Author:
Singh Lavanya,Anyaneji Ugochukwu J.,Ndifon Wilfred,Turok Neil,Mattison Stacey A.,Lessells Richard,Sinayskiy Ilya,San Emmanuel J.,Tegally Houriiyah,Barnett Shaun,Lorimer Trevor,Petruccione Francesco,de Oliveira Tulio
Abstract
AbstractThe 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 (LFA) tests.
Funder
Department of Science and Innovation, South Africa
Publisher
Springer Science and Business Media LLC
Reference23 articles.
1. Hu, B., Guo, H., Zhou, P. & Shi, Z.-L. Characteristics of SARS-CoV-2 and COVID-19. Nat. Rev. Microbiol. 19, 1–14 (2020).
2. Long, S. W. et al. Molecular architecture of early dissemination and massive second wave of the SARS-CoV-2 virus in a major metropolitan area. MBio 11 (2020).
3. Tegally, H. et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv (2020).
4. Vahidy, F. S. et al. Characteristics and outcomes of COVID-19 patients during initial peak and resurgence in the Houston metropolitan area. JAMA 324, 998–1000 (2020).
5. de Oliveira, T. et al. A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa. medRxiv (2021).
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