Detection of HIV-1 in alternative specimen types using the APTIMA® HIV-1 RNA Qualitative Assay

Nugent, C. Thomas; Dockter, Janel; Bernardin, Flavien; Hecht, Richard D.; Smith, Davey M.; Delwart, Eric; Pilcher, Christopher D.; Richman, Douglas D.; Busch, Michael P.; Giachetti, Cristina

doi:10.1016/j.jviromet.2009.02.015

Cited by 20 publications

(15 citation statements)

References 14 publications

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“…usRNA can be easily detected with a seminested or nested quantitative reverse transcription PCR (qRT-PCR) (36-39) or by ddPCR, using a set of primers and probe against Pol or Gag (17, 30, 33, 39). Alternatively, some investigators have adapted commercial quantitative tests for HIV-1 plasma viremia, such as Amplicor (Roche Diagnostics) (40,41) or APTIMA HIV-1 Qualitative assay (Hologic) (42,43) for the quantitation of caRNA. msRNA primers are designed to amplify a region containing the Tat/Rev (or Tat/Nef) exon-exon junction and can be quantified by nested qRT-PCR (36, 38, 39) or ddPCR (17,39,44).…”

Section: Pcr-based Assays To Measure the Latent Reservoirmentioning

confidence: 99%

Measuring the latent reservoir in vivo

Massanella¹,

Richman²

2016

Journal of Clinical Investigation

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Section: Pcr-based Assays To Measure the Latent Reservoirmentioning

confidence: 99%

Measuring the latent reservoir in vivo

Massanella¹,

Richman²

2016

Journal of Clinical Investigation

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“…The pooling of sera or plasma specimens has long been used to improve the accuracy, costeffectiveness, and throughput of screening for many infections (e.g., HIV-1, hepatitis B virus, hepatitis C virus, and West Nile virus) in low-prevalence settings, such as blood banks (4,26). We recently reported methods for pooled analysis of dried blood spots for HIV-1 nucleic acids (1,18).…”

mentioning

confidence: 99%

PCR-Based Pooling of Dried Blood Spots for Detection of Malaria Parasites: Optimization and Application to a Cohort of Ugandan Children

Hsiang¹,

Lin²,

Dokomajilar

et al. 2010

J Clin Microbiol

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Sensitive, high-throughput methods to detect malaria parasites in low-transmission settings are needed. PCR-based pooling strategies may offer a solution. We first used laboratory-prepared samples to compare 2 DNA extraction and 4 PCR detection methods across a range of pool sizes and parasite densities. Pooled Chelex extraction of DNA, followed by nested PCR of cytochrome b, was the optimal strategy, allowing reliable detection of a single low-parasitemic sample (100 parasites/l) in pool sizes up to 50. This PCR-based pooling strategy was then compared with microscopy using 891 dried blood spots from a cohort of 77 Ugandan children followed for 2 years in an urban setting of low endemicity. Among 419 febrile episodes, 35 cases of malaria were detected using the PCR-based pooling strategy and 40 cases using microscopy. All five cases of malaria not detected by PCR were from samples stored for >2 years with parasitemia of <6,000/l, highlighting the issue of possible DNA degradation with long-term storage of samples. Among 472 samples collected from asymptomatic children as part of routine surveillance, 15 (3.2%) were positive by PCR-based pooling compared to 4 (0.8%) by microscopy (P ‫؍‬ 0.01). Thus, this PCR-based pooling strategy for detection of malaria parasites using dried blood spots offers a sensitive and efficient approach for malaria surveillance in low-transmission settings, enabling improved detection of asymptomatic submicroscopic infections and dramatic savings in labor and costs.Due to large-scale implementation of effective control measures, many countries where malaria is endemic are experiencing dramatic declines in disease burden. With this success has come a shift in the end goal from control to elimination (9, 10). However, when the goal is elimination, accurate detection of persons infected with malaria parasites becomes essential (11). Standard surveillance systems depend on diagnosis by microscopy, a method that is technically challenging, labor-intensive, and often inaccurate in operational settings. More recently available rapid diagnostic tests (RDTs) provide convenience and ease of use, but they have limitations in specificity, sensitivity, species identification, and cost (22).PCR-based methods for malaria parasite detection are relatively simple and provide improved sensitivity compared to microscopy and RDTs, especially in settings where infections have low parasitemia or contain mixed species (22). PCR can also be performed on dried blood spots, which are convenient for collection, storage, and transport. Nonetheless, PCR has a long turnaround time, making it an impractical tool for clinical care of individual patients. One exception would be real-time PCR, which has a short turnaround time but carries with it cost and capacity constraints that make it unavailable for rapid diagnosis in most settings. However, there is a potential role for PCR in situations where large numbers of samples are being screened: a high-throughput system could allow accurate, rapid, and cost-effective ass...

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“…The % clinical sensitivity=number of samples reactive by pooled NAAT/number of samples reactive by IDT-NAAT at the lowest limit of detection × 100. A strong agreement, in analytical sensitivity and specificity was also reported using different pool sizes, specimen types (including DBS) and assays, compared to individual donor testing ruling out the speculated serious negative impact of dilution (optimum at 10 to 45 different donor samples) [4][5][6]8,9,21,26,27,32,34,35]. The sensitivity obviously negatively correlates with the pool size, particularly from 96 to 128.…”

Section: Discussionmentioning

confidence: 63%

“…enrichment by hard spinning) and the incidence of HIV in the targeted population are quite critical to the success and cost effectiveness of MP-NAAT. Low viral load sero-conversion panels are prone to viral RNA dilution of the mini-pools, below the detection threshold of the NAAT, though various studies have confirmed its reliability [4][5][6]8,9,17,21,26,27,32,34,35]. An average clinical sensitivity of 98% was recorded for pooled NAAT using IDT NAAT as v from the studies included in this review.…”

Section: Resultsmentioning

confidence: 95%

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Current Trends in the detection of Acute HIV Infection among Blood Donors: Reliability of Pooled Nucleic Acid Amplification Technology and the Need for Population Specific Algorithms: A Systematic Review

PJ¹,

P²

2015

J Antivir Antiretrovir

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We conducted a systematic review of quantitative studies that evaluated the accuracy of nucleic acid amplification testing technologies (NAAT) compared their cost effectiveness and evaluated minipool NAAT against individual donor testing NAAT. PubMed, Cochrane and Google Scholar were used to identify relevant peer-reviewed journal articles published in English language between 1999 (when NAAT was introduced) and 2013. MeSH key words included: Human immunodeficiency virus OR HIV AND nucleic acid amplification techniques OR pooled NAAT AND blood donors. Additional filters include: minipool-NAAT and individual donor testing-NAAT. After screening for duplication and relevance, 50 out of 4,181 articles were selected. Thirty six (36) studies which included 5 review article, 5 retrospective cohort studies, 20 cross sectional studies, 2 statistical modeling's, 2 national guidelines and 2 prospective cohort studies were further synthesized. Articles were further sub-divided into 8 groups based their focus area which includes: prevalence, clinical sensitivity of the assay, analytical sensitivity, test technology, testing algorithm, limit of detection and cost effectiveness.Four of six studies with pool sizes of 10 to 50 donor plasmas with standard centrifugation recorded a clinical sensitivity of 100% while the remaining two whose plasma pool size of 96 and128 had sensitivities of 92.3% and 95.3%, respectively. All four studies that focused on analytical sensitivity using different samples and controls, including cadaveric samples reported 100% analytical sensitivity using various pool sizes. We recommend minipool NAAT testing after running a third generation ELISA as highly sensitive and cost effective algorithm for low income countries.

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Detection of HIV-1 in alternative specimen types using the APTIMA® HIV-1 RNA Qualitative Assay

Cited by 20 publications

References 14 publications

Measuring the latent reservoir in vivo

Measuring the latent reservoir in vivo

PCR-Based Pooling of Dried Blood Spots for Detection of Malaria Parasites: Optimization and Application to a Cohort of Ugandan Children

Current Trends in the detection of Acute HIV Infection among Blood Donors: Reliability of Pooled Nucleic Acid Amplification Technology and the Need for Population Specific Algorithms: A Systematic Review

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