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PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance

Since the start of the COVID-19 pandemic in 2020, wastewater surveillance programs were established, or upscaled, in many countries around the world and have proven to be a cost-effective way of monitoring infectious disease pathogens. Many of these programs use RT-qPCR, and quantify the viral conce...

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Autores principales: Nagelkerke, Erwin, Hetebrij, Wouter A., Koelewijn, Jaap M., Kooij, Jannetje, van der Drift, Anne-Merel R., van der Beek, Rudolf F. H. J., de Jonge, Eline F., Lodder, Willemijn J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10652756/
https://www.ncbi.nlm.nih.gov/pubmed/38026384
http://dx.doi.org/10.3389/fpubh.2023.1141494
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author Nagelkerke, Erwin
Hetebrij, Wouter A.
Koelewijn, Jaap M.
Kooij, Jannetje
van der Drift, Anne-Merel R.
van der Beek, Rudolf F. H. J.
de Jonge, Eline F.
Lodder, Willemijn J.
author_facet Nagelkerke, Erwin
Hetebrij, Wouter A.
Koelewijn, Jaap M.
Kooij, Jannetje
van der Drift, Anne-Merel R.
van der Beek, Rudolf F. H. J.
de Jonge, Eline F.
Lodder, Willemijn J.
author_sort Nagelkerke, Erwin
collection PubMed
description Since the start of the COVID-19 pandemic in 2020, wastewater surveillance programs were established, or upscaled, in many countries around the world and have proven to be a cost-effective way of monitoring infectious disease pathogens. Many of these programs use RT-qPCR, and quantify the viral concentrations in samples based on standard curves, by including preparations of a reference material with known nucleic acid or virus concentrations in the RT-qPCR analyses. In high-throughput monitoring programs it is possible to combine data from multiple previous runs, circumventing the need for duplication and resulting in decreased costs and prolonged periods during which the reference material is obtained from the same batch. However, over time, systematic shifts in standard curves are likely to occur. This would affect the reliability and usefulness of wastewater surveillance as a whole. We aim to find an optimal combination of standard curve data to compensate for run-to-run measurement variance while ensuring enough flexibility to capture systematic longitudinal shifts. Based on more than 4000 observations obtained with the CDC N1 and N2 assays, taken as a part of the National Sewage Surveillance program at the Dutch National Institute for Public Health and the Environment, we show that seasonal and long-term shifts in RT-qPCR efficiency and sensitivity occur. We find that in our setting, using five days of standard-curve data to quantify, results in the least error prone curve or best approximation. This results in differences up to 100% in quantified viral loads when averaged out over a nationwide program of >300 treatment plants. Results show that combining standard curves from a limited set of runs can be a valid approach to quantification without obscuring the trends in the viral load of interest.
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spelling pubmed-106527562023-11-02 PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance Nagelkerke, Erwin Hetebrij, Wouter A. Koelewijn, Jaap M. Kooij, Jannetje van der Drift, Anne-Merel R. van der Beek, Rudolf F. H. J. de Jonge, Eline F. Lodder, Willemijn J. Front Public Health Public Health Since the start of the COVID-19 pandemic in 2020, wastewater surveillance programs were established, or upscaled, in many countries around the world and have proven to be a cost-effective way of monitoring infectious disease pathogens. Many of these programs use RT-qPCR, and quantify the viral concentrations in samples based on standard curves, by including preparations of a reference material with known nucleic acid or virus concentrations in the RT-qPCR analyses. In high-throughput monitoring programs it is possible to combine data from multiple previous runs, circumventing the need for duplication and resulting in decreased costs and prolonged periods during which the reference material is obtained from the same batch. However, over time, systematic shifts in standard curves are likely to occur. This would affect the reliability and usefulness of wastewater surveillance as a whole. We aim to find an optimal combination of standard curve data to compensate for run-to-run measurement variance while ensuring enough flexibility to capture systematic longitudinal shifts. Based on more than 4000 observations obtained with the CDC N1 and N2 assays, taken as a part of the National Sewage Surveillance program at the Dutch National Institute for Public Health and the Environment, we show that seasonal and long-term shifts in RT-qPCR efficiency and sensitivity occur. We find that in our setting, using five days of standard-curve data to quantify, results in the least error prone curve or best approximation. This results in differences up to 100% in quantified viral loads when averaged out over a nationwide program of >300 treatment plants. Results show that combining standard curves from a limited set of runs can be a valid approach to quantification without obscuring the trends in the viral load of interest. Frontiers Media S.A. 2023-11-02 /pmc/articles/PMC10652756/ /pubmed/38026384 http://dx.doi.org/10.3389/fpubh.2023.1141494 Text en Copyright © 2023 Nagelkerke, Hetebrij, Koelewijn, Kooij, van der Drift, van der Beek, de Jonge and Lodder. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Public Health
Nagelkerke, Erwin
Hetebrij, Wouter A.
Koelewijn, Jaap M.
Kooij, Jannetje
van der Drift, Anne-Merel R.
van der Beek, Rudolf F. H. J.
de Jonge, Eline F.
Lodder, Willemijn J.
PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance
title PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance
title_full PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance
title_fullStr PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance
title_full_unstemmed PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance
title_short PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance
title_sort pcr standard curve quantification in an extensive wastewater surveillance program: results from the dutch sars-cov-2 wastewater surveillance
topic Public Health
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10652756/
https://www.ncbi.nlm.nih.gov/pubmed/38026384
http://dx.doi.org/10.3389/fpubh.2023.1141494
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