Characterization of the Hepatitis C virus in Pakistan: comprehensive molecular and epidemiological insights

Hepatitis C virus affects the liver. Persistent infections lead to serious complications like hepatocellular carcinoma and liver-cirrhosis. Pakistan has very high HCV prevalence. With a national seroprevalence of 5.31%-7.5% and much lower yet concerning 1.05%-5.78% prevalence rate for PCR confirmed active infection. We have analyzed recent trends in its demography, biochemistry, molecular biology, and epidemiology within multi-regional laboratory-referred cohorts in Pakistan. Three cohorts of samples were established. For first cohort, 1200 HCV-positive serum samples were collected from Punjab, KPK, and Sindh provinces of Pakistan. Patient demographics, gender, age, and geographical region of the samples were recorded. Alanine transaminase levels were quantified. Real-time PCR and HCV genotyping were carried out. The second cohort comprised 200 random samples of healthy volunteers, not related to any liver ailment. Third cohort included a hundred HBV-positive samples. All these samples were confirmed for active infection via RT-PCR. Statistical analyses were carried out for the first cohort. Prevalence was evaluated in the last two cohorts as a pilot study proposing further analysis. For the first cohort, significant ALT levels association was found with different age groups from 5 to 77 years in both genders ( p < .001), while both ALT levels and high viral titers showed significant associations with gender. Higher tendency of viral loads exhibiting significant association ( p < .001) was observed from Punjab and KPK samples. These descriptive variations were supported by clear effect sizes (Cramer’s V > 0.50). Genotypes 1, 2, 3, and 3a (most prevalent 85.06%) were detected. Second and third pilot cohorts showed a prevalence of 4.6% (95%CI = 1.5%–10.4%) and 11.26% (95%CI = 5.0%–21.0%) respectively. The three-fold difference in prevalence between these cohorts indicates the survivorship bias inherent in clinical based reporting. In this laboratory-based convenience cohort, we identified descriptive associations of elevated ALT and higher viral loads with older age in Punjab and KPK regions. We also found much lower incidence of HCV in our pilot cohorts of convenience samples not associated with liver disease and coinfected with hepatitis B virus. Given the cross-sectional nature of the study, these findings represent a preliminary association and point towards a need for systematic, population-based surveillance to accurately map HCV epidemiology in Pakistan. Not applicable.