of HLA I (in genotype 3) bound peptides are conserved. The peptides IPIVSVASL, KGAQRLAAL, LAVFLICVL and FRTLFGGMS, VFLICVLTV, are top ranking with potential super antigenic property by binding to all HLA allele members of B7 and DR4 super-types, respectively. This data finds application in the design and development of short peptide vaccine candidates and diagnostic agents for JE following adequate validation and verification.