High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods
Autor (es)
Quer, Josep; Gregori, Josep; Rodríguez-Frias, Francisco; Buti, Maria; Madejon, Antonio; Perez-del-Pulgar, Sofia; Garcia-Cehic, Damir; Casillas, Rosario; Blasi, Maria; Homs, Maria; Tabernero, David; Alvarez-Tejado, Miguel; Muñoz, Jose Manuel; Cubero, Maria; Caballero, Andrea; Campo, Jose Antonio del; Domingo, Esteban; Belmonte, Irene; Nieto, Leonardo; Lens, Sabela; Muñoz-de-Rueda, Paloma; Sanz-Cameno, Paloma; Sauleda, Silvia; Bes, Marta; Gomez, Jordi; Briones, Carlos; Perales, Celia; Sheldon, Julie; Castells, Lluis; Viladomiu, Lluis; Salmerón, Javier; Ruiz-Extremera, Angela; Quiles-Pérez, Rosa; Moreno-Otero, Ricardo; López-Rodríguez, Rosario; Allende, Helena; Romero-Gómez, Manuel; Guardia, Jaume; Esteban, Rafael; Garcia-Samaniego, Javier; Forns, Xavier; Esteban, Juan IgnacioEntidad
UAM. Departamento de Medicina; Centro de Biología Molecular Severo Ochoa (CBM)Editor
American Society for MicrobiologyFecha de edición
2015-01-01Cita
10.1128/JCM.02093-14
Journal of Clinical Microbiology 53.1 (2015): 219-226
ISSN
0095-1137; 1098-660X (on line)DOI
10.1128/JCM.02093-14Financiado por
This study has been supported by CDTI (Centro para el Desarrollo Tecnológico Industrial), Spanish Ministry of Economics and Competitiveness (MINECO), IDI-20110115; MINECO projects SAF 2009-10403; and also by the Spanish Ministry of Health, Instituto de Salud Carlos III (FIS) projects PI10/01505, PI12/01893, and PI13/00456. CIBERehd is funded by the Instituto de Salud Carlos III, Madrid, Spain. Work at CBMSO was supported by grant MINECO-BFU2011-23604, FIPSE, and Fundación Ramón Areces. X. Forns received unrestricted grant support from Roche and has acted as advisor for MSD, Gilead, and Abbvie. M. Alvarez-Tejado, J. Gregori, and J. M. Muñoz work in Roche DiagnosticsProyecto
Gobierno de España. IDI-20110115; Gobierno de España. SAF 2009-10403; Gobierno de España. BFU2011-23604,Versión del editor
http://dx.doi.org/10.1128/JCM.02093-14Materias
Hepatitis C; Antivirals; HCV; MedicinaDerechos
© 2015, American Society for MicrobiologyResumen
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
Lista de ficheros
Google Scholar:Quer, Josep
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Gregori, Josep
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Rodríguez-Frias, Francisco
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Buti, Maria
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Madejon, Antonio
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Perez-del-Pulgar, Sofia
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Garcia-Cehic, Damir
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Casillas, Rosario
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Blasi, Maria
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Homs, Maria
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Tabernero, David
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Alvarez-Tejado, Miguel
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Muñoz, Jose Manuel
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Cubero, Maria
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Caballero, Andrea
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Campo, Jose Antonio del
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Domingo, Esteban
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Belmonte, Irene
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Nieto, Leonardo
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Lens, Sabela
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Muñoz-de-Rueda, Paloma
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Sanz-Cameno, Paloma
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Sauleda, Silvia
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Bes, Marta
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Gomez, Jordi
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Briones, Carlos
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Perales, Celia
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Sheldon, Julie
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Castells, Lluis
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Viladomiu, Lluis
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Salmerón, Javier
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Ruiz-Extremera, Angela
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Quiles-Pérez, Rosa
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Moreno-Otero, Ricardo
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López-Rodríguez, Rosario
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Allende, Helena
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Romero-Gómez, Manuel
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Guardia, Jaume
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Esteban, Rafael
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Garcia-Samaniego, Javier
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Forns, Xavier
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Esteban, Juan Ignacio
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