A pooled RT-PCR testing strategy for more efficient COVID-19 pandemic management

Abstract

ABSTRACT: Objectives: Reverse transcription polymerase chain reaction (RT-PCR) testing is indispensable in management of the coronavirus disease 2019 (COVID-19) pandemic. However, with the emergence of new variants of severe acute respiratory syndrome coronavirus-2, the cause of COVID-19, the screening capacity of RT-PCR testing is overburdened, and new strategies and capabilities need to be established. One option is pooled RT-PCR testing. Design: This study used various mixtures of COVID-19 samples known to be negative and positive, and investigated the impact of pool size and mixture level on final cycle threshold (Ct) values. More specifically, 5, 10 and 20 negative samples were combined with one, two or three low Ct or high Ct positive samples. Results: Average baseline Ct and numbers of high and low Ct samples in the pool were found to be the main drivers of the final Ct value, making detectability easier. Pool size was not significantly associated with final Ct, but was suggestive. Conclusions: A pooled RT-PCR testing strategy does not reduce the sensitivity of RT-PCR, and thus provides a practical way to expand RT-PCR screening capacity in pandemic management. The pool size was not found to be significant, so it is recommended that a pool size of 20 would be a practical number to reduce the time taken to obtain the results and the cost of RT-PCR testing.

Keywords

• COVID-19 testing
• Pooled RT-PCR
• Cycle threshold
• Pandemic management
• Virus screening