title: Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing.
abstract: 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.
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: James C
authors.identifier: http://orcid.org/0000-0001-7276-9829
authors.initials: JC
authors.lastname: Iles
authors.affiliation: Service de Virologie, Centre Pasteur du Cameroun, Yaounde, Cameroon.
authors.forename: Richard
authors.initials: R
authors.lastname: Njouom
authors.affiliation: Service de Virologie, Centre Pasteur du Cameroun, Yaounde, Cameroon.
authors.forename: Yacouba
authors.initials: Y
authors.lastname: Foupouapouognigni
authors.affiliation: Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Bonsall
authors.affiliation: Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom.
authors.forename: Rory
authors.initials: R
authors.lastname: Bowden
authors.affiliation: Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom.
authors.forename: Amy
authors.initials: A
authors.lastname: Trebes
authors.affiliation: Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom.
authors.forename: Paolo
authors.initials: P
authors.lastname: Piazza
authors.affiliation: Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom.
authors.forename: Ellie
authors.initials: E
authors.lastname: Barnes
authors.affiliation: Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Canada.
authors.forename: Jacques
authors.initials: J
authors.lastname: Pépin
authors.affiliation: Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom.
authors.forename: Paul
authors.initials: P
authors.lastname: Klenerman
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom oliver.pybus@zoo.ox.ac.uk.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
mesh_terms: D000368:Aged; D002163:Cameroon; D016000:Cluster Analysis; D005260:Female; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*