Background:  We investigated the genetic diversity of hepatitis C virus (HCV) among rural populations in southern Cameroon where HIV-1 has been previously characterized. HCV infection is endemic in Sub-Saharan Africa where a broad sequence diversity of predominantly genotypes 1, 2, and 4 has been reported from convenience samples, urban clinics, and single villages. Correspondingly, HIV-1 genetic variability is pronounced in Central Africa where Cameroon is situated. We sought to characterize HCV genetic variants among inhabitants of 4 widely dispersed villages in the rainforest in Cameroon, focusing on those who reported exposure to non-human primate blood.

Methods:  The core/E1 region of 34 HCV RNA-positive samples was sequenced directly from RT-PCR product and compared with known sequences from GenBank. Phylogenetic analysis of HCV was performed using PHYLIP, PAUP*, and SimPlot, and clades supported in less than 700 of 1000 permuted trees were considered insignificant.

Results:  HCV sequences clustered with genotypes 1, 2, and 4, and formed distinct clades at a depth consistent with subtypes, but not with previously identified subtypes. These results suggest as many as 8 novel subtypes including 4 of genotype 1, which is the most prevalent and treatment-resistant genotype worldwide. Only 1 individual was co-infected with HIV-1 and HCV.

Conclusions:  These data indicate the emergence of HCV variants among rural populations in Cameroon where the risk of transmission is low. Genotypes 1, 2, and 4 of HCV are prevalent in this population, comparable with data from other studies in urban populations in Cameroon. The detection of divergent HCV strains and HIV-1 second generation recombinants in this population, raises concern regarding the performance of diagnostic tests, response to therapy and development of vaccines.

Keywords: rural; population; cameroon