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J Clin Virol. 2014 Jul;60(3):301-4. doi: 10.1016/j.jcv.2014.04.005. Epub 2014 Apr 14.

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

Author information

1
Alberta Provincial Laboratory for Public Health, Edmonton, Alberta, Canada.
2
Alberta Provincial Laboratory for Public Health, Calgary, Alberta, Canada.
3
Alberta Provincial Laboratory for Public Health, Calgary, Alberta, Canada; Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
4
Alberta Provincial Laboratory for Public Health, Edmonton, Alberta, Canada; Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada. Electronic address: jwtang49@hotmail.com.

Abstract

BACKGROUND:

Hepatitis 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 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-LiPA HCV 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 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.

CONCLUSIONS:

The 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.

PMID:
24794397
DOI:
10.1016/j.jcv.2014.04.005
[Indexed for MEDLINE]

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