Molecular Epidemiology of Hepatitis B Virus (HBV) Genotypes Prevalent in KP

Abstract

Hepatitis B virus (HBV) infection is a major public health dilemma affecting about 2 billion of world population and more than 350 million people are chronic HBV carriers including Pakistan with an estimated prevalence rate of 3%. HBV can be categorized into 10 genotypes (A-H) clarified by more than 8% of sequence divergence based on the whole genome. Although Pakistan is highly endemic to HBV no large scale study of HBV genotypes based on sequence analysis has been reported yet so the ongoing research study was aimed to explore the existing patterns of HBV genotypes based on sequencing method and phylogenetic analysis of HBV S gene distributed in Khyber Pakhtukhwa (KP)which isone of the third most populated province of Pakistan. A total of 3000 chronically HBV positive samples were collected from 7 most populous districts of KP and were analyzed by ICT followed by qualitative PCR for confirmation. Type-specific PCR or restriction fragment length polymorphism (RFLP) and random sequencing of the partial Sgene were carried out for HBV genotypes characterization. We obtained a 100 of, S gene nucleotide sequences out of which 28 nucleotide sequences demonstrating the whole diversity of the sequenced types were further used for phylogenetic study using Mega 6 software. Active infection of HBV was confirmed in all patients through qualitative PCR and three genotypes A, C, and D were confirmed by type specific PCR and RFLP. The most prevalent genotype detected was genotype D 68.3% followed by genotype A 22.6% and genotype C 8.53%. Phylogenetic analysis of the obtained sequences based on HBV S gene revealed that some of our HBV sequences clustered with some local isolates showing close homology with them while other clustered together with some foreign isolates with a high bootstrap value. However, one isolate didn’t match or show any similarity with any of HBV strain available in online repositories that point towards a great divergence and a distinctive origin of the strain.