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Pakistan has second highest burden of hepatitis C virus (HCV) infected patients in the World. Little is known about the molecular epidemiology and risk factors for prevailing HCV genotypes in Pakistan. Considering this a multicenter cross-sectional study was conducted at 23different viral hepatitis control and prevention centers. A total of 175,897 patients were registered and screened for HCV, out of which 73,180 (41.6%) were found positive on Architect screening test. The screened positive patients were sequentially tested on RT-PCR; where 41,241 (56.35%) were detected positive. Molecular characterization results showed genotype 3 (73.9%) as the most prevalent type, followed by genotype 1 (9.7%), and genotype 4 (0.3%) was isolated for the first time in Pakistan. On regression analysis; risk factors associated with genotype 3 and 1 included; age group of 30–50 years, rural residence, exposure to >10 injections, barber shaving, circumcision by barbers, and low literacy rate. Phylogenetic analysis based on genotypes identified in this study and sequences isolated from Pakistan in last 10 years demonstrated that genotype 3 and 1 are endemic locally in Punjab province. The high prevalence rate of HCV is a threat for a generalized epidemic and genetic recombination with such variability of genotypes identified here is an alarming condition. More focused attention and resources should be spent in awareness of the population to prevent the spread of HCV among high risk population. • its the first study in Pakistan reporting HCV genotype 4 in a large cohort. • sequence analysis and genotyping is carried out on a large sample size. • this study reports an emerging pattern of HCV endemic highlighting the threat of epidemic in the country. [ABSTRACT FROM AUTHOR]