Differences between Two Real-Time PCR-Based Hepatitis C Virus (HCV) Assays (RealTime HCV and Cobas AmpliPrep/Cobas TaqMan) and One Signal Amplification Assay (Versant HCV RNA 3.0) for RNA Detection and Quantification

Abstract

Hepatitis C virus (HCV) RNA detection and quantification are the key diagnostic tools for the management of hepatitis C. Commercially available HCV RNA assays are calibrated to the HCV genotype 1 (gt1)-based WHO standard. Significant differences between assays have been reported. However, it is unknown which assay matches the WHO standard best, and little is known about the sensitivity and linear quantification of the assays for non-gt1 specimens. Two real-time reverse transcriptase PCR-based assays (RealTime HCV and Cobas Ampliprep/Cobas TaqMan HCV [CAP/CTM]) and one signal amplification-based assay (the Versant HCV RNA, version 3.0, branched DNA [bDNA] assay) were compared for their abilities to quantify HCV RNA in clinical specimens (n ‫؍‬ 65) harboring HCV isolates of gt1 to g5. The mean differences in the amounts detected by RealTime HCV in comparison to those detected by the bDNA assay and CAP/CTM were ؊0.02 and 0.72 log 10 IU/ml HCV RNA, respectively, for gt1; ؊0.22 and 0.03 log 10 IU/ml HCV RNA, respectively, for gt2; ؊0.27 and ؊0.22 log 10 IU/ml HCV RNA, respectively, for gt3; ؊0.19 and ؊1.27 log 10 IU/ml HCV RNA, respectively, for gt4; and ؊0.03 and 0.09 log 10 IU/ml HCV RNA, respectively, for gt5. The lower limits of detection for RealTime HCV and CAP/CTM were 16.8 and 10.3 IU/ml, respectively, for the WHO standard and in the range of 4.7 to 9.0 and 3.4 to 44.4 IU/ml, respectively, for clinical specimens harboring gt1 to gt6. Direct comparison of the two assays with samples of the WHO standard (code 96/798) with high titers yielded slightly smaller amounts by RealTime HCV (؊0.2 log 10 at 1,500 IU/ml and ؊0.3 log 10 at 25,000 IU/ml) and larger amounts by CAP/CTM (0.3 log 10 at 1,500 IU/ml and 0.2 log 10 at 25,000 IU/ml). Finally, all three tests were linear between 4.0 ؋ 10 3 and 1.0 ؋ 10 6 IU/ml (correlation coefficient, >0.99). In conclusion, the real-time PCR based assays sensitively detected all genotypes and showed comparable linearities for the quantification of HCV RNA, with the exception of gt1 and gt4. The previously reported differences in the absolute quantification of samples harboring gt1 were confirmed and may be explained by different calibrations to the WHO standard.Hepatitis C virus (HCV) infection is a common cause of chronic liver disease that can lead to end-stage liver disease, including hepatocellular carcinoma.At present, combination therapy with pegylated interferon and ribavirin is the standard of care. However, this treatment regimen appears to be effective in only 40% to 50% of patients infected with genotype 1 and approximately 80% of patients infected with genotypes 2 and 3 (12, 13, 16).A sustained virologic response, defined as undetectable HCV RNA at least 6 months after the completion of therapy, may be predicted by a number of host and viral factors, including age, race, liver fibrosis, the HCV genotype, and the baseline viral load.Recent reports suggest that decisions on the optimal treatment duration may be made on the basis of the baseline viral load and the virologi...

Development of a Second Version of the Cobas AmpliPrep/Cobas TaqMan Hepatitis C Virus Quantitative Test with Improved Genotype Inclusivity

“…Among these, several report underestimation of HCV RNA levels in up to 30% of GT4 specimens compared to competitor assays (2,16,17,20,22). Recently, the hypothesis was established that these findings were linked to the occurrence of GT4 specimens harboring amino acid substitutions at positions 145 (G to A) and 165 (A to T) in the 5ЈUTR of the HCV genome (1,3,8,10).…”

“…The CAP/CTM assay is widely used in clinical research and practice, and it has been evaluated in a number of studies (2,12,14,16,17,20,22). Among these, several report underestimation of HCV RNA levels in up to 30% of GT4 specimens compared to competitor assays (2,16,17,20,22).…”

Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine

“…With the advent of novel antiviral therapies for human immunodeficiency virus (HIV) and hepatitis C virus (HCV), assays for virus quantification with high sensitivity are becoming increasingly important for optimal patient management. 26 The gold standards for viral infection detection have traditionally been viral culture, where host cells are cultured to detect structural changes caused by viral invasion, and immunoassays for detection of antigens and antibodies to viral proteins. These methods are expensive and timeconsuming, require designated laboratories, and cannot always identify the viral serotype.…”

“…27 Recently, FDA has approved several assays and platforms for detection of genomic and messenger viral RNA, summarized in Table I. 26,[28][29][30][31][32][33][34] These platforms offer a limit of detection (LOD) of 10-200 copies/ml, and linear quantification up to 10 À8 copies/ml. Such new point-of care diagnostic assays capable of achieving comparable or lower limits of detection than current ones would allow better patient management with antiviral therapies and maybe even allow higher cure rates.…”

Evaluation of the Performance Characteristics of an In-House One Step TaqMan Real Time-Polymerase Chain Reaction Assay for Detection and Quantification of Hepatitis C Virus

“…In the last decade, several commercial or in-house TaqMan real time systems have been introduced with acceptable performance characteristics (8,(10)(11)(12)(13)(14)(15)(16)(17)(18). Due to increasing sensitivity of quantitative assays, they are recommended for detection and quantification of HCV RNA in seropositive patients (7).…”