Sample Pooling is a Viable Strategy for SARS-CoV-2 Detection in Low-Prevalence Settings (preprint)

ABSTRACT

BACKGROUNDThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has significantly increased demand on laboratory throughput and reagents for nucleic acid extraction and polymerase chain reaction (PCR). Reagent shortages may limit the expansion of testing required to scale back isolation measures. AIMTo investigate the viability of sample pooling as a strategy for increasing test throughput and conserving PCR reagents; to report our early experience with pooling of clinical samples. METHODSA pre-implementation study was performed to assess the sensitivity and theoretical efficiency of two, four, and eight-sample pools in a real-time reverse transcription PCR-based workflow. A standard operating procedure was developed and implemented in two laboratories during periods of peak demand, inclusive of over 29,000 clinical samples processed in our laboratory. RESULTSSensitivity decreased (mean absolute increase in cycle threshold value of 0.6, 2.3, and 3.0 for pools of two, four, and eight samples respectively) and efficiency increased as pool size increased. Gains from pooling diminished at high disease prevalence. Our standard operating procedure was successfully implemented across two laboratories. Increased workflow complexity imparts a higher risk of errors, and requires risk mitigation strategies. Turnaround time for individual samples increased, hence urgent samples should not be pooled. CONCLUSIONSPooling is a viable strategy for high-throughput testing of SARS-CoV-2 in low-prevalence settings.