High capacity clinical SARS-CoV-2 molecular testing using combinatorial pooling.

Area of Science:

• Infectious Disease Epidemiology
• Molecular Diagnostics
• Public Health Surveillance

Background:

• The COVID-19 pandemic created immense demand for SARS-CoV-2 testing, leading to global delays.
• Traditional pooled-testing methods were limited to low positivity rates (<2%) due to practical constraints.

Purpose of the Study:

• To develop and validate a single-stage pooled-testing strategy for efficient SARS-CoV-2 detection.
• To assess the clinical utility of this strategy during periods of high viral prevalence.

Main Methods:

• Development and clinical validation of P-BEST (pooled-testing by enhanced single-stage testing).
• Side-by-side clinical validation using 3636 samples.
• Implementation in Israel for large-scale testing during Alpha and Delta waves.

Main Results:

• P-BEST demonstrated high accuracy in detecting positive samples and estimating Ct values.
• Clinical application in 2021 tested over 837,000 samples with a 3.1-fold reduction in PCR tests.
• The strategy remained effective even when positivity rates exceeded 10%.

Conclusions:

• P-BEST serves as a proof-of-concept for large-scale single-stage pooled-testing.
• It offers reduced costs and increased efficiency for pathogen surveillance and pandemic response.
• A tablet-based solution facilitates manual pooling in resource-limited settings.