Nested pool testing strategy for the reliable identification of virally infected individuals

INÉS ARMENDÁRIZ; JOSÉ MARIO MARTÍNEZ; PABLO A. FERRARI; HUGO G. MENZELLA; DANIEL FRAIMAN; SILVINA PONCE DAWSON

Scientific Reports

Nature Research

Lugar: London; Año: 2021 vol. 11 p. 1 - 30

The progress of the SARS-CoV-2 pandemic requires the design of large-scale, cost-effective testing programs. Pooling samples provides a solution if the RNA detection method is sensitive enough. The use of the gold standard, RT-qPCR, raises some concerns for the reliable identification of infected individuals with pooled samples. Recently, droplet digital PCR (ddPCR) was shown to be 10-100 times more sensitive than RT-qPCR, making it more suitable for pooling. Furthermore, ddPCR quantifies the RNA content directly, a feature that, as shown in this paper, can be used to identify unviable samples in pools. Cost-effective strategies require the definition of efficient deconvolution and re-testing procedures for the identification of the carrier. In this paper we analyze the practical implementation of an efficient nested pooling strategy which we have recently introduced, determining the best ways to proceed when there are impediments for the use of the absolute optimum or when multiple pools are tested simultaneously. We also show how the ddPCR RNA quantification and the nested nature of the strategy can be combined to perform self-consistency tests for a better identification of infected individuals and unviable samples. The studies are useful to those considering pool testing for the identification of SARS-CoV-2 infected individuals.