Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing

The importance of recombination in the evolution and genetic diversity of the hepatitis C virus (HCV) is currently uncertain. Only a small number of intergenotypic recombinants have been identified so far, and each has core and envelope genes classified as belonging to genotype 2. Here, we investigated two putative genotype 4/1 recombinants from southern Cameroon using a number of approaches, including standard Sanger sequencing, genotype-specific PCR amplification, and non-HCV-specific Illu-mina RNA sequencing (RNA-seq). Recombination between genotypes 1 and 4 was confirmed in both samples, and the parental lineages of each recombinant belong to HCV subtypes that are cocirculating at a high prevalence in Cameroon. Using the RNA-seq approach, we obtained a complete genome for one sample, which contained a recombination breakpoint at the E2/P7 gene junction.We developed and applied a newmethod, called Deep SimPlot, which can be used to visualize and identify viral recom-bination directly from the short sequence reads created by next-generation sequencing in conjunction with a consensus sequence. Hepatitis C virus (HCV) is a globally prevalent and geneticallydiverse virus that infects approximately 170 million people worldwide (1). HCV is classified into seven genotypes (1 to 7), with an average 35 % nucleotide divergence between strains be-longing to different genotypes (2). All genotypes except 5 and 7 are subdivided into numerous subtypes (1a, 1b, 1c, 2a, 2b, etc.), an