title: In-silico analysis of putative HCV epitopes against Pakistani human leukocyte antigen background: An approach towards development of future vaccines for Pakistani population.
abstract: Mounting burden of HCV-infected individuals and soaring cost of treatment is a serious source of unease for developing countries. Numbers of various approaches have been anticipated to develop a vaccine against HCV but the majority of them proved ineffective. Development of vaccine by considering geographical distribution of HCV genotypes and host genetics shows potential. In this research article, we have tried to predict most putative HCV epitopes which are efficiently restricted by most common HLA alleles in Pakistani population through different computational algorithms. Thirteen selected, experimentally identified epitopes sequences were used to derived consensus sequences in all genotypes of HCV. Obtained consensus sequences were used to predict their binding affinities with most prevalent HLA alleles in Pakistani population. Two Class-I epitopes from NS4B region, one from Class-I epitope from NS5A and one Class-II epitope from NS3 region showed effective binding and proved to be highly putative to boost immune response. A cocktail of these four have been checked for population coverage and they gave 75.53% for Pakistani Asian and 70.77% for Pakistani Mixed populations with no allergenic response. Computational algorithms are robust way to shortlist potential candidate epitopes for vaccine development but further, in vivo and in-vitro studies are required to confirm their immunogenic properties.
authors.affiliation: Department of Biochemistry & Molecular Biology, University of Gujrat, Punjab, Pakistan. Electronic address: naeem.mahmood@uog.edu.pk.
authors.forename: Naeem Mahmood
authors.initials: NM
authors.lastname: Ashraf
authors.affiliation: Department of Pathology, Nawaz Sharif Medical College, University of Gujrat, Punjab, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Bilal
authors.affiliation: Institute of Biochemistry and Biotechnology, University of the Punjab, Punjab, Pakistan.
authors.forename: Malik Siddique
authors.initials: MS
authors.lastname: Mahmood
authors.affiliation: Department of Biochemistry & Molecular Biology, University of Gujrat, Punjab, Pakistan.
authors.forename: Aadil
authors.initials: A
authors.lastname: Hussain
authors.affiliation: Department of Biochemistry & Molecular Biology, University of Gujrat, Punjab, Pakistan.
authors.forename: Muhammad Zubair
authors.initials: MZ
authors.lastname: Mehboob
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D016384:Consensus Sequence; D018984:Epitopes, T-Lymphocyte / Q000235:genetics* / Q000276:immunology; D005838:Genotype; D006680:HLA Antigens / Q000737:chemistry* / Q000276:immunology; D016174:Hepacivirus / Q000235:genetics* / Q000276:immunology; D006801:Humans; D010154:Pakistan; D014612:Vaccines / Q000276:immunology*
chemical_list: D018984:Epitopes, T-Lymphocyte; D006680:HLA Antigens; D014612:Vaccines
keywords: Epitope-based vaccines; HCV genotypes; HLA; Pakistani population