Prediction of promiscuous T cell epitopes in RNA dependent RNA polymerase of Chikungunya virus

作     者：Yasir Waheed Sher Zaman Safi Muzammil Hasan Najmi Hafsa Aziz Muhammad Imran 

作者机构：Foundation University Medical CollegeFoundation University IslamabadDHA-I Islamabad(44000)Pakistan Interdisciplinary Research Centre in Biomedical Materials(IRCBM)COMSATS Institute of Information TechnologyLahore CampusLahorePakistan Nuclear Medicine Oncology and Radiotherapy Institute IslamabadIslamabad(44000)Pakistan Department of Medical Laboratory Sciences(DMLS)Faculty of Health and Allied Sciences(FHAS)Imperial College of Business Studies(ICBS)LahorePakistan Department of MicrobiologyUniversity of Health SciencesLahorePakistan 

出 版 物：《Asian Pacific Journal of Tropical Medicine》 (亚太热带医药杂志（英文版）)

年 卷 期：2017年第10卷第8期

页      面：825-829页

核心收录：

学科分类：1007[医学-药学(可授医学、理学学位)] 100705[医学-微生物与生化药学] 1001[医学-基础医学(可授医学、理学学位)] 100103[医学-病原生物学] 10[医学] 

主　　题：Chikungunya virus Epitope vaccine HLA binding T cell epitopes 

摘      要：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. PropredⅠand Propred software were used to predict HLAⅠ and HLAⅡ 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 HLAⅠ 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 classⅠepitopes 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 HLAⅠI alleles with antigenicity scores of 0.754 9 and 1.013 0 respectively. Epitope YSPPINVRL was predicted to bind 18 HLAⅠ 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