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Reference: Iles, JC, Njouom, R, Foupouapouognigni, Y et al., (2015). Characterisation of hepatitis C virus recombination in Cameroon using non-specific next generation sequencing. Journal of Clinical Microbiology, 53 (10), 3155-3164.Citable link to this page:

 

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

Abstract: 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.

Peer Review status:Peer reviewedPublication status:PublishedVersion:Publisher's versionNotes:Copyright © 2015, Iles et al. This is an open-access article distributed under theterms of the Creative Commons Attribution 3.0 Unported license.

Bibliographic Details

Publisher: American Society for Microbiology

Publisher Website: http://www.asm.org/

Journal: Journal of Clinical Microbiologysee more from them

Publication Website: http://jcm.asm.org/

Issue Date: 2015

pages:3155-3164Identifiers

Urn: uuid:44353acc-eda8-4197-a787-885de7057aee

Source identifier: 535876

Eissn: 1098-660X

Doi: https://doi.org/10.1128/jcm.00483-15

Issn: 0095-1137 Item Description

Type: Journal article;

Language: eng

Version: Publisher's version Tiny URL: pubs:535876

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Autor: Iles, JC - - - Njouom, R - - - Foupouapouognigni, Y - - - Bonsall, D - - - Bowden, R - - - Trebes, A - - - Piazza, P - - - Barnes

Fuente: https://ora.ox.ac.uk/objects/uuid:44353acc-eda8-4197-a787-885de7057aee



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