Assessment of a novel automatic real-time PCR assay on the cobas 4800 analyzer as a screening platform for Hepatitis C virus genotyping in clinical practice: Comparison with massive sequencing

Leonardo Nieto-Aponte, Josep Quer, Alicia Ruiz-Ripa, David Tabernero, Carolina Gonzalez, Josep Gregori, Marta Vila, Miriam Asensio, Damir Garcia-Cehic, Gerardo Ruiz, Qian Chen, Laura Ordeig, Meritxell Llorens, Montserrat Saez, Juan I. Esteban, Rafael Esteban, Maria Buti, Tomas Pumarola, Francisco Rodriguez-Frias

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11 Citations (Scopus)

Abstract

© 2017 American Society for Microbiology. The unequivocal identification of hepatitis C virus (HCV) subtypes 1a/1b and genotypes 2 to 6 is required for optimizing the effectiveness of interferon-free, direct-acting antiviral therapies. We compared the performance of a new real-time HCV genotyping assay used on the Cobas 4800 system (C4800) with that of highresolution HCV subtyping (HRCS). In total, 502 samples were used, including 184 samples from chronic HCV patients (from routine laboratory activity during April 2016), 5 stored samples with double HCV genotype infections for testing the limitations of the method, and 313 samples from a screening protocol implemented in our hospital (from May to August 2016) based on the new method to further determine its genotyping accuracy. A total of 282 samples, including 171 from April 2016 (the 13 remaining had too low of a viral load for HRCS), 5 selected with double infections, and 106 from screening, were analyzed by both methods, and 220 were analyzed only by the C4800. The C4800 correctly subtyped 125 of 126 1a/1b samples, and the 1 remaining sample was reported as genotype 1. The C4800 correctly genotyped 38 of 45 non-1a/1b samples (classified by HRCS), and it reported the remaining 7 samples as indeterminate. One hundred two of 106 non-1a/1b genotype samples that were identified using the C4800 for screening were confirmed by HRCS. In the 4 remaining samples, 3 were correctly reported as genotype 1 (without defining the subtype) and 1 was reported as indeterminate. None of the samples were misgenotyped. Four of 7 samples with double HCV infections were correctly genotyped by the C4800. Excluding the 5 selected double-infected samples, the C4800 showed 95.7% concordant results for genotyping HCVs 2 to 6 and 1a/1b subtyping, and 99.2% concordance for subtyping 1a/1b single infections in clinical samples. To improve laboratory workflow, we propose using the C4800 as a first-line test for HCV genotyping and 1a/1b classification, followed by transferring non-1a/1b samples to a center where HRCS is available, if further characterization is needed.
Original languageEnglish
Pages (from-to)504-509
JournalJournal of Clinical Microbiology
Volume55
Issue number2
DOIs
Publication statusPublished - 1 Feb 2017

Keywords

  • Diagnostics
  • Genotype identification
  • Hepatitis C virus
  • Molecular subtyping

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