Cross-sectional Pakistani HCV convenience cohort identifies dominant genotype 3a

A cross-sectional, laboratory-based study of hepatitis C virus in Pakistan found that genotype 3a accounted for 85.06% of classified infections in a cohort of 1,200 HCV-positive samples referred from Punjab, Khyber Pakhtunkhwa and Sindh. The analysis also identified descriptive associations between older age, elevated alanine transaminase (ALT) and higher viral loads in samples from Punjab and Khyber Pakhtunkhwa. Because the main cohort was assembled through laboratory referrals rather than probability-based population sampling, the findings characterize selected clinical samples and do not provide a nationally representative estimate of Pakistan’s HCV prevalence or genotype distribution.

Researchers established three sample groups. The principal cohort consisted of 1,200 HCV-positive serum specimens collected in Punjab, Khyber Pakhtunkhwa and Sindh. For these samples, investigators recorded demographic information, including age, sex and geographic region, and quantified ALT levels. Real-time polymerase chain reaction and HCV genotyping were used to characterize infection. The second group comprised 200 randomly selected samples from healthy volunteers with no liver ailment, while the third contained 100 hepatitis B virus (HBV)-positive samples. Reverse-transcription PCR confirmed active HCV infection in the two comparison groups, which were evaluated as pilot cohorts rather than as comprehensive population surveys.

The main cohort included participants ranging from 5 to 77 years old. ALT levels were significantly associated with age groups in both sexes, with a reported p-value below 0.001, and both ALT levels and high viral titers were significantly associated with sex. Samples from Punjab and Khyber Pakhtunkhwa also showed a greater tendency toward high viral loads than samples from Sindh, with the association reported at p below 0.001. The researchers described these demographic and regional patterns as supported by large effect sizes, including Cramer’s V values greater than 0.50. These are associations within the sampled groups; the cross-sectional design does not establish that age, sex or region caused the observed biochemical or virological differences.

Molecular analysis detected HCV genotypes 1, 2, 3 and 3a, with genotype 3a the most prevalent at 85.06% of classified infections. The broad age range and coverage of three provinces give the main cohort a substantial clinical scope, but its referral-based composition remains an important limitation. The genotype proportions may therefore reflect the people whose specimens reached the participating laboratories rather than the distribution of HCV across Pakistan’s population. Similarly, the reported age and regional patterns describe the main cohort and should not be interpreted as population-wide trends.

The two pilot cohorts yielded markedly different estimates of PCR-confirmed HCV prevalence. Active infection was detected in 4.6% of the healthy-volunteer group, with a 95% confidence interval of 1.5% to 10.4%, and in 11.26% of the HBV-positive group, with a 95% confidence interval of 5.0% to 21.0%. The authors said the roughly threefold difference between the groups indicates survivorship bias in clinically based reporting. Both estimates came from small convenience samples, however, and the authors characterized them as preliminary. The source places these pilot findings against reported national HCV seroprevalence estimates of 5.31% to 7.5% and PCR-confirmed active-infection prevalence estimates of 1.05% to 5.78%, but the study itself does not constitute a population-prevalence survey.

Pakistan’s hepatitis C burden provides the context for examining the virus through several related dimensions. HCV affects the liver, and persistent infection can lead to cirrhosis and hepatocellular carcinoma, according to the study background. By combining demographic information, ALT measurements, viral-load comparisons and genotyping, the research offers a detailed laboratory view of infection in the main cohort while also testing how prevalence appeared in two smaller comparison groups. Its central result is the marked predominance of genotype 3a among the classified HCV-positive referrals, accompanied by measurable demographic and regional associations. The authors conclude that systematic, population-based surveillance is needed to establish HCV epidemiology more accurately in Pakistan and determine whether the observed genotype, age, ALT and viral-load patterns extend beyond laboratory-referred patients and the limited pilot samples examined here.

Subject of Research: Molecular and epidemiological characterization of HCV in Pakistani laboratory-referred and pilot cohorts

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

Article References: Nawaz, R., Nawaz, A., Arif, M. A., Rehman, Z., Shah, R., Shafi, F., Javaid, M., Idrees, H., Shahid, M., Amin, I., Afzal, S., Ahad, A., Ali, M. R., Khan, M. A., Sajjad, S., Rafique, S., & Idrees, M. (2026). Characterization of the Hepatitis C virus in Pakistan: comprehensive molecular and epidemiological insights. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14248-9

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14248-9

Keywords: hepatitis C, HCV genotype 3a, Pakistan, cross-sectional study, viral load, alanine transaminase, laboratory cohort, prevalence, Punjab, Khyber Pakhtunkhwa, Characterization, Hepatitis