Hepatitis C virus genotyping: Comparison of the Abbott RealTime HCV Genotype II assay and NS5B sequencing

Département de virologie, hôpital Paul-Brousse, AP-HP, 12, avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.
Pathologie Biologie (Impact Factor: 1.2). 11/2009; 58(2):175-8. DOI: 10.1016/j.patbio.2009.07.023
Source: PubMed


Hepatitis C virus genotyping is needed for treatment decision and monitoring. The results of a genotyping assay based on real-time PCR and TaqMan chemistry were compared with the results of NS5B region sequencing.
One hundred and two sera (genotypes 1-6) were tested. Amplification and detection of viral RNA were performed with the Abbott RealTime HCV Genotype II assay targeting 5'non-coded region (5'NC) for the identification of genotypes 1 to 6 and NS5B, for 1a and 1b subtypes detection. Sequencing of 5'NC fragment was used to resolve discrepant results.
No indeterminate results were obtained. Concordance with NS5B sequencing was 93% (95 on 102), 96% at the genotype level (98 on 102) and 93% for genotype 1 subtyping (40 on 43). Discordant genotyping results were a 2f subtype identified as 5, a 6a typed as 1, a 3a identified as a 1-3 co-infection and a 4r identified as a 1-4 co-infection. Discordant subtyping results were 2 1b subtypes only typed as 1 and a 1e identified as 1a.
Abbott RealTime HCV Genotype II assay is a rapid, automated and simple to interpret method for HCV genotyping. It allows the detection of possible mixed infections which might have a negative impact on therapeutic response. However, the discrepant results found in this small series underline the need for assay optimization.

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    • "AU, Australia; CH, Switzerland; CN, China; DE, Germany; ES, Spain; FR, France; GB, United Kingdom; ID, Indonesia; IN, India; IT, Italy; JP, Japan; PK, Pakistan; RU, Russian Federation; TH, Thailand; US, United States. used the current assay version9101112. Another study that focused on HCV-1-infected patients and employed a larger sample size only found 2 out of 495 (0.4%) specimens to be indeterminate[13]. Interestingly, 18 of the 19 indeterminate results in our study were phylogenetically classified as HCV-3, with 17 of them subtype 3a. "

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