Abstract
BackgroundThe purpose of this study was to explore molecular epidemiology of HCV genotype 3a in Peshawar based on sequencing and phylogenetic analysis of Core region of HCV genome.MethodsChronically infected Hepatitis C virus infected patients enrolled under the Prime Minister Hepatitis C control program at three Tertiary care units of Peshawar [Khyber Teaching Hospital Peshawar, Lady Reading Hospital Peshawar, Hayat Abad Medical Complex Peshawar] were included in this cross sectional observational study. Qualitative detection of HCV and HCV genotyping was carried out by a modified reverse transcription-polymerase chain reaction (RT-PCR) and type specific genotyping assay. The Core gene of HCV genotype 3a was amplified, cloned and sequenced. The sequences obtained were used for phylogenetic analysis using MEGA 6 software.ResultsAmong the 422 (82.75 %) PCR positive samples, 192 (45.5 %) were identified as having HCV genotype 3a infection. HCV Core gene sequencing was carried out randomly for the characterization of HCV 3a. Nucleotide sequence analysis of the obtained viral genomic sequences based on partial HCV 3a Core gene sequences with reference sequences from different countries showed that our sequences clustered with some local and regional sequences with high bootstrap values.ConclusionHCV 3a is highly prevalent in Peshawar, Pakistan and its phylogenetics based on Core gene sequences indicate the prevalence of different lineages of HCV 3a in Peshawar which may have consequences for disease management strategies causing more economic pressure on the impoverished population due to possible antiviral resistance.
Highlights
The purpose of this study was to explore molecular epidemiology of Hepatitis C virus (HCV) genotype 3a in Peshawar based on sequencing and phylogenetic analysis of Core region of HCV genome
For identification of HCV genotype 3a infection among the actively infected HCV samples, RT PCR followed by Type specific nested PCR based genotyping assay was carried out
For authentication of HCV genotype 3a, Core gene amplification and sequencing was carried out by randomly selecting a representative number (58/192) of samples and it was established that the patients had HCV 3a infection
Summary
The purpose of this study was to explore molecular epidemiology of HCV genotype 3a in Peshawar based on sequencing and phylogenetic analysis of Core region of HCV genome. In Pakistan, approximately 10–17 million people are chronically infected with HCV [5, 6] with an overall prevalence rate of 5 % [7]. HCV genome shows substantial nucleotide sequence variability in both the structural and nonstructural coding regions, with different isolates of HCV showing as much as 30 % nucleotide sequence divergence over the entire genome which is sufficient to alter the antigenic and biological characteristics of seven major genotypes of HCV [12]. Identification of HCV genotype is extremely important as different genotypes are relevant to the epidemiology and clinical management of
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