The need for a sequencing-based assay to supplement the Abbott m2000 RealTime HCV Genotype II assay: A 1 year analysis

Background: Hepatitis C (HCV) genotyping is important for treatment planning. The Abbott m2000 Real-Time HCV Genotype II assay is a PCR-based assay targeting specific regions of the 5'NCR gene for genotypes 1-6, and the NS5b gene for subgenotypes 1a/1b. However, not all genotypes can be resolved, with results being reported as: Indeterminate', 'mixed', 'genotype X reactivity with Y', or just the major genotype 1 alone. Objectives and study design: To assess the supplementary testing required for these unresolved HCV genotypes, these samples were tested further using an in-house core/E1 sequencing assay. The resulting genotypes/subgenotypes were assigned using phylogenetic analysis with reference HCV genotype sequences. Additional testing was conducted using the INNO-LiPAHCV II assay for truly mixed genotypes. Results: Out of 1052 samples tested, 89 (8.5%) underwent further sequencing to determine the HCV genotype: 16 that were Indeterminate' on the m2000, were mostly genotype 2s and 3s by sequencing; 12 that were 'mixed', were mostly one of the genotypes reported in the mixture; 7 that were 'X reactivity with Y', were usually genotype X; 54 that gave just a major genotype 1 result were mostly la, with some 6 and 1b, and a few 1 c. For three truly mixed genotypes, additional testing using the VERSANT (R) HCV Genotype Assay (LiPA) 2.0, showed two mixed 1 and 3, and one indistinguishable 6c-6l genotypes. Conclusions: The Abbott m2000 Real-Time HCV Genotype II assay can resolve most (similar to 90%) HCV genotypes. However in 9-10% of cases, to fully resolve the genotype, additional testing is required. (C) 2014 Elsevier B.V. All rights reserved.