Molecular characterization of Hepatitis C virus 3a in Peshawar

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.

Real Time PCR Based Detection of Hepatitis C Virus Major Genotypes in Chronic HCV Patients in Khyber Pakhtunkhwa

“…This higher percentage indicates a new shift in HCV epidemiology, although the presence of genotype 1a and 1b has been reported by other studies conducted in Pakistan (16). A more recent study conducted in the Khyber Pakhtunkhwa province has also reported a shift the distribution of HCV types with higher percentage of HCV 1b or its mixed infections (21).…”

Genetic Diversity of Hepatitis C Virus Genotype 3a Based on Complete Core Protein in Peshawar, Pakistan

“…In the present study, genetic relatedness with local isolates points to the prior presence of similar types in other parts of Pakistan. Recently, Gul et al (17) described the evolutionary analysis of HCV genotype 3a isolates from Peshawar.…”

“…Hepatitis C Virus genotype 3a is more prevalent in Pakistan, and few studies were con-ducted on complete core protein sequences and phylogenetic analysis in the north-west of Pakistan. Studies performed locally revealed a prevalence of genotype 3a from 26% to 45% (17,18). According to a national survey conducted in 2007, 4.8% of the Pakistani population was infected with HCV, which corresponds to nearly 9.9 million of overall HCV cases in Pakistan.…”

Anti-viral effect of Indigoferra gerardiana on core protein of HCV and clinical significance of serum markers in chronic HCV genotype 3a patients in district Peshawar

“…A baseline investigation along with genotyping and viral load quantification was done. HCV RNA was detected using quantitative PCR (Q-PCR) according to the operating manual of the test kit (Qiagen, Germany) followed by HCV genotyping [36].…”

“…The P value (< 0.05) was labeled significant. HCV genotype determination was carried out as described earlier [36]. For HCV genotype determination, RNA extraction was carried according kit protocol.…”