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Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples

Facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. During the first emergency phase of the epidemic, RT-qPCR on nasopharyngeal (NP) swabs, which is the most reliable technique to detect ongoing infections, exhibited limitation...

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Autores principales: Baccini, Michela, Rocco, Emilia, Paganini, Irene, Mattei, Alessandra, Sani, Cristina, Vannucci, Giulia, Bisanzi, Simonetta, Burroni, Elena, Peluso, Marco, Munnia, Armelle, Cellai, Filippo, Pompeo, Giampaolo, Micio, Laura, Viti, Jessica, Mealli, Fabrizia, Carozzi, Francesca Maria
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8130965/
https://www.ncbi.nlm.nih.gov/pubmed/34003878
http://dx.doi.org/10.1371/journal.pone.0251589
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author Baccini, Michela
Rocco, Emilia
Paganini, Irene
Mattei, Alessandra
Sani, Cristina
Vannucci, Giulia
Bisanzi, Simonetta
Burroni, Elena
Peluso, Marco
Munnia, Armelle
Cellai, Filippo
Pompeo, Giampaolo
Micio, Laura
Viti, Jessica
Mealli, Fabrizia
Carozzi, Francesca Maria
author_facet Baccini, Michela
Rocco, Emilia
Paganini, Irene
Mattei, Alessandra
Sani, Cristina
Vannucci, Giulia
Bisanzi, Simonetta
Burroni, Elena
Peluso, Marco
Munnia, Armelle
Cellai, Filippo
Pompeo, Giampaolo
Micio, Laura
Viti, Jessica
Mealli, Fabrizia
Carozzi, Francesca Maria
author_sort Baccini, Michela
collection PubMed
description Facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. During the first emergency phase of the epidemic, RT-qPCR on nasopharyngeal (NP) swabs, which is the most reliable technique to detect ongoing infections, exhibited limitations due to availability of reagents and budget constraints. This stressed the need to develop screening procedures that require fewer resources and are suitable to be extended to larger portions of the population. RT-qPCR on pooled samples from individual NP swabs seems to be a promising technique to improve surveillance. We performed preliminary experimental analyses aimed to investigate the performance of pool testing on samples with low viral load and we evaluated through Monte Carlo (MC) simulations alternative screening protocols based on sample pooling, tailored to contexts characterized by different infection prevalence. We focused on the role of pool size and the opportunity to develop strategies that take advantage of natural clustering structures in the population, e.g. families, school classes, hospital rooms. Despite the use of a limited number of specimens, our results suggest that, while high viral load samples seem to be detectable even in a pool with 29 negative samples, positive specimens with low viral load may be masked by the negative samples, unless smaller pools are used. The results of MC simulations confirm that pool testing is useful in contexts where the infection prevalence is low. The gain of pool testing in saving resources can be very high, and can be optimized by selecting appropriate group sizes. Exploiting natural groups makes the definition of larger pools convenient and potentially overcomes the issue of low viral load samples by increasing the probability of identifying more than one positive in the same pool.
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spelling pubmed-81309652021-05-27 Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples Baccini, Michela Rocco, Emilia Paganini, Irene Mattei, Alessandra Sani, Cristina Vannucci, Giulia Bisanzi, Simonetta Burroni, Elena Peluso, Marco Munnia, Armelle Cellai, Filippo Pompeo, Giampaolo Micio, Laura Viti, Jessica Mealli, Fabrizia Carozzi, Francesca Maria PLoS One Research Article Facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. During the first emergency phase of the epidemic, RT-qPCR on nasopharyngeal (NP) swabs, which is the most reliable technique to detect ongoing infections, exhibited limitations due to availability of reagents and budget constraints. This stressed the need to develop screening procedures that require fewer resources and are suitable to be extended to larger portions of the population. RT-qPCR on pooled samples from individual NP swabs seems to be a promising technique to improve surveillance. We performed preliminary experimental analyses aimed to investigate the performance of pool testing on samples with low viral load and we evaluated through Monte Carlo (MC) simulations alternative screening protocols based on sample pooling, tailored to contexts characterized by different infection prevalence. We focused on the role of pool size and the opportunity to develop strategies that take advantage of natural clustering structures in the population, e.g. families, school classes, hospital rooms. Despite the use of a limited number of specimens, our results suggest that, while high viral load samples seem to be detectable even in a pool with 29 negative samples, positive specimens with low viral load may be masked by the negative samples, unless smaller pools are used. The results of MC simulations confirm that pool testing is useful in contexts where the infection prevalence is low. The gain of pool testing in saving resources can be very high, and can be optimized by selecting appropriate group sizes. Exploiting natural groups makes the definition of larger pools convenient and potentially overcomes the issue of low viral load samples by increasing the probability of identifying more than one positive in the same pool. Public Library of Science 2021-05-18 /pmc/articles/PMC8130965/ /pubmed/34003878 http://dx.doi.org/10.1371/journal.pone.0251589 Text en © 2021 Baccini et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Baccini, Michela
Rocco, Emilia
Paganini, Irene
Mattei, Alessandra
Sani, Cristina
Vannucci, Giulia
Bisanzi, Simonetta
Burroni, Elena
Peluso, Marco
Munnia, Armelle
Cellai, Filippo
Pompeo, Giampaolo
Micio, Laura
Viti, Jessica
Mealli, Fabrizia
Carozzi, Francesca Maria
Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples
title Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples
title_full Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples
title_fullStr Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples
title_full_unstemmed Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples
title_short Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples
title_sort pool testing on random and natural clusters of individuals: optimisation of sars-cov-2 surveillance in the presence of low viral load samples
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8130965/
https://www.ncbi.nlm.nih.gov/pubmed/34003878
http://dx.doi.org/10.1371/journal.pone.0251589
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