Abstract
Repeated testing of a population is critical for limiting the spread of the SARS-CoV-2 virus and for the safe reopening of educational institutions such as kindergarten—grade 12 (K-12) schools and colleges. Many screening efforts utilize the CDC RT-PCR based assay which targets two regions of the novel Coronavirus nucleocapsid gene. The standard approach of testing each person individually, however, poses a financial burden to these institutions and is therefore a barrier to using testing for re-opening. Pooling samples from multiple individuals into a single test is an attractive alternate approach that promises significant cost savings—however the specificity and sensitivity of such approaches needs to be assessed prior to deployment. To this end, we conducted a pilot study to evaluate the feasibility of analyzing samples in pools of eight by the established RT-PCR assay. Participants (1,576) were recruited from amongst the Tufts University community undergoing regular screening. Each volunteer provided two swabs, one analyzed separately and the other in a pool of eight. Because the positivity rate was very low, we spiked approximately half of the pools with laboratory-generated swabs produced from known positive cases outside the Tufts testing program. The results of pooled tests had 100% correspondence with those of their respective individual tests. We conclude that pooling eight samples does not negatively impact the specificity or sensitivity of the RT-PCR assay and suggest that this approach can be utilized by institutions seeking to reduce surveillance costs.
Highlights
Shutdowns resulting from an effort to control the ongoing COVID-19 pandemic have had a detrimental effect on the education of kindergarten—grade 12 (K-12) school children, especially those in at-risk socioeconomic groups and those with special needs [1, 2]
Samples were couriered to the Broad Institute 4– 6 times per day and analyzed by the established CDC reverse transcriptionpolymerase chain reaction (RT-PCR) assay with fluorescent detection (FAM-labeled probes) [11]
Pooled sample testing is an effective strategy to reduce the cost of regular screening testing during pandemics
Summary
Shutdowns resulting from an effort to control the ongoing COVID-19 pandemic have had a detrimental effect on the education of K-12 school children, especially those in at-risk socioeconomic groups and those with special needs [1, 2]. The simplest form of pooling is known as Dorfman or two-stage hierarchical pooling [5]. By this method, each pool contains a set number of samples. More complex methods assign a single sample to more than one pool to better predict positive samples, reducing the number of individual retests necessary [6,7,8]. Dorfman pooling for SARS-CoV-2 RT-PCR testing has been shown to be effective at the level of eight samples per group [9]
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