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Molecular characterization of Hepatitis C virus 3a in Peshawar
Amina Gul1,2, Nabeela Zahid3, Jawad Ahmed1
1Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Peshawar, Pakistan.
Insights
Hepatitis C virus (HCV) genotype 3a is common in Peshawar, Pakistan. Phylogenetic analysis of the HCV Core gene reveals diverse local lineages, potentially impacting treatment strategies and increasing healthcare costs.
Area of Science:
- Virology
- Molecular Epidemiology
- Public Health
Background:
- Hepatitis C virus (HCV) genotype 3a is a significant global health concern.
- Understanding the molecular epidemiology of HCV is crucial for effective control programs.
- Peshawar, Pakistan, has a high burden of HCV infection.
Purpose of the Study:
- To investigate the molecular epidemiology of HCV genotype 3a in Peshawar.
- To perform phylogenetic analysis of the HCV Core gene for genotype 3a strains.
- To understand the genetic diversity of HCV 3a in the region.
Main Methods:
- Cross-sectional observational study involving chronically HCV-infected patients in Peshawar.
- HCV detection and genotyping using modified reverse transcription-polymerase chain reaction (RT-PCR).
- Amplification, sequencing, and phylogenetic analysis of the HCV genotype 3a Core gene using MEGA 6 software.
Main Results:
- HCV genotype 3a infection was identified in 45.5% of PCR-positive samples (192 out of 422).
- Sequencing of the HCV Core gene was performed for characterization of genotype 3a strains.
- Phylogenetic analysis showed that local sequences clustered with regional and international strains, indicating established transmission networks.
Conclusions:
- HCV genotype 3a demonstrates high prevalence in Peshawar, Pakistan.
- Phylogenetic analysis based on Core gene sequences highlights the presence of diverse HCV 3a lineages in Peshawar.
- The identified genetic diversity may influence disease management and potentially lead to increased economic burden due to antiviral resistance.
Background:
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.
Methods:
Chronically 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.
Results:
Among 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.
Conclusion:
HCV 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.
