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Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing

Current HCV genotyping methods may have some limitations in detecting mixed infections. We aimed to determine the accuracy of genotyping and the detection of mixed-genotype infections using the Abbott-RealTime HCV Genotype II assay (Abbott-RT-PCR) in comparison with a Roche-Next Generation Sequencin...

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Autores principales: Fernández-Caso, Belén, Fernández-Caballero, Jose Ángel, Chueca, Natalia, Rojo, Eukene, de Salazar, Adolfo, García Buey, Luisa, Cardeñoso, Laura, García, Federico
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592891/
https://www.ncbi.nlm.nih.gov/pubmed/31239457
http://dx.doi.org/10.1038/s41598-019-42605-z
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author Fernández-Caso, Belén
Fernández-Caballero, Jose Ángel
Chueca, Natalia
Rojo, Eukene
de Salazar, Adolfo
García Buey, Luisa
Cardeñoso, Laura
García, Federico
author_facet Fernández-Caso, Belén
Fernández-Caballero, Jose Ángel
Chueca, Natalia
Rojo, Eukene
de Salazar, Adolfo
García Buey, Luisa
Cardeñoso, Laura
García, Federico
author_sort Fernández-Caso, Belén
collection PubMed
description Current HCV genotyping methods may have some limitations in detecting mixed infections. We aimed to determine the accuracy of genotyping and the detection of mixed-genotype infections using the Abbott-RealTime HCV Genotype II assay (Abbott-RT-PCR) in comparison with a Roche-Next Generation Sequencing assay (Roche-NGS). Plasma samples collected from 139 HCV-infected patients tested with Abbott-RT-PCR, 114 with single genotype (GT) and 25 with mixed GTs were genotyped using Roche-NGS. Roche-NGS confirmed all single GTs obtained with Abbott-RT-PCR. One case of Abbott GT 4 was found as GT 1a using Roche-NGS. Genotype 5 was confirmed using Roche-NGS in 75% cases (3 out of 4 cases). Twenty-five patients were identified as having mixed HCVinfections using Abbott-RT-PCR. The concordance between Abbott-RT-PCR and Roche-NGS was 76% (19 out of 25 cases). Three mixed-GT infections identified with the Abbott assay (two (1b + 4); one (1a + 3)) were reported as pure 1b using Roche-NGS. Very divergent results were found for the other three samples. When compared to Roche-NGS, Abbott-RT-PCR has performed excellently for the determination of patients infected with single GTs. For patients that are categorized as having a mixed infection using Abbott-RT-PCR, we recommend an NGS assay as a confirmation test.
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spelling pubmed-65928912019-07-03 Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing Fernández-Caso, Belén Fernández-Caballero, Jose Ángel Chueca, Natalia Rojo, Eukene de Salazar, Adolfo García Buey, Luisa Cardeñoso, Laura García, Federico Sci Rep Article Current HCV genotyping methods may have some limitations in detecting mixed infections. We aimed to determine the accuracy of genotyping and the detection of mixed-genotype infections using the Abbott-RealTime HCV Genotype II assay (Abbott-RT-PCR) in comparison with a Roche-Next Generation Sequencing assay (Roche-NGS). Plasma samples collected from 139 HCV-infected patients tested with Abbott-RT-PCR, 114 with single genotype (GT) and 25 with mixed GTs were genotyped using Roche-NGS. Roche-NGS confirmed all single GTs obtained with Abbott-RT-PCR. One case of Abbott GT 4 was found as GT 1a using Roche-NGS. Genotype 5 was confirmed using Roche-NGS in 75% cases (3 out of 4 cases). Twenty-five patients were identified as having mixed HCVinfections using Abbott-RT-PCR. The concordance between Abbott-RT-PCR and Roche-NGS was 76% (19 out of 25 cases). Three mixed-GT infections identified with the Abbott assay (two (1b + 4); one (1a + 3)) were reported as pure 1b using Roche-NGS. Very divergent results were found for the other three samples. When compared to Roche-NGS, Abbott-RT-PCR has performed excellently for the determination of patients infected with single GTs. For patients that are categorized as having a mixed infection using Abbott-RT-PCR, we recommend an NGS assay as a confirmation test. Nature Publishing Group UK 2019-06-25 /pmc/articles/PMC6592891/ /pubmed/31239457 http://dx.doi.org/10.1038/s41598-019-42605-z Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Fernández-Caso, Belén
Fernández-Caballero, Jose Ángel
Chueca, Natalia
Rojo, Eukene
de Salazar, Adolfo
García Buey, Luisa
Cardeñoso, Laura
García, Federico
Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing
title Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing
title_full Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing
title_fullStr Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing
title_full_unstemmed Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing
title_short Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing
title_sort infection with multiple hepatitis c virus genotypes detected using commercial tests should be confirmed using next generation sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592891/
https://www.ncbi.nlm.nih.gov/pubmed/31239457
http://dx.doi.org/10.1038/s41598-019-42605-z
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