Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR

Detection of SARS-CoV-2 has created an enormous workload for laboratories worldwide resulting in a restriction at the time of massive testing. Pool testing is a strategy that reduces time and costs. However, beyond the detection of infectious diseases in blood banks, this approach is rarely implemen...

Descripción completa

Guardado en:
Detalles Bibliográficos
Autores principales: Heckel, Sofía, Pacini, Antonella, Paredes, Franco, Petreli, María Victoria, Perez, Marilina, Adriani, Natalia, Ibarra, Guadalupe, Menzella, Hugo G., Colaneri, Alejandro, Sesma, Juliana
Formato: article artículo publishedVersion
Lenguaje:Inglés
Publicado: Public Library of Science 2023
Materias:
COVID-19
Pandemics
Real-time polymerase chain reaction
SARS-CoV-2
COVID-19 testing
Sensitivity and specificity
Specimen handling
Acceso en línea:http://hdl.handle.net/2133/25149
http://hdl.handle.net/2133/25149
Aporte de:
Repositorio Hipermedial de la Universidad Nacional de Rosario (UNR) de Universidad Nacional de Rosario
id I15-R121-2133-25149
record_format dspace
institution Universidad Nacional de Rosario
institution_str I-15
repository_str R-121
collection Repositorio Hipermedial de la Universidad Nacional de Rosario (UNR)
language Inglés
topic COVID-19
Pandemics
Real-time polymerase chain reaction
SARS-CoV-2
COVID-19 testing
Sensitivity and specificity
Specimen handling
spellingShingle COVID-19
Pandemics
Real-time polymerase chain reaction
SARS-CoV-2
COVID-19 testing
Sensitivity and specificity
Specimen handling
Heckel, Sofía
Pacini, Antonella
Paredes, Franco
Petreli, María Victoria
Perez, Marilina
Adriani, Natalia
Ibarra, Guadalupe
Menzella, Hugo G.
Colaneri, Alejandro
Sesma, Juliana
Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR
topic_facet COVID-19
Pandemics
Real-time polymerase chain reaction
SARS-CoV-2
COVID-19 testing
Sensitivity and specificity
Specimen handling
description Detection of SARS-CoV-2 has created an enormous workload for laboratories worldwide resulting in a restriction at the time of massive testing. Pool testing is a strategy that reduces time and costs. However, beyond the detection of infectious diseases in blood banks, this approach is rarely implemented in routine laboratories. Therefore, what was learned from the SARS-CoV-2 pool testing should represent an opportunity to increase diagnostic capabilities. The present work, carried out in the context of a diagnostic laboratory of a public hospital during the COVID-19 pandemic, represents a contribution to this end. The main limitation of pool testing is the risk of false negatives that could have been identified by individual tests. These limitations are the dilution of samples with a low virus load during pooling and that the integrity of the sample may be affected by the quality of the sample collection. Fortunately, both limitations coincide with the main strengths of droplet digital PCR (ddPCR). ddPCR is a third-generation PCR that splits the amplification into thousands of droplets that work in parallel, increasing sensitivity and resistance to inhibitors. Therefore, ddPCR is particularly useful for pool testing. Here we show how to factor between test sensitivity and savings in test time and resources. We have identified and optimized critical parameters for pool testing. The present study, which analyzed 1000 nasopharyngeal samples, showed that the pool testing could detect even a single positive sample with a CT value of up to 30 in pools of 34 samples. This test was performed using three different standard extraction methods, the simplest being heating only, which resulted in substantial savings of extraction reagents in addition to PCR reagents. Moreover, we show that pooling can be extended to use saliva, which is less invasive and allows self-collection, reducing the risk for health personnel.
format article
artículo
publishedVersion
author Heckel, Sofía
Pacini, Antonella
Paredes, Franco
Petreli, María Victoria
Perez, Marilina
Adriani, Natalia
Ibarra, Guadalupe
Menzella, Hugo G.
Colaneri, Alejandro
Sesma, Juliana
author_facet Heckel, Sofía
Pacini, Antonella
Paredes, Franco
Petreli, María Victoria
Perez, Marilina
Adriani, Natalia
Ibarra, Guadalupe
Menzella, Hugo G.
Colaneri, Alejandro
Sesma, Juliana
author_sort Heckel, Sofía
title Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR
title_short Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR
title_full Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR
title_fullStr Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR
title_full_unstemmed Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR
title_sort practical considerations to establish a validated platform for pooled detection of sars-cov-2 by droplet digital pcr
publisher Public Library of Science
publishDate 2023
url http://hdl.handle.net/2133/25149
http://hdl.handle.net/2133/25149
work_keys_str_mv AT heckelsofia practicalconsiderationstoestablishavalidatedplatformforpooleddetectionofsarscov2bydropletdigitalpcr
AT paciniantonella practicalconsiderationstoestablishavalidatedplatformforpooleddetectionofsarscov2bydropletdigitalpcr
AT paredesfranco practicalconsiderationstoestablishavalidatedplatformforpooleddetectionofsarscov2bydropletdigitalpcr
AT petrelimariavictoria practicalconsiderationstoestablishavalidatedplatformforpooleddetectionofsarscov2bydropletdigitalpcr
AT perezmarilina practicalconsiderationstoestablishavalidatedplatformforpooleddetectionofsarscov2bydropletdigitalpcr
AT adrianinatalia practicalconsiderationstoestablishavalidatedplatformforpooleddetectionofsarscov2bydropletdigitalpcr
AT ibarraguadalupe practicalconsiderationstoestablishavalidatedplatformforpooleddetectionofsarscov2bydropletdigitalpcr
AT menzellahugog practicalconsiderationstoestablishavalidatedplatformforpooleddetectionofsarscov2bydropletdigitalpcr
AT colanerialejandro practicalconsiderationstoestablishavalidatedplatformforpooleddetectionofsarscov2bydropletdigitalpcr
AT sesmajuliana practicalconsiderationstoestablishavalidatedplatformforpooleddetectionofsarscov2bydropletdigitalpcr
bdutipo_str Repositorios
_version_ 1764820412780249088

Ejemplares similares