The Cobas AmpliPrep/Cobas TaqMan HCV Test,Version 2.0, Real-Time PCR Assay Accurately Quantifies Hepatitis C Virus Genotype 4 RNA

Accurate hepatitis C virus (HCV) RNA quantification is mandatory for the management of chronic hepatitis C therapy. The first-generation Cobas AmpliPrep/Cobas TaqMan HCV test (CAP/CTM HCV) underestimated HCV RNA levels by >1-log₁₀ international units/ml in a number of patients infected with HCV genotype 4 and occasionally failed to detect it. The aim of this study was to evaluate the ability of the Cobas AmpliPrep/Cobas TaqMan HCV test, version 2.0 (CAP/CTM HCV v2.0), to accurately quantify HCV RNA in a large series of patients infected with different subtypes of HCV genotype 4. Group A comprised 122 patients with chronic HCV genotype 4 infection, and group B comprised 4 patients with HCV genotype 4 in whom HCV RNA was undetectable using the CAP/CTM HCV. Each specimen was tested with the third-generation branched DNA (bDNA) assay, CAP/CTM HCV, and CAP/CTM HCV v2.0. The HCV RNA level was lower in CAP/CTM HCV than in bDNA in 76.2% of cases, regardless of the HCV genotype 4 subtype. In contrast, the correlation between bDNA and CAP/CTM HCV v2.0 values was excellent. CAP/CTM HCV v2.0 accurately quantified HCV RNA levels in the presence of an A-to-T substitution at position 165 alone or combined with a G-to-A substitution at position 145 of the 5′ untranslated region of HCV genome. In conclusion, CAP/CTM HCV v2.0 accurately quantifies HCV RNA in genotype 4 clinical specimens, regardless of the subtype, and can be confidently used in clinical trials and clinical practice with this genotype.     

Necessity for Reassessment of Patients with Serogroup 2 Hepatitis C Virus (HCV) and Undetectable Serum HCV RNA

We encountered a patient positive for anti-hepatitis C virus (HCV) whose serum HCV RNA was undetectable with the Roche AmpliPrep/Cobas TaqMan HCV assay (CAP/CTM) version 1 but showed a high viral load with the Abbott RealTime HCV assay (ART). Discrepancies in the detectability of serum HCV RNA were investigated among 891 consecutive patients who were positive for anti-HCV. Specific nucleotide variations causing the undetectability of HCV RNA were determined and confirmed by synthesizing RNA coding those variations. Serum samples with the discrepancies were also reassessed by CAP/CTM version 2. Among the 891 anti-HCV-positive patients, 4 patients had serum HCV RNA levels that were undetectable by CAP/CTM version 1 despite having levels of >5 log IU/ml that were detected by ART. All four patients had HCV genotype 2a and high titers of anti-HCV. Sequencing of the HCV 5′ noncoding regions revealed 2 common variations, A at nucleotide (nt) 145 and T at nt 151. Synthesized RNAs of the HCV 5′ noncoding region with standard (NCR145G151C) and variant nucleotides at nt 145 and nt 151 were quantified with CAP/CTM. RNAs of NCR145G151C and NCR145G151T were quantifiable with CAP/CTM version 1, while those of NCR145A151T and NCR145A151C went undetected. The substitution from G to A at nt 145 specifically conferred this undetectability, while this undetectability was reverted in synthesized HCV RNA with correction of this variation. Reassessment of these samples by CAP/CTM version 2 resulted in similar levels of HCV RNA being detected by ART. We conclude that HCV patients with undetectable HCV RNA by CAP/CTM version 1 should be reassessed for viral quantification.     

Second-Generation Cobas AmpliPrep/Cobas TaqMan HCV Quantitative Test for Viral Load Monitoring: a Novel Dual-Probe Assay Design

Hepatitis C virus (HCV) RNA viral load (VL) monitoring is a well-established diagnostic tool for the management of chronic hepatitis C patients. HCV RNA VL results are used to make treatment decisions with the goal of therapy to achieve an undetectable VL result. Therefore, a sensitive assay with high specificity in detecting and accurately quantifying HCV RNA across genotypes is critical. Additionally, a lower sample volume requirement is desirable for the laboratory and the patient. This study evaluated the performance characteristics of a second-generation real-time PCR assay, the Cobas AmpliPrep/Cobas TaqMan HCV quantitative test, version 2.0 (CAP/CTM HCV test, v2.0), designed with a novel dual-probe approach and an optimized automated extraction and amplification procedure. The new assay demonstrated a limit of detection and lower limit of quantification of 15 IU/ml across all HCV genotypes and was linear from 15 to 100,000,000 IU/ml with high accuracy (<0.2-log₁₀ difference) and precision (standard deviation of 0.04 to 0.22 log₁₀). A specificity of 100% was demonstrated with 600 HCV-seronegative specimens without cross-reactivity or interference. Correlation to the Cobas AmpliPrep/Cobas TaqMan HCV test (version 1) was good (n = 412 genotype 1 to 6 samples, R² = 0.88; R² = 0.94 without 105 genotype 4 samples). Paired plasma and serum samples showed similar performance (n = 25, R² = 0.99). The sample input volume was reduced from 1 to 0.65 ml in the second version. The CAP/CTM HCV test, v2.0, demonstrated excellent performance and sensitivity across all HCV genotypes with a smaller sample volume. The new HCV RNA VL assay has performance characteristics that make it suitable for use with currently available direct-acting antiviral agents.     

Performance of Version 2.0 of the Cobas AmpliPrep/Cobas TaqMan Real-Time PCR Assay for Hepatitis B Virus DNA Quantification

The detection and quantification of hepatitis B virus (HBV) DNA are essential for the diagnosis and treatment of chronic HBV infection. The use of real-time PCR assays for HBV DNA quantification is strongly recommended. The goal of this study was to evaluate the intrinsic characteristics and clinical performance of version 2.0 (v2.0) of the Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) assay, a fully automated platform for HBV DNA quantification in serum or in plasma with a claimed lower limit of detection of 20 IU/ml and a claimed upper limit of quantification of 1.7 × 10⁸ IU/ml. The specificity of the assay was 99% (95% confidence interval, 94.7 to 100%). Intra-assay and interassay coefficients of variation ranged from 0.21% to 2.67% and from 0.65% to 2.25%, respectively. The calibration of the assay was found to be satisfactory. Study of blood specimens from patients infected with HBV genotypes A to F showed good correspondence between HBV DNA levels measured by the CAP/CTM v2.0 assay, version 1.0 of the same assay, and the third-generation “branched DNA” assay. The CAP/CTM v2.0 assay quantified HBV DNA levels in serum or plasma from the same patients equally. In conclusion, the new version of the CAP/CTM assay is sensitive, specific, and reproducible. It accurately quantifies HBV DNA levels in patients chronically infected with HBV genotypes A to F. Improvements made to ensure equal quantification of HBV DNA in serum and plasma have been successful. Overall, the CAP/CTM assay, version 2.0, is well suited to monitoring clinical HBV DNA levels according to current clinical practice guidelines.Chronic hepatitis B virus (HBV) infection is associated with a large spectrum of liver diseases, ranging from a low-viremia inactive carrier state to chronic active hepatitis, which may subsequently evolve toward cirrhosis and hepatocellular carcinoma (HCC). Morbidity and mortality are linked to the persistence of viral replication, and hepatic complications develop in 15% to 40% of patients chronically infected with HBV. Overall, HBV-related end-stage liver disease and HCC are responsible for more than 750,000 deaths worldwide per year (5).The detection and quantification of HBV DNA are essential for diagnosing ongoing HBV infection and establishing the prognosis of related liver disease, influence the decision to treat, and are indispensable for monitoring the virological response to antiviral therapy and the emergence of resistance in order to tailor therapy (4). A number of HBV DNA detection and quantification assays are available. For many years, such methods were based on either hybrid capture, signal amplification by means of branched DNA (bDNA) technology, or classical PCR, all of which suffered from poor analytical sensitivity and a narrow range of HBV DNA quantification (3). More recently, assays based on real-time PCR quantification have been developed. Their use for the routine detection and quantification of HBV DNA is recommended, because of their excellent analytical sensitivity (lower limit of detection, 10 to 20 IU/ml), their specificity, their accuracy, and their broad dynamic range of linear quantification, which fully covers clinical needs (9). Among these assays, we recently evaluated the first-generation (V1.0) Cobas AmpliPrep/Cobas TaqMan (CAP/CTM; Roche Molecular Systems, Pleasanton, CA) assay. This assay was found to be sensitive, specific, and reproducible and to accurately quantify HBV DNA levels in patients chronically infected by HBV genotypes A to F (2). However, this assay could be used only for the quantification of HBV DNA in plasma.A second version of the CAP/CTM assay (v2.0) has been released recently. Several changes have been made; in particular, the assay can be used on both serum and plasma, and it requires 650 μl of sample instead of 850 μl. Its claimed dynamic range of quantification is 20 IU/ml to 1.7 × 10⁸ IU/ml (1.3 to 8.2 log₁₀ IU/ml). The goal of this study was to evaluate the intrinsic characteristics and clinical performance of the CAP/CTM v2.0 assay.     

Evaluation of the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 Test and Identification of Rare Polymorphisms Potentially Affecting Assay Performance

We evaluated the FDA-approved Roche Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) HIV-1 viral load assay for sensitivity, reproducibility, linearity, HIV-1 subtype detection, and correlation to the Roche Amplicor HIV-1 monitor test, version 1.5 (Amplicor). The limit of detection calculated by probit analysis was 23.8 copies/ml using the 2nd International WHO Standard and 30.8 copies/ml using Viral Quality Assurance (VQA) standard material. Serial dilutions of six patient samples were used to determine inter- and intra-assay reproducibility and linearity, which were very good (<8% coefficient of variation [CV]; between ∼1.7 and 7.0 log₁₀ copies/ml). Subtype detection was evaluated in the CAP/CTM, Amplicor, and Bayer Versant HIV-1 bDNA 3.0 (Versant) assays using a commercially available panel. Versant averaged 0.829 log₁₀ copies/ml lower than CAP/CTM and Amplicor averaged 0.427 log₁₀ copies/ml lower than CAP/CTM for the subtype panel. Correlation with samples previously tested by Amplicor was excellent (R² = 0.884; average difference [Amplicor value minus CAP/CTM value], 0.008 log₁₀ copies/ml). Of the 305 HIV samples tested, 7 samples generated CAP/CTM titers between 1.0 and 2.75 log₁₀ copies/ml lower than those for Amplicor. Three of these samples revealed primer and probe mismatches that could account for the discrepancies. Otherwise, the CAP/CTM assay exhibits excellent sensitivity, dynamic range, reproducibility, and correlation with Amplicor in an automated format.Measurement of HIV-1 RNA in the plasma of infected patients is critical for guiding treatment. Over the past decade, several commercial quantitative HIV-1 RNA assays have become available that utilize endpoint PCR, isothermal amplification, or signal amplification techniques. Most recently, Abbott Molecular (Des Plaines, IL) and Roche Molecular Systems (Branchburg, NJ) received FDA approval for their real-time PCR-based systems, the RealTime HIV-1 assay and Cobas AmpliPrep/Cobas TaqMan HIV-1 Test (CAP/CTM), respectively. Each assay has its own advantages and disadvantages in terms of sensitivity, equipment requirements, throughput, dynamic range, subtype detection, and cost (1a, 4, 6, 7, 8, 11, 13, 15, 16).The CAP/CTM test includes a “docked” version that permits automated “sample in—results out” analysis of specimens without user intervention. We evaluated this configuration and compared its performance to those of the Roche Amplicor HIV-1 monitor test, version 1.5 (Amplicor), and the Bayer Versant HIV-1 bDNA 3.0 assay (Versant). Seven samples which gave discrepant Amplicor versus CAP/CTM results were further evaluated by sequencing analysis.     

Evaluation of an automated, highly sensitive, real-time PCR-based assay (COBAS Amplipreptrade mark/COBAS TaqMantrade mark) for quantification of HCV RNA

BACKGROUND: Diagnosis of hepatitis C virus (HCV) infection and its therapy is based on qualitative and quantitative measurement of HCV RNA. OBJECTIVES: A new assay that employs automated specimen extraction and real-time RT-PCR (COBAS Amplipreptrade mark/COBAS TaqMantrade mark, "CAP/CTM", Roche Diagnostics, Pleasanton, USA) was designed for linear quantification and highly sensitive detection of HCV RNA. STUDY DESIGN: The performance characteristics of CAP/CTM were compared to standard RT-PCR-based COBAS Amplicor Monitor 2.0 (CAM) assay in a multicenter study. RESULTS: The limit of detection of CAP/CTM was 7.4IU/ml (95% CI 6.2-10.6) and clinical specificity was 99%. The linear range of HCV RNA quantification by CAP/CTM was between 28 and 1.4x10(7)IU/ml, with a correlation coefficient between expected and observed results of >0.99. A fivefold dilution of serum- or plasma-samples showed a linear correlation of HCV RNA levels in undiluted and diluted samples. Analyses of the mean intra- and inter-assay imprecision within the linear range of quantification showed a coefficient of variation of 3% and 3%, respectively. HCV genotypes 1a/b, 2b, 3a, 4, 5 and 6 were equally quantified by the CAP/CTM and CAM assay with mean deviations ranging from -0.29log(10) to 0.32log(10)IU/ml. HCV RNA quantification by CAP/CTM and CAM was highly concordant (correlation coefficient of 0.96). CONCLUSIONS: The CAP/CTM assay is a reliable and robust assay for highly sensitive detection and quantification of HCV RNA within a broad linear range.     

Predictive value of early virologic response in HIV/hepatitis C virus-coinfected patients treated with an interferon-based regimen plus ribavirin

BACKGROUND: As a result of adverse events, a moderate rate of virologic response, and high costs associated with hepatitis C virus (HCV) therapy, finding early markers of sustained treatment response is a clinical priority. In the HCV-monoinfected population, a reduction >or=2 log in plasma HCV RNA at week 12 of therapy (early virologic response [EVR]) predicts a sustained virologic response (SVR). Few data are available in HIV/HCV-coinfected patients, however. METHODS: A subanalysis of data from HIV/HCV-coinfected patients treated with pegylated interferon-alpha-2b (PEG, 100-150 mug/wk) or interferon-alpha-2b (IFN, 3 MIU 3 times per week) plus ribavirin (RBV, 800-1200 mg/d) was conducted in a randomized single-center clinical trial. The duration of treatment was 48 weeks (only 24 weeks for HCV genotype 2 or 3 with a baseline HCV RNA level <800,000 IU/mL). RESULTS: Ninety-five patients were randomized (43 assigned to IFN + RBV and 52 assigned to PEG + RBV). Eighty patients completed at least 12 weeks on therapy and were included in the EVR analysis. Thirty-five (43%) of them attained an SVR (56% and 30% of patients treated with PEG and IFN, respectively; P = 0.026). An EVR occurred in 55 (69%; 80% of PEG + RBV group and 56% of IFN + RBV group). Overall, 35 of 55 patients with an EVR were sustained responders, yielding a positive predictive value of 64% (70% in PEG + RBV arm and 55% in IFN + RBV arm). None of the patients who demonstrated an HCV RNA decline of <2 logs at week 12 reached an SVR (negative predictive value of 100%). CONCLUSION: Our results confirm the utility of an EVR to predict the chance of the lack of an SVR in HIV/HCV-coinfected patients, particularly those treated with PEG.     

Detection and quantitation of HCV RNA using real-time PCR after automated sample processing

There is considerable evidence that the loss of hepatitis C virus (HCV) RNA during the first 3 months of treatment with pegylated interferon plus ribavirin is a prognostic marker of response to therapy. Real-time polymerase chain reaction (PCR) assays for quantifying HCV RNA in plasma or serum are now commercially available. The extraction of HCV RNA can also be automated. This report analyses the performance of the COBAS Ampliprep-COBAS Taqman 48 (CAP/CTM) real-time PCR assay and compares this new test with the COBAS Amplicor HCV Monitor v 2.0 assay (CAM). CAP/CTM was 100% specific. The assay was linear across a wide range of HCV RNA concentrations without sample dilution. The intra-assay variation was 0.3-3.3% and the interassay variation was 1.5-6.7%. A total of 118 clinical samples with different HCV genotypes were assayed using both methods. The results obtained using the two methods were well correlated (r = 0.89, P < 0.001). The mean difference [CAP/CTM-CAM] was 0.17 log IU/ml and it was not influenced by the HCV genotype or by the subtype. It is concluded that the new CAP/CTM system is adequate for quantifying HCV RNA in clinical practice.     

Patterns of viral load decline with telaprevir-based therapy in patients with genotype 1 chronic HCV infection

BackgroundTelaprevir-based therapy is associated with rapid decline in HCV RNA, enabling the application of early futility rules.ObjectivesTo familiarize physicians with this paradigm, a comprehensive analysis of the most frequent HCV viral load profiles observed during treatment with telaprevir/Peg-IFN/RBV in Phase III trials is provided.DesignHCV RNA profiles were analyzed from 320 HCV genotype 1 treatment-naïve patients enrolled in the ADVANCE study, and 225 prior Peg-IFN/RBV treatment-experienced patients enrolled in the REALIZE study. Patients received 12 weeks of telaprevir with either 24 or 48 weeks of Peg-IFN alfa-2a/RBV. Patients with missing SVR assessments during follow-up, detectable HCV RNA at end of treatment but who did not have viral breakthrough (vBT), or with early vBT who discontinued telaprevir before time of failure were excluded.ResultsAll analyzed patients experienced a rapid decline in HCV RNA (>2.0 log₁₀) by Day 14, irrespective of baseline characteristics and/or prior response to Peg-IFN/RBV (relapse, partial response and null response). Subsequently, HCV RNA continued to decline to undetectable levels in most patients. These patients went on to have one of the following outcomes: sustained virologic response, late vBT (after Week 12, i.e. during the Peg-IFN/RBV phase), or relapse. In the small subset of patients with early vBT or meeting a futility rule before Week 12, HCV RNA usually never became undetectable and/or increased rapidly after reaching the nadir.ConclusionsHCV RNA profiles with telaprevir/Peg-IFN/RBV are different from those with Peg-IFN/RBV alone. It is important that clinicians understand these HCV RNA profiles and monitor patient viral load in order to apply futility rules correctly.     

Clinical evaluation of the COBAS Ampliprep/COBAS TaqMan for HCV RNA quantitation in comparison with the branched-DNA assay

Diagnosis and monitoring of HCV infection relies on sensitive and accurate HCV RNA detection and quantitation. The performance of the COBAS AmpliPrep/COBAS TaqMan 48 (CAP/CTM) (Roche, Branchburg, NJ), a fully automated, real-time PCR HCV RNA quantitative test was assessed and compared with the branched-DNA (bDNA) assay. Clinical evaluation on 576 specimens obtained from patients with chronic hepatitis C showed a good correlation (r = 0.893) between the two test, but the CAP/CTM scored higher HCV RNA titers than the bDNA across all viral genotypes. The mean bDNA versus CAP/CTM log10 IU/ml differences were -0.49, -0.4, -0.54, -0.26 for genotype 1a, 1b, 2a/2c, 3a, and 4, respectively. These differences reached statistical significance for genotypes 1b, 2a/c, and 3a. The ability of the CAP/CTM to monitor patients undergoing antiviral therapy and correctly identify the weeks 4 and 12 rapid and early virological responses was confirmed. The broader dynamic range of the CAP/CTM compared with the bDNA allowed for a better definition of viral kinetics. In conclusion, the CAP/CTM appears as a reliable and user-friendly assay to monitor HCV viremia during treatment of patients with chronic hepatitis. Its high sensitivity and wide dynamic range may help a better definition of viral load changes during antiviral therapy.     

An OPTIMIZE Study Retrospective Analysis for Management of Telaprevir-Treated Hepatitis C Virus (HCV)-Infected Patients by Use of the Abbott RealTime HCV RNA Assay

Protease inhibitor (PI)-based response-guided triple therapies for hepatitis C virus (HCV) infection are still widely used. Noncirrhotic treatment-naive and prior relapser patients receiving telaprevir-based treatment are eligible for shorter, 24-week total therapy if HCV RNA is undetectable at both weeks 4 and 12. In this study, the concordance in HCV RNA assessments between the Roche High Pure System/Cobas TaqMan and Abbott RealTime HCV RNA assays and the impacts of different HCV RNA cutoffs on treatment outcome were evaluated. A total of 2,629 samples from 663 HCV genotype 1 patients receiving telaprevir/pegylated interferon/ribavirin in OPTIMIZE were analyzed using the High Pure System and reanalyzed using Abbott RealTime (limits of detection, 15.1 IU/ml versus 8.3 IU/ml; limits of quantification, 25 IU/ml versus 12 IU/ml, respectively). Overall, good concordance was observed between the assays. Using undetectable HCV RNA at week 4, 34% of the patients would be eligible for shorter treatment duration with Abbott RealTime versus 72% with the High Pure System. However, using <12 IU/ml for Abbott RealTime, a similar proportion (74%) would be eligible. Of the patients receiving 24-week total therapy, 87% achieved a sustained virologic response with undetectable HCV RNA by the High Pure System or <12 IU/ml by Abbott RealTime; however, 92% of the patients with undetectable HCV RNA by Abbott RealTime achieved a sustained virologic response. Using undetectable HCV RNA as the cutoff, the more sensitive Abbott RealTime assay would identify fewer patients eligible for shorter treatment than the High Pure System. Our data confirm the <12-IU/ml cutoff, as previously established in other studies of the Abbott RealTime assay, to determine eligibility for shortened PI-based HCV treatment. (The study was registered with ClinicalTrials.gov under registration no. {"type":"clinical-trial","attrs":{"text":"NCT01241760","term_id":"NCT01241760"}}NCT01241760.)     

Performance of the Abbott RealTime and Roche Cobas TaqMan hepatitis C virus (HCV) assays for quantification of HCV genotypes

We evaluated the Abbott RealTime (ART) and Roche Cobas TaqMan Hepatitis C virus (HCV) viral load assays for quantification of HCV genotypes in patient specimens. The ART HCV assay was a more sensitive and precise tool for accurate HCV viral load quantification across the HCV genotypes tested, especially genotype 1b.     

Comparison between the automated Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 assay and its version 1 and Nuclisens HIV-1 EasyQ version 2.0 assays when measuring diverse HIV-1 genotypes in China

Background

Several commercially available HIV-1 viral load assays based on real-time detection technology and automated platforms are available. It is not clear how the diversity of HIV-1 genotypes impacts the ability to consistently detect HIV-1 viral loads.

Objectives

To examine whether the diversity of HIV-1 genotypes impacts the ability of the Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 (CAP/CTM v2.0), its version 1.0 (CAP/CTM v1.0) and the NucliSens EasyQ HIV-1 version 2.0 (EasyQ v2.0) assays to consistently determine the viral loads.

Study design

The three assays were used to measure the viral load in 178 plasma samples with diverse genotypes from treatment-naive patients.

Results

CAP/CTM v2.0 showed significant correlation and high agreement with CAP/CTM v1.0 and EasyQ v2.0. CAP/CTM v2.0 showed excellent detection of clade B samples compared with CAP/CTM v1.0 and EasyQ v2.0. However, significant differences were observed when using CAP/CTM v2.0 to test clade BC and AE samples. The HIV-1 load measured by CAP/CTM v2.0 differed by >0.5 log IU/ml in 59.52% and 72.62% of clade BC samples, and in 57.14% and 85.71% of clade AE samples, compared with CAP/CTM v1.0 and EasyQ v2.0, respectively. CAP/CTM v2.0 was more precise (13.18%) than EasyQ v2.0 (29.21%), and both assays showed good linearity (R ≥ 0.9926).

Conclusions

The three assays may not deliver consistent results for samples belonging to clades BC and AE. It is strongly suggested that the version of the HIV-1 viral load assay used initially is also used at follow-up.