Sample pooling is a viable strategy for SARS-CoV-2 detection in low-prevalence settings

Area of Science:

• Clinical diagnostics
• Virology
• Molecular biology

Background:

• The COVID-19 pandemic strained laboratory resources, increasing demand for nucleic acid extraction and PCR testing.
• Reagent shortages posed a significant challenge to expanding SARS-CoV-2 testing capacity.

Purpose of the Study:

• To evaluate sample pooling as a strategy to enhance testing throughput and conserve PCR reagents.
• To assess the sensitivity and efficiency of pooling clinical samples in a real-time RT-PCR workflow.

Main Methods:

• A pre-implementation study assessed the sensitivity and theoretical efficiency of 2, 4, and 8-sample pools.
• A standard operating procedure for sample pooling was developed and implemented in two laboratories.
• Over 29,000 clinical samples were processed using the developed pooling strategy.

Main Results:

• Sensitivity decreased as pool size increased (mean Ct increase of 0.6, 2.3, and 3.0 for pools of 2, 4, and 8, respectively).
• Testing efficiency increased with larger pool sizes.
• The benefits of pooling diminished in settings with high disease prevalence.

Conclusions:

• Sample pooling is a viable strategy for high-throughput SARS-CoV-2 testing, particularly in low-prevalence settings.
• Increased workflow complexity necessitates risk mitigation strategies to minimize errors.
• Urgent samples should not be pooled due to increased turnaround times.