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, espec...

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Autores principales:	Lavanya Singh, Ugochukwu J. Anyaneji, Wilfred Ndifon, Neil Turok, Stacey A. Mattison, Richard Lessells, Ilya Sinayskiy, Emmanuel J. San, Houriiyah Tegally, Shaun Barnett, Trevor Lorimer, Francesco Petruccione, Tulio de Oliveira
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/00d2faa17b5f49e284e8c2228bbcd2de
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spelling	oai:doaj.org-article:00d2faa17b5f49e284e8c2228bbcd2de2021-12-02T19:12:35ZImplementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing10.1038/s41598-021-96934-z2045-2322https://doaj.org/article/00d2faa17b5f49e284e8c2228bbcd2de2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-96934-zhttps://doaj.org/toc/2045-2322Abstract 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 (LFA) tests.Lavanya SinghUgochukwu J. AnyanejiWilfred NdifonNeil TurokStacey A. MattisonRichard LessellsIlya SinayskiyEmmanuel J. SanHouriiyah TegallyShaun BarnettTrevor LorimerFrancesco PetruccioneTulio de OliveiraNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-7 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lavanya Singh Ugochukwu J. Anyaneji Wilfred Ndifon Neil Turok Stacey A. Mattison Richard Lessells Ilya Sinayskiy Emmanuel J. San Houriiyah Tegally Shaun Barnett Trevor Lorimer Francesco Petruccione Tulio de Oliveira Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing
description	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 (LFA) tests.
format	article
author	Lavanya Singh Ugochukwu J. Anyaneji Wilfred Ndifon Neil Turok Stacey A. Mattison Richard Lessells Ilya Sinayskiy Emmanuel J. San Houriiyah Tegally Shaun Barnett Trevor Lorimer Francesco Petruccione Tulio de Oliveira
author_facet	Lavanya Singh Ugochukwu J. Anyaneji Wilfred Ndifon Neil Turok Stacey A. Mattison Richard Lessells Ilya Sinayskiy Emmanuel J. San Houriiyah Tegally Shaun Barnett Trevor Lorimer Francesco Petruccione Tulio de Oliveira
author_sort	Lavanya Singh
title	Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing
title_short	Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing
title_full	Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing
title_fullStr	Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing
title_full_unstemmed	Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing
title_sort	implementation of an efficient sars-cov-2 specimen pooling strategy for high throughput diagnostic testing
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/00d2faa17b5f49e284e8c2228bbcd2de
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Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing

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