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

Improving Linkage to Care of Hepatitis C: Clinical Validation of GeneXpert® HCV Viral Load Point-of-Care Assay in Indonesia

Hepatitis C virus (HCV) infection large-scale diagnosis and treatment are hampered by lack of a simple, rapid, and reliable point-of-care (POC) test, which poses a challenge for the elimination of hepatitis C as a public health problem. This study aimed to evaluate Cepheid Xpert^® HCV Viral Load performance in comparison with the Roche Cobas^® TaqMan^® HCV Test using serum samples of HCV-infected patients in Indonesia. Viral load quantification was performed on 243 anti-HCV positive patients’ samples using both Xpert HCV VL and Roche HCV tests, followed by HCV genotyping by reverse hybridization. Strength of the relationship between the assays was measured by Pearson correlation coefficient, while level of agreement was analyzed by Deming regression and Bland–Altman plot analysis using log₁₀-transformed viral load values. Quantifiable viral load was detected in 180/243 (74.1%), with Xpert HCV VL sensitivity of 100% (95% CI 0.98, 1.00) and specificity of 98.4% (95% CI 0.91, 0.99) based on the Roche HCV test, while HCV genotypes were determined in 172/180 (95.6%) samples. There was a good correlation between both assays (r = 0.97, P < 0.001), overall and per genotype, with good concordance by Deming regression and a mean difference of −0.25 log₁₀ IU/mL (95% CI −0.33, −0.18) by Bland–Altman plot analysis. Xpert HCV VL test was demonstrated as a POC platform with good performance for HCV diagnosis and treatment decision that would be beneficial for decentralized services in resource-limited areas. HCV testing sites, alongside additional GeneXpert modular systems distributed toward the fight against COVID-19, could ensure some continuity, once this pandemic is controlled.

Diverse HCV Strains And HIV URFS Identified Amongst People Who Inject Drugs In India

Although the prevalences of HIV and HCV are significantly higher amongst PWID in India compared to the general population, the strains circulating within this group have not been well-characterized. Through subgenomic sequencing of viruses present in residual plasma from an HIV/HCV prevalence study conducted amongst PWID across five cities in India in 2016-2017, a total of N = 498 HCV and N = 755 HIV strains were classified from N = 975 study participants. Considerable HCV diversity was identified, with different strains predominating in each region of the country. Overall, the most common strain was genotype 3a (39.0%), with genotypes 1a (26.9%), 1b (3.0%), 1c (0.2%), 3b (20.7%), 3i (2.0%), 4a (0.2%), 4d (1.0%), 6 (1.8%), 6n (4.8%), 6 v (0.2%) and one unclassifiable recombinant specimen (0.2%) also identified. The majority of the HIV specimens were subtype C (96.7%), although subtype A (0.4%), CRF01_AE (0.4%) and unique recombinant forms (URFs, 2.5%) were also detected. Notably, the geographical restriction of HIV subtype A and CRF01_AE, and HCV genotypes 4 and 6 to specific sites suggests distinct novel introductions of HIV and HCV into PWID populations, potentially via drug trafficking routes from neighboring countries where these strains are common.

Analytical and clinical performance of the Hologic Aptima HCV Quant Dx Assay for the quantification of HCV RNA in plasma samples

BACKGROUND

Chronic hepatitis C virus (HCV) infection can be effectively treated with directly acting antiviral (DAA) therapy. Measurement of HCV RNA is used to evaluate patient compliance and virological response during and after treatment.

OBJECTIVES

To compare the analytical performance of the Aptima HCV Quant Dx Assay (Aptima) and the COBAS Ampliprep/COBAS TaqMan HCV Test v2.0 (CAPCTMv2) for the quantification of HCV RNA in plasma samples, and compare the clinical utility of the two tests in patients undergoing treatment with DAA therapy.

STUDY DESIGN

Analytical performance was evaluated on two sets of plasma samples: 125 genotyped samples and 172 samples referred for quantification of HCV RNA. Furthermore, performance was evaluated using dilutions series of four samples containing HCV genotype 1a, 2b, 3a, and 4a, respectively. Clinical utility was evaluated on 118 plasma samples obtained from 13 patients undergoing treatment with DAAs.

RESULTS

Deming regression of results from 187 plasma samples with HCV RNA >2 Log IU/mL indicated that the Aptima assay quantified higher than the CAPCTMv2 test for HCV RNA >4.9 Log IU/mL. The linearity of the Aptima assay was excellent across dilution series of four HCV genotypes (slope of the regression line: 1.00-1.02). The Aptima assay detected significantly more replicates below targeted 2 Log IU/mL than the CAPCTMv2 test, and yielded clearly interpretable results when used to analyze samples from patients treated with DAAs.

CONCLUSIONS

The analytical performance of the Aptima assay makes it well suited for monitoring patients with chronic HCV infection undergoing antiviral treatment.

Chronic Hepatitis B, C, and D

Chronic hepatitis B, C, and D virus infections contribute significantly to the morbidity and mortality of immunocompromised individuals. To contextualize discussion of these infections in immunocompromised patients, this paper provides an overview of aspects of infection in normal hosts. It then describes differences in disease, diagnostic testing, and therapeutic management observed in immunocompromised patients.

A European multicentre study on the comparison of HCV viral loads between VERIS HCV assay and COBAS® TaqMan® HCV Test and RealTime HCV Assay

BACKGROUND

Beckman Coulter has developed the VERIS HCV Assay for use on the new fully automated DxN VERIS Molecular Diagnostic System^¥ for HCV viral load monitoring.

OBJECTIVES

Evaluate the clinical performance of the new quantitative VERIS HCV Assay.

STUDY DESIGN

Comparison was performed on 279 plasma specimens from HCV infected patients tested with the VERIS HCV Assay and COBAS^® Ampliprep/COBAS^® Taqman^® HCV Test and 369 specimens tested with the VERIS HCV Assay and RealTime HCV Assay. Patient monitoring sample results from four time points were also compared.

RESULTS

The average bias between the VERIS HCV Assay and the COBAS^® Ampliprep/COBAS^® Taqman^® HCV Test was 0.04 log₁₀IU/mL, while between the VERIS HCV Assay and the RealTime HCV Assay average bias was 0.21 log₁₀IU/mL. Bias, however, was not consistent across the measuring range. Analysis at the lower end of quantification levels 50, 100, and 1000IU/mL showed a predicted bias for VERIS HCV Assay versus COBAS^® Ampliprep/COBAS^® Taqman^® HCV Test between -0.42 and -0.22 log₁₀IU/mL and for VERIS HCV Assay versus RealTime HCV Assay between 0.00 and 0.13 log₁₀IU/mL. Patient monitoring of HCV viral load over time demonstrated similar levels between VERIS HCV Assay results and COBAS^® Ampliprep/COBAS^® Taqman^® HCV Test (52 samples from 13 patients) and RealTime HCV Assay (112 samples from 28 patients).

CONCLUSIONS

VERIS HCV Assay for use on the DxN VERIS Molecular Diagnostic System represents a reliable new tool for easy sample to result HCV RNA viral load monitoring.

Identification of rare HIV-1 Group N, HBV AE, and HTLV-3 strains in rural South Cameroon

Surveillance of emerging viral variants is critical to ensuring that blood screening and diagnostic tests detect all infections regardless of strain or geographic location. In this study, we conducted serological and molecular surveillance to monitor the prevalence and diversity of HIV, HBV, and HTLV in South Cameroon. The prevalence of HIV was 8.53%, HBV was 10.45%, and HTLV was 1.04% amongst study participants. Molecular characterization of 555 HIV-1 specimens identified incredible diversity, including 7 subtypes, 12 CRFs, 6 unclassified, 24 Group O and 2 Group N infections. Amongst 401 HBV sequences were found a rare HBV AE recombinant and two emerging sub-genotype A strains. In addition to HTLV-1 and HTLV-2 strains, sequencing confirmed the fifth known HTLV-3 infection to date. Continued HIV/HBV/HTLV surveillance and vigilance for newly emerging strains in South Cameroon will be essential to ensure diagnostic tests and research stay a step ahead of these rapidly evolving viruses.

European Multicenter Study on Analytical Performance of DxN Veris System HCV Assay

The analytical performance of the Veris HCV Assay for use on the new and fully automated Beckman Coulter DxN Veris Molecular Diagnostics System (DxN Veris System) was evaluated at 10 European virology laboratories. Precision, analytical sensitivity, specificity, and performance with negative samples, linearity, and performance with hepatitis C virus (HCV) genotypes were evaluated. Precision for all sites showed a standard deviation (SD) of 0.22 log₁₀ IU/ml or lower for each level tested. Analytical sensitivity determined by probit analysis was between 6.2 and 9.0 IU/ml. Specificity on 94 unique patient samples was 100%, and performance with 1,089 negative samples demonstrated 100% not-detected results. Linearity using patient samples was shown from 1.34 to 6.94 log₁₀ IU/ml. The assay demonstrated linearity upon dilution with all HCV genotypes. The Veris HCV Assay demonstrated an analytical performance comparable to that of currently marketed HCV assays when tested across multiple European sites.

Hepatitis C RNA assay differences in results: Potential implications for shortened therapy and determination of Sustained Virologic Response

Approval of Ledipasvir/Sofosbuvir for the treatment of chronic hepatitis C (HCV) includes the truncation of therapy from 12 to 8 weeks in treatment naïve, non-cirrhotic patients with baseline HCV RNA levels <6 million IU/mL (6.8 log10 IU/mL). The aim of this study was to evaluate this clinical cutoff with a different widely used commercially available HCV RNA test. Results from samples tested prospectively with Roche High Pure TaqMan HCV 2.0 test (HPS) were compared to those tested retrospectively with the Abbott RealTime HCV RNA test (ART). Using 6 million IU/mL as the cut-off, pre-treatment results were concordant in 70.4% of cases. When results with the same test measured at screening and baseline, clinical decisions could be impacted in 14.4% and 6.2% of cases for HPS and ART respectively. Using only HCV RNA cutoff of 6 million IU/mL, 29.55% of subjects would receive a different and potentially incorrect treatment duration based solely on HCV RNA test method used. A further 6-14% of subjects would have treatment decision change based on the day the sample was taken.

Analytical performance of the VERIS MDx system HCV assay for detecting and quantifying HCV RNA

BACKGROUND

The diagnosis of HCV relies on the detection of viral RNA.

OBJECTIVE

To evaluate the performance of the VERIS/MDx System HCV Assay, a new automated system for quantifying HCV RNA, and to compare with the COBAS^® Ampliprep/COBAS^® Taqman™ (CAPCTM) HCV Test version 2.0.

STUDY DESIGN

The limit of detection was determined by Probit analysis with the 3rd International WHO HCV standard and precision by assaying in duplicate control samples with HCV RNA concentrations of 7.9; 5.0; 3.4; 1.6 and 0logIU/ml over 20 days. Analytical specificity was assessed by assaying 180 samples from negative anti-HCV and HCV RNA blood donors and linearity with replicates of serial dilutions of a clinical plasma (6.4-0.6logIU/ml). We compared the VERIS MDx HCV and CAPCTM HCV assays by testing 209 samples.

RESULTS

The limit of detection was 6.1IU/ml [CI 95%: 5.0-8.3] and the precision, given by the standard deviation, was ≤0.11logIU/ml. Specificity was 100%. The linearity ranged from 1.5 to 6.4logIU/ml. Passing-Bablok regression analysis gave: VERIS logIU/ml=-0.33+[1.04× CAPCTM] logIU/ml, with biases for the 25th, 50th, 75th percentiles of 0.18, -0.10 and -0.06logIU/ml. The two assays were well correlated (ρ=0.92, p<0.001) and Bland-Altman analysis gave biases of 0.12, logIU/ml for genotype 1, -0.19 for genotype 2, -0.26 for genotype 3, and -0.77 for genotype 4.

CONCLUSION

The VERIS MDx HCV assay performed well. But, we observed an under-quantification of the genotype 4 samples.

Significance of HCV RNA monitoring in the era of new potent therapies

INTRODUCTION

The development and approval of direct-acting-antivirals (DAA) has revolutionized the treatment of hepatitis C within a few years and opened the door to a new era of shorter, well-tolerated but also highly expensive treatment options.

AREAS COVERED

Nowadays, reductions of viral load below quantification limits may often be achieved within the first weeks of therapy. Viral breakthroughs during treatment are rarely observed and unfavourable viral genotypes or an advanced liver disease do not necessarily lower the prospect of eradication. For this reason, pan-genotypic DAA-only therapies are about to replace interferon/ribavirin-regimens as the standard of care worldwide. Expert commentary: Consequently, it has become essential to reevaluate the utility of HCV RNA quantification in predicting treatment outcomes and to guide clinical decisions. Is there still a need for a close-meshed monitoring or is it reasonable to limit HCV RNA monitoring to baseline and post-treatment results? This review discusses the pro- and contra arguments in this regard.

Real-Time PCR Assays for the Quantification of HCV RNA: Concordance, Discrepancies and Implications for Response Guided Therapy

BACKGROUND AND AIMS

Monitoring of chronic Hepatitis C (CHC) treatment relies on HCV RNA quantification by means of real-time PCR methods. Assay specific analytical sensitivities may impact therapy management.

METHODS

Comparative analysis between three commercial assays (Roche COBAS AmpliPrep/COBAS TaqMan Version 1 (CAP/CTM Ver. 1), Version 2 (CAP/CTM Ver. 2) and the Abbott RealTime HCV (ART) assay) was performed on 247 available samples taken at key decision time points during antiviral therapy of 105 genotype 1 patients (triple therapy: n = 70; dual therapy: n = 35).

RESULTS

Overall concordance of HCV RNA measurements was high between the two Roche systems (89%; n = 220/247) but lower between the Roche assays and the ART (CAP/CTM Ver. 1 vs ART: 77.3%; n = 191/247 and CAP/CTM v.2 vs ART: 80.1%; n = 198/247). Most discrepancies were noted in week 4/8 samples with residual viremia (

CONCLUSION

An abbreviated course of treatment can safely be applied in patients with residual viremia ( Collapse

Key Words Collapse

MESH Headings

• Female
• Hepatitis C, Chronic/blood
• Hepatitis C, Chronic/drug therapy
• Humans
• Male
• Monitoring, Physiologic/instrumentation
• Monitoring, Physiologic/methods
• RNA, Viral/blood
• Real-Time Polymerase Chain Reaction/instrumentation
• Real-Time Polymerase Chain Reaction/methods

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Grants Collapse

Affiliation(s)

Robert Strassl Department of Laboratory Medicine, Division of Clinical Virology, Medical University of Vienna, Vienna, Austria
Karoline Rutter Department of Internal Medicine III, Division of Gastroenterology & Hepatology, Medical University of Vienna, Vienna, Vienna, Austria
Albert Friedrich Stättermayer Department of Internal Medicine III, Division of Gastroenterology & Hepatology, Medical University of Vienna, Vienna, Vienna, Austria
Sandra Beinhardt Department of Internal Medicine III, Division of Gastroenterology & Hepatology, Medical University of Vienna, Vienna, Vienna, Austria
Michael Kammer Center for Medical Statistics, Informatics, and Intelligent Systems (CeMSIIS), Medical University of Vienna, Vienna, Austria
Harald Hofer Department of Internal Medicine III, Division of Gastroenterology & Hepatology, Medical University of Vienna, Vienna, Vienna, Austria
Peter Ferenci Department of Internal Medicine III, Division of Gastroenterology & Hepatology, Medical University of Vienna, Vienna, Vienna, Austria
Theresia Popow-Kraupp Department of Laboratory Medicine, Division of Clinical Virology, Medical University of Vienna, Vienna, Austria

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Variation analysis of six HCV viral load assays using low viremic HCV samples in the range of the clinical decision points for HCV protease inhibitors

In the range of clinical decision points for response-guided therapy of HCV, there is still insufficient data concerning the conformity of quantification results obtained by different assays and their correlation with the HPS/CTM v2 assay which was used for initial clinical studies. In a head-to-head comparison, assay accuracy and detection rates of six quantitative assays [artus HCV QS-RGQ, COBAS Ampliprep/COBAS TaqMan HCV v1/v2, High Pure System/COBAS TaqMan (HPS), RealTime HCV, and Versant HCV1.0] were assessed by measuring WHO and PEI standards at dilution steps near clinical decision points. Detection rates and mean differences between assays were evaluated by analyzing twenty clinical samples at 10, 100, and 1,000 IU/mL. Ten replicates from specimens with different HCV genotypes were used to analyze pan-genotypic intra-assay variation. At ≤ 25 IU/mL, RealTime demonstrated the highest detection rates. With 0.1 log difference when testing clinical samples, results obtained from the Versant and RealTime assays matched best with results from HPS. Mean difference analysis across all assay results revealed wide differences between 0.01 and 0.75 log IU/mL. RealTime showed the lowest intra-assay variation across genotypes 1-4 (25, 100, 1,000 IU/mL). There are substantial analytical differences between viral load assays clinicians should be aware of. These variations may have impact on clinical decisions for patients on HCV triple therapy and may argue for assay-specific decision points equivalent to reference values established in studies using HPS. A comparison of quantification is recommended prior to a switch of assays during ongoing therapy.

Utility of hepatitis C viral load monitoring on direct-acting antiviral therapy

BACKGROUND

Hepatitis C virus (HCV) RNA loads serve as predictors of treatment response during interferon-based therapy. We evaluated the predictive ability of HCV RNA levels at end of treatment (EOT) for sustained virologic response (SVR12) during interferon-sparing direct-acting antiviral therapies.

METHODS

HCV genotype 1-infected, treatment-naive patients were treated with sofosbuvir and ribavirin for 24 weeks (n = 55), sofosbuvir and ledipasvir for 12 weeks (n = 20), sofosbuvir, ledipasvir, and GS-9669 for 6 weeks (n = 20), or sofosbuvir, ledipasvir, and GS-9451 for 6 weeks (n = 19). Measurements of HCV RNA were performed using the Roche COBAS TaqMan HCV test and the Abbott RealTime HCV assay. Positive predictive value (PPV) and negative predictive value (NPV) of HCV RNA less than the lower limit of quantification (

RESULTS

All 55 patients treated with sofosbuvir and ribavirin had HCV RNA

CONCLUSIONS

Contrary to past experience with interferon-containing treatments, low levels of quantifiable HCV RNA at EOT do not preclude treatment success.

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Key Words

• HCV RNA
• direct-acting antiviral
• hepatitis C
• viral load

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MESH Headings

• Adult
• Aged
• Antiviral Agents/pharmacology
• Antiviral Agents/therapeutic use
• Drug Monitoring/methods
• Female
• Hepacivirus/drug effects
• Hepatitis C/drug therapy
• Hepatitis C/epidemiology
• Hepatitis C/virology
• Humans
• Male
• Middle Aged
• Predictive Value of Tests
• RNA, Viral/blood
• Viral Load/drug effects

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Grants

• HHSN261200800001C NCI NIH HHS
• HHSN261200800001E NCI NIH HHS
• HHSN261200800001E NCI NIH HHS

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Affiliation(s)

Sreetha Sidharthan Critical Care Medicine Department, National Institutes of Health Clinical Center, National Institutes of Health, Bethesda
Anita Kohli Critical Care Medicine Department, National Institutes of Health Clinical Center, National Institutes of Health, Bethesda
Zayani Sims Critical Care Medicine Department, National Institutes of Health Clinical Center, National Institutes of Health, Bethesda
Amy Nelson Institute of Human Virology, University of Maryland, Baltimore Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
Anu Osinusi Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland Gilead Sciences Inc, Foster City, California
Henry Masur Critical Care Medicine Department, National Institutes of Health Clinical Center, National Institutes of Health, Bethesda
Shyam Kottilil Institute of Human Virology, University of Maryland, Baltimore Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland

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HCV RNA assay sensitivity impacts the management of patients treated with direct-acting antivirals

BACKGROUND

Application of response-guided therapy (RGT) rules to the treatment of HCV infection with pegylated interferon-α2a and ribavirin, and direct-acting antivirals (DAAs) such as the NS3/4A protease inhibitors (PIs) boceprevir and telaprevir, relies on the determination of viral genotype and on-treatment HCV RNA level. Currently there are few data available regarding the clinical impact of the analytical differences that exist between different HCV RNA quantification assays on treatment decisions such as those involved in RGT.

METHODS

We sought to ascertain the concordance between two HCV RNA quantification assays, the Roche/High-Pure-System COBAS(®) TaqMan (CTM) version 2 and Abbott RealTime HCV (ART), and to understand the impact of different assay characteristics on treatment decisions. We evaluated 1,336 specimens collected from 74 patients enrolled in the Phase II CHAMPION-2 study of the investigational DAAs ABT-450 (an acylsulfonamide NS3/4A PI), ABT-072 and ABT-333 (both non-nucleoside NS5B polymerase inhibitors).

RESULTS

HCV RNA level results were highly correlated, but CTM values were higher than those from ART by an average of 0.46 log IU/ml. Use of ART HCV RNA level results led to a higher positive predictive value of week 4 viral load for the achievement of a sustained virological response 24 weeks after the end of treatment (100% versus 87% using the lower limit of detection as the threshold).

CONCLUSIONS

This study suggests that HCV viral load assay performance characteristics need to be taken into consideration when managing HCV patients with RGT. Further studies are required to determine whether a consensus HCV RNA level threshold can be established or whether HCV viral load assays with greater sensitivity can increase cure rates with RGT.

The importance of HCV RNA measurement for tailoring treatment duration

The introduction of telaprevir and boceprevir in the treatment of chronically HCV genotype 1 infected patients has led to substantially improved sustained virologic response rates and shorter treatment duration for a growing group of patients. Management and monitoring of patients receiving protease inhibitor-based triple therapy is of major importance and has become more complicated. Close monitoring of HCV RNA levels for patients on protease inhibitor-based therapy to identify subjects who are eligible for shortening of treatment duration, are virological non-responders or are in danger of experiencing a viral breakthrough is strongly recommended. Several virological tools including qualitative and quantitative HCV RNA assays for detection and quantification of HCV RNA are commercially available. We review these methods and their implications for HCV therapy as well as current sustained virologic response definition, stopping rules and recommendations for protease inhibitor-based treatment durations.

Genotype impact on HCV RNA levels determined with the VERSANT HCV RNA 1.0 assay (kPCR)

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 log(10) units. For the panel member containing HCV subtype 2a, the HCV RNA concentration was found to be >0.5 log(10) 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 log(10) units lower with the Siemens assay while that of certain HCV subtype 3a and 4a isolates were found to be >1.0 log(10) 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.