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Title: Using NS5B Sequencing for Hepatitis C Virus Genotyping Reveals Discordances with Commercial Platforms.
Authors: Chueca, Natalia
Rivadulla, Isidro
Lovatti, Rubén
Reina, Gabriel
Blanco, Ana
Fernandez-Caballero, Jose Angel
Cardeñoso, Laura
Rodriguez-Granjer, Javier
Fernandez-Alonso, Miriam
Aguilera, Antonio
Alvarez, Marta
Galán, Juan Carlos
García, Federico
metadata.dc.contributor.authoraffiliation: [Chueca,N; Fernandez-Caballero,JA; Alvarez,M; García,F] Servicio de Microbiología, Complejo Hospitalario Universitario Granada, Hospital San Cecilio. Instituto de Investigación Biosanitaria IBS, Granada, Spain. [Rivadulla,I] Departamento de Microbiología y Parasitología USC. Servicio de Microbiología Hospital Conxo-CHUS Santiago de Compostela, A Coruña, Spain. [Lovatti,R; Galán,JC] Servicio de Microbiología, Hospital Ramón y Cajal. Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. [Reina,G; Fernandez-Alonso,M] Servicio de Microbiología, Clínica Universidad de Navarra. Navarra Institute for Health Research (IdiSNA), Pamplona, Spain. [Blanco,A; Cardeñoso,L] Servicio de Microbiología, Hospital la Princesa, Madrid, Spain. [Rodriguez-Granjer,J] Servicio de Microbiología, Complejo Hospitalario Universitario Granada, Hospital Virgen de las Nieves, Granada, Spain.
Keywords: Antivirales;Genotipo;Técnicas de genotipaje;Hepacivirus;España
metadata.dc.subject.mesh: Medical Subject Headings::Chemicals and Drugs::Chemical Actions and Uses::Pharmacologic Actions::Therapeutic Uses::Anti-Infective Agents::Antiviral Agents
Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genotype
Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Genotyping Techniques
Medical Subject Headings::Organisms::Viruses::Hepatitis Viruses::Hepacivirus
Medical Subject Headings::Geographicals::Geographic Locations::Europe::Spain
Issue Date: 20-Apr-2016
Publisher: Public Library of Science
Citation: Chueca N, Rivadulla I, Lovatti R, Reina G, Blanco A, Fernandez-Caballero JA, et al. Using NS5B Sequencing for Hepatitis C Virus Genotyping Reveals Discordances with Commercial Platforms. PLoS ONE. 2016; 11(4):e0153754
Abstract: We aimed to evaluate the correct assignment of HCV genotypes by three commercial methods-Trugene HCV genotyping kit (Siemens), VERSANT HCV Genotype 2.0 assay (Siemens), and Real-Time HCV genotype II (Abbott)-compared to NS5B sequencing. We studied 327 clinical samples that carried representative HCV genotypes of the most frequent geno/subtypes in Spain. After commercial genotyping, the sequencing of a 367 bp fragment in the NS5B gene was used to assign genotypes. Major discrepancies were defined, e.g. differences in the assigned genotype by one of the three methods and NS5B sequencing, including misclassification of subtypes 1a and 1b. Minor discrepancies were considered when differences at subtype levels, other than 1a and 1b, were observed. The overall discordance with the reference method was 34% for Trugene and 15% for VERSANT HCV2.0. The Abbott assay correctly identified all 1a and 1b subtypes, but did not subtype all the 2, 3, 4 and 5 (34%) genotypes. Major discordances were found in 16% of cases for Trugene HCV, and the majority were 1b- to 1a-related discordances; major discordances were found for VERSANT HCV 2.0 in 6% of cases, which were all but one 1b to 1a cases. These results indicated that the Trugene assay especially, and to a lesser extent, Versant HCV 2.0, can fail to differentiate HCV subtypes 1a and 1b, and lead to critical errors in clinical practice for correctly using directly acting antiviral agents.
Description: Journal Article;
metadata.dc.identifier.doi: 10.1371/journal.pone.0153754
ISSN: 1932-6203 (Online)
Appears in Collections:01- Artículos - Complejo Hospitalario Universitario de Granada
01- Artículos - ibsGRANADA. Instituto de Investigación Biosanitaria de Granada

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