Identification of a novel HCV subtype 6xl in Baoshan, China

Abstract Background Hepatitis C virus (HCV) infection remains a major global public health concern, particularly in border regions. Baoshan, located in Yunnan Province, China, borders Myanmar and serves as a key regional hub; however, the epidemiological characteristics of HCV in this area remain poorly understood. Methods A total of 160 newly reported HCV antibody-positive individuals in Baoshan were enrolled from June 2022 to October 2023. The C/E2 and NS5B gene fragments were amplified and sequenced, followed by phylogenetic analysis, pairwise genetic distance calculation, recombination analysis, and Bayesian phylogeographic analysis. Results Sequences were successfully obtained from 128 samples of 160. The predominant genotypes were genotype 6 (52.3%) and genotype 3 (40.6%), with lower proportions of genotype 1 (6.3%) and genotype 2 (0.8%). Nine known subtypes and one novel HCV subtype 6xl were identified, with the latter accounting for 8.6% of the study population. Phylogenetic analysis revealed that this HCV-6 novel subtype was most closely related to 6xk, forming an independent clade with no evidence of recombination. Bayesian analysis estimated its time to the most recent common ancestor to be approximately 1985–1991, with its effective population size showing a slight decline before 2021 and remaining stable thereafter. Conclusions These findings reveal a unique HCV genotype distribution in Baoshan dominated by genotypes 6 and 3, and identify a novel subtype of genotype 6 for the first time in this region. This highlights the importance of continuous molecular epidemiological surveillance in border areas for the detection of novel subtypes and the implementation of targeted prevention and control strategies.