Dataset Information

Dorfman pooling enhances SARS-CoV-2 large-scale community testing efficiency.

ABSTRACT: PCR-based analysis is the gold standard for detection of SARS-CoV-2 and was used broadly throughout the pandemic. However, heightened demand for testing put strain on diagnostic resources and the adequate amount of PCR-based testing required exceeded existing testing capacity. Pooled testing strategies presented an effective method to increase testing capacity by decreasing the number of tests and resources required for laboratory PCR analysis of SARS-CoV-2. We sought to conduct an analysis of SARS-CoV-2 pooling schemes to determine the sensitivity of various sized Dorfman pooling strategies and evaluate the utility of using such pooling strategies in diagnostic laboratory settings. Overall, a trend of decreasing sensitivity with larger pool sizes was observed, with modest sensitivity losses in the largest pools tested, and high sensitivity in all other pools. Efficiency data was then calculated to determine the optimal Dorfman pool sizes based on test positivity rate. This was correlated with current presumptive test positivity to maximize the number of tests saved, thereby increasing testing capacity and resource efficiency in the community setting. Dorfman pooling methods were evaluated and found to offer a high-throughput solution to SARS-CoV-2 clinical testing that improve resource efficiency in low-resource environments.

SUBMITTER: Burtniak J

PROVIDER: S-EPMC10112776 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Dorfman pooling enhances SARS-CoV-2 large-scale community testing efficiency.

Burtniak Julian J Hedley Adam A Dust Kerry K Van Caeseele Paul P Bullard Jared J Stein Derek R DR

PLOS global public health 20230418 4

PCR-based analysis is the gold standard for detection of SARS-CoV-2 and was used broadly throughout the pandemic. However, heightened demand for testing put strain on diagnostic resources and the adequate amount of PCR-based testing required exceeded existing testing capacity. Pooled testing strategies presented an effective method to increase testing capacity by decreasing the number of tests and resources required for laboratory PCR analysis of SARS-CoV-2. We sought to conduct an analysis of S ...[more]

PMID: 37071604

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Project description:Real-world data are needed to establish SARS-CoV-2 rapid antigen testing (RAT) as an effective and reliable approach for SARS-CoV-2 screening. This study included 1,952,931 individuals who provided upper respiratory specimens during SARS-CoV-2 screening at CityMD urgent care locations in the New York metropolitan area from October 2020 to March 2021. Positive and negative results, as determined by the BD Veritor™ System for Rapid Detection of SARS-CoV-2 antigen (Veritor), were obtained for all individuals, with reflex reverse transcriptase-polymerase chain reaction (RT-PCR) testing performed on a case-by-case basis, per standard of care. Using verification bias adjustment, two alternative model assumptions were utilized for RAT results with missing reflex RT-PCR results. The worst antigen diagnostic performance estimates asserted that missing RT-PCR results would show a distribution similar to those RT-PCR results actually obtained, based on symptom category. The best antigen diagnostic performance estimates asserted that individuals without RT-PCR results had a clinical presentation consistent with RAT results, and, therefore, missing RT-PCR results would agree with RAT results. For patients with symptoms or high-risk exposure, 25.3% (n = 86,811/343,253) of RAT results were positive; vs. 3.4% (n = 53,046/1,559,733) positive for asymptomatic individuals without high-risk exposure. Reflex RT-PCR results were obtained from 46.3% (n = 158,836/343,253) and 13.8% (n = 215,708/1,559,733) of symptomatic and asymptomatic individuals, respectively. RT-PCR confirmed 94.4% (4,265/4,518) of positive and 90.6% (139,759/154,318) of negative RAT results in symptomatic individuals; and confirmed 83.4% (6,693/8,024) of positive and 95.3% (197,955/207,684) of negative RAT results in asymptomatic individuals. Applied assumptions for missing reflex RT-PCR results led to worst performance sensitivity estimates of 77.2 and 38.5% in the symptomatic and asymptomatic populations, respectively; assumptions for best performance estimates led to sensitivity values of 85.6 and 84.2%, respectively. Specificity values, regardless of assumptions or symptom category, ranged from 97.9-99.9%. At 10% SARS-CoV-2 prevalence, RAT positive predictive value was 86.9 and 99.0% for worst and best performance estimates across the total population, respectively; negative predictive values were >95% regardless of the applied assumption. Veritor test performance was consistent with that listed in the manufacturer instructions for use for symptomatic individuals. Real-world evidence should be gathered on RATs to support their efficacy as SARS-CoV-2 persists.

Project description:BackgroundThe development of new large-scale saliva pooling detection strategies can significantly enhance testing capacity and frequency for asymptomatic individuals, which is crucial for containing SARS-CoV-2.ObjectiveThis study aims to implement and scale-up a SARS-CoV-2 screening method using pooled saliva samples to control the virus in critical areas and assess its effectiveness in detecting asymptomatic infections.MethodsBetween August 2020 and February 2022, our laboratory received a total of 928,357 samples. Participants collected at least 1 mL of saliva using a self-sampling kit and registered their samples via a smartphone app. All samples were directly processed using AutoMate 2550 for preanalytical steps and then transferred to Microlab STAR, managed with the HAMILTON Pooling software for pooling. The standard pool preset size was 20 samples but was adjusted to 5 when the prevalence exceeded 2% in any group. Real-time polymerase chain reaction (RT-PCR) was conducted using the Allplex SARS-CoV-2 Assay until July 2021, followed by the Allplex SARS-CoV-2 FluA/FluB/RSV assay for the remainder of the study period.ResultsOf the 928,357 samples received, 887,926 (95.64%) were fully processed into 56,126 pools. Of these pools, 4863 tested positive, detecting 5720 asymptomatic infections. This allowed for a comprehensive analysis of pooling's impact on RT-PCR sensitivity and false-negative rate (FNR), including data on positive samples per pool (PPP). We defined Ctref as the minimum cycle threshold (Ct) of each data set from a sample or pool and compared these Ctref results from pooled samples with those of the individual tests (ΔCtP). We then examined their deviation from the expected offset due to dilution [ΔΔCtP = ΔCtP - log2]. In this work, the ΔCtP and ΔΔCtP were 2.23 versus 3.33 and -0.89 versus 0.23, respectively, comparing global results with results for pools with 1 positive sample per pool. Therefore, depending on the number of genes used in the test and the size of the pool, we can evaluate the FNR and effective sensitivity (1 - FNR) of the test configuration. In our scenario, with a maximum of 20 samples per pool and 3 target genes, statistical observations indicated an effective sensitivity exceeding 99%. From an economic perspective, the focus is on pooling efficiency, measured by the effective number of persons that can be tested with 1 test, referred to as persons per test (PPT). In this study, the global PPT was 8.66, reflecting savings of over 20 million euros (US $22 million) based on our reagent prices.ConclusionsOur results demonstrate that, as expected, pooling reduces the sensitivity of RT-PCR. However, with the appropriate pool size and the use of multiple target genes, effective sensitivity can remain above 99%. Saliva pooling may be a valuable tool for screening and surveillance in asymptomatic individuals and can aid in controlling SARS-CoV-2 transmission. Further studies are needed to assess the effectiveness of these strategies for SARS-CoV-2 and their application to other microorganisms or biomarkers detected by PCR.

Dataset Information

Dorfman pooling enhances SARS-CoV-2 large-scale community testing efficiency.

Publications

Dorfman pooling enhances SARS-CoV-2 large-scale community testing efficiency.

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