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Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater

Since the beginning of the COVID-19 pandemic, the wastewater-based epidemiology (WBE) of SARS-CoV-2 has been used as a complementary indicator to follow up on the trends in the COVID-19 spread in Belgium and in many other countries. To further develop the use of WBE, a multiplex digital polymerase c...

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Autores principales: Boogaerts, Tim, Van den Bogaert, Siel, Van Poelvoorde, Laura A. E., El Masri, Diala, De Roeck, Naomi, Roosens, Nancy H. C., Lesenfants, Marie, Lahousse, Lies, Van Hoorde, Koenraad, van Nuijs, Alexander L. N., Delputte, Peter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8953730/
https://www.ncbi.nlm.nih.gov/pubmed/35337017
http://dx.doi.org/10.3390/v14030610
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author Boogaerts, Tim
Van den Bogaert, Siel
Van Poelvoorde, Laura A. E.
El Masri, Diala
De Roeck, Naomi
Roosens, Nancy H. C.
Lesenfants, Marie
Lahousse, Lies
Van Hoorde, Koenraad
van Nuijs, Alexander L. N.
Delputte, Peter
author_facet Boogaerts, Tim
Van den Bogaert, Siel
Van Poelvoorde, Laura A. E.
El Masri, Diala
De Roeck, Naomi
Roosens, Nancy H. C.
Lesenfants, Marie
Lahousse, Lies
Van Hoorde, Koenraad
van Nuijs, Alexander L. N.
Delputte, Peter
author_sort Boogaerts, Tim
collection PubMed
description Since the beginning of the COVID-19 pandemic, the wastewater-based epidemiology (WBE) of SARS-CoV-2 has been used as a complementary indicator to follow up on the trends in the COVID-19 spread in Belgium and in many other countries. To further develop the use of WBE, a multiplex digital polymerase chain reaction (dPCR) assay was optimized, validated and applied for the measurement of emerging SARS-CoV-2 variants of concern (VOC) in influent wastewater (IWW) samples. Key mutations were targeted in the different VOC strains, including SΔ69/70 deletion, N501Y, SΔ241 and SΔ157. The presented bioanalytical method was able to distinguish between SARS-CoV-2 RNA originating from the wild-type and B.1.1.7, B.1.351 and B.1.617.2 variants. The dPCR assay proved to be sensitive enough to detect low concentrations of SARS-CoV-2 RNA in IWW since the limit of detection of the different targets ranged between 0.3 and 2.9 copies/µL. This developed WBE approach was applied to IWW samples originating from different Belgian locations and was able to monitor spatio-temporal changes in the presence of targeted VOC strains in the investigated communities. The present dPCR assay developments were realized to bring added-value to the current national WBE of COVID-19 by also having the spatio-temporal proportions of the VoC in presence in the wastewaters.
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spelling pubmed-89537302022-03-26 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater Boogaerts, Tim Van den Bogaert, Siel Van Poelvoorde, Laura A. E. El Masri, Diala De Roeck, Naomi Roosens, Nancy H. C. Lesenfants, Marie Lahousse, Lies Van Hoorde, Koenraad van Nuijs, Alexander L. N. Delputte, Peter Viruses Article Since the beginning of the COVID-19 pandemic, the wastewater-based epidemiology (WBE) of SARS-CoV-2 has been used as a complementary indicator to follow up on the trends in the COVID-19 spread in Belgium and in many other countries. To further develop the use of WBE, a multiplex digital polymerase chain reaction (dPCR) assay was optimized, validated and applied for the measurement of emerging SARS-CoV-2 variants of concern (VOC) in influent wastewater (IWW) samples. Key mutations were targeted in the different VOC strains, including SΔ69/70 deletion, N501Y, SΔ241 and SΔ157. The presented bioanalytical method was able to distinguish between SARS-CoV-2 RNA originating from the wild-type and B.1.1.7, B.1.351 and B.1.617.2 variants. The dPCR assay proved to be sensitive enough to detect low concentrations of SARS-CoV-2 RNA in IWW since the limit of detection of the different targets ranged between 0.3 and 2.9 copies/µL. This developed WBE approach was applied to IWW samples originating from different Belgian locations and was able to monitor spatio-temporal changes in the presence of targeted VOC strains in the investigated communities. The present dPCR assay developments were realized to bring added-value to the current national WBE of COVID-19 by also having the spatio-temporal proportions of the VoC in presence in the wastewaters. MDPI 2022-03-15 /pmc/articles/PMC8953730/ /pubmed/35337017 http://dx.doi.org/10.3390/v14030610 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Boogaerts, Tim
Van den Bogaert, Siel
Van Poelvoorde, Laura A. E.
El Masri, Diala
De Roeck, Naomi
Roosens, Nancy H. C.
Lesenfants, Marie
Lahousse, Lies
Van Hoorde, Koenraad
van Nuijs, Alexander L. N.
Delputte, Peter
Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater
title Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater
title_full Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater
title_fullStr Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater
title_full_unstemmed Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater
title_short Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater
title_sort optimization and application of a multiplex digital pcr assay for the detection of sars-cov-2 variants of concern in belgian influent wastewater
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8953730/
https://www.ncbi.nlm.nih.gov/pubmed/35337017
http://dx.doi.org/10.3390/v14030610
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