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Online Journal of Bioinformatics ©

Volume 11 (1): 47-58, 2010.

Identification & HLA distribution analysis of CD4+ epitope-based vaccine candidates for H1N1 Swine Influenza.


Aditya N Sarangi¹, Bhawna Rathi¹, Nidhi Trivedi1, Stuti Gupta1


¹Biomedical Informatics Centre, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India.




Sarangi AN, Rathi B, Trivedi N, Gupta S., Identification & HLA distribution analysis of CD4+ epitope-based vaccine candidates for H1N1 Swine Influenza, Onl J Bioinform., 11 (1): 47-58, 2010. Swine Influenza is an infectious disease of pigs caused by type A influenza virus which is the prime source of influenza outbreaks in pigs. Humoral immune response based vaccines against influenza target external viral coat proteins.  As these proteins are conserved for a given strain, such vaccines may be ineffective against heterologous strains with serologically distinct coat protein. In cell mediated immune responses, T cells play an important role by targeting internal proteins common to heterologous viral strains. Nucleoprotein (NP) sequence of Swine Influenza A was selected for T-cell epitope prediction because NP undergoes relatively minor variation within types. Entropy based analysis of the NP sequence of swine influenza was done to check the degree of variability of the peptide and to infer the evolutionary stability. NetMHCIIPan server was used to predict and analyze proteome promiscuous Helper T Lymphocytes (HTL) epitopes for nucleoprotein of Swine Influenza. Population coverage tool of IEDB was employed to determine the fraction of individuals expected to respond to a given set of epitopes. The predicted epitopes may provide the support for serodiagnosis or as protective peptide immunogen in vaccine design against Swine Influenza.


Key words: Swine flu, Peptide vaccine, T-cell epitope, MHC polymorphism, HTL, Population coverage.