Background Accurate quantitation of hepatitis C virus (HCV) RNA is mandatory for the management of anti-HCV therapy. Objectives The genotype-dependent performance of the new commercially available VERSANT HCV RNA 1.0 Assay (kPCR) and the COBAS AmpliPrep/COBAS TaqMan HCV Quantitative Test, version 2.0 was investigated. Study design The molecular assays for quantitation of HCV RNA were performed according to the manufacturer's package insert instructions. HCV genotypes/subtypes/isolates, and mutations in the 5′NCR were detected by direct sequencing. Results When members of a worldwide HCV performance panel including HCV subtypes 1a, 1b, 2a, 3b, and 4a were tested with the Siemens assay and the results were compared with those obtained by the Roche assay, the mean log10 unit differences for members containing HCV subtypes 1a, 1b, 3b, and 4a were found to be within ±0.5 log10 units. For the panel member containing HCV subtype 2a, the HCV RNA concentration was found to be >0.5 log10 units lower with the Siemens assay. When clinical samples were tested, the HCV RNA concentration of all samples containing HCV subtype 2a were found to be >0.5 log10 units lower with the Siemens assay while that of certain HCV subtype 3a and 4a isolates were found to be >1.0 log10 units lower. Conclusion The VERSANT HCV RNA 1.0 Assay substantially underestimates HCV RNA concentrations in HCV subtype 2a samples and in HCV subtype 3a and 4a samples containing certain isolates. This may be caused by mismatches with the target sequences due to the primer and/or probe design.
