Characterisation of hepatitis C virus recombination in Cameroon using non-specific next generation sequencing.

The importance of recombination for the evolution and genetic diversity of the hepatitis C virus (HCV) is currently uncertain. Only a small number of inter-genotypic recombinants have been so far identified, and each has core and envelope genes classified as genotype 2. Here we investigate 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 Illumina RNAseq sequencing. Recombination between genotypes 1 and 4 is confirmed in both samples and the parental lineages of each recombinant belong to HCV subtypes that are co-circulating at high prevalence in Cameroon. Using the RNAseq 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 new method, called Deep SimPlot, that can be used to visualise and identify viral recombination directly from the short sequence reads created by next-generation sequencing in conjunction with a consensus sequence.