Optimizing Screening for Acute Human Immunodeficiency Virus Infection with Pooled Nucleic Acid Amplification Tests

Abstract

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.Nucleic acid amplification testing (NAAT) has revolutionized testing for infectious diseases (17), but the technique remains expensive (6, 9, 27) and exhibits poor predictive value in many settings. In the last decade, laboratories have turned to specimen pooling or group testing strategies to increase both the efficiency and the predictive value of NAAT for use in screening for rare diseases (23,24,27,31). In group testing, biological specimens are pooled together, and these pools (rather than the individual specimens) are initially tested. If a pool tests positive, further testing is required to identify individual positive specimens; however, if the pool tests negative, all specimens in that pool are declared negative. Thus, group testing can lead to a decrease in the average number of tests required per specimen evaluated compared to individual testing. Group testing can also lead to higher specificity and thus to higher positive predictive values in a screening setting.

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

“…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.…”

“…In contrast, of those anti-HIV repeat reactive samples that tested NAAT nonreactive and Western blot negative or indeterminate, 98.5% had an Abbott ELISA signal-cutoff ratio less than 15 [15]. The need for an optimized and realistic algorithm and pool size that is cost effective, for different settings and incidences via-as-vis methodology (such as hard spinning), taking into account HIV 1 genetic diversity, primerprobe mismatch and platforms as summarized in Table 6 below, cannot be over emphasized [16][17][18][19][20][21][22][23]26,27,[36][37][38][39][40][41][42][43][44][45]. Cannillo et al recently, reported that CAD as the most frequent cardiac complication in HIV patients (particularly those with low CD4 and high viral load) treated with HAART.…”

“…The need for population specific NAAT algorithm and optimization of assays and pool sizes including modelling and simulation cannot be over emphasized [15,17,19,31]. Tang and Ou have summarized various molecular diagnostic techniques, their application, turnaround time, including blood donor screening in a review [18].…”

Primary HIV infection: a medical and public health emergency requiring rapid specialist management

“…In these situations, confirmation of an HIV diagnosis can be made from venous blood samples sent to a virology laboratory where the presence of viral proteins (p24) or viral HIV DNA or RNA can be made. 13 Laboratory third generation tests do not detect viral gag protein (p24) and therefore are less able to detect early infection prior to the development of detectable levels of HIV antibody. The lack of detectable antibodies in the initial stages of infection makes this a difficult diagnosis to make using current standard tests.…”

Integrating Acute HIV Infection within Routine Public Health Surveillance Practices in New York City

“…The diagnostic challenge posed by AHI has inspired screening efforts involving complex and expensive laboratory procedures using pooled nucleic acid amplification test (pNAAT) algorithms. 5,15,16 Programs designed to increase the ascertainment of AHI by pNAAT have been conducted and described in North Carolina, 5,17 Seattle (Washington), 18 Los Angeles (California), 19 San Francisco (California), 20 and New York City (NYC). 21 While effective in increasing the detection of AHI, such pNAAT programs are costly, and targeting their use to the highest-yield populations to maximize efficiency has been recommended.…”