Implementation of an efficient sample pooling strategy for high throughput diagnostic testing of Severe Acute Respiratory Syndrome Corona Virus-2.
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Date
2022
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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 of up to 32. We report on the 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 costs than lateral flow antigen
tests.
Description
Masters Degree. University of KwaZulu-Natal, Durban.