Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing

Abstract

The rapid identification and isolation of infected individuals remains a key strategy for controlling the spread of SARS-CoV-2. Frequent testing of populations to detect infection early in asymptomatic or presymptomatic individuals can be a powerful tool for intercepting transmission, especially when the viral prevalence is low. However, RT-PCR testing – the gold standard of SARS-CoV-2 diagnosis – is expensive, making regular testing of every individual unfeasible. Sample pooling is one approach to lowering costs. By combining samples and testing them in groups the number of tests required is reduced, substantially lowering costs. Here we report on the implementation of pooling strategies using 3-d and 4-d hypercubes to test a professional sports team in South Africa. We have shown that infected samples can be reliably detected in groups of 27 and 81, with minimal loss of assay sensitivity for samples with individual Ct values up to 32. We report on automation of sample pooling, using a liquid-handling robot and an automated web interface to identify positive samples. We conclude that hypercube pooling allows for the reliable RT-PCR detection of SARS-CoV-2 infection, at significantly lower cost than lateral flow antigen (LFA) tests.

Ferrobotic swarms enable accessible and adaptable automated viral testing

“…Accordingly, accessible and adaptable automated platforms that in decentralized settings perform nucleic acid amplification tests resource-efficiently are required [10][11][12][13][14] . Pooled testing can be extremely efficient if the pooling strategy is based on local viral prevalence [15][16][17][18][19][20] ; however, it requires automation, small sample volume handling and feedback not available in current bulky, capital-intensive liquid handling technologies [21][22][23][24][25][26][27][28][29] . Here we use a swarm of millimetre-sized magnets as mobile robotic agents ('ferrobots') for precise and robust handling of magnetized sample droplets and high-fidelity delivery of flexible workflows based on nucleic acid amplification tests to overcome these limitations.…”

“…However, current automated NAAT-based testing platforms are unable to perform the integrated liquid handling, analysis and automated feedback processes that are necessary to achieve these flexible workflows [21][22][23] . In addition, they use bulky, expensive and reagentwasteful robotic liquid handlers and bioinstruments, with heavy installations and maintenance needs, and thus, they are restricted to centralized laboratory settings [24][25][26][27][28][29] .…”