Molecular Epidemiology of Hepatitis C Virus Genotypes in Northern Thailand: A Retrospective Study from 2016 to 2024

Abstract

Background: Hepatitis C virus (HCV) remains a significant public health concern in Thailand, with genotype-specific, drug-dependent variations influencing treatment response and disease progression. Despite the availability of pan-genotypic direct-acting antivirals (DAAs), genotype surveillance remains essential for optimizing national elimination strategies. This study thus aims to characterize the molecular distribution of HCV genotypes in northern Thailand. Methods: We conducted a retrospective molecular epidemiological study on 1737 HCV-infected patients who attended the Clinical Microbiology Service Unit (CMSU) Laboratory, Faculty of Associated Medical Sciences, Chiang Mai University between April 2016 and June 2024. HCV genotyping was performed using Sanger sequencing and reverse hybridization line probe assay (LiPA). Results: Genotype 3 was the most prevalent (36.6%), followed by genotype 1 (35.8%) and genotype 6 (27.2%). Subtype 3a (27.2%) predominated, along with 1a (22.1%), 1b (12.6%), and genotype 6 subtypes including 6c to 6l (13.5%) and 6n (6.6%). Males had a higher prevalence of genotype 1, while genotype 3 was more common among females. Temporal analysis revealed a relative increase in genotype 6 prevalence since 2021. Genotype 6 also exhibited significantly higher median viral loads compared to genotypes 1 and 3 (p < 0.0001). Conclusions: This study provides updated evidence on the shifting distribution of HCV genotypes in northern Thailand, particularly the increasing prevalence of genotype 6. These findings underscore the importance of continued molecular surveillance to guide genotype-specific treatment strategies and support Thailand's 2030 HCV elimination goals.

Keywords: HCV genotypes; Thailand; antiviral therapy; genotype distribution; hepatocellular carcinoma; liver disease.

Figure 1

Overall distribution of HCV genotypes in 1737 patients diagnosed at CMSU from 2016 to 2024.

Figure 2

Geographical distribution of HCV genotypes by province in northern Thailand (2016–2024).

Figure 3

Temporal trends in HCV genotype distribution in northern Thailand (2016–2024). Stacked area chart showing annual proportions of HCV genotypes 1, 2, 3, 4, and 6 across the study period.

Figure 4

Distribution of HCV genotypes based on sex differences. Different genotypes were indicated by different colors in the key. The percentage was calculated based on the proportion of different HCV genotypes with the total number of males or females. n, the total number of cases who are male or female.

Figure 5

Association between HCV genotypes and level of viral load. The x-axis represents different HCV genotypes, including genotypes 1, 3, and 6. Genotype 2 was missing due to no data for HCV viral load. Each dot represents an individual sample in each genotype. The yellow line indicates the median values and the magenta lines represent the interquartile range. Black lines show the link between two different genotypes. * p < 0.01, ** p < 0.001.