HIV-1 viral load assays for resource-limited settings

Centrifugation improves the detection of HIV-1 p24 antigen in plasma from children born to mothers infected with HIV-1

Detection of HIV proteins and/or nucleic acids is necessary for the diagnosis of perinatal HIV infection. Despite its low sensitivity, detection of p24 antigen in plasma is a simple and economic method for the diagnosis of HIV in exposed children. The aim of this study was to improve the sensitivity of detection of p24 using centrifugation of plasma. Forty-seven selected stored samples from 37 children (23 infected, 14 uninfected, median age of 137 days) were examined. Plasma samples (volume 0.3-1.5 ml) were defrosted, centrifuged at 23,500 x g at 4 degrees C for 60 min and determination of p24 was carried out in the resuspended pellet (0.12 ml). In 32 plasma samples from infected children, p24 was found originally in 6 (18.7%) and resulted positive in 24 (75%) pellets. When only one sample per child was considered, sensitivity was significantly higher in pellets, 3/23 uncentrifuged plasma samples and 15/23 pellets (McNemar Test, p<0.001). Specificity was 100%. The absorbance/cut-off ratio was always higher in the pellets from positive children (p=0.028). Plasma samples with volumes of 1 ml or more achieved a higher sensitivity (91.7% vs. 36.4%, p=0.009). Centrifugation of plasma samples prior to determination of p24 in pediatric patients resulted in a significant increase in sensitivity.

In-house HIV-1 RNA real-time RT-PCR assays: principle, available tests and usefulness in developing countries

The principle of currently available licensed HIV-1 RNA assays is based on real-time technologies that continuously monitor the fluorescence emitted by the amplification products. Besides these assays, in-house quantitative (q) real-time reverse transcription (RT)-PCR (RT-qPCR) tests have been developed and evaluated particularly in developing countries, for two main reasons. First, affordable and generalized access to HIV-1 RNA viral load is urgently needed in the context of expected universal access to prevention and antiretroviral treatment programs in these settings. Second, since many non-B subtypes, circulating recombinant forms and unique recombinant forms circulate in these areas, in-house HIV-1 RNA RT-qPCR assays are ideal academic tools to thoroughly evaluate the impact of HIV-1 genetic diversity on the accuracy of HIV-1 RNA quantification, as compared with licensed techniques. To date, at least 15 distinct in-house assays have been designed. They differ by their chemistry and the HIV-1 target sequence (located in gag, Pol-IN or LTR gene). Analytical performances of the tests that have been extensively evaluated appear at least as good as (or even better than) those of approved assays, with regard to HIV-1 strain diversity. Their clinical usefulness has been clearly demonstrated for early diagnosis of pediatric HIV-1 infection and monitoring of highly active antiretroviral therapy efficacy. The LTR-based HIV-1 RNA RT-qPCR assay has been evaluated by several groups under the auspices of the Agence Nationale de Recherches sur le SIDA et les hépatites virales B et C. It exists now as a complete standardized commercial test.

Diagnosis of human immunodeficiency virus type 1 infection in infants by use of dried blood spots and an ultrasensitive p24 antigen assay

We tested 617 dried blood spots (DBS) from human immunodeficiency virus-exposed infants from five countries using an ultrasensitive p24 antigen assay (Up24). The sensitivity was 94.4% (67/71) and the specificity was 100% (431/431) for infants with DBS specimens <or=20 months old; DBS older than 30 months demonstrated only 72.2% sensitivity (39/54) (P < 0.001) but displayed 100% specificity (61/61).

Cost assessment of the automated VERSANT 440 Molecular System versus the semi-automated System 340 bDNA Analyzer platforms

Labor, supply and waste were evaluated for HIV-1 and HCV bDNA on the semi-automated System 340 bDNA Analyzer and the automated VERSANT 440 Molecular System (V440). HIV-1 sample processing was evaluated using a 24- and 48-position centrifuge rotor. Vigilance time (hands-on manipulations plus incubation time except initial target hybridization) and disposables were approximately 37 and 12% lower for HIV-1, and 64 and 31% lower for HCV bDNA, respectively, with V440. Biohazardous solid waste was approximately twofold lower for both assays and other waste types were the same for either assay on both platforms. HIV-1 sample processing vigilance time for the 48-position rotor was reduced by 2 h. V440 provides cost savings and improved workflow.

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.

Optimizing screening for acute human immunodeficiency virus infection with pooled nucleic acid amplification tests

Recent studies have shown the public health importance of identifying individuals with acute human immunodeficiency virus infection (AHI); however, the cost of nucleic acid amplification testing (NAAT) makes individual testing of at-risk individuals prohibitively expensive in many settings. Pooled NAAT (or group testing) can improve efficiency and test performance of testing for AHI, but optimizing the pooling algorithm can be difficult. We developed simple, flexible biostatistical models of specimen pooling with NAAT for the identification of AHI cases; these models incorporate group testing theory, operating characteristics of biological assays, and a model of viral dynamics during AHI. Pooling algorithm sensitivity, efficiency (test kits used per individual specimen evaluated), and positive predictive value (PPV) were modeled and compared for three simple pooling algorithms: two-stage minipools (D2), three-stage hierarchical pools (D3), and square arrays with master pools (A2m). We confirmed the results by stochastic simulation and produced reference tables and a Web calculator to facilitate pooling by investigators without specific biostatistical expertise. All three pooling strategies demonstrated improved efficiency and PPV for AHI case detection compared to individual NAAT. D3 and A2m algorithms generally provided better efficiency and PPV than D2; additionally, A2m generally exhibited better PPV than D3. Used selectively and carefully, the simple models developed here can guide the selection of a pooling algorithm for the detection of AHI cases in a wide variety of settings.

SMARThivVLmos: a complexity-free and cost effective dynamic model technology for monitoring HIV viral load in resource-poor settings

We design a "simple" and "low cost" model technology for monitoring HIV viral load in resource-poor settings: SMARThivVLmos. Cost and complexity are the major challenges to the developing world, in monitoring HIV patients viral load. We have previously demonstrated in our SMARThivPack model that cost and complexity of laboratory monitoring of HIV patients, may be reduced not only at a first technology development level, but also at a second technology implementation, and at a third global coordination levels. In our SMARThivPack model, the P24 HIV viral load monitoring system passed both the "cost" and the "complexity" tests. However, compared to other alternative viral monitoring systems such as the Cavidi EXAVIR, the sensitivity of the P24 system is too low. Here we describe a dynamic model technology that overcomes the sensitivity barrier of the P24 system while maintaining simplicity and low cost.

SMARThivPack: a complexity free and cost effective "three tests" combo kit model for improving HIV patients monitoring standards in resource poor settings

We propose a second method at an implementation level with cost and complexity reductions for monitoring HIV patients in resource-limited settings. The model is SMARThivPack, a "three tests" combo kit. Cost and complexity reductions of HIV patient monitoring technologies were described in a first model (at a technology development stage) proposed earlier. In developed countries, HIV patient clinical management programs comport three laboratory tests containing CD4 count, viral load measurement and pharmaco-resistance testing. In most developing countries only CD4 count is performed without the other two tests. Cost and complexity of required technologies are the major challenges to the developing world to meeting the "three tests" standard. SMARThivPack model achieves the "three tests" standard in the developing world by optimizing technology choice as to favour cross-use of equipments, thereby reducing equipment cost at the laboratory implementation level. Equipment cross use also reduces complexity by reducing training time, promoting specialization and substantiating experience in equipment use. The second level cost and complexity reductions model sets the grounds for a third level, global coordination cost and complexity reductions model.

Evaluation of two commercially available alternatives for HIV-1 viral load testing in resource-limited settings

There is an urgent need for low-cost assays for HIV-1 quantitation to ensure adequate follow-up of HIV-infected patients on antiretroviral therapy (ART) in resource-limited countries. Two low-cost viral load assays are evaluated, a reverse transcriptase activity assay (ExavirLoad v2, Cavidi) and a real-time reverse transcriptase PCR assay (Generic HIV viral load, Biocentric). Both tests were compared with the ultrasensitive HIV Amplicor Monitor assay. Samples were collected in Mombasa, Kenya, from 20 HIV-1 seronegative and 150 HIV-1 seropositive individuals of whom 50 received antiretroviral treatment (ART). The ExavirLoad and the Generic HIV viral load assay were performed in a local laboratory in Mombasa, the Amplicor Monitor assay (version 1.5, Roche Diagnostics) was performed in Ghent, Belgium. ExavirLoad and Generic HIV viral load reached a sensitivity of 98.3% and 100% and a specificity of 80.0% and 90.0%, respectively. Linear regression analyses revealed good correlations between the Amplicor Monitor and the Generic HIV viral load (r=0.935, p<0.001) with high accuracy (100.1%), good precision (5.5%) and a low percent similarity coefficient of variation (5.4%). Bland-Altman analysis found 95% of the samples within clinically acceptable limits of agreement (-1.19 to 0.87logcopies/ml). Although, the ExavirLoad also showed a good linear correlation with the Amplicor Monitor (r=0.901, p<0.001), a problem with false positive results was more significant. The cost per test remains relatively high (US$ 30 for ExavirLoad and US$ 20 for the Generic HIV viral load). Hence, false positive results and the need for an expensive PCR instrument for the Generic HIV viral load assays still limit the implementation of these tests in less equipped, less experienced laboratories.

Feasibility of detecting human immunodeficiency virus type 1 drug resistance in DNA extracted from whole blood or dried blood spots

Due to high cost, availability of human immunodeficiency virus type 1 (HIV-1) drug resistance testing in resource-poor settings is still limited. We therefore evaluated the usefulness of viral DNA extracted from either whole blood or dried blood spots (DBS). Samples were collected from 50 patients receiving therapy and 10 therapy-naïve patients. Amplification and sequencing of RNA and DNA was performed using an in-house assay. Protease (PR) and reverse transcriptase (RT) sequences of plasma viral RNA were obtained for 96.6% and 89.7%, respectively, of the 29 patients with a detectable viral load. For cellular viral DNA, useful PR and RT sequences were obtained for 96.6% and 93.1% of the whole-blood-cell samples and for 93.1% and 93.1% of the DBS samples, respectively. For the 31 patients with an undetectable viral load, PR and RT sequences were obtained for 67.7% and 61.3% of the whole-blood-cell DNA preparations and for 54.8% and 58.1% of the DBS DNA preparations, respectively. A good correlation between RNA and DNA sequences was found; most discordances were caused by the detection of mixed amino acids. Of the RT drug-resistant mutations, 13 (38.2%) were seen in RNA only, 6 (17.6%) in DNA only, and 15 (44.1%) in both. Repeated amplification and sequencing of DNA extracts revealed a lack of reproducibility for the detection of drug resistance mutations in a number of samples, indicating a possible founder effect. In conclusion, this study shows the feasibility of genotypic drug resistance testing on whole blood cells or DBS and its possible usefulness for HIV-1 subtyping or examining the overall distribution of drug resistance in a population. For individual patients, RNA sequencing was shown to be superior to DNA sequencing, especially for patients who experienced early treatment failure. The use of DNA extracted from whole blood or DBS for the detection of archived drug resistance mutations deserves further study.

Potential of a simplified p24 assay for early diagnosis of infant human immunodeficiency virus type 1 infection in Haiti

With global efforts to scale up the prevention of mother-to-child transmission services and pediatric antiretroviral therapy, there is an urgent need to introduce a simple, low-cost infant human immunodeficiency virus test in the field. We postulated that the p24 antigen capture enzyme-linked immunosorbent assay could be simplified by eliminating signal amplification without compromising diagnostic accuracy.