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 investiga...

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Published inJournal of clinical microbiology Vol. 53; no. 10; pp. 3155 - 3164
Main Authors Iles, James C, Njouom, Richard, Foupouapouognigni, Yacouba, Bonsall, David, Bowden, Rory, Trebes, Amy, Piazza, Paolo, Barnes, Ellie, Pépin, Jacques, Klenerman, Paul, Pybus, Oliver G
Format Journal Article
LanguageEnglish
Published United States American Society for Microbiology 01.10.2015
Subjects
Aged
Cameroon
Cluster Analysis
Female
Genotype
Hepacivirus - classification
Hepacivirus - genetics
Hepacivirus - isolation & purification
Hepatitis C - virology
High-Throughput Nucleotide Sequencing - methods
Humans
Male
Middle Aged
Molecular Sequence Data
Phylogeny
Recombination, Genetic
Sequence Analysis, DNA - methods
Virology
Cameroon
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Summary: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 Illumina 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 new method, called Deep SimPlot, which can be used to visualize and identify viral recombination directly from the short sequence reads created by next-generation sequencing in conjunction with a consensus sequence.
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Citation Iles JC, Njouom R, Foupouapouognigni Y, Bonsall D, Bowden R, Trebes A, Piazza P, Barnes E, Pépin J, Klenerman P, Pybus OG. 2015. Characterization of hepatitis C virus recombination in Cameroon by use of nonspecific next-generation sequencing. J Clin Microbiol 53:3155–3164. doi:10.1128/JCM.00483-15.
J.C.I. and R.N. contributed equally to this article.
ISSN:0095-1137
1098-660X
DOI:10.1128/JCM.00483-15