Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources

Abdalhamid, Baha; Bilder, Christopher R.; McCutchen, Emily; Hinrichs, Steven H.; Koepsell, Scott A.; Iwen, Peter C.

doi:10.1101/2020.04.03.20050195

Cited by 64 publications

(112 citation statements)

References 6 publications

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“…However, in a recent study, it has been documented that viral loads are similar in symptomatic and asymptomatic patients; thus, pool testing will produce similar results in all patients with COVID‐19 5 . The present study is concordant with the findings of Abdalhamid et al 6 who reported that pool testing is effective in saving resources in the population having prevalence less than 10%. Laboratories have begun to demonstrate that SARS‐CoV‐2 can be detected in RT‐qPCR performed on pooled samples, despite potential dilution.…”

Section: Discussionsupporting

confidence: 91%

Evaluation of sample pooling for diagnosis of COVID‐19 by real time‐PCR: A resource‐saving combat strategy

Garg

Singh

Pandey

et al. 2020

Journal of Medical Virology

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Background and Objectives Although about 80% of coronavirus disease‐2019 (COVID‐19) cases are reported to be mild, the remaining 20% of cases often result in severe disease with the potential of crushing already overstrained health care services. There has been sustainable growth of COVID‐19 cases worldwide since mid‐May 2020. To keep tabs on community transmission of COVID‐19 infection screening of the samples from a large population is needed which includes asymptomatic/symptomatic individuals along with the migrant population. This requires extra resources, man power, and time for detection of severe acute respiratory syndrome coronavirus 2 by real‐time polymerase chain reaction (RT‐PCR). In the current scenario, the pooled sample testing strategy advocated by the Indian Council of Medical Research, New Delhi is a new approach that is very promising in resource‐limited settings. In this study, we have evaluated the pooled strategy in terms of accurate testing results, utilization of consumables, and identification of borderline positive cases. Materials and Methods Between April and June 2020, we performed COVID‐19 testing by RT‐PCR from areas with varying prevalence of population referred to COVID laboratory, Dr Ram Manohar Lohia Institute of Medical Sciences, Lucknow. In the first step, the samples are collated into pools of 5 or 10. These pools are tested by RT‐PCR. Negative pools were reported as negative whereas positive pools of 5 and 10 are then deconvoluted and each sample is tested individually. Results In the present study, we tested 4620 samples in 462 pools of 10 and 14 940 samples in 2990 pools of 5. Among 10 samples pool, 61 (13%) pools flagged positive in the first step. In the second step, among 61 pools (610 samples) deconvoluted strategy was followed in which 72 individual samples came positive. The pooled‐sample testing strategy helps saves substantial resources and time during surge testing and enhanced pandemic surveillance. This approach requires around 76% to 93% fewer tests done in low to moderate prevalence settings and group sizes up to 5–10 in a population, compared to individual testing. Conclusions Pooled‐sample PCR analysis strategies can save substantial resources and time for COVID‐19 mass testing in comparison with individual testing without compromising the resulting outcome of the test. In particular, the pooled‐sample approach can facilitate mass screening in the early coming stages of COVID‐19 outbreaks, especially in low‐ and middle‐income settings, and control the spread by meticulous testing of all risk groups.

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Section: Discussionsupporting

confidence: 91%

Evaluation of sample pooling for diagnosis of COVID‐19 by real time‐PCR: A resource‐saving combat strategy

Garg

Singh

Pandey

et al. 2020

Journal of Medical Virology

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show abstract

“…While pooling of samples has been widely proposed as a way to expand testing capacity for large scale screening [9][10][11] , there has been limited empirical evidence on pooling performance to properly inform projections of both feasibility and cost-effectiveness. Therefore, we investigated the potential of pooling saliva for SARS-CoV-2 detection in the laboratory setting, then used our findings to inform a model exploring the benefits of pooled sample testing at different rates of virus prevalence in the population.…”

Section: Discussionmentioning

confidence: 99%

Pooling saliva to increase SARS-CoV-2 testing capacity

Watkins¹,

Fenichel

Weinberger³

et al. 2020

Preprint

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Expanding testing capabilities is integral to managing the further spread of SARS-CoV-2 and developing reopening strategies, particularly in regards to identifying and isolating asymptomatic and pre-symptomatic individuals. Central to meeting testing demands are specimens that can be easily and reliably collected and laboratory capacity to rapidly ramp up to scale. We and others have demonstrated that high and consistent levels of SARS-CoV-2 RNA can be detected in saliva from COVID-19 inpatients, outpatients, and asymptomatic individuals. As saliva collection is non-invasive, extending this strategy to test pooled saliva samples from multiple individuals could thus provide a simple method to expand testing capacity. However, hesitation towards pooled sample testing arises due to the dilution of positive samples, potentially shifting weakly positive samples below the detection limit for SARS-CoV-2 and thereby decreasing the sensitivity. Here, we investigated the potential of pooling saliva samples by 5, 10, and 20 samples prior to RNA extraction and RT-qPCR detection of SARS-CoV-2. Based on samples tested, we conservatively estimated a reduction of 7.41%, 11.11%, and 14.81% sensitivity, for each of the pool sizes, respectively. Using these estimates we modeled anticipated changes in RT-qPCR cycle threshold to show the practical impact of pooling on results of SARS-CoV-2 testing. In tested populations with greater than 3% prevalence, testing samples in pools of 5 requires the least overall number of tests. Below 1% however, pools of 10 or 20 are more beneficial and likely more supportive of ongoing surveillance strategies.

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“…One strategy many countries have adopted to increase testing capacity is to combine samples into pools that are tested together [1,2,3,4,5]. If such a pool is tested negative, all individual samples within the pool are declared free of SARS-CoV-2, whereas if it is tested positive then all individuals in that pool must be retested individually in a second round.…”

Section: Introductionmentioning

confidence: 99%

Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing

Ghosh

Rajwade

Krishna

et al. 2020

Preprint

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The COVID-19 pandemic has strained testing capabilities worldwide. There is an urgent need to find economical and scalable ways to test more people. We present Tapestry, a novel quantitative nonadaptive pooling scheme to test many samples using only a few tests. The underlying molecular diagnostic test is any real-time RT-PCR diagnostic panel approved for the detection of the SARS-CoV-2 virus. In cases where most samples are negative for the virus, Tapestry accurately identifies the status of each individual sample with a single round of testing in fewer tests than simple two-round pooling. We also present a companion Android application BYOM Smart Testing which guides users through the pipetting steps required to perform the combinatorial pooling. The results of the pooled tests can be fed into the application to recover the status and estimated viral load for each individual sample. NOTE: This protocol has been validated with in vitro experiments that used synthetic RNA and DNA fragments and additionally, its expected behavior has been confirmed using computer simulations. Validation with clinical samples is ongoing. We are looking for clinical collaborators with access to patient samples. Please contact the corresponding author if you wish to validate this protocol on clinical samples.

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Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources

Cited by 64 publications

References 6 publications

Evaluation of sample pooling for diagnosis of COVID‐19 by real time‐PCR: A resource‐saving combat strategy

Evaluation of sample pooling for diagnosis of COVID‐19 by real time‐PCR: A resource‐saving combat strategy

Pooling saliva to increase SARS-CoV-2 testing capacity

Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing

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