PMID- 28942824
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20191120
IS  - 2352-4146 (Electronic)
IS  - 1995-7645 (Linking)
VI  - 10
IP  - 8
DP  - 2017 Aug
TI  - Prediction of promiscuous T cell epitopes in RNA dependent RNA polymerase of 
      Chikungunya virus.
PG  - 760-764
LID - S1995-7645(17)30573-4 [pii]
LID - 10.1016/j.apjtm.2017.07.023 [doi]
AB  - 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.
CI  - Copyright (c) 2017 Hainan Medical University. Production and hosting by Elsevier 
      B.V. All rights reserved.
FAU - Waheed, Yasir
AU  - Waheed Y
AD  - Foundation University Medical College, Foundation University Islamabad, DHA-I, 
      Islamabad 44000, Pakistan. Electronic address: yasir_waheed_199@hotmail.com.
FAU - Safi, Sher Zaman
AU  - Safi SZ
AD  - Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS 
      Institute of Information Technology, Lahore Campus, Lahore, Pakistan.
FAU - Najmi, Muzammil Hasan
AU  - Najmi MH
AD  - Foundation University Medical College, Foundation University Islamabad, DHA-I, 
      Islamabad 44000, Pakistan.
FAU - Aziz, Hafsa
AU  - Aziz H
AD  - Nuclear Medicine Oncology and Radiotherapy Institute Islamabad, Islamabad 44000, 
      Pakistan.
FAU - Imran, Muhammad
AU  - Imran M
AD  - Department of Medical Laboratory Sciences (DMLS), Faculty of Health and Allied 
      Sciences (FHAS), Imperial College of Business Studies (ICBS), Lahore, Pakistan; 
      Department of Microbiology, University of Health Sciences, Lahore, Pakistan.
LA  - eng
PT  - Journal Article
DEP - 20170819
PL  - India
TA  - Asian Pac J Trop Med
JT  - Asian Pacific journal of tropical medicine
JID - 101533720
OTO - NOTNLM
OT  - Chikungunya virus
OT  - Epitope vaccine
OT  - HLA binding
OT  - T cell epitopes
EDAT- 2017/09/26 06:00
MHDA- 2017/09/26 06:01
CRDT- 2017/09/26 06:00
PHST- 2017/04/03 00:00 [received]
PHST- 2017/06/28 00:00 [revised]
PHST- 2017/06/30 00:00 [accepted]
PHST- 2017/09/26 06:00 [entrez]
PHST- 2017/09/26 06:00 [pubmed]
PHST- 2017/09/26 06:01 [medline]
AID - S1995-7645(17)30573-4 [pii]
AID - 10.1016/j.apjtm.2017.07.023 [doi]
PST - ppublish
SO  - Asian Pac J Trop Med. 2017 Aug;10(8):760-764. doi: 10.1016/j.apjtm.2017.07.023. 
      Epub 2017 Aug 19.