Increased detectability of plasma HIV-1 RNA after introduction of a new assay and altered specimen-processing procedures

Systematic review of the accuracy of plasma preparation tubes for HIV viral load testing

Expanding access to HIV viral load testing is essential to improving the care and treatment of people living with HIV/AIDS and ending the AIDS epidemic. Though significant investments have been made in the past five years, many high burden, low resource countries continue to have viral load access rates below 50%. Plasma preparation tubes (PPTs) can simplify storage, transport, and preparation of plasma used for viral load testing. A systematic review was conducted to evaluate the accuracy of plasma preparation tubes for HIV viral load testing. Study results regarding the accuracy of PPT viral load measurements across various storage and transportation conditions were examined. The quality of evidence was evaluated using GRADE and QUADAS-2 criteria. The review identified 16 studies using PPTs with data from 6,141 individuals from 1995 to 2014. Overall the quality of evidence was rated as moderate, with unclear applicability for studies evaluating viral load assays that are no longer commercially available. Significantly elevated viral load results (>0.3 log copies/ml difference) have been observed with PPTs; however, when manufacturer handling instructions are followed, when plasma is aliquoted into a secondary tube, or when PPTs are centrifuged prior to testing, PPT results only differed from standard EDTA plasma testing using commercially available viral load assays by a range on average of -0.03 to +0.08 log copies/ml across studies. Although spuriously elevated viral load results have been observed with PPTs, following proper sample handing techniques have been shown to provide accurate results. PPTs, therefore, provide a high quality alternative specimen type for countries seeking solutions to infrastructure and specimen transportation challenges in an effort to scale-up viral load testing and achieve 90-90-90 targets.

Estimation of measurement error in plasma HIV-1 RNA assays near their limit of quantification

BACKGROUND

Plasma HIV-1 RNA levels (pVLs), routinely used for clinical management, are influenced by measurement error (ME) due to physiologic and assay variation.

OBJECTIVE

To assess the ME of the COBAS HIV-1 Ampliprep AMPLICOR MONITOR ultrasensitive assay version 1.5 and the COBAS Ampliprep Taqman HIV-1 assay versions 1.0 and 2.0 close to their lower limit of detection. Secondly to examine whether there was any evidence that pVL measurements closest to the lower limit of quantification, where clinical decisions are made, were susceptible to a higher degree of random noise than the remaining range.

METHODS

We analysed longitudinal pVL of treatment-naïve patients from British Columbia, Canada, during their first six months on treatment, for time periods when each assay was uniquely available: Period 1 (Amplicor): 08/03/2000-01/02/2008; Period 2 (Taqman v1.0): 07/01/2010-07/03/2012; Period 3 (Taqman v2.0): 08/03/2012-30/06/2014. ME was estimated via generalized additive mixed effects models, adjusting for several clinical and demographic variables and follow-up time.

RESULTS

The ME associated with each assay was approximately 0.5 log10 copies/mL. The number of pVL measurements, at a given pVL value, was not randomly distributed; values ≤250 copies/mL were strongly systematically overrepresented in all assays, with the prevalence decreasing monotonically as the pVL increased. Model residuals for pVL ≤250 copies/mL were approximately three times higher than that for the higher range, and pVL measurements in this range could not be modelled effectively due to considerable random noise of the data.

CONCLUSIONS

Although the ME was stable across assays, there is substantial increase in random noise in measuring pVL close to the lower level of detection. These findings have important clinical significance, especially in the range where key clinical decisions are made. Thus, pVL values ≤250 copies/mL should not be taken as the "truth" and repeat pVL measurement is encouraged to confirm viral suppression.

Aptima HIV-1 Quant Dx--A fully automated assay for both diagnosis and quantification of HIV-1

BACKGROUND

Separate assays are available for diagnosis and viral load (VL) monitoring of HIV-1. Studies have shown that using a single test for both confirmatory diagnosis and VL increases linkage to care.

OBJECTIVE

To validate a single assay for both diagnosis and VL monitoring of HIV-1 on the fully automated Panther platform.

STUDY DESIGN

Validate the assay by assessing specificity, sensitivity, subtype detection, seroconversion, reproducibility and linearity. Also assess diagnostic agreement with the Procleix(®) Ultrio Elite™ discriminatory assay (Procleix), and agreement of VL results (method comparison) with Ampliprep/COBAS TaqMan HIV-1 version 2.0 (CAP/CTM), using clinical samples.

RESULTS

The assay was specific (100%) and sensitive with a 95% limit of detection of 12 copies/mL with the 3rd WHO standards. Aptima detected HIV in seroconversion panels 6 and 11 days before p24 antigen and antibody tests, respectively. Diagnostic agreement with Procleix, was 100%. Regression analysis showed good agreement of VL results between Aptima and CAP/CTM with a slope of 1.02, intercept of 0.07, and correlation coefficient (R(2)) of 0.97. Aptima was more sensitive than CAP/CTM. Equivalent quantification was seen on testing clinical samples and isolates belonging to HIV group M, N, O and P and commercially available subtype panels. Assay results were linear (R(2) 0.9994) with standard deviation of <0.17 log copies across assay range.

CONCLUSIONS

The good specificity, sensitivity, precision, subtype performance and clinical agreement with other assays demonstrated by Aptima combined with the complete automation provided by the Panther platform makes Aptima a good candidate for both VL monitoring and diagnosis of HIV-1.

Low-level HIV-1 viraemia in patients on HAART: risk factors and management in clinical practice

OBJECTIVES

Characterization of the conditions favouring HIV-1 low-level viraemia (LLV) during treatment is required to guide strategies for prevention and cure.

METHODS

The characteristics and treatments of 171 patients experiencing a confirmed LLV of 50-1000 copies/mL (PLLVs) were compared with those of 146 patients with persistently controlled viraemia. We analysed the risk factors for LLV, the parameters affecting the level of viraemia and the presence of resistance-associated mutations (RAMs). We compared outcomes for PLLVs on fully effective HAART as a function of treatment modifications.

RESULTS

LLV was <500 copies/mL in at least 90% of cases. A higher zenith viral load (VL) (5.27 versus 4.91 log10 copies/mL, OR 2.23; P = 0.0003), a shorter time on continuous HAART (4.3 versus 6.8 years, OR 0.88; P = 0.0003) and previously detected RAMs (43% versus 23%, OR 2.42; P = 0.0033) were independent predictors of LLV. NNRTIs were less frequently used in PLLVs and were associated with more stable treatment. The presence of any RAM during LLV was associated with a lower zenith VL and a higher LLV. In the absence of resistance, virological success was achieved in similar proportions of patients with and without treatment modification.

CONCLUSIONS

Viraemia >500 copies/mL should no longer be considered to be LLV. In patients with a high zenith VL, several years on continuous HAART may be required to decrease the HIV reservoir and prevent LLV. Resistance testing is useful to detect RAMs, leading if necessary to treatment modifications. In the absence of resistance, treatment changes seemed dispensable.

Comparative performances of HIV-1 RNA load assays at low viral load levels: results of an international collaboration

Low-level viremia during antiretroviral therapy and its accurate measurement are increasingly relevant. Here, we present an international collaboration of 4,221 paired blood plasma viral load (pVL) results from four commercial assays, emphasizing the data with low pVL. The assays compared were the Abbott RealTime assay, the Roche Amplicor assay, and the Roche TaqMan version 1 and version 2 assays. The correlation between the assays was 0.90 to 0.97. However, at a low pVL, the correlation fell to 0.45 to 0.85. The observed interassay concordance was higher when detectability was defined as 200 copies/ml than when it was defined as 50 copies/ml. A pVL of ∼100 to 125 copies/ml by the TaqMan version 1 and version 2 assays corresponded best to a 50-copies/ml threshold with the Amplicor assay. Correlation and concordance between the viral load assays were lower at a low pVL. Clear guidelines are needed on the clinical significance of low-level viremia.

Successful use of Plasma Preparation Tubes™ (PPTs) in the COBAS® AmpliPrep/COBAS® TaqMan® HIV-1 test

BACKGROUND

Since switching to the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HIV-1 Test, v. 1.0 from the Amplicor HIV-1 Monitor Test, v. 1.5, an increase in detectable viral load results was noted. We were concerned that this was due to the use of Plasma Preparation Tubes (PPT) in this test.

OBJECTIVE

To assess the impact of different pre-analytical processing conditions on HIV-1 viral load results on the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HIV-1 Test.

STUDY DESIGN

Sixty-three HIV-infected patients were consented and had 3 PPTs and 1 K2EDTA drawn for HIV-1 viral load testing. Three methods of PPT processing were compared against the referent K2EDTA tube which was spun at 1100 × g for 20 min, poured off and frozen; PPT1 was refrigerated with an additional centrifugation prior to testing, PPT2 was processed similarly to EDTA, and PPT3 was centrifuged, frozen and centrifuged again prior to testing.

RESULTS

PPT1 and PPT3 yielded results that were most similar to the referent EDTA processing, with a concordance correlation coefficient (CCC) of 0.80 and 0.85, compared to PPT2 with CCC of 0.37. Both PPT1 and PPT3 involved additional centrifugation prior to testing. In 26 patients with residual samples from the PPT2 processing, 9 (34.6%) were found to have the presence of proviral DNA, which likely contributed to the elevated HIV-1 RNA viral loads in these individuals.

CONCLUSION

PPTs can be used in the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HIV-1 Test with an additional centrifugation in order to avoid misleading elevated HIV-1 RNA viral loads that may change patient management.

Past, present and future molecular diagnosis and characterization of human immunodeficiency virus infections

Substantive and significant advances have been made in the last two decades in the characterization of human immunodeficiency virus (HIV) infections using molecular techniques. These advances include the use of real-time measurements, isothermal amplification, the inclusion of internal quality assurance protocols, device miniaturization and the automation of specimen processing. The result has been a significant increase in the availability of results to a high level of accuracy and quality. Molecular assays are currently widely used for diagnostics, antiretroviral monitoring and drug resistance characterization in developed countries. Simple and cost-effective point-of-care versions are also being vigorously developed with the eventual goal of providing timely healthcare services to patients residing in remote areas and those in resource-constrained countries. In this review, we discuss the evolution of these molecular technologies, not only in the context of the virus, but also in the context of tests focused on human genomics and transcriptomics.

Long-Term Resolution of Viral Breakthrough after Changing HIV Viral Load Assay

BACKGROUND

Viral load (VL) measurement assays differ in their sensitivity with polymerase chain reaction assays (PCR) being more sensitive than branched DNA (bDNA) assays. We evaluated virologic outcomes of patients and physicians' response to increased VL after a switch from bDNA to PCR assay.

METHOD

Retrospective, case-control study on 65 HIV+ patients receiving highly active antiretroviral therapy (HAART). Cases included patients with undetectable VL by bDNA that became detectable after the switch; controls were patients that remained undetectable. Records were reviewed up to 1 year after the switch.

RESULTS

A total of 58.5% patients had detectable VL after the switch. Repeat VL testing and resistance testing were ordered in 15.4% and 23.1% of these patients, respectively. By 1 year, VL was undetectable in 82.8% of cases and 92% of controls (P = .30), without change in HAART.

CONCLUSION

Transient viremia after changing VL assay reflects the different sensitivity of these assays with no impact on patients' outcomes compared to controls.

Comparative RNA quantification of HIV-1 group M and non-M with the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 v2.0 and Abbott Real-Time HIV-1 PCR assays

BACKGROUND

A new version of the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 assay (CA/CTM v2.0) has been introduced to overcome the underquantification observed with the first version.

METHODS

We compared the Roche Cobas CA/CTM v2.0 and Abbott RealTime HIV-1 assays for HIV-1 group M and non-M viral load measurement.

RESULTS

We found a good correlation (r = 0.96) between the 2 techniques for the 260 HIV-1 group M plasma samples tested. The Roche Cobas assay gave significantly higher values than the Abbott assay, and 51 samples (20%) yielded differences greater than 0.5 log10 copies per milliliter. Conversely, 2 samples were more than 0.5 log10 copies per milliliter higher with the Abbott assay than with the Roche Cobas assay. Among the 84 samples with undetectable viral load in the Abbott assay (detection limit 40 copies/mL), 17 (20%) were detectable with the CA/CTM v2.0 assay (detection limit 20 copies/mL), with values ranging from 41 to 897 copies per milliliter. Extrapolation of the Abbott curves led to 10/17 (59%) of these samples being quantifiable. HIV-1 groups O and P were similarly quantified by the two techniques.

CONCLUSION

The results of the Roche Cobas CA/CTM v2.0 and Abbott RealTime HIV-1 assays correlate well. The new version of the CA/CTM assay shows improved sensitivity. Nevertheless, the 2 assays differ by more than 0.5 log₁₀ copies per milliliter for some samples.

Evaluation of effect of specimen-handling parameters for plasma preparation tubes on viral load measurements obtained by using the Abbott RealTime HIV-1 load assay

HIV-1 viral load testing is essential to the management of HIV-1-infected patients, and proper specimen handling ensures accurate viral load (VL) results. This study was performed to (i) evaluate the effect of freezing plasma in situ in BD Vacutainer plasma preparation tubes (PPT) on the accuracy of HIV-1 viral load results using the Abbott RealTime HIV-1 assay and (ii) evaluate the effect of whole-blood storage in the PPT for 6 h at room temperature prior to centrifugation (PPT6H) rather than 2 h as specified in the PPT product insert. Of the 64 HIV-positive subjects evaluated, 29 had average viral load counts of >40 copies/ml in at least one of the tubes tested and 35 subjects had a result of either "undetected target" or "below the limit of quantification" (LOQ) for all or some of the tubes regardless of handling condition. For the 29 subjects with VLs that were >LOQ, the mean biases between plasma from Vacutainer K(2)EDTA tubes and plasma frozen in situ in PPT and between K(2)EDTA tube plasma and plasma from PPT6H (log(10) copies/ml) were 0.005 and -0.001, respectively, and r(2) was >0.92 for all correlations. We conclude that VLs determined from plasma frozen in situ in PPT are equivalent to VLs in K(2)EDTA tube plasma and can be used for accurate quantification of HIV-1 RNA in the Abbott RealTime HIV-1 assay. Furthermore specimens collected in PPT can be stored for 6 h at room temperature with no effect on viral load results as measured by the Abbott RealTime HIV-1 assay.

Defining treatment failure in resource-rich settings

PURPOSE OF REVIEW

To define treatment failure in resource-rich settings; summarizing current guidelines, assays, the significance of detectable viremia, and definitions of treatment failure in clinical and research settings.

RECENT FINDINGS

The goal of treatment should be full viral suppression, even in highly treatment-experienced patients.

SUMMARY

Treatment failure is defined as repeated HIV RNA values above the lower limit of detection of a sensitive assay (usually 50 copies/ml). This criterion is based on evidence that the maximum clinical benefit of antiretroviral therapy is derived by keeping the viral load as low as possible. Full viral suppression should be achievable in all patients, both treatment-naïve and experienced. Transient, low-detectable viremia ('blips') may not predict virologic breakthrough. However, consecutive or higher-level transient viremia is associated with risk of treatment failure. Defining failure by a confirmed HIV RNA more than 50 copies/ml is the most conservative approach, but the use of such low limits of detection in clinical trials may lead to a high false-positive 'failure' rate, thus a definition of 200 copies/ml may be preferable. Variation in clinical trial endpoint definitions creates a challenge for comparing results between studies. For example, using a composite endpoint to define treatment failure may result in a high proportion of 'failures' that are not related to poor virologic response.

Coamplification of HIV-1 proviral DNA and viral RNA in assays used for quantification of HIV-1 RNA

Elevated HIV-1 viral load (VL) observed in specimens frozen in situ in plasma preparation tubes (PPTs) compared to EDTA plasma specimens may affect therapeutic monitoring of HIV-infected patients. The increase in viral load is cell associated and minimized when plasma from the PPT is aspirated or recentrifuged prior to freezing. This study investigates the contribution of integrated HIV-1 proviral DNA to elevated VL in the quantification of HIV-1 RNA in plasma. Fifty paired specimens collected in EDTA tubes and PPTs frozen in situ were used for analysis. HIV-1 VL was measured using the COBAS Amplicor Monitor ultrasensitive test version 1.5. Contaminating proviral DNA was detected using a nested PCR targeting the Alu repeat in human genomic DNA and HIV pol gene simultaneously. Treatment of the specimen with DNase resulted in significantly lower quantifiable HIV-1 RNA in specimens from PPTs compared to the corresponding EDTA tubes (P = 0.004). After the RNA was destroyed by heat treatment, the mean HIV-1 RNA VL decreased by 79% in the EDTA tube compared to 65% in the PPT. The nested PCR amplified integrated proviral DNA in nucleic acid extracted from plasma in PPT and EDTA specimens with high viral load values. Likewise, a semiquantitative densitometric analysis revealed that the total amount of genomic DNA in the PPT was higher than that in the EDTA tube. Our investigation clearly shows that both proviral DNA and intracellular RNA are amplified simultaneously in the COBAS Amplicor HIV-1 Monitor assay and that proviral DNA contributes to the elevated VL in plasma frozen in PPTs.

Viral load assay sensitivity and low level viremia in HAART treated HIV patients

BACKGROUND

The recent introduction of highly sensitive viral load assays resulted in a significant increase in number of treated HIV-infected patients with a detectable viral load. The significance of a viral load between 20 and 50 copies/mL remains unclear.

OBJECTIVES

To compare the performance of three viral load assays, with special attention for specificity and sensitivity at the lowest level of quantification.

STUDY DESIGN

Samples (n=181) were selected from 62 HIV-positive individuals that experience viral blips or episodes of low but detectable viremia under antiretroviral treatment, and from 216 HIV-negative individuals. Each sample was tested in at least two of three assays: the Cobas Amplicor HIV-1 Monitor (CAP/CA), the Cobas Ampliprep/Cobas TaqMan HIV-1 version 1 (CAP/CTM1) and the Cobas Ampliprep/Cobas TaqMan HIV-1 version 2 (CAP/CTM2).

RESULTS

No false positive results were recorded. Kappa statistics revealed fair to moderate agreement between the results of the three assays, but important differences in sensitivity were observed, with the highest sensitivity reported for CAP/CTM2 followed by CAP/CTM1 and CAP/CA. The differences in sensitivity remained after equalization of the detection limit for all assays at 50 copies/mL. Analysis of samples collected over time showed that patients with single blips in CAP/CA present with recurrent blips in CAP/CTM1 and persistent detectable viremia in CAP/CTM2.

CONCLUSIONS

Viral load results between 20 and 50 copies/mL in either CAP/CTM1 or CAP/CTM2, indicate true viremia. The availability of highly sensitive assays force reconsideration of the terms 'undetectable' viral load and 'virological success' of antiretroviral treatment.

Increased reporting of detectable plasma HIV-1 RNA levels at the critical threshold of 50 copies per milliliter with the Taqman assay in comparison to the Amplicor assay

OBJECTIVE

To investigate the application of the new COBAS Ampliprep Taqman HIV-1 assay in comparison with the COBAS HIV-1 Ampliprep AMPLICOR MONITOR ultrasensitive assay version 1.5, with a particular focus on the most clinically relevant region near the lower limit of quantification.

METHODS

Scatterplots and the Bland-Altman plot were used to inspect the degree of agreement between the 2 assays when tested on samples from the British Columbia Centre for Excellence in HIV/AIDS monitoring and evaluation system. Consistency of clinically applicable values at low HIV-1 RNA copy number was assessed from samples from individuals with previously undetectable Amplicor results.

RESULTS

Despite general agreement of these assays over a wide dynamic range, the Taqman assay resulted in a nearly 2-fold increase (from 3.6% to 6.9%) in the number of patients experiencing a plasma HIV-1 RNA level >50 copies per milliliter after being suppressed to levels <50 copies per milliliter consistently during the previous year (P < 0.01). In addition, rare discrepancies between the 2 assays were observed to be as high as 0.7 log10 copies per milliliter. The kappa statistic was 0.19, indicating only slight agreement at the critical threshold of 50 HIV RNA copies per milliliter, with 43% of undetectable samples in the Amplicor assay testing detectable in the Taqman assay (median 70 copies/mL; interquartile range 60-83 copies/mL).

CONCLUSIONS

The increased frequency of detectable plasma HIV-1 RNA levels at the threshold of 50 copies per milliliter with the new Taqman assay has important implications for highly active antiretroviral therapy monitoring. Until there is clinical evidence that patients with detectable HIV by the Taqman assay (but undetectable HIV with Amplicor) have differential outcomes, it is unclear whether the Taqman assay is appropriate for routine management of HIV-1 therapy, and caution is required in the interpretation of low-level viremia by the Taqman assay until a clinical validation of a new cutoff is performed.

Overestimation of human immunodeficiency virus type 1 load caused by the presence of cells in plasma from plasma preparation tubes

The human immunodeficiency virus type 1 (HIV-1) load is an important marker of disease progression and treatment efficacy in patients with HIV-1 infection. In recent years, an increase in the number of samples with detectable HIV-1 RNA has been reported among patients with previously suppressed viral loads, affecting clinical patient care and leading to repeat measurements of viral load and drug resistance. This rise seems to have coincided with the increased use of plasma preparation tubes (PPTs) for sample collection, and we have aimed to explain why PPTs might yield elevated HIV-1 RNA levels. The impacts of different sample-processing procedures on HIV-1 RNA levels were compared retrospectively. Prospectively, the presence of different cells and cell-associated HIV-1 nucleic acids in paired plasma samples from PPTs centrifuged before (PPT1) and after (PPT2) transportation to the laboratory was compared. A retrospective analysis of 4,049 patient samples with <1,000 HIV-1 RNA copies/ml showed elevated HIV-1 RNA levels in plasma from PPT1 compared with the levels from PPT2 and standard EDTA-containing tubes. Prospective data revealed cell-associated HIV-1 nucleic acids and abundant blood cells in plasma from PPT1 but not from the corresponding PPT2. The levels of HIV-1 RNA correlated with the lymphocyte counts in plasma in PPT1. Cells could be removed by the recentrifugation of PPT1 before analysis. In conclusion, the transportation of PPTs after centrifugation may render cells in the plasma fraction containing cell-associated HIV-1 nucleic acids that contribute significantly to the HIV-1 RNA copy numbers in patients with low viral loads.