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

Abstract

Objectives To establish the optimal parameters for group testing of pooled specimens for the detection of SARS-CoV-2. Methods The most efficient pool size was determined to be five specimens using a web-based application. From this analysis, 25 experimental pools were created using 50 µL from one SARS-CoV-2 positive nasopharyngeal specimen mixed with 4 negative patient specimens (50 µL each) for a total volume of 250 µL. Viral RNA was subsequently extracted from each pool and tested using the CDC SARS-CoV-2 RT-PCR assay. Positive pools were consequently split into individual specimens and tested by extraction and PCR. This method was also tested on an unselected group of 60 nasopharyngeal specimens grouped into 12 pools. Results All 25 pools were positive with cycle threshold (Ct) values within 0 and 5.03 Ct of the original individual specimens. The analysis of 60 specimens determined that 2 pools were positive followed by identification of 2 individual specimens among the 60 tested. This testing was accomplished while using 22 extractions/PCR tests, a savings of 38 reactions. Conclusions When the incidence rate of SARS-CoV-2 infection is 10% or less, group testing will result in the saving of reagents and personnel time with an overall increase in testing capability of at least 69%.

Group testing for SARS-CoV-2 allows for up to 10-fold efficiency increase across realistic scenarios and testing strategies

“…13 Similarly, a US American research group performed a test with 12 pools of 5 specimens, each from individuals at risk, and were able to correctly identify the two infected individuals out of the 60 with only 22 tests. 14 The main goal of these works is to demonstrate the feasibility of the experimental design; they propose to use the original group testing design by Dorfman of including each specimen into exactly one pool then testing every specimen of the pool again individually in case of a positive outcome of the group test. 7 Other works over the last weeks have suggested refined approaches, typically based on examples or, from a more theoretical viewpoint, with a simplified model.…”

“…Such connections have been established by Abdalhamid, Bilder and McCutchen by incorporating a decision step regarding how to optimize the number of samples within each pool based on the estimated infection rate -this led to the choice of 5 for the pool size. 14 The problem of choosing the right pool size had previously been analyzed in many works. [22][23][24] The theoretical and practical understanding of group testing developed since the first results of Dorfman, 7 however, goes far beyond merely optimizing the pool sizes.…”

Evaluating efficiency of pooling specimens for PCR-based detection of COVID-19

“…A previous study found that pooling at ratio of 1 to 5 (50 μL of each specimen for total of 250 μL pooled extraction) retained accuracy of the test and resulted in greater efficiency of test resources 10 as well as demonstrating that when the prevalence of COVID-19 is 1%, the optimal specimen pool size is 11 with an overall increase in testing efficiency calculated at 400%. In this study, a 10-specimen pool size (100 μL each specimen) was chosen based on the capacity of the RNA extraction system in the laboratory where this study was performed, and the result was similar to 5 samples pooling 10 .…”

Pooling for SARS-CoV-2 Control in Care Institutions

“…With a prevalence < 2% for more than 85% people in Care Houses, pooling could achieve maximum usefulness. After reviewing the literature, and due to the absence of accumulated experience with this type of strategy for SARS-CoV-2, a more conservative sizepools of 20 and sub pools of 5 samples were chosen [4] [5] [18].…”

“…Pooling strategies have proven to preserve SARS-CoV-2 testing resources and time with an increase in testing capability of the 69% for an incidence rate of SARS-CoV-2 infection of 10% or less [4,5,6,7], but it could be associated with a decrease in detection [8,9].…”