Characterization of Samples Identified as Hepatitis C Virus Genotype 1 without Subtype by Abbott RealTime HCV Genotype II Assay Using the New Abbott HCV Genotype Plus RUO Test.

Camelia Mokhtari,Sandra Merlin,Stéphanie Proust,Anne-Marie Roque-Afonso,Anne Ebel,Birgit Reinhardt,Y.-W Tang

doi:10.1128/jcm.02264-15

Camelia Mokhtari, Sandra Merlin + Show 5 more

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https://doi.org/10.1128/jcm.02264-15

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Abstract

Hepatitis C virus (HCV) genotyping continues to be relevant for therapeutic strategies. Some samples are reported as genotype 1 (gt 1) without subtype by the Abbott RealTime HCV Genotype II (GT II) test. To characterize such samples further, the Abbott HCV Genotype Plus RUO (Plus) assay, which targets the core region for gt 1a, gt 1b, and gt 6 detection, was evaluated as a reflex test in reference to NS5B or 5′-untranslated region (UTR)/core region sequencing. Of 3,626 routine samples, results of gt 1 without subtype were received for 171 samples (4.7%), accounting for 11.5% of gt 1 specimens. The Plus assay and sequencing were applied to 98 of those samples. NS5B or 5′-UTR/core region sequencing was successful for 91/98 specimens (92.9%). Plus assay and sequencing results were concordant for 87.9% of specimens (80/91 samples). Sequencing confirmed Plus assay results for 82.6%, 85.7%, 100%, and 89.3% of gt 1a, gt 1b, gt 6, and non-gt 1a/1b/6 results, respectively. Notably, 12 gt 6 samples that had been identified previously as gt 1 without subtype were assigned correctly here; for 25/28 samples reported as “not detected” by the Plus assay, sequencing identified the samples as gt 1 with subtypes other than 1a/1b. The genetic variability of HCV continues to present challenges for the current genotyping platforms regardless of the applied methodology. Samples identified by the GT II assay as gt 1 without subtype can be further resolved and reliably characterized by the new Plus assay.

Highlights

It is estimated that more than 185 million people have been infected with hepatitis C virus (HCV) [1]
The 5= untranslated region (UTR), a highly conserved part of the Hepatitis C virus (HCV) genome, is used by diagnostic HCV RNA assays and is a common target for HCV genotyping by most commercial assays
98 routine samples that had been identified by the Genotype II (GT II) assay as gt 1 without subtype assignment were retested using the Plus assay and NS5B and/or 5=-UTR/core region sequencing

Summary

Introduction

It is estimated that more than 185 million people have been infected with hepatitis C virus (HCV) [1]. The 5= untranslated region (UTR), a highly conserved part of the HCV genome, is used by diagnostic HCV RNA assays and is a common target for HCV genotyping by most commercial assays. The results without 1a/1b amplification curves might indicate a gt 1 subtype other than 1a or 1b or gt 6 subtypes with 5=-UTR sequences identical to that of subtype 1b [14] To characterize these samples further, the manufacturer has developed a new assay, the Abbott HCV Genotype Plus RUO (Plus) assay, targeting the core region and identifying genotypes 1a, 1b, and 6. The present study analyzes the performance of this new assay as a supplementary test for samples with gt 1 results without subtype identification, in reference to NS5B and 5=-UTR/core region sequencing

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