Publication: Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing.
Loading...
Identifiers
Date
2019-04-01
Authors
Fernandez-Caso, Belen
Fernandez-Caballero, Jose Angel
Chueca, Natalia
Rojo, Eukene
de Salazar, Adolfo
Garcia Buey, Luisa
Cardeñoso, Laura
Garcia, Federico
Advisors
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Publishing Group
Abstract
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.
Description
MeSH Terms
Adult
Aged
Aged, 80 and over
Cohort Studies
Female
Genotype
Genotyping Techniques
Hepacivirus
Hepatitis C
High-Throughput Nucleotide Sequencing
Humans
Male
Middle Aged
Real-Time Polymerase Chain Reaction
Viral Nonstructural Proteins
Aged
Aged, 80 and over
Cohort Studies
Female
Genotype
Genotyping Techniques
Hepacivirus
Hepatitis C
High-Throughput Nucleotide Sequencing
Humans
Male
Middle Aged
Real-Time Polymerase Chain Reaction
Viral Nonstructural Proteins
DeCS Terms
Estudios de cohortes
Hepacivirus
Proteínas no estructurales virales
Reacción en cadena en tiempo real de la polimerasa
Secuenciación de nucleótidos de alto rendimiento
Técnicas de genotipaje
Hepacivirus
Proteínas no estructurales virales
Reacción en cadena en tiempo real de la polimerasa
Secuenciación de nucleótidos de alto rendimiento
Técnicas de genotipaje
CIE Terms
Keywords
Citation
Fernández-Caso B, Fernández-Caballero JÁ, Chueca N, Rojo E, de Salazar A, García Buey L, et al. Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing. Sci Rep. 2019 Jun 25;9(1):9264.