TY - JOUR
T1 - High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods
AU - Quer, Josep
AU - Gregori, Josep
AU - Rodríguez-Frias, Francisco
AU - Buti, Maria
AU - Madejon, Antonio
AU - Perez-del-Pulgar, Sofia
AU - Garcia-Cehic, Damir
AU - Casillas, Rosario
AU - Blasi, Maria
AU - Homs, Maria
AU - Tabernero, David
AU - Alvarez-Tejado, Miguel
AU - Muñoz, Jose Manuel
AU - Cubero, Maria
AU - Caballero, Andrea
AU - DelCampo, Jose Antonio
AU - Domingo, Esteban
AU - Belmonte, Irene
AU - Nieto, Leonardo
AU - Lens, Sabela
AU - Muñoz-de-Rueda, Paloma
AU - Sanz-Cameno, Paloma
AU - Sauleda, Silvia
AU - Bes, Marta
AU - Gomez, Jordi
AU - Briones, Carlos
AU - Perales, Celia
AU - Sheldon, Julie
AU - Castells, Lluis
AU - Viladomiu, Lluis
AU - Salmeron, Javier
AU - Ruiz-Extremera, Angela
AU - Quiles-Pérez, Rosa
AU - Moreno-Otero, Ricardo
AU - López-Rodríguez, Rosario
AU - Allende, Helena
AU - Romero-Gómez, Manuel
AU - Guardia, Jaume
AU - Esteban, Rafael
AU - Garcia-Samaniego, Javier
AU - Forns, Xavier
AU - Esteban, Juan Ignacio
PY - 2015/1/1
Y1 - 2015/1/1
N2 - 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.
AB - 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.
U2 - 10.1128/JCM.02093-14
DO - 10.1128/JCM.02093-14
M3 - Article
SN - 0095-1137
VL - 53
SP - 219
EP - 226
JO - Journal of Clinical Microbiology
JF - Journal of Clinical Microbiology
IS - 1
ER -
