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Online Journal of Bioinformatics
 Established 1995

ISSN  1443-2250

21(3): 225-235, 2020.

In Silico prediction of putative epitopes in structural polyprotein of Chikungunya virus


J. Asnet Mary1 (MSc, ADBI), S. Kavitha1 (MSc), V. Victoria1(MSc), R. Paramasivan2 (PhD), R.Shenbagarathai1(PhD)*,

P. Selvanayagam1 (PhD), T. Madhanmohan3 (PhD).


1. Bioinformatics Centre, Department of Biotechnology, Lady Doak College, 2. CRME (ICMR), Madurai 3. Department of Biotechnology, New Delhi, India.




Asnet Mary J, Kavitha S, Victoria V, Paramasivan R, Shenbagarathai R, Selvanayagam P, Madhanmohan T., In Silico prediction of putative epitopes in structural polyprotein of Chikungunya virus, Onl J Bioinform., 21(3): 225-235, 2020. Chikungunya (CHIKF) is associated with acute fever, including asthenia, skin rash, polyarthritis and occasionally, encephalitis in humans. The virus is transmitted by Aedes aegypti and Aedes albopictus and there is no specific treatment or vaccine as of this date. We predict putative epitopes of Chikungunya virus from In silico analysis of genome sequences with Open reading frame (ORF) and putative proteins by BLAST. 3D structure of viral polyproteins and 17 B-cell epitopes were determined for accessibility, flexibility, hydrophilicity, β-turn and linearity by BCPred server. One epitope capsid protein with residues range 85 104 amino acid was immunogenic in the entire structural polyprotein of CHIKV in BCIPED database with maximum score. We used PROPREDL to test B-cell epitope for T-cell epitopes and MHC class I binding sites. We found binding with 25 MHC alleles in humans supporting further assessment of these putative epitopes of CHIKV In Vivo.


Keywords: Chikungunya virus, genome, epitopes, BCPred, Bcipep, MHC binding, vaccine.