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Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater

Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for...

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Autores principales: Heijnen, Leo, Elsinga, Goffe, de Graaf, Miranda, Molenkamp, Richard, Koopmans, Marion P.G., Medema, Gertjan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Authors. Published by Elsevier B.V. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8332926/
https://www.ncbi.nlm.nih.gov/pubmed/34371414
http://dx.doi.org/10.1016/j.scitotenv.2021.149456
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author Heijnen, Leo
Elsinga, Goffe
de Graaf, Miranda
Molenkamp, Richard
Koopmans, Marion P.G.
Medema, Gertjan
author_facet Heijnen, Leo
Elsinga, Goffe
de Graaf, Miranda
Molenkamp, Richard
Koopmans, Marion P.G.
Medema, Gertjan
author_sort Heijnen, Leo
collection PubMed
description Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.
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spelling pubmed-83329262021-08-04 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater Heijnen, Leo Elsinga, Goffe de Graaf, Miranda Molenkamp, Richard Koopmans, Marion P.G. Medema, Gertjan Sci Total Environ Article Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination. The Authors. Published by Elsevier B.V. 2021-12-10 2021-08-04 /pmc/articles/PMC8332926/ /pubmed/34371414 http://dx.doi.org/10.1016/j.scitotenv.2021.149456 Text en © 2021 The Authors Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Heijnen, Leo
Elsinga, Goffe
de Graaf, Miranda
Molenkamp, Richard
Koopmans, Marion P.G.
Medema, Gertjan
Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater
title Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater
title_full Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater
title_fullStr Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater
title_full_unstemmed Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater
title_short Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater
title_sort droplet digital rt-pcr to detect sars-cov-2 signature mutations of variants of concern in wastewater
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8332926/
https://www.ncbi.nlm.nih.gov/pubmed/34371414
http://dx.doi.org/10.1016/j.scitotenv.2021.149456
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