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Abstract
Hepatitis C virus (HCV), a small, single-stranded RNA virus with a 9.6 kb genome, is one of the most common causes of liver diseases. Sequencing of the 5ʹ untranslated region (UTR) is usually used for HCV genotyping, but it is less important in numerous subtypes due to its scarce sequence variations. This study aimed to identify genotypes using the 5ʹ UTR of HCV from cirrhotic patients of Khyber Pakhtunkhwa (KP). Serum RNA samples (44) were screened by real time PCR to determine the HCV viral load. Nested PCR was performed to identify cDNA and the 5ʹ UTR. The HCV 5′ UTR was sequenced using the Sanger method. MEGA-7 software was used to analyze evolutionary relatedness. After 5ʹ UTR sequencing, 26 samples (59%) were identified as genotype 3, and 2 samples (6%) were identified as genotypes 1, 2 and 4. The most predominant genotype was 3a, and genotype 4 was rarely reported in the phylogenetic tree. Analysis of the HCV 5ʹ UTR is an efficient alternative method for confirmation of various genotypes. Phylogenetic analysis showed that genotype 3 was dominant in the area of KP, Pakistan.
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Details
1 Abasyn University Peshawar, Department of Microbiology and Biotechnology, Khyber Pakhtunkhwa, Pakistan (GRID:grid.444982.7) (ISNI:0000 0004 0471 0173)
2 University Hospital of Cologne, Institute of Pathology, Laboratory of Translational Molecular Pathology, Cologne, Germany (GRID:grid.411097.a) (ISNI:0000 0000 8852 305X)
3 Gandhara University Peshawar, Kabir Medical College Peshawar, Khyber Pakhtunkhwa, Pakistan (GRID:grid.444987.2) (ISNI:0000 0004 0609 3121)
4 University of the Punjab Lahore, Centre of Excellence in Molecular Biology, Lahore, Pakistan (GRID:grid.11173.35) (ISNI:0000 0001 0670 519X)
5 The University of Lahore, Institute of Molecular Biology and Biotechnology, Lahore, Pakistan (GRID:grid.440564.7) (ISNI:0000 0001 0415 4232)
6 Swat University, Department of Biotechnology and Microbiology, Khyber Pakhtunkhwa, Pakistan (GRID:grid.449683.4) (ISNI:0000 0004 0522 445X)
7 Hong Kong University of Science and Technology, Division of Life Sciences, Center for Cancer Research and State Key Lab for Molecular Neuroscience, Clear Water Bay, Hong Kong (GRID:grid.24515.37) (ISNI:0000 0004 1937 1450)
8 Bacha Khan University Charsadda, Institute of Biotechnology and Microbiology, Khyber Pakhtunkhwa, Pakistan (GRID:grid.459380.3) (ISNI:0000 0004 4652 4475)
9 Riphah Faculty of Pharmaceutical Sciences, Islamabad, Pakistan (GRID:grid.459380.3)