Cobas AmpliPrep/Cobas TaqMan Research Articles

Development and validation of the first HBV qRT-PCR assay in the Mediterranean area targeting the X region

Hepatitis B virus (HBV) infection is a global public health burden and affects approximatively 300 million people around the world. Since, HBV population is represented with genetic diversity, having different viral effects. Development of a new prognosis method play a key role on the efficiency of the different treatment. The HBx protein of HBV has a potential role in Hepatocellular Carcinoma (HCC), which makes it a valuable target for HCC prognosis. In this context, the first quantitative real-time PCR (qRT-PCR) assay in the Mediterranean area was developed and validated.Specific primers and probes of a conserved X region across all HBV genotypes were designed and the qRT-PCR was performed with the TaqPath 1-Step Multiplex Master Mix on 441 Moroccan plasma samples in Pasteur Institute of Morocco.The assay demonstrated a linear quantification range of 1010–101 IU/reaction (R2 = 0.99) and a quantification limit of 15 IU/mL. Comparative evaluations with the COBAS Ampliprep/COBAS TaqMan (CAP/CTM) HBV, v2.0 and the artus HBV QS-RGQ assays showed strong correlations (R2 = 0.92 and R2 = 0.89, respectively).Our test is fast, highly sensitive, specific, reproducible, and labor-saving. This system will be of great advantage to Mediterranean countries in their efforts to eliminate viral hepatitis B and C by 2030, enabling precise monitoring and effective treatment of HBV infections.

More HIV-1 RNA detected and quantified with the Cobas 6800 system in patients on antiretroviral therapy.

Target-detected (TD) results or low-level viraemia (LLV) can be observed in HIV-1 patients on ART, which regularly raises questions. We describe here the impact on HIV-1 RNA quantification of switching from the COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) to the Cobas 6800 system (C6800), based on analyses of viraemia close to the lower limit of quantification (LLoQ). We retrospectively selected two groups of patients: 200 individuals whose viral loads (VLs) were consistently <50 copies/mL with CAP/CTM for at least 3 years before switching to C6800 (group 1), and 35 other patients with confirmed LLV when C6800 was in use (group 2). In both groups, we compared several consecutive VL results performed before and after the change of quantification assay. Analyses were performed with McNemar's paired tests or Fisher's exact tests. In group 1, the frequency of TD results (below or above the LLoQ) increased significantly after the switch to C6800 for patients with <25% of results being TD for VLs performed with CAP/CTM (P < 0.0001). Significantly more patients had at least one VL ≥20 or ≥50 copies/mL with C6800, in both group 1 (37.0% versus 18.5%; P < 0.0001 and 6.5% versus 0%; P = 0.0009, respectively) and group 2 (100% versus 66%; P = 0.0015 and 97% versus 40%; P < 0.0001, respectively). C6800 revealed residual or low-level HIV-1 RNA that was not detected with CAP/CTM, resulting in twice as many patients being found to have a VL ≥20 copies/mL. Physicians and patients should be aware of possible differences in results between assays, and it is crucial to specify the quantitative assay used in studies.

Validation of the point-of-care (POC) technologies Xpert HIV-1 Qual and m-PIMA HIV 1/2 detect for early diagnosis of HIV-1 and HIV-2 in Senegal.

early infant diagnosis (EID) is crucial in the prevention of mother to child transmission (PMTCT) of human immunodeficiency virus (HIV) and is an essential component for the elimination of HIV. EID can be strengthened in resource-limited countries by the introduction and the roll out of real-time polymerase chain reaction (PCR) technologies via point-of-care (POC) devices which improves treatment in remote areas and reduces turnaround time for clinicians and patients to receive results and linkage to care. The objective of this study was to evaluate the performance of Xpert® HIV-1 Qual Assay (Cepheid) and m-PIMA™ HIV 1/2 Detect (ABBOTT) for EID of HIV-1 and HIV-2. the performance of the Xpert® HIV-1 qual device was evaluated with 192 samples including 100 dried blood spot (DBS) samples from the National Reference Laboratory biobank (71 negative and 29 positive samples) and an additional 92 whole blood samples collected from infants from neonatal departments. These infants from seven treatment centers in the Dakar region were born to mothers infected with HIV-1 (n=91), HIV-2 (n= 8) or HIV-1/2 (n=1). The m-PIMA™ HIV 1/2 detect assay was evaluated on whole blood samples (n=100) with 92 HIV-1 samples and 8 HIV-2 samples from children born to HIV-infected mothers. The Cobas AmpliPreP/Cobas TaqMan (CAP/CTM) platform from Roche Diagnostic Laboratories was used as a reference for HIV-1 diagnosis and the Generic HIV-2 Viral Load Assay (Biocentric) was used as a reference for HIV-2 diagnosis. Performance was evaluated by calculating sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV) and Cohen's kappa coefficient. for HIV-1 detection on GeneXpert and m-PIMA, no discordance was found on the samples tested, i.e. a sensitivity of 100% (95% CI: 93.9-100%), a specificity of 100% (95% CI: 97.5-100%), a positive predictive value (PPV) of 100% (95% CI: 93.9-100%) and a negative predictive value (NPV) of 100% (95% CI: 97.5-100%). Agreement with Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) was 100% with a Kappa coefficient of 1 (p<0.001, 95% CI) for both techniques. Similarly, the comparison between m-PIMA and generic biocentric for the detection of HIV-2 on the 8 samples tested showed perfect agreement. these results confirm the excellent performance of the Xpert® HIV-1 qual and m-PIMA™ HIV1/2 detect tests for the detection of HIV-1 and HIV-2 and encourage the extension of POC tests to improve access to EID in Senegal.

Suitability of Different Diagnostic Platforms for Virological Testing of Blood Samples from Cornea Donors

Background: To minimize the risk of disease transmission in cornea transplantation, donor screening for blood-derived viral infections is mandatory. Ideally, pre-mortem blood samples are used, but based on availability, cadaveric blood samples of cornea donors may also be used. However, serological and nucleic acid amplification tests (NATs) need to be validated for the use of cadaveric specimens. Methods: Hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus (HIV), human T-lymphotropic virus (HTLV) 1/2, and Treponema pallidum (syphilis)-specific serological and/or NAT assays were validated on different platforms (Abbott Alinity i, Alinity m, Roche Cobas 6800, and Roche Cobas AmpliPrep/Cobas TaqMan (CAP/CTM)) using (un)spiked paired pre- and post-mortem cornea donor blood samples from the same individual (up to 23.83 h after death) of 28 individuals in accordance with the specifications of the German Federal Institute for Vaccines and Biomedicines (Paul-Ehrlich-Institut [PEI]). In addition, routinely HBV-, HCV- and HIV-PCR-negative tested post-mortem blood samples of 24 individuals were used to assess NAT specificity. Results: For the majority of serological parameters on the Abbott Alinity i (HBsAg, anti-HBc, anti-HBs, anti-HCV, anti-HIV, anti-HTLV 1/2, and anti-Treponema pallidum), ratios of generated test results of (un)spiked paired pre- and post-mortem blood samples differed ≤25%, with an agreement of qualitative pre- and post-mortem test results ranging from 91.2 to 100%. For NAT parameters (HBV, HCV, and HIV) on the Cobas 6800, Alinity m, and CAP/CTM, no significant deviation in virus concentrations (factor >5) of spiked pre- and post-mortem blood samples could be observed. Ct-values of corresponding internal controls did also not differ significantly (>1.5 Ct-values). In addition, no false-positive test results were generated when specificity was assessed. Conclusion: Overall, fluctuations of test results for serological and NAT parameters in pre- and post-mortem blood samples examined in this study, were only limited and within the range of what is also observed when routinely testing fresh patient specimens. We conclude that all examined assays are eligible for the screening of blood samples taken up to about 24 h after the occurrence of death.

Successful Use of Near Point-of-Care Early Infant Diagnosis in NAMPHIA to Improve Turnaround Times in a National Household Survey.

In the population-based HIV impact assessment surveys, early infant diagnosis (EID) was provided to infants <18 months without a prior diagnosis. For the Namibia population-based HIV impact assessment (NAMPHIA), the GeneXpert platform was assessed for the feasibility of near POC EID testing compared with the standard Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) platform. Quality assurance measures and turnaround time were compared to improve EID results reporting. NAMPHIA participants were screened for HIV exposure using Determine HIV-1/2 rapid test; samples reactive on Determine received EID testing on the GeneXpert instrument and Xpert HIV-1 Qual assay using whole blood. Results were confirmed at the Namibia Institute of Pathology using dried blood spots on the Roche CAP/CTM platform per national guidelines. Of the 762 screened infants, 61 (8.0%) were Determine-reactive and considered HIV-exposed. Of the 61 exposed infants, 2 were found to be HIV-infected whereas 59 were negative on both GeneXpert and Roche platforms, achieving 100% concordance. Average turnaround time was 3.4 days for the Xpert HIV-1 Qual assay, and average time from collection to testing was 1.0 days for GeneXpert compared with 10.7 days for Roche. No samples failed using GeneXpert whereas 1 sample failed using Roche and was repeated. Quality POC EID testing is feasible in a national survey through extensive training and external quality assurance measures. The use of decentralized POC EID for national testing would provide rapid diagnosis and improve TATs which may prevent loss to follow-up, ensure linkage to care, and improve clinical outcomes for infants.

Clinical significance of detectable and quantifiable HCV RNA at the end of treatment with ledipasvir/sofosbuvir in GT1 patients.

AASLD/IDSA treatment guidelines for hepatitis C virus (HCV) infection state that testing for quantitative HCV RNA can be considered at the end of antiviral treatment (EOT) with interferon-free regimens. However, it remains unclear how to respond to a detectable or even quantifiable HCV RNA result. The aim of this study was to analyse the frequency and predictive value of detectable and quantifiable HCV RNA results at the EOT in patients with HCV genotype 1 infection treated with ledipasvir (LDV) and sofosbuvir (SOF)±ribavirin (RBV) in a large real-world cohort. A retrospective analysis of the DHC-R (Deutsches Hepatitis C-Register, German Hepatitis C-Registry) cohort was performed including all patients who were treated with LDV/SOF±RBV and in whom HCV RNA testing was done with either the Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) or the Abbott RealTime HCV assay (ART). The frequency of detectable HCV RNA at the EOT was 7% in this real-world study involving 471 patients. Furthermore, 3% of the patients (n=14/471) even had quantifiable viral load at the EOT. Detectable and quantifiable results were more frequent if the ART was used for testing. However, SVR was achieved by 32/33 patients (97%) with detectable and even by all 14 patients (100%) with quantifiable HCV RNA results at the EOT. Detectable and even quantifiable HCV RNA results are quite frequent if highly sensitive HCV RNA assays are used. However, treatment prolongation is not indicated, as SVR rates remain high in these patients.

Multicountry Validation of SAMBA - A Novel Molecular Point-of-Care Test for HIV-1 Detection in Resource-Limited Setting.

Early diagnosis of HIV-1 infection and the prompt initiation of antiretroviral therapy are critical to achieving a reduction in the morbidity and mortality of infected infants. The Simple AMplification-Based Assay (SAMBA) HIV-1 Qual Whole Blood Test was developed specifically for early infant diagnosis and prevention of mother-to-child transmission programs implemented at the point-of-care in resource-limited settings. We have evaluated the performance of this test run on the SAMBA I semiautomated platform with fresh whole blood specimens collected from 202 adults and 745 infants in Kenya, Uganda, and Zimbabwe. Results were compared with those obtained with the Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HIV-1 assay as performed with fresh whole blood or dried blood spots of the same subjects, and discrepancies were resolved with alternative assays. The performance of the SAMBA and CAP/CTM assays evaluated at 5 laboratories in the 3 countries was similar for both adult and infant samples. The clinical sensitivity, specificity, positive predictive value, and negative predictive value for the SAMBA test were 100%, 99.2%, 98.7%, and 100%, respectively, with adult samples, and 98.5%, 99.8%, 99.7%, and 98.8%, respectively, with infant samples. Our data suggest that the SAMBA HIV-1 Qual Whole Blood Test would be effective for early diagnosis of HIV-1 infection in infants at point-of-care settings in sub-Saharan Africa.

Prevalence and outcomes of HIV-1 diagnostic challenges during universal birth testing - an urban South African observational cohort.

Introduction: HIV‐1 polymerase chain reaction (PCR) testing at birth aims to facilitate earlier initiation of antiretroviral therapy (ART) for HIV‐infected neonates. Data from two years of universal birth testing implementation in a high‐burden South African urban setting are presented to demonstrate the prevalence and outcomes of diagnostic challenges in this context. Methods: HIV‐exposed neonates born at Rahima Moosa Mother and Child Hospital between 5 June 2014 and 31 August 2016 were routinely screened at birth for HIV‐1 on whole blood samples using the COBAS® AmpliPrep/COBAS® TaqMan (CAP/CTM) HIV‐1 Qualitative Test, version 2.0 (Roche Molecular Systems, Inc., Branchburg, NJ, USA). Virological results were interpreted according to standard operating procedures with the South African National Health Laboratory Service. All neonates with non‐negative results were actively followed‐up and categorized according to HIV infection status as positive, negative, uncertain and lost to follow‐up (LTFU). Results: 104 (1.8%) of 5743 HIV‐exposed neonates received a non‐negative birth PCR result, for which laboratory data were available for 102 (98%) cases – 78 (76%) tested positive and 24 (24%) indeterminate. HIV infection status was confirmed positive in 83 (81%) infants, negative in 8 (8%), uncertain in 5 (5%) and LTFU in 6 (6%) cases. The positive predictive value (excluding cases of uncertain diagnosis and inadequate testing) following a non‐negative HIV‐1 PCR screening test at birth was 0.91 (83/91; 95% confidence interval: 0.85–0.96). Neonates testing positive at birth had significantly higher viral load (VL) results than those testing indeterminate at birth of 4.5 and 3.0 log copies/ml (p = 0.0007), respectively. Similarly, mothers of neonates with positive as compared to indeterminate birth test results had higher VLs of 4.5 and 2.7 log copies/ml (p = 0.0013), respectively. Half of neonates with an indeterminate birth test were shown to be HIV‐infected on subsequent confirmatory testing, with time to final diagnosis 30 days longer for these neonates (p < 0.0001). Conclusion: Indeterminate HIV‐1 PCR results accounted for a quarter of non‐negative results at birth and were associated with a high risk of infection in comparison to the risk of in utero transmission. Indeterminate birth results with positive HIV PCR results on repeat testing were associated with later final diagnosis. The HIV‐1 status remains uncertain in a minority of cases because of repeatedly indeterminate results, highlighting the need for more sensitive and specific virological tests.

Field Evaluation of Dried Blood Spots for HIV-1 Viral Load Monitoring in Adults and Children Receiving Antiretroviral Treatment in Kenya: Implications for Scale-up in Resource-Limited Settings.

The World Health Organization recommends viral load (VL) as the preferred method for diagnosing antiretroviral therapy failure; however, operational challenges have hampered the implementation of VL monitoring in most resource-limited settings. This study evaluated the accuracy of dried blood spot (DBS) VL testing under field conditions as a practical alternative to plasma in determining virologic failure (VF). From May to December 2013, paired plasma and DBS specimens were collected from 416 adults and 377 children on antiretroviral therapy for ≥6 months at 12 clinics in Kenya. DBSs were prepared from venous blood (V-DBS) using disposable transfer pipettes and from finger-prick capillary blood using microcapillary tubes (M-DBS) and directly spotting (D-DBS). All samples were tested on the Abbott m2000 platform; V-DBS was also tested on the Roche COBAS Ampliprep/COBAS TaqMan (CAP/CTM) version 2.0 platform. VF results were compared at 3 DBS thresholds (≥1000, ≥3000, and ≥5000 copies/mL) and a constant plasma threshold of ≥1000 copies/mL. On the Abbott platform, at ≥1000-copies/mL threshold, sensitivities, specificities, and kappa values for VF determination were ≥88.1%, ≥93.1%, and ≥0.82%, respectively, for all DBS methods, and it had the lowest percentage of downward misclassification compared with higher thresholds. V-DBS performance on CAP/CTM had significantly poorer specificity at all thresholds (1000%-33.0%, 3000%-60.9%, and 5000%-77.0%). No significant differences were found between adults and children. VL results from V-DBS, M-DBS, and D-DBS were comparable with those from plasma for determining VF using the Abbott platform but not with CAP/CTM. A 1000-copies/mL threshold was optimal and should be considered for VF determination using DBS in adults and children.

Detection and quantification of HIV-1 RNA with a fully automated transcription-mediated-amplification assay

BackgroundNucleic acid testing is the major method used to monitor HIV viral load. Commercial systems based on real-time PCR assays are available for high-volume centralized laboratory testing, but they are not fully automated. Objectives and study designWe have compared the diagnostic performance of the Hologic Aptima HIV-1 Quant Dx assay (Aptima) (based on real-time TMA) on the Panther instrument, a fully-automated random access platform, to that of, the Roche Cobas Ampliprep Cobas TaqMan (CAP/CTM) HIV-1 version 2.0 (based on real-time PCR). ResultsProbit analysis of replicate dilutions of NIBSC WHO International HIV-1 Standard, gave LODs of 8.6 c/ml for Aptima and 15.2 c/ml for CAP/CTM. The agreement between the assays was excellent when measuring HIV RNA in a calibrated reference (κ=0.90, p<0.001) and good when measuring clinical samples (κ=0.62, p<0.001). The correlation among the samples quantified by the two methods was very good (r=0.95, p<0.001) and the mean difference between the values obtained with the two assays was 0.02 log c/ml for B and non-B subtypes. The vast majority of results showed <0.5 log variance between the two assays (89%); only one sample showed results that differed by over 1.0 log c/ml. ConclusionThe performance of the new fully automated Aptima assay is adequate for clinical monitoring of HIV-1 RNA during infections and treatment. The Aptima assay is well suited for routine laboratory use.

Clinical efficacy of the highly sensitive hepatitis C virus RNA quantitative assay in patients with relapse following interferon-based therapy with second-generation direct-acting antivirals.

For refractory chronic hepatitis C, interferon (IFN)-based triple-agent combination therapy with second-generation direct-acting antivirals (DAAs) has been established as the standard treatment method. The rate of decrease in the viral load and the negative conversion of hepatitis C virus (HCV) RNA in the early phase following treatment initiation are considered important factors for predicting the therapeutic outcome. In the present study, the Roche Cobas AmpliPrep/COBAS TaqMan (CAP/CTM) HCV v2.0 assay and the AccuGENE m-HCV RNA quantitative assay [Abbott RealTime HCV (ART) assay] were analyzed for their clinical efficacy and ability to predict therapeutic outcomes in the early phase in patients with relapse following IFN-based second-generation DAA therapy. Of the 56 patients who received IFN-based second-generation DAA therapy since December 2013, 6 achieved an end-of-treatment response (ETR), but subsequently experienced relapse. In these 6 patients, fluctuations in viral loads in the early phase detected by the CAP/CTM and ART assays were compared. At 4 weeks after treatment initiation, 4 of the 6 patients were diagnosed as negative by the CAP/CTM assay, whereas 2 of these 4 patients were not identified as negative by the ART assay. Of the 2 patients, one was signal-positive with an HCV RNA load <1.08 Log IU/ml, and the other patient had a viral load of 1.12 Log IU/ml. At 8 weeks after treatment initiation, 1 patient was found to be negative by the CAP/CTM assay, but signal-positive with a viral load <1.08 Log IU/ml by the ART assay. From 4 to 8 weeks after treatment initiation, 3 of the 6 patients appeared to be discrepant cases. In conclusion, of the 6 patients who achieved an ETR, 4 were determined to have achieved a rapid virological response (RVR) by the CAP/CTM assay, but may not have actually become negative. The ART assay is highly sensitive, has a wide measurement range, may be suitable for monitoring HCV RNA loads, and is expected to have an important role in providing a predictive marker for early therapeutic outcomes. In discrepant cases in which no RVR is proved by either assay, it was assumed important to consider continuation of treatment and to attempt to achieve a sustained virological response.

Applicability of Hepatitis C Virus RNA Viral Load Thresholds for 8-Week Treatments in Patients With Chronic Hepatitis C Virus Genotype 1 Infection.

Interferon-free treatment of chronic hepatitis C virus (HCV) genotype 1 infection may be shortened to 8 weeks in treatment-naive, noncirrhotic patients with baseline HCV RNA levels of <4 or <6 million (M) IU/mL based on post-hoc analyses of phase 3 trial data. The applicability of these viral load thresholds in clinical practice is unknown. Pretreatment and on-treatment serum samples (n = 740) from patients with HCV genotype 1 infection were included for HCV RNA analysis with 2 widely used assays, Cobas AmpliPrep/CobasTaqMan (CAP/CTM) and Abbott RealTime HCV (ART) assays. HCV RNA levels were significantly higher with CAP/CTM than with ART (overall difference, +0.11 log10 IU/mL; P < .001). In treatment-naive, noncirrhotic patients, discordance rates around the clinical cutoffs at 4M and 6M IU/mL were 23% and 18%, respectively. The mean differences between assays in discordant samples were 0.38 (4M) and 0.41 (6M) log10 IU/mL, respectively. Overall, 87% and 95% of treatment-naive, noncirrhotic patients, respectively, had baseline HCV RNA levels below 4M and 6M IU/mL with ART. These rates were significantly higher than those measured with CAP/CTM (64% and 78%, respectively; P < .001). Finally, discordance rates around the proposed thresholds in 2 consecutive samples of the same patient were in the range of 1%-2% for ART and 13%-17% for CAP/CTM. Selection of patients for 8-week regimens on the basis of a single HCV RNA determination may not be reliable because viral load levels around the proposed clinical thresholds show significant interassay and intrapatient variability.

Cost analysis of residual viremia detected by two real-time PCR assays for response-guided (dual or triple) therapy of HCV genotype 1 infection

Introduction The duration of interferon-based dual and triple therapies for HCV-G1 is determined by assessment of early viral kinetics. We conducted a cost analysis to determine the mean cost of dual or triple therapy treatment for a patient with HCV-G1, where the therapy duration (24 or 48 weeks) is guided by HCV-RNA assay. Methods HCV-RNA was assessed by two widely used real-time PCR-based assays, Cobas Ampliprep/Cobas TaqMan (CAP-CTM) and Real-Time HCV (ART). As far as the dual therapy (PegINFα-2b and RBV) is concerned, at week 12 of treatment 16.0% of patients (27/169) were eligible to receive a shorter duration of therapy (24 weeks) according to CAP-CTM and 8.9% (15/169) according to ART: 26 patients achieved SVR (15.4%) with CAP-CTM and 15 with ART (8.9%). With regard to triple therapy (TPV, PegINFα-2a and RBV), at week 12 of treatment 59.6% of patients (31/52) were eligible to receive a shorter duration of therapy (24 weeks) according to CAP-CTM and 28.8% (15/52) according to ART: 30 patients achieved SVR (57.7%) with CAP-CTM and 13 with ART (25.0%). The cost analysis was conducted from the perspective of the Italian National Health Service (NHS). Only drug (TPV, PegINFα-2a, PegINFα-2b and RBV) and test (CAP-CTM and ART) costs were taken into account. Ex-factory prices (included all discounts) and national tariffs were used to calculate drug consumptions and tests, respectively. Costs were assessed in Euros 2015. Results With regard to dual therapy, the overall mean treatment cost per patient with CAP-CTM (€9,572.77) was lower than with ART (€9,876.19). With regard to triple therapy, the overall mean treatment cost per patient was lower with CAP-CTM (€31,354.40) than with ART (€33,155.26). Conclusions CAP-CTM HCV-RNA assay was cost-saving from the Italian NHS perspective compared with ART HCV-RNA assay in the dual (-€303.42 per patient) and triple (-€1,800.96 per patient) HCV therapy.

Impact of HCV kinetics on treatment outcome differs by the type of real-time HCV assay in NS3/4A protease inhibitor-based triple therapy

Repeated measurement of the HCV RNA level is essential for properly monitoring treatment efficacy. The aim of this study was to determine the utility of two HCV real-time assays in the evaluation of the impact of hepatitis C virus (HCV) kinetics on the outcome of triple therapy with NS3/4A protease inhibitors (PIs), telaprevir or simeprevir. This study consisted of 171 Japanese patients infected with HCV genotype 1. All 3266 serum samples taken during and post treatment were tested with both the COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HCV Test v2.0 and the Abbott RealTime (ART) HCV Test. Of the 2597 samples undetectable (lower limit of detection [<LOD]) for HCV RNA by the CAP/CTM assay from the on and post treatment, 400 (15.4%) (369 detectable/less than the lower limitation of quantification [<LLOQ] and 31 quantifiable) were detectable by the ART assay. HCV RNA < LOD within the first four weeks by ART was associated with sustained virological response (SVR) for the difficult-to-treat group that included patients with advanced fibrosis or prior partial/null response. In contrast, for the non-difficult-to-treat group, almost all of the late responders by ART achieved SVR, unlike by CAP/CTM. Despite HCV RNA being once < LOD by ART, 33.1% patients experienced the reappearance of residual HCV RNA (detectable/<LLOQ) during treatment. This event in the first 12 weeks (with PI-treatment period) was not related to treatment failure, however, relapse was observed in all patients with a reappearance of residual HCV RNA after 12 weeks (without PI-treatment period). The superior ability to detect low-level HCV RNA by ART could be useful for predicting SVR by difficult-to-treat patients in the early period and relapse in the late period.

Infection Burden of Double Stranded DNA (dsDNA) Viruses after CD34+ Selected, T-Cell Depleted (TCD) Hematopoietic Cell Transplantation (HCT) for Myeloid Malignancies at Memorial Sloan Kettering Cancer Center (MSK)

Background: Ex vivo T-cell depletion (TCD) by CD34+ selection has been used successfully for graft-versus-host disease prevention alleviating the need for additional pharmacologic immunosuppressants. TCD has been associated with higher rates of viral infections and cytomegalovirus (CMV) disease in particular compared to conventional (CONV) HCT. Modern methods of TCD achieve up to 5 log reduction of T-cells. At MSK, TCD HCT recipients (R) are routinely monitored for CMV, adenovirus (ADV), Epstein-Barr virus (EBV), and human herpes virus 6 (HHV6) in the blood by quantitative polymerase chain reaction (qPCR) assays. We report the incidence of viremia and end organ disease (EOD) by these viruses in TCD HCT recipients.Methods: Retrospective review of adults with acute leukemia (AL) and myelodysplastic syndrome (MDS) patients (pts) who received TCD HCT at MSK from June 2010 -December 2014. TCD was performed by the FDA approved CliniMACS CD34+ reagent system (Miltenyi Biotec, Gladbach, Germany). CMV was monitored at least weekly from day 14-100 and at least every 14 days until day 180. EBV was monitored through day 180. Monitoring for CMV and EBV was performed by the Clinical Microbiology Laboratory at MSK using Roche analyte specific reagents, and since March 2013, the Cobas Ampliprep/Cobas Taqman (CAP/CTM) CMV qPCR in plasma. Monitoring for ADV/HHV6 was performed by Viracor-IBT laboratories (Lenexa, KS). Preemptive treatment for CMV was started for ≥2 consecutive PCR >500copies/ml in whole blood or >300 IU/ml in plasma. Treatment of ADV/HHV6 viremia was at clinician's discretion. EBV post-transplant lymphoproliferative disorder (PTLD) was treated with rituximab as primary therapy. During the study, 11 pts were enrolled in CMV prevention trials of brincidofovir (BCV), and 5 pts received BCV for treatment of ADV. EOD was scored by standard criteria. Follow up was through June 2015. The cumulative incidence (CI) was estimated for viremia at 180 days and EOD at 365 days for CMV, ADV, HHV6, and EBV. Kaplan-Meier method and log-rank test were used to compare CI between groups. P <0.05 was deemed statistically significant.Results: Of239 pts (median age 56.3 years, range 19.6-73.3), 161 (67%) pts had AL and 78 (33%) pts had MDS. Donors were matched-related 76 (32%), matched unrelated 116 (48%), or mismatched (related or unrelated) 47(20%); CMV R+ 148 (62%) or R- 91 (38%). CMV infection had the earliest onset post HCT at a median of 28 days (d) (IQR: 25-33), followed by HHV6 33d (25-52), ADV 71d (44-89), and EBV 85d (58-107). 188 (79%) pts had ≥1 dsDNA viral infection with 182 (76%) pts experiencing infection prior to d100. The CIs of viremia were: CMV 42% (68% in R+ vs 0% in R-, P <0.0001), ADV 7% (10% in R+ vs 5% in R-, P =0.02), EBV 19%, and HHV6 61%. The CI of EBV and HHV6 viremia were similar between R+ and R- (P =NS). Among 100 pts with CMV viremia, 62 (62%) had dsDNA viral coinfections; including 40 (40%) with 1 coinfection, 19 (19%) with 2 coinfections, and 3 (3%) with 3 coinfections. Antiviral treatment was given to 99 pts for CMV (99% of CMV viremic pts, 67% of R+, 41% of total pts), 9pts for ADV (56% of ADV viremic pts; 4% of total), and 19 for HHV6 (16% of HHV6 viremic pts; 8% of total). In total, 42 (18%) pts developed EOD by dsDNA viruses. The most common EOD was EBV PTLD (20 pts, 9%), followed by CMV (14 pts, 7%; but 11% among CMV R+ pts), ADV (8 pts, 4%), and HHV6 (2 pts, 1%). Among 14 pts with CMV disease, 6 had pneumonitis, 5 colitis, 3 duodenitis, and 3 retinitis. Three pts had 2 sites of CMV EOD. Among 8 pts with ADV disease, 3 had colitis, 3 pneumonitis, 1 nephritis, and 1 hepatitis/colitis. Two pts had HHV6 pneumonitis.Conclusions: 1) Viremias by dsDNA viruses occurred frequently and early post TCD HCT: 189 (79%) pts had at least 1 dsDNA viral infection, with onset of first infection before d100 in 183 (77%) pts. Around 58% of pts with CMV had coinfections with additional dsDNA virus(es). 2) Two thirds (67%) of CMV R+ and 41% of total pts received CMV antiviral treatment. 3) Overall, 18% of patients developed end organ disease by dsDNA viruses. 4) Viremias were managed effectively with intense monitoring and antiviral treatment, and rates of EOD were comparable to those of CONV HCT. Our data highlights the need for effective strategies to reduce the total burden of dsDNA viruses after TCD HCT. [Display omitted] [Display omitted] [Display omitted] DisclosuresPerales:Merck: Membership on an entity's Board of Directors or advisory committees; Astellas: Membership on an entity's Board of Directors or advisory committees. Giralt:TAKEDA: Consultancy, Honoraria, Research Funding; JAZZ: Consultancy, Honoraria, Research Funding, Speakers Bureau; AMGEN: Consultancy, Research Funding; SANOFI: Consultancy, Honoraria, Research Funding; CELGENE: Consultancy, Honoraria, Research Funding.

Hepatitis C Virus RNA Real-Time Quantitative RT-PCR Method Based on a New Primer Design Strategy

Viral nucleic acids are unstable when improperly collected, handled, and stored, resulting in decreased sensitivity of currently available commercial quantitative nucleic acid testing kits. Using known unstable hepatitis C virus RNA, we developed a quantitative RT-PCR method based on a new primer design strategy to reduce the impact of nucleic acid instability on nucleic acid testing. The performance of the method was evaluated for linearity, limit of detection, precision, specificity, and agreement with commercial hepatitis C virus assays. Its clinical application was compared to that of two commercial kits--Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) and Kehua. The quantitative RT-PCR method delivered a good performance, with a linearity of R(2) = 0.99, a total limit of detection (genotypes 1 to 6) of 42.6 IU/mL (95% CI, 32.84 to 67.76 IU/mL), a CV of 1.06% to 3.34%, a specificity of 100%, and a high concordance with the CAP/CTM assay (R(2) = 0.97), with a means ± SD value of -0.06 ± 1.96 log IU/mL (range, -0.38 to 0.25 log IU/mL). The method was superior to commercial assays in detecting unstable hepatitis C virus RNA (P < 0.05). This quantitative RT-PCR method can effectively eliminate the influence of RNA instability on nucleic acid testing. The principle of primer design strategy may be applied to the detection of other RNA or DNA viruses.

Irreproducible positive results on the Cobas AmpliPrep/Cobas TaqMan HIV‐1 Qual test are different qualitatively from confirmed positive results

Criteria that define low positive results on the COBAS® AmpliPrep/COBAS® TaqMan (CAP/CTM) HIV-1 Qual test as inconclusive have been adopted by all academic centres in South Africa that conduct infant HIV PCR, following previous investigations that showed poor specificity of these results. Retesting all inconclusive specimens has considerable cost implications. Therefore, it was attempted to characterise such inconclusive results, by comparing those that prove to be either negative or positive on follow-up testing. This retrospective, laboratory-based study found that 193 of 211 (91.5%) patients with previous inconclusive results (defined as reported positive by CAP/CTM but with cycle threshold [Ct ] values of >32 and/or fluorescence intensity [FI] values of <5) tested negative and only 18 (8.5%) tested positive using independently obtained follow-up samples after a median of 28 days. The only significant independent predictor of a later positive result was a higher FI value (3.326 vs. 0.495, P < 0.0001), whereas Ct values were not predictive independently. Specimens from patients negative on follow-up testing differed qualitatively from specimens that proved to be true positives. As the lower FI values in false-positive compared to true-positive results probably are indicative of a non-specific signal, the incorporation of stringent amplification slope criteria in the assay's test definition file may improve correct classification and thus reduce the need for repeat testing of a large number of inconclusive specimens.

Evaluation of Quantification of HIV-1 RNA Viral Load in Plasma and Dried Blood Spots by Use of the Semiautomated Cobas Amplicor Assay and the Fully Automated Cobas Ampliprep/TaqMan Assay, Version 2.0, in Kisumu, Kenya

In Kenya, HIV-1 viral load monitoring is commonly performed with the Cobas Amplicor using plasma specimens. Interest is growing in transitioning to real-time PCR (RT-PCR), such as the Cobas Ampliprep/Cobas TaqMan (CAP/CTM), using dried blood spots (DBS). Before implementation, direct evaluation of the two assays using DBS field specimens is required. This study compares the sensitivity, specificity, negative and positive predictive values (NPV and PPV, respectively), concordance, and agreement between HIV-1 viral load measurements using plasma and DBS specimens obtained from 512 HIV-1-infected pregnant females enrolled in the Kisumu Breastfeeding Study and tested with the Cobas Amplicor and CAP/CTM assays. The sensitivity and NPV of viral load detection in DBS specimens were higher with CAP/CTM (sensitivity, 100%; 95% confidence interval [CI], 99.1 to 100.0%; NPV, 100%; 95% CI, 59.0 to 100.0%) than the Cobas Amplicor (sensitivity, 96.6%; 95% CI, 94.3 to 98.1%; NPV, 58.8%; 95% CI, 40.7 to 75.4%). The PPVs were comparable between both assays when using DBS. The specificity of viral load detection in DBS specimens was lower with CAP/CTM (77.8%; 95% CI, 40.0 to 97.2%) than that of the Cobas Amplicor (95.2%; 95% CI, 76.2 to 99.9%). Good concordance and agreement were observed when paired plasma and DBS specimens were tested with both assays. Lower specificity with the CAP/CTM is likely due to proviral HIV-1 DNA amplification and lower detection limits with RT-PCR. However, the CAP/CTM has better sensitivity and higher throughput than the Cobas Amplicor. These findings suggest that DBS may be a suitable alternative to plasma when using RT-PCR, which could increase access to viral load monitoring in resource-limited settings.

Analytical sensitivity of three real-time PCR assays for measuring subtype B HIV-1 RNA

BackgroundLack of HIV RNA during antiretroviral therapy (ART) is regarded as a desirable outcome. Commercial assays of HIV virus load now need to detect virus RNA concentrations below 50c/ml and several of them have claimed a limit of detection (LOD) of 20–45c/ml. Objectives and study designWe have compared the performances of three commercial assays of HIV RNA, the Abbott RealTime HIV-1, the Qiagen Artus RG HIV-1 and the Roche Cobas Ampliprep Cobas TaqMan (CAPCTM) HIV-1 vs 2.0 using replicate of specimens with HIV-1 subtype B RNA concentrations of 20–200c/ml. ResultsDespite fair-to-moderate agreement between the three assays, probit analysis showed that their LODs differed; they were 81, 65 and 18c/ml respectively. The CAPCTM HIV-1 vs 2.0 values were higher than those of the other two; the maximum difference was 0.26logc/ml. By testing 20 replicate of each concentration, coefficients of variation were between 0.6% and 9.2% (Abbott RealTime HIV-1), 10.3% and 38% (Qiagen Artus RG HIV-1) and 5.2% and 13.1% (Roche CAPCTM HIV-1 vs 2.0). The three assays also differed in their reproducibility and linearity for virus loads of 50–200c/ml. ConclusionThe analytical performances of commercial virus load assays differ. Direct comparisons of widely used commercial assays in clinical studies could help to identify the residual viremia that is clinically relevant for effective long term therapy.

Early Diagnosis of In Utero and Intrapartum HIV Infection in Infants Prior to 6 Weeks of Age

Early initiation of antiretroviral therapy reduces HIV-related infant mortality. The early peak of pediatric HIV-related deaths in South Africa occurs at 3 months of age, coinciding with the earliest age at which treatment is initiated following PCR testing at 6 weeks of age. Earlier diagnosis is necessary to reduce infant mortality. The performances of the Amplicor DNA PCR, COBAS AmpliPrep/COBAS TaqMan (CAP/CTM), and Aptima assays for detecting early HIV infection (acquired in utero and intrapartum) up to 6 weeks of age were compared. Dried blood spots (DBS) were collected at birth and at 2, 4, and 6 weeks from HIV-exposed infants enrolled in an observational cohort study in Johannesburg, South Africa. HIV status was determined at 6 weeks by DNA PCR on whole blood. Serial DBS samples from all HIV-infected infants and two HIV-uninfected, age-matched controls were tested with the 3 assays. Of 710 infants of known HIV status, 38 (5.4%) had in utero (n = 29) or intrapartum (n = 9) infections. By 14 weeks, when treatment should have been initiated, 13 (45%) in utero-infected and 2 (22%) intrapartum-infected infants had died or were lost to follow-up. The CAP/CTM and Aptima assays identified 76.3% of all infants with early HIV infections at birth and by 4 weeks were 96% sensitive. DNA PCR demonstrated lower sensitivities at birth and 4 weeks of 68.4% and 87.5%, respectively. All assays had the lowest sensitivity at 2 weeks of age. CAP/CTM was the only assay with 100% specificity at all ages. Testing at birth versus 6 weeks of age identifies a higher total number of HIV-infected infants, irrespective of the assay.