Highly efficient and sensitive membrane-based concentration process allows quantification, surveillance, and sequencing of viruses in large volumes of wastewater Article Swipe
Ghina El Soufi
,
Léo Di Jorio
,
Zuzana Gerber
,
Nicolas Cluzel
,
J Van Assche
,
Damien Delafoy
,
Robert Olaso
,
Christian Daviaud
,
Thomas Loustau
,
Christian Schwartz
,
Dominique Trébouet
,
Olivier Hernalsteens
,
Vincent Maréchal
,
Stéphanie Raffestin
,
Dominique Rousset
,
Carine Van Lint
,
J.-F. Deleuze
,
Mickaël Boni
,
Olivier Rohr
,
M. Villain-Gambier
,
Clémentine Wallet
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1016/j.watres.2023.120959
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1016/j.watres.2023.120959
Wastewater-based epidemiology is experiencing exponential development. Despite undeniable advantages compared to patient-centered approaches (cost, anonymity, survey of large populations without bias, detection of asymptomatic infected peoples…), major technical limitations persist. Among them is the low sensitivity of the current methods used for quantifying and sequencing viral genomes from wastewater. In situations of low viral circulation, during initial stages of viral emergences, or in areas experiencing heavy rains, the extremely low concentrations of viruses in wastewater may fall below the limit of detection of the current methods. The availability during crisis and the cost of the commercial kits, as well as the requirement of expensive materials such as high-speed centrifuge, can also present major blocks to the development of wastewater-based epidemiological survey, specifically in low-income countries. Thereby, highly sensitive, low cost and standardized methods are still needed, to increase the predictability of the viral emergences, to survey low-circulating viruses and to make the results from different labs comparable. Here, we outline and characterize new protocols for concentrating and quantifying SARS-CoV-2 from large volumes (500 mL-1 L) of untreated wastewater. In addition, we report that the methods are applicable for monitoring and sequencing. Our nucleic acid extraction technique (the routine C: 5 mL method) does not require sophisticated equipment such as automatons and is not reliant on commercial kits, making it readily available to a broader range of laboratories for routine epidemiological survey. Furthermore, we demonstrate the efficiency, the repeatability, and the high sensitivity of a new membrane-based concentration method (MBC: 500 mL method) for enveloped (SARS-CoV-2) and non-enveloped (F-specific RNA phages of genogroup II / FRNAPH GGII) viruses. We show that the MBC method allows the quantification and the monitoring of viruses in wastewater with a significantly improved sensitivity compared to the routine C method. In contexts of low viral circulation, we report quantifications of SARS-CoV-2 in wastewater at concentrations as low as 40 genome copies per liter. In highly diluted samples collected in wastewater treatment plants of French Guiana, we confirmed the accuracy of the MBC method compared to the estimations done with the routine C method. Finally, we demonstrate that both the routine C method processing 5 mL and the MBC method processing 500 mL of untreated wastewater are both compatible with SARS-CoV-2 sequencing. We show that the quality of the sequence is correlated with the concentration of the extracted viral genome. Of note, the quality of the sequences obtained with some MBC processed wastewater was improved by dilutions or enzyme substitutions suggesting the presence of specific enzyme inhibitors in some wastewater. To the best of our knowledge, our MBC method is one of the first efficient, sensitive, and repeatable method characterized for SARS-CoV-2 quantification and sequencing from large volumes of wastewater.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1016/j.watres.2023.120959
- https://ars.els-cdn.com/content/image/1-s2.0-S0043135423013994-ga1_lrg.jpg
- OA Status
- hybrid
- Cited By
- 6
- References
- 34
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4389286691
All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4389286691Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1016/j.watres.2023.120959Digital Object Identifier
- Title
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Highly efficient and sensitive membrane-based concentration process allows quantification, surveillance, and sequencing of viruses in large volumes of wastewaterWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-12-03Full publication date if available
- Authors
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Ghina El Soufi, Léo Di Jorio, Zuzana Gerber, Nicolas Cluzel, J Van Assche, Damien Delafoy, Robert Olaso, Christian Daviaud, Thomas Loustau, Christian Schwartz, Dominique Trébouet, Olivier Hernalsteens, Vincent Maréchal, Stéphanie Raffestin, Dominique Rousset, Carine Van Lint, J.-F. Deleuze, Mickaël Boni, Olivier Rohr, M. Villain-Gambier, Clémentine WalletList of authors in order
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https://doi.org/10.1016/j.watres.2023.120959Publisher landing page
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https://ars.els-cdn.com/content/image/1-s2.0-S0043135423013994-ga1_lrg.jpgDirect link to full text PDF
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://ars.els-cdn.com/content/image/1-s2.0-S0043135423013994-ga1_lrg.jpgDirect OA link when available
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Wastewater, Environmental science, Biochemical engineering, Computer science, Engineering, Environmental engineeringTop concepts (fields/topics) attached by OpenAlex
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6Total citation count in OpenAlex
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2025: 2, 2024: 4Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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