T-cell epitopes predicted from the Nucleocapsid protein of Sin Nombre virus restricted to 30 HLA alleles common to the North American population



Sathish Sankar*, Mageshbabu Ramamurthy, Balaji Nandagopal, Gopalan Sridharan



Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India;




Article Type




Received March 9, 2017; Accepted March 16, 2017; Published March 31, 2017



Hantavirus cardiopulmonary syndrome in North America is caused by Sin Nombre virus (SNV) and poses a public health problem. We identified T-cell epitopes restricted to HLA alleles commonly seen in the N. American population. Nucleocapsid (N) protein is 428 aminoacid in length and binds to RNA and functions also as a key molecule between virus and host cell processes. The predicted epitopes from N protein that bind to class I MHC were analyzed for human proteasomes cleavage, TAP efficiency, immunogenicity and antigenicity. We identified 8 epitopes through MHC binding prediction, proteasomal cleavage prediction and TAP efficiency. Epitope VMGVIGFSF had highest Vaxijen score and the epitope, TNRAYFITR had highest immunogenicity score. Epitope AAVSALETK and TIACGLFPA had 100% homology to many HCPS causing viruses. Our study focused on T-cell epitope prediction
specific to restricted HLA haplotypes of racial groups in North America for the potential vaccine development. Among the candidate epitopes, FLAARCPFL was conserved in SNV, which is suitable for vaccine specific to the virus genotype. Peptide-based vaccines can be designed to include multiple determinants from several hantavirus genotypes, or multiple epitopes from the same genotype.
Thereby, immune response will focus solely on relevant epitopes, avoiding non-protective responses or immune evasion. The other advantages include absence of infectious material unlike in live or attenuated vaccines. There is no risk of reversion or formation of adverse reassortants leading to virulence and no risk of genetic integration or recombination forming a rationale for vaccine design
including for distinct geographical regions.



T cell epitopes; Hantaviruses; Sin Nombre; nucleocapsid; MHC



Sankar et al. Bioinformation 13(3): 94-100 (2017)


Edited by

P Kangueane






Biomedical Informatics



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