Identification and Molecular Characterization of 10 Novel Recombinant Variants of Hepatitis C Virus (HCV) in Cameroon Using Oxford Nanopore Sequencing and Phylogenomic Analysis.

Hepatitis C virus (HCV) remains a major global public health concern due to the absence of an effective vaccine and its diversity, which complicate diagnosis, genotyping, and clinical management despite the widespread use of direct-acting antivirals (DAAs). In regions where multiple HCV genotypes co-circulate, inter-genotypic recombination represents an additional challenge for accurate classification and molecular surveillance. In this study, we investigate the presence and characterize inter-genotypic recombinant strains of HCV in Cameroon. Among 512 chronically infected patients initially genotyped by Sanger sequencing of Core and NS5B regions, 10 samples (1.9%) showed genotypic discordance, suggesting putative recombination. Whole-genome sequencing using Oxford Nanopore technology, combined with phylogenomic and recombinant analysis, confirmed the recombinant nature of all 10 isolates. Most recombinant (7/10) shared a unique breakpoint in the NS2/NS3 region, primarily displaying a genotype 2/1 genomic profile, while one group had a breakpoint in the E2/p7 region (genotype 4/1 genomic profile). One isolate exhibited a more complex structure with two successive breakpoints (4/2 followed by 2/1). Genotypes 1 and 2 were the most frequently involved parental lineages. These findings demonstrate the ongoing circulation of diverse natural HCV recombinant forms in Cameroon and identify genomic regions that appear preferentially involved in recombination events. Our results highlight the limitations of genotypic approaches based on partial genomes and underscore the importance of comprehensive genomic characterization to improve HCV genotype classification, surveillance, and therapeutic strategies in Central Africa.