Overestimation and underestimation of hepatitis C virus RNA levels in a widely used real-time polymerase chain reaction–based method

Authors

  • Stéphane Chevaliez,

    1. French National Reference Center for Viral Hepatitis B, C, and Delta, Department of Virology, Hôpital Henri Mondor, Créteil, France
    2. Institut National de la Santé et de la Recherche Médicale U841, Créteil, France
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  • Magali Bouvier-Alias,

    1. French National Reference Center for Viral Hepatitis B, C, and Delta, Department of Virology, Hôpital Henri Mondor, Créteil, France
    2. Institut National de la Santé et de la Recherche Médicale U841, Créteil, France
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  • Rozenn Brillet,

    1. French National Reference Center for Viral Hepatitis B, C, and Delta, Department of Virology, Hôpital Henri Mondor, Créteil, France
    2. Institut National de la Santé et de la Recherche Médicale U841, Créteil, France
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  • Jean-Michel Pawlotsky

    Corresponding author
    1. French National Reference Center for Viral Hepatitis B, C, and Delta, Department of Virology, Hôpital Henri Mondor, Créteil, France
    2. Institut National de la Santé et de la Recherche Médicale U841, Créteil, France
    • Department of Virology, Hôpital Henri Mondor, 51 Avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France
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    • fax: +33-1-4981-4831


  • Potential conflict of interest: Nothing to report.

  • This work is part of the activity of the VIRGIL European Network of Excellence on Antiviral Drug Resistance

Abstract

The quantification of hepatitis C virus (HCV) RNA is essential for the everyday management of chronic hepatitis C therapy. Real-time polymerase chain reaction (PCR) techniques are potentially more sensitive than classical PCR techniques, are not prone to carryover contamination, and have a consistently wider dynamic range of quantification. Thus, they are rapidly replacing other technologies for the routine quantification of HCV RNA. We extensively evaluated the intrinsic characteristics and clinical performance of Cobas Ampliprep/Cobas TaqMan (CAP/CTM), the most widely used real-time PCR assay for HCV RNA quantification. This study shows that CAP/CTM is sensitive, specific, precise, and reproducible and has a broad dynamic range of quantification well suited to HCV RNA monitoring in clinical practice. However, we identified 2 technical issues that will have an impact in clinical practice. First, the CAP/CTM assay overestimates HCV RNA levels in undiluted patient samples by approximately 0.6 log10 international units per milliliter on average, and this overestimation increases with the viral load. Second, the CAP/CTM assay substantially underestimates HCV RNA levels in approximately 15% of genotype 2 samples and 30% of genotype 4 samples, probably because of mismatches with the target sequences due to the primer and/or probe design. Conclusion: As the CAP/CTM platform is widely available, easy to use, and suited to high-throughput screening for viral genomes, the manufacturer should improve the HCV RNA kit to resolve these 2 important technical issues that may affect everyday management of hepatitis C therapy. (HEPATOLOGY 2007.)

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