High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods
| Autor: | Xavier Forns, Marta Bes, Javier García-Samaniego, Manuel Romero-Gómez, Rafael Esteban, Josep Gregori, Maria Buti, Julie Sheldon, Silvia Sauleda, Sofía Pérez-del-Pulgar, Maria Homs, Miguel Álvarez-Tejado, Celia Perales, David Tabernero, Rosa Quiles-Pérez, L Viladomiu, Jose Antonio delCampo, Jordi Gómez, Carlos Briones, Antonio Madejón, Sabela Lens, Jose Manuel Muñoz, Maria Blasi, Francisco Rodriguez-Frias, Lluis Castells, Rosario López-Rodríguez, Maria Cubero, Jaume Guardia, Rosario Casillas, Josep Quer, Andrea Caballero, Damir Garcia-Cehic, Paloma Muñoz-de-Rueda, Paloma Sanz-Cameno, Juan Ignacio Esteban, Javier Salmerón, Irene Belmonte, Helena Allende, Ricardo Moreno-Otero, L. Nieto, Angela Ruiz-Extremera, Esteban Domingo |
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| Přispěvatelé: | [Quer,J, Gregori,J, Buti,M, Garcia-Cehic,D, Cubero,M, Castells,L, Viladomiu,L, Guardia,J, Esteban,R, Esteban,JI] Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca—Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain. [Quer,J, Rodríguez-Friaas,F, Madejon,A, Perez-del-Pulgar,S, Casillas,R, Blasi,M, Homs,M, Tabernero,D, Cubero, del Campo,JA, Domingo,E, Lens,S, Muñoz-de-Rueda,P, Sanz-Cameno,P, Sauleda,S, Bes,M, Gomez,J, Briones,C, Perales,C, Sheldon,J, Salmeron,J, Ruiz-Extremera,A, Quiles-Pérez,R, Moreno-Otero,R, López-Rodríguez,R, Romero-Gómez,M, Garcia-Samaniego,J, Forns,X, Esteban,JI] Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain. [Quer,J, Rodríguez-Frias,F, Esteban,JI] Universitat Autònoma de Barcelona, Barcelona, Spain. [Gregori,J, Alvarez-Tejado,M, Muñoz,JM] Roche Diagnostics SL, Barcelona, Spain. [Rodrígue-Frias,F, Casilla,R, Caballero,A, Belmonte,I, Nieto,L] Biochemistry Unit, Virology Unit /Microbiology Department, HUVH, Barcelona, Spain. [Madejo,A, Garcia-Samaniego,J] Liver Unit, Hospital La Paz-Carlos III, Madrid, Spain. [Perez-del-Pulgar,S, Forns,X] Liver Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain. [del Campo,JA, Romero-Gomez,M] Hospital Universitario Virgen de Valme, Seville, Spain.[Domingo,E, Sheldon,J] Centro de Biología Molecular Severo Ochoa-Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain. [Muñoz-de-Rueda,P, Ruiz Extremera,A, Quiles-Pérez,R] Hospital San Cecilio, Granada, Spain. [San-Cameno,P, López-Rodríguez,R] Hospital de la Princesa, Madrid, Spain. [Sauleda,S, Bes,M] Banc de Sang i de Teixits, Institut Català de la Salut, Barcelona, Spain. [Gomez,J] CSIC, Instituto de Parasitología y Biomedicina López Neyra, Granada, Spain. [Briones,C] Centro de Astrobiología (CSIC-INTA), Madrid, Spain. [Allende,H] Pathological Anatomy Department, VHIR-HUVH, Barcelona, Spain., 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., UAM. Departamento de Medicina, Centro de Biología Molecular Severo Ochoa (CBM), Centro para el Desarrollo Tecnológico Industrial (España), Ministerio de Economía y Competitividad (España), Ministerio de Sanidad y Consumo (España), Fundación para la Investigación y la Prevención del Sida en España, Fundación Ramón Areces, Instituto de Salud Carlos III |
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Microbiology (medical)
Genotyping Techniques Genotype Medicina Hepatitis C virus Population Organisms::Viruses::Hepatitis Viruses::Hepacivirus [Medical Subject Headings] Diseases::Virus Diseases::Hepatitis Viral Human::Hepatitis C [Medical Subject Headings] Chemicals and Drugs::Chemical Actions and Uses::Specialty Uses of Chemicals::Laboratory Chemicals::Indicators and Reagents::Reagent Kits Diagnostic [Medical Subject Headings] Hepacivirus Biology Viral Nonstructural Proteins medicine.disease_cause Deep sequencing Técnicas de genotipaje Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans [Medical Subject Headings] chemistry.chemical_compound symbols.namesake Proteínas no estructurales virales Virology medicine Humans Chemicals and Drugs::Amino Acids Peptides and Proteins::Proteins::Viral Proteins::Viral Nonstructural Proteins [Medical Subject Headings] education NS5B Genotyping Phylogeny Sanger sequencing education.field_of_study Analytical Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Genotyping Techniques [Medical Subject Headings] High-Throughput Nucleotide Sequencing Antivirals Hepatitis C Subtyping Author Corrections Humanos Juego de reactivos para diagnóstico Filogenia chemistry HCV symbols Phenomena and Processes::Genetic Phenomena::Phylogeny [Medical Subject Headings] Phenomena and Processes::Genetic Phenomena::Genotype [Medical Subject Headings] Reagent Kits Diagnostic |
| Zdroj: | Repositorio Institucional de la Consejería de Sanidad de la Comunidad de Madrid Consejería de Sanidad de la Comunidad de Madrid Biblos-e Archivo. Repositorio Institucional de la UAM instname Digital.CSIC. Repositorio Institucional del CSIC |
| Popis: | 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. 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. |
| Databáze: | OpenAIRE |
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