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%.

Keywords: COVID-19; Group testing; SARS CoV-2.

Figure 1

Optimal sample pool size. Graphical comparison of initial pool size compared to expected number of tests per individual using the Shiny application for pooled testing available at https://www.chrisbilder.com/shiny. The optimal sample pool size was determined based on the least number of tests and the following parameters: prevalence rate (5%), a lower limit of detection of 1 to 3 RNA copies/µL, an assay sensitivity of either 95% or 100%, and an assay specificity of 100%.