High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods

Josep Quer, Josep Gregori, Francisco Rodríguez-Frias, Maria Buti, Antonio Madejon, Sofia Perez-del-Pulgar, Damir Garcia-Cehic, Rosario Casillas, Maria Blasi, Maria Homs, David Tabernero, Miguel Alvarez-Tejado, Jose Manuel Muñoz, Maria Cubero, Andrea Caballero, Jose Antonio DelCampo, Esteban Domingo, Irene Belmonte, Leonardo Nieto, Sabela LensPaloma Muñoz-de-Rueda, Paloma Sanz-Cameno, Silvia Sauleda, Marta Bes, Jordi Gomez, Carlos Briones, Celia Perales, Julie Sheldon, Lluis Castells, Lluis Viladomiu, Javier Salmeron, Angela Ruiz-Extremera, Rosa Quiles-Pérez, Ricardo Moreno-Otero, Rosario López-Rodríguez, Helena Allende, Manuel Romero-Gómez, Jaume Guardia, Rafael Esteban, Javier Garcia-Samaniego, Xavier Forns, Juan Ignacio Esteban

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60 Citations (Scopus)

Abstract

Copyright © 2015, American Society for Microbiology. All Rights Reserved. HepatitisCvirus(HCV)is classified into seven major genotypesand67 subtypes. Recent studies haveshownthat inHCVgenotype 1-infected patients, response rates to regimens containingdirect-acting antivirals(DAAs)are subtype dependent. Currently available genotypingmethods have limited subtyping accuracy.Wehave evaluated theperformanceof adeep-sequencing-basedHCVsubtyping assay, developed for the 454/GS-Junior platform, in comparisonwith thoseof two commercial assays (VersantHCVgenotype 2.0andAbbott Real-timeHCVGenotype II)andusingdirectNS5Bsequencing as a gold standard (direct sequencing), in 114 clinical specimenspreviously tested by first-generation hybridization assay (82 genotype 1and32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 callingbypopulation Sanger sequencing(69%1b,31%1a) in 81 specimensandidentified amixed-subtype infection (1b/3a/1a) in one sample. Similarly,amongthe 32previously indeterminate specimens, identical genotypeandsubtype results were obtained by directanddeep sequencing in all but four samples with dual infection. In contrast, both VersantHCVGenotype 2.0andAbbott Real-timeHCVGenotype II failed subtype 1 calling in 13 (16%) samples eachandwere unable to identify theHCVgenotype and/or subtype inmore than half of the nongenotype 1 samples.Weconcluded that deep sequencing ismore efficient forHCVsubtyping than currently available methodsandallows qualitative identificationofmixed infectionsandmay bemorehelpfulwith respect to informing treatment strategies withnewDAA-containing regimens across allHCVsubtypes.
Original languageEnglish
Pages (from-to)219-226
JournalJournal of Clinical Microbiology
Volume53
Issue number1
DOIs
Publication statusPublished - 1 Jan 2015

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