Facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. During the 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 requiring fewer resources and suitable to be extended to larger proportions 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 take advantage of natural clustering structure 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 it convenient the definition of larger pools and potentially overcomes the issue of low viral load samples by increasing the probability of identifying more than one positive in the same pool.

Pool testing on random and natural clusters of individuals: optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples / Michela Baccini, Alessandra Mattei, Irene Paganini, Emilia Rocco, Cristina Sani, Giulia Vannucci, Simonetta Bisanzi, Elena Burroni, Marco Peluso, Armelle Munnia, Filippo Cellai, Giampaolo Pompeo, Laura Micio, Jessica Viti, Fabrizia Mealli, Francesca Carozzi. - ELETTRONICO. - (2020).

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

Michela Baccini;Alessandra Mattei;Emilia Rocco;Giulia Vannucci;Fabrizia Mealli;Francesca Carozzi
2020

Abstract

Facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. During the 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 requiring fewer resources and suitable to be extended to larger proportions 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 take advantage of natural clustering structure 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 it convenient the definition of larger pools and potentially overcomes the issue of low viral load samples by increasing the probability of identifying more than one positive in the same pool.
File in questo prodotto:
File Dimensione Formato  
SARSCOV2_pooling_11102020_EP1.pdf

Accesso chiuso

Descrizione: Articolo principale
Tipologia: Pdf editoriale (Version of record)
Licenza: Tutti i diritti riservati
Dimensione 366.61 kB
Formato Adobe PDF
366.61 kB Adobe PDF   Richiedi una copia

I documenti in FLORE sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/1214684
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus ND
  • ???jsp.display-item.citation.isi??? ND
social impact