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

• The Abbott m2000 HCV genotyping II assay resolves over 90% of the HCV genotypes (G).
• Out of 1052 samples tested, 89 (8.5%) required further sequencing.
• Of these 89, 54 G1 samples were mostly sub-genotyped as 1a, with some 6, 1b and 1c.
• Of these 89, 16 ‘indeterminate’ samples were mostly G2s and G3s.
• Of these 89, 12 ‘mixed’ samples were mostly one of the genotypes from the mixture.

BackgroundHepatitis C (HCV) genotyping is important for treatment planning. The Abbott m2000 RealTime 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 designTo 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-LiPA HCV II assay for truly mixed genotypes.ResultsOut 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 1a, with some 6 and 1b, and a few 1c. For three truly mixed genotypes, additional testing using the VERSANT® HCV Genotype Assay (LiPA) 2.0, showed two mixed 1 and 3, and one indistinguishable 6c–6l genotypes.ConclusionsThe Abbott m2000 RealTime HCV Genotype II assay can resolve most (∼90%) HCV genotypes. However in 9–10% of cases, to fully resolve the genotype, additional testing is required.