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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MDPI AG
2022-03-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/3/610 |
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| author | Tim Boogaerts Siel Van den Bogaert Laura A. E. Van Poelvoorde Diala El Masri Naomi De Roeck Nancy H. C. Roosens Marie Lesenfants Lies Lahousse Koenraad Van Hoorde Alexander L. N. van Nuijs Peter Delputte |
| author_facet | Tim Boogaerts Siel Van den Bogaert Laura A. E. Van Poelvoorde Diala El Masri Naomi De Roeck Nancy H. C. Roosens Marie Lesenfants Lies Lahousse Koenraad Van Hoorde Alexander L. N. van Nuijs Peter Delputte |
| author_sort | Tim Boogaerts |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T12:16:22Z |
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| id | doaj.art-f4844b50236a4da48b6a8bc91478dd66 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T12:16:22Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-f4844b50236a4da48b6a8bc91478dd662023-11-30T22:47:03ZengMDPI AGViruses1999-49152022-03-0114361010.3390/v14030610Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent WastewaterTim Boogaerts0Siel Van den Bogaert1Laura A. E. Van Poelvoorde2Diala El Masri3Naomi De Roeck4Nancy H. C. Roosens5Marie Lesenfants6Lies Lahousse7Koenraad Van Hoorde8Alexander L. N. van Nuijs9Peter Delputte10Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, BelgiumLaboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, BelgiumScientific Directorate of Biological Health Risks, Service Transerversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, BelgiumLaboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, BelgiumLaboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, BelgiumScientific Directorate of Biological Health Risks, Service Transerversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, BelgiumScientific Directorate of Epidemiology and Public Health, Service Epidemiology of Infectious Diseases, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, BelgiumDepartment of Bioanalysis, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, BelgiumScientific Directorate of Infectious Diseases in Humans, Service Foodborne Pathogens, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, BelgiumToxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, BelgiumLaboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, BelgiumSince 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.https://www.mdpi.com/1999-4915/14/3/610wastewater-based epidemiologyvariants of concerndigital polymerase chain reactionBelgiumSARS-CoV-2 |
| spellingShingle | Tim Boogaerts Siel Van den Bogaert Laura A. E. Van Poelvoorde Diala El Masri Naomi De Roeck Nancy H. C. Roosens Marie Lesenfants Lies Lahousse Koenraad Van Hoorde Alexander L. N. van Nuijs Peter Delputte Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater Viruses wastewater-based epidemiology variants of concern digital polymerase chain reaction Belgium SARS-CoV-2 |
| 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 | wastewater-based epidemiology variants of concern digital polymerase chain reaction Belgium SARS-CoV-2 |
| url | https://www.mdpi.com/1999-4915/14/3/610 |
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