Comparative evaluation of the Cobas Amplicor HIV-1 Monitor Ultrasensitive Test, the new Cobas AmpliPrep/Cobas Amplicor HIV-1 Monitor Ultrasensitive Test and the Versant HIV RNA 3.0 assays for quantitation of HIV-1 RNA in plasma samples

The Development of a Standardized Quality Assessment Material to Support Xpert® HIV-1 Viral Load Testing for ART Monitoring in South Africa

The tiered laboratory framework for human immunodeficiency virus (HIV) viral load monitoring accommodates a range of HIV viral load testing platforms, with quality assessment critical to ensure quality patient testing. HIV plasma viral load testing is challenged by the instability of viral RNA. An approach using an RNA stabilizing buffer is described for the Xpert^® HIV-1 Viral Load (Cepheid) assay and was tested in remote laboratories in South Africa. Plasma panels with known HIV viral titres were prepared in PrimeStore molecular transport medium for per-module verification and per-instrument external quality assessment. The panels were transported at ambient temperatures to 13 testing laboratories during 2017 and 2018, tested according to standard procedures and uploaded to a web portal for analysis. A total of 275 quality assessment specimens (57 verification panels and two EQA cycles) were tested. All participating laboratories met study verification criteria (n = 171 specimens) with an overall concordance correlation coefficient (ρ_c) of 0.997 (95% confidence interval (CI): 0.996 to 0.998) and a mean bias of −0.019 log copies per milliliter (cp/mL) (95% CI: −0.044 to 0.063). The overall EQA ρ_c (n = 104 specimens) was 0.999 (95% CI: 0.998 to 0.999), with a mean bias of 0.03 log cp/mL (95% CI: 0.02 to 0.05). These panels are suitable for use in quality monitoring of Xpert^® HIV-1 VL and are applicable to laboratories in remote settings.

Mathematical Modeling of HIV Dynamics After Antiretroviral Therapy Initiation: A Review

This review shows the potential ground-breaking impact that mathematical tools may have in the analysis and the understanding of the HIV dynamics. In the first part, early diagnosis of immunological failure is inferred from the estimation of certain parameters of a mathematical model of the HIV infection dynamics. This method is supported by clinical research results from an original clinical trial: data just after 1 month following therapy initiation are used to carry out the model identification. The diagnosis is shown to be consistent with results from monitoring of the patients after 6 months. In the second part of this review, prospective research results are given for the design of individual anti-HIV treatments optimizing the recovery of the immune system and minimizing side effects. In this respect, two methods are discussed. The first one combines HIV population dynamics with pharmacokinetics and pharmacodynamics models to generate drug treatments using impulsive control systems. The second one is based on optimal control theory and uses a recently published differential equation to model the side effects produced by highly active antiretroviral therapy therapies. The main advantage of these revisited methods is that the drug treatment is computed directly in amounts of drugs, which is easier to interpret by physicians and patients.

Single-copy quantification of HIV-1 in clinical samples

HIV replication in humans proceeds with substantial viral RNA levels in plasma. Antiretroviral therapy results in suppression but not eradication of HIV infection. Continuous therapy is essential for durable clinical responses. Discontinuing antiretroviral therapy results in prompt rebound in viremia. The source of HIV during suppressive therapy and mechanisms of persistence remain uncertain. Sensitive assays for HIV have been useful in quantifying viremia in response to antiretroviral therapy and in experimental studies of drug intensification, drug simplification, and potential anatomic sanctuary site investigations. As clinical eradication strategies move forward, robust, sensitive quantitative assays for HIV at low levels represent essential laboratory support modalities. Here we describe in detail an assay for HIV-1 RNA with single-copy sensitivity.

Comparison of the COBAS/Ampliprep Taqman and Amplicor HIV-1 monitor tests in Lagos, Nigeria

Background

The use of real-time Polymerase chain reaction (PCR) technology options is increasing in resource-limited settings because they are faster, improve assay sensitivity, have higher throughput, larger dynamic ranges and reduced rates of contamination. In 2010, UNAIDS ranked Nigeria as the second highest population of people living with HIV and AIDS (2.98 million people) in the world.

Objective

The objective of this study was to compare the analytical performances of the Amplicor HIV-1 Monitor (version 1.5) and the COBAS Ampliprep/Taqman (version 2.0) used in monitoring HIV disease progression in HIV-infected individuals.

Method

In a cross-sectional study, HIV-1 RNA values obtained with the Amplicor HIV-1 monitor version 1.5 were compared with those of the COBAS/Ampliprep TaqMan HIV-1 version 2.0 in a routine clinical setting. Between May and November 2011, 176 plasma samples collected were analysed in parallel using both techniques. Data analysis was done using statgraphics Centurion XVI and Medcalc version 12.0.

Result

The correlation coefficient for the two assays was 0.83 and the level of agreement using a Bland–Altman plot was 94.2%.

Conclusion

These findings suggest that the results from the two methods were comparable, hence the COBAS/Ampliprep Taqman version 2.0 is recommended for high-volume laboratories.

Viral load testing in a resource-limited setting: quality control is critical

BACKGROUND

World Health Organization guidelines now recommend routine use of viral load testing, where available, for patients receiving antiretroviral treatment (ART). However, its use has not been routinely implemented in many resource-limited settings due to cost, availability and accessibility. Viral load testing is complex, making its application in resource-limited settings challenging. We describe the issues encountered by Médecins Sans Frontières (MSF) when using routine viral load testing in a large HIV programme in sub-Saharan Africa.

METHODS

Between October 2005 and August 2006, more than 1200 patients on ART had viral load tests at baseline and at three-month intervals performed by a local reference laboratory that was quality assured by an experienced international institution. Concerns with reliability of results halted testing. The quality control measures instituted with a second laboratory and outcomes of these were documented.

RESULTS

In 2005 and 2006, only 178 of 334 (53%) previously ART-naïve patients tested after six to 12 months of treatment had viral loads of less than 1000 copies/mL. Similar MSF programmes elsewhere demonstrated virological suppression rates of more than 85%, and duplicate testing showed unacceptable discordance. Laboratory problems encountered included: disregarded quality control; time delays; requirement for retesting; and duplicate sample variations. Potentially harmful clinical outcomes of inaccurate viral load results include: unnecessary ART regimen changes; unnecessary enhanced adherence counselling after "false failures"; and undetected virological failure.

CONCLUSIONS

Viral load testing performed without rigorous quality control carries the risk of erroneous and potentially damaging results. Viral load testing should be utilized only if robust quality assurance has been implemented. Our experience in this and other settings led to the development of a guide for assessing the suitability of a laboratory for viral load testing that can be used to help achieve reliable results.

Comparison of an Automated and a Manual Method of Viral Load Determination in HIV-Infected Persons in Yaounde, Cameroon

OBJECTIVES

Although access to antiretroviral therapy is being improved in the resource-limited settings most affected by the HIV pandemic, the assessment of treatment success or failure remains a challenge. Methods of viral load determination that are inexpensive, easy to use, and practicable at peripheral health centers are required. This study aimed at evaluating the validity and relative cost of a manual method compared to an automated method of viral load quantification.

METHODS

HIV-1 viral load was determined by both the COBAS Amplicor HIV-1 Monitor and the Amplicor HIV-1 Monitor assays in 18 patients in Yaounde, Cameroon.

RESULTS

There was a strong correlation between values of viral load obtained by the automated method and the manual method (r = .83, P value < .0001). Also, both methods were not statistically different from each other (Wilcoxon rank-sum statistic P value .99).

CONCLUSIONS

The manual method of determining HIV viral load was correlated with the automated method and should be considered as a viable alternative.

Viral load levels measured at set-point have risen over the last decade of the HIV epidemic in the Netherlands

Background

HIV-1 RNA plasma concentration at viral set-point is associated not only with disease outcome but also with the transmission dynamics of HIV-1. We investigated whether plasma HIV-1 RNA concentration and CD4 cell count at viral set-point have changed over time in the HIV epidemic in the Netherlands.

Methodology/Principal Findings

We selected 906 therapy-naïve patients with at least one plasma HIV-1 RNA concentration measured 9 to 27 months after estimated seroconversion. Changes in HIV-1 RNA and CD4 cell count at viral set-point over time were analysed using linear regression models. The ATHENA national observational cohort contributed all patients who seroconverted in or after 1996; the Amsterdam Cohort Studies (ACS) contributed seroconverters before 1996. The mean of the first HIV-1 RNA concentration measured 9–27 months after seroconversion was 4.30 log₁₀ copies/ml (95% CI 4.17–4.42) for seroconverters from 1984 through 1995 (n = 163); 4.27 (4.16–4.37) for seroconverters 1996–2002 (n = 232), and 4.59 (4.52–4.66) for seroconverters 2003–2007 (n = 511). Compared to patients seroconverting between 2003–2007, the adjusted mean HIV-1 RNA concentration at set-point was 0.28 log₁₀ copies/ml (95% CI 0.16–0.40; p<0.0001) and 0.26 (0.11–0.41; p = 0.0006) lower for those seroconverting between 1996–2002 and 1984–1995, respectively. Results were robust regardless of type of HIV-1 RNA assay, HIV-1 subtype, and interval between measurement and seroconversion. CD4 cell count at viral set-point declined over calendar time at approximately 5 cells/mm³/year.

Conclusion

The HIV-1 RNA plasma concentration at viral set-point has increased over the last decade of the HIV epidemic in the Netherlands. This is accompanied by a decreasing CD4 cell count over the period 1984–2007 and may have implications for both the course of the HIV infection and the epidemic.

Molecular assays for monitoring HIV infection and antiretroviral therapy

Infection with HIV results in lifelong persistence of the virus in the body of infected persons, independent of antiretroviral treatment. Therefore, efficient and meaningful therapy monitoring has been developed since its introduction in the 1980s. Whereas, primarily, the measurement of the CD4 cell count was the most important clinical marker of disease progression, nowadays the estimation of plasma viral load with molecular methods plays a major role as a marker of therapy success. To optimize therapy changes in patients failing on antiretroviral therapy regimen, HIV-1 genotyping has been introduced and is now widely accepted as an additional diagnostic tool. Due to this increase in diagnostic parameters, clinicians and virologists have to cope with many different methods. This review should give a brief overview of the current commercially available assays for detection and quantification of HIV, as well as for HIV-1 genotypic resistance testing. Quantitative reverse transcriptase PCR, real-time PCR, nucleic acid sequence-based amplification and the branched DNA system are described in detail, and the advantages and disadvantages are discussed. In addition, two commercially available HIV-1 genotyping assays are compared. However, a general recommendation to favor one system over the other cannot be given, because the final decision of which system to use should be decided on the individual requirements.

Performance of three commercial viral load assays, Versant human immunodeficiency virus type 1 (HIV-1) RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2, testing HIV-1 non-B subtypes and recombinant variants

Monitoring antiretroviral therapy requires that human immunodeficiency virus type 1 (HIV-1) viremia assays are applicable to all distinct variants. This study evaluates the performance of three commercial viral load assays-Versant HIV-1 RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2-in testing 83 plasma specimens from patients carrying HIV-1 non-B subtypes and recombinants previously defined by phylogenetic analysis of the pol gene. All 28 specimens from patients under treatment presented viremia values below the detection limit with the three methods. In the remaining 55 specimens from naive individuals viremia could not be detected in 32.7, 20, and 14.6% using the NucliSens, Versant, or TaqMan tests, respectively, suggesting potential viral load underestimation of some samples by all techniques. Only 32 (58.2%) samples from naive subjects were quantified by the three methods; the NucliSens test provided the highest HIV RNA values (mean, 4.87 log copies/ml), and the Versant test provided the lowest (mean, 4.16 log copies/ml). Viremia differences of greater than 1 log were seen in 8 (14.5%) of 55 specimens, occurring in 10.9, 7.3, and 5.4%, respectively, of the specimens in comparisons of Versant versus NucliSens, Versant versus TaqMan, and TaqMan versus NucliSens. Differences greater than 0.5 log, considered significant for clinicians, occurred in 45.5, 27.3, and 29% when the same assays were compared. Some HIV-1 strains, such as subtype G and CRF02_AG, showed more discrepancies in distinct quantification methods than others. In summary, an adequate design of primers and probes is needed for optimal quantitation of plasma HIV-RNA in non-B subtypes. Our data emphasize the need to use the same method for monitoring patients on therapy and also the convenience of HIV-1 subtyping.

HIV-1 and HCV viral load cost models for bDNA: 440 Molecular System versus real-time PCR AmpliPrep/TaqMan test

Comparative cost models were developed to assess cost-per-reportable result and annual costs for HIV-1 and HCV bDNA and AmpliPrep/TaqMan Test (PCR). Model cost components included kit, disposables, platform and related equipment, equipment service plan, equipment maintenance, equipment footprint, waste and labor. Model assessment was most cost-effective when run by bDNA with 36 or more clinical samples and PCR with 30 or fewer clinical samples. Lower costs are attained with maximum samples (84-168) run daily. Highest cost contributors include kit, platform and PCR proprietary disposables. Understanding component costs and the most economic use of HIV-1 and HCV viral load will aid in attaining lowest costs through selection of the appropriate assay and effective negotiations.

Impact of the COBAS AmpliPrep/COBAS AMPLICOR HIV-1 MONITOR Test, Version 1.5, on clinical laboratory operations

The COBAS AmpliPrep/COBAS AMPLICOR HIV-1 MONITOR Test, version 1.5 (CAP/CA), and the COBAS AMPLICOR HIV-1 MONITOR Test, version 1.5, were compared. CAP/CA reduced and consolidated labor while modestly increasing assay throughput without increased failure rates or direct costs, regardless of batch size and assay format.

Fully automated quantification of human immunodeficiency virus (HIV) type 1 RNA in human plasma by the COBAS AmpliPrep/COBAS TaqMan system

BACKGROUND

HIV-1 RNA is a key parameter for reliable diagnosis and treatment of HIV-1 infection. The determination of HIV-1 RNA reduces the pre-seroconversion period in the diagnosis of HIV-1 infection and supports clinical management of HIV-1-infected patients.

OBJECTIVES AND STUDY DESIGN

The COBAS AmpliPrep/COBAS TaqMan HIV-1 Test combines automated extraction of total nucleic acids on the COBAS AmpliPrep Instrument with real-time PCR on the COBAS TaqMan Analyzer, thus greatly reducing hands-on time during sample preparation and amplification/detection. The test was evaluated for sensitivity, dynamic range, precision, subtype inclusivity, interfering substances, diagnostic and analytical specificity, as well as correlation with three other commercial tests for HIV-1 RNA quantification.

RESULTS

The COBAS AmpliPrep/COBAS TaqMan HIV-1 Test demonstrated an assay sensitivity of 40 copies/mL, a greater than 5 log(10) measuring range of 40-1.0E+07 copies/mL (1.6-7.0 log(10)) and a reliable determination of HIV-1 group M and N subtypes in EDTA plasma. Quantification results were highly correlated with those obtained by the COBAS AMPLICOR HIV-1 MONITOR Test v1.5, the COBAS AmpliPrep/COBAS AMPLICOR HIV-1 MONITOR Test v1.5 and the VERSANT HIV-1 RNA 3.0 assay.

CONCLUSIONS

The COBAS AmpliPrep/COBAS TaqMan HIV-1 Test excellently satisfies the requirements for reliable quantification of HIV-1 RNA in clinical specimens by a broad linear measuring range and a fully automated quantification procedure. It is highly appropriate for therapy monitoring and routine management of HIV-1 infection.

Diagnosis of pediatric human immunodeficiency virus infection in resource-constrained settings

The majority of children infected with human immunodeficiency virus live in resource-constrained settings and die without an established diagnosis. Definitive laboratory diagnosis in children younger than 12-18 months requires virologic testing; however, antibody testing is often the only option available. Antibody testing provides a definitive diagnosis in older children but is frequently not used. Children meeting clinical criteria should be treated regardless of availability of laboratory diagnoses.

HIV-1 load quantitation: a 17-year perspective

During the past decade and a half, quantitation of plasma-associated human immunodeficiency virus type 1 (HIV-1) RNA level, or HIV-1 load, has been validated in clinical practice and clinical trials as an important surrogate marker of HIV-1 disease progression and of the potency and durability of antiretroviral regimens. This review highlights some of the history, accomplishments, and impact of Tom Merigan's laboratory on the use of HIV-1 load as a marker, as well as on updating technologies for determining HIV-1 load, their performance, interpretation of the results, and their use in clinical practice.

HIV/AIDS epidemiology, pathogenesis, prevention, and treatment

The HIV-1 pandemic is a complex mix of diverse epidemics within and between countries and regions of the world, and is undoubtedly the defining public-health crisis of our time. Research has deepened our understanding of how the virus replicates, manipulates, and hides in an infected person. Although our understanding of pathogenesis and transmission dynamics has become more nuanced and prevention options have expanded, a cure or protective vaccine remains elusive. Antiretroviral treatment has transformed AIDS from an inevitably fatal condition to a chronic, manageable disease in some settings. This transformation has yet to be realised in those parts of the world that continue to bear a disproportionate burden of new HIV-1 infections and are most affected by increasing morbidity and mortality. This Seminar provides an update on epidemiology, pathogenesis, treatment, and prevention interventions pertinent to HIV-1.