Nested pool testing strategy for the diagnosis of infectious diseases

Abstract 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 tests are sensitive enough. In this regard, the use of the gold standard, RT-qPCR, raises some concerns. Recently, droplet digital PCR (ddP...

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Autores principales:	Inés Armendáriz, Pablo A. Ferrari, Daniel Fraiman, José M. Martínez, Hugo G. Menzella, Silvina Ponce Dawson
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/378315dab86a4c6c9bbf18677a663c71
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spelling	oai:doaj.org-article:378315dab86a4c6c9bbf18677a663c712021-12-02T17:25:33ZNested pool testing strategy for the diagnosis of infectious diseases10.1038/s41598-021-97534-72045-2322https://doaj.org/article/378315dab86a4c6c9bbf18677a663c712021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97534-7https://doaj.org/toc/2045-2322Abstract 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 tests are sensitive enough. In this regard, the use of the gold standard, RT-qPCR, raises some concerns. 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 we show, can be used to identify nonviable samples in pools. Cost-effective strategies require the definition of efficient deconvolution and re-testing procedures. In this paper we analyze the practical implementation of an efficient hierarchical pooling strategy for which we have recently derived the optimal, determining the best ways to proceed when there are impediments for the use of the absolute optimum or when multiple pools are tested simultaneously and there are restrictions on the throughput time. 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 nonviable samples. The studies are useful to those considering pool testing for the identification of infected individuals.Inés ArmendárizPablo A. FerrariDaniel FraimanJosé M. MartínezHugo G. MenzellaSilvina Ponce DawsonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Inés Armendáriz Pablo A. Ferrari Daniel Fraiman José M. Martínez Hugo G. Menzella Silvina Ponce Dawson Nested pool testing strategy for the diagnosis of infectious diseases
description	Abstract 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 tests are sensitive enough. In this regard, the use of the gold standard, RT-qPCR, raises some concerns. 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 we show, can be used to identify nonviable samples in pools. Cost-effective strategies require the definition of efficient deconvolution and re-testing procedures. In this paper we analyze the practical implementation of an efficient hierarchical pooling strategy for which we have recently derived the optimal, determining the best ways to proceed when there are impediments for the use of the absolute optimum or when multiple pools are tested simultaneously and there are restrictions on the throughput time. 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 nonviable samples. The studies are useful to those considering pool testing for the identification of infected individuals.
format	article
author	Inés Armendáriz Pablo A. Ferrari Daniel Fraiman José M. Martínez Hugo G. Menzella Silvina Ponce Dawson
author_facet	Inés Armendáriz Pablo A. Ferrari Daniel Fraiman José M. Martínez Hugo G. Menzella Silvina Ponce Dawson
author_sort	Inés Armendáriz
title	Nested pool testing strategy for the diagnosis of infectious diseases
title_short	Nested pool testing strategy for the diagnosis of infectious diseases
title_full	Nested pool testing strategy for the diagnosis of infectious diseases
title_fullStr	Nested pool testing strategy for the diagnosis of infectious diseases
title_full_unstemmed	Nested pool testing strategy for the diagnosis of infectious diseases
title_sort	nested pool testing strategy for the diagnosis of infectious diseases
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/378315dab86a4c6c9bbf18677a663c71
work_keys_str_mv	AT inesarmendariz nestedpooltestingstrategyforthediagnosisofinfectiousdiseases AT pabloaferrari nestedpooltestingstrategyforthediagnosisofinfectiousdiseases AT danielfraiman nestedpooltestingstrategyforthediagnosisofinfectiousdiseases AT josemmartinez nestedpooltestingstrategyforthediagnosisofinfectiousdiseases AT hugogmenzella nestedpooltestingstrategyforthediagnosisofinfectiousdiseases AT silvinaponcedawson nestedpooltestingstrategyforthediagnosisofinfectiousdiseases
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Nested pool testing strategy for the diagnosis of infectious diseases

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