Prediction of promiscuous T cell epitopes in RNA dependent RNA polymerase of Chikungunya virus
Journal Title: Asian Pacific Journal of Tropical Medicine - Year 2017, Vol 10, Issue 8
Abstract
Objective: To explore RNA dependent RNA polymerase of Chikungunya virus (CHIKV) and develop T cell based epitopes with high antigenicity and good binding affinity for the human leukocyte antigen (HLA) classes as targets for epitopes based CHIKV vaccine. Methods: In this study we downloaded 371 non-structural protein 4 protein sequences of CHIKV belonging to different regions of the world from the US National Institute of Allergy and Infectious Diseases (NIAID) virus pathogen resource database. All the sequences were aligned by using CLUSTALW software and a consensus sequence was developed by using Uni Pro U Gene Software version 1.2.1. Propred I and Propred software were used to predict HLA I and HLA II binding promiscuous epitopes from the consensus sequence of non-structural protein 4 protein. The predicted epitopes were analyzed to determine their antigenicity through Vaxijen server version 2.0. All the HLA I binding epitopes were scanned to determine their immunogenic potential through the Immune Epitope Database (IEDB). All the predicted epitopes of our study were fed to IEDB database to determine whether they had been tested earlier. Results: Twenty two HLA class II epitopes and eight HLA class I epitopes were predicted. The promiscuous epitopes WMNMEVKII at position 486–494 and VRRLNAVLL at 331– 339 were found to bind with 37 and 36 of the 51 HLA class II alleles respectively. Epitope MANRSRYQS at position 58–66 and epitopes YQSRKVENM at positions 64–72 were predicted to bind with 12 and 9 HLA II alleles with antigenicity scores of 0.754 9 and 1.013 0 respectively. Epitope YSPPINVRL was predicted to bind 18 HLA I alleles and its antigenicity score was 1.425 9 and immunogenicity score was 0.173 83. This epitope is very useful in the preparation of a universal vaccine against CHIKV infection. Conclusions: Epitopes reported in this study showed promiscuity, antigenicity as well as good binding affinity for the HLA classes. These epitopes will provide the baseline for development of efficacious vaccine for CHIKV.
Authors and Affiliations
Yasir Waheed
Keywords
Related Articles
- EP ID EP279740
- DOI 10.1016/j.apjtm.2017.07.023
- Views 52
- Downloads 0
Zika virus from a Southeast Asian perspective
Phylogenic evidence suggests that the strain of Zika virus causing an unprecedented outbreak of disease in the Americas had its origin in Southeast Asia, where reports of isolated cases of Zika virus infection have occur...
Influence of light intensity and water content of medium on total dendrobine of Dendrobium nobile Lindl
Objective: To ascertain the influence of light intensity and water content of medium on the total dendrobine of Dendrobium nobile (D. nobile). Method: The principal component analysis combined with total dendrobine accum...
Annona muricata fruit extract protects against diethylnitrosamineinduced hepatocellular cancer in rats
Objective: To evaluate the anticancer potentials of Annona muricata fruit by in vitro and in vivo methods. Methods: The ethanolic extract of Annona muricata fruit was prepared by Soxhlet extraction method and further fra...
Optimized combinations of statins and azoles against Acanthamoeba trophozoites and cysts in vitro
Objective: To evaluate the combination of several statins (atorvastatin, fluvastatin and simvastatin) and azoles (voriconazole, posaconazole and itraconazole) against Acanthamoeba spp. Methods: The efficiency of the diff...
Anticancer activity of Mahonia leschenaultii methanolic root extract and berberine on Dalton’s ascitic lymphoma in mice
Objective: To evaluate the effects of methanol root extract of Mahonia leschenaultii and berberine of Mahonia leschenaultii on Dalton’s ascitic lymphoma in Swiss Albino mice. Methods: The methanol root extracts of Mahoni...