Prediction of promiscuous T cell epitopes in RNA dependent RNA polymerase of Chikungunya virus
10.1016/j.apjtm.2017.07.023
- Author:
Yasir WAHEED
1
;
Muzammil Hasan NAJMI
1
;
Sher Zaman SAFI
2
;
Hafsa AZIZ
3
;
Muhammad IMRAN
4
;
Muhammad IMRAN
5
Author Information
1. Foundation University Medical College, Foundation University Islamabad, DHA-I
2. Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS Institute of Information Technology, Lahore Campus
3. Nuclear Medicine Oncology and Radiotherapy Institute Islamabad
4. Department of Medical Laboratory Sciences (DMLS), Faculty of Health and Allied Sciences (FHAS), Imperial College of Business Studies (ICBS)
5. Department of Microbiology, University of Health Sciences
- Publication Type:Journal Article
- Keywords:
Chikungunya virus;
Epitope vaccine;
HLA binding;
T cell epitopes
- From:
Asian Pacific Journal of Tropical Medicine
2017;10(8):760-764
- CountryChina
- Language:Chinese
-
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.
