Genotyping of HCV RNA Reveals That 3a Is the Most Prevalent Genotype in Mardan, Pakistan

The clinical outcomes of patients infected with hepatitis C virus (HCV) range from acute resolving hepatitis to chronic liver diseases such as liver cirrhosis or hepatocellular carcinoma. Identification of the infecting virus genotype is indispensable for the exploration of many aspects of HCV infection, including epidemiology, pathogenesis, and response to antiviral therapy. 1419 individuals were screened for anti-HCV in this study, of which 166 (11.7%) were found reactive by ICT (Immunochromatographic test). These 166 anti-HCV positive and 26 normal individuals were further analyzed. RNA was extracted from serum and reverse-transcribed to cDNA and the core region of HCV genome was targeted and amplified by multiplex PCR. HCV RNA was detected in 121 individuals, of which 87 were male and 34 were female. Genotype 3a was the most prevalent among all the genotypes observed followed by 3b. Genotypes 1a, 2a, and 2b were found in 10.89%, 13.22%, and 6.61% patients, respectively. 25.41% of the HCV RNA positive samples were not typed. 6.05% of patients were found having mixed genotypes. These findings will not only help the physicians to prescribe more appropriate treatment for the HCV infection but will also draw the attention of health-related policy makers to devise strategies to curb the disease more effectively. 1. Introduction Hepatitis C virus (HCV) is the most frequent cause of chronic viral hepatitis worldwide. In the recent years, infection with HCV has emerged as one of the most common causes of acute and chronic liver diseases all over the world [1]. HCV is a member of the Flaviviridae family that bears approximately 10？kb long positive sense single-stranded RNA (ssRNA) genome. Since anti-HCV testing alone cannot differentiate between acute, chronic, or resolved infection, a supplementary test must also be carried out, involving measurement of anti-HCV immunoglobulin G activity index [2] or antibody reactivities to specific HCV structural and nonstructural proteins [3], to confirm a positive anti-HCV result [1]. HCV is known to have high rate of genetic heterogeneity [4]. This has allowed HCV strains to be classified into a number of genetically distinct groups, known as genotypes, subtypes, isolates, and quasispecies [5]. The genetic variability among HCV strains is 65.8%–68.7% nucleotide sequence identities of full-length sequences for types, 76.9%–80.1% nucleotide sequence identities of full-length sequences for subtypes, and 90.8%–99% nucleotide sequence identities of full-length sequences for isolates and quasispecies [6]. Six major genotypes,