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Phylogenetic Characterization of the 5' Untranslated Region of Untypable HCV Genotypes Circulating in Pakistan
Usman Ghani1, Irshad Ur Rehman1, Muhammad Ali2
1Center of Biotechnology and Microbiology (COBAM), University of Peshawar, Peshawar, Pakistan.
Introduction:
Commercial methods for HCV genotyping is challenged by the increased prevalence of untypable genotypes in Pakistan.
Objective:
The aim of the current study was to perform nucleotide sequencing of 5' UTR region for genotyping of viral isolates circulating in Peshawar, Pakistan.
Methods:
The total number of commercially untypable samples were 94 in which 18 samples were sequenced for the characterization of 5' UTR region. Post-sequencing analysis was performed for genotype identification (n = 18) and molecular phylogenetic analysis.
Results:
The current study reveals different genotypes, that is, 10/18 viral isolates were found to be genotype 3a (55.55%), 3 isolates (genotype 3b, 16.66%), 2 isolates (genotype 6h/6g, 11.11%), 2 (6g/d, 11.11%), and 1 sample (genotype 1c, 5.55%). In addition, genotype 3a is the dominant representative of HCV circulating in Pakistan and has been increasing across the country.
Conclusion:
The current study also reveals that genotype 6 (2 were genotype 6h/6g and 2 were 6g/d) is also circulating in Pakistan and not restricted to South China and Hong Kong.
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