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Dostálková A, Zdeňková K, Bartáčková J, Čermáková E, Kapisheva M, Lopez Marin MA, Kouba V, Sýkora P, Chmel M, Bartoš O, Dresler J, Demnerová K, Rumlová M, Bartáček J. Prevalence of SARS-CoV-2 variants in Prague wastewater determined by nanopore-based sequencing. CHEMOSPHERE 2024; 351:141162. [PMID: 38218235 DOI: 10.1016/j.chemosphere.2024.141162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
The early detection of upcoming disease outbreaks is essential to avoid both health and economic damage. The last four years of COVID-19 pandemic have proven wastewater-based epidemiology is a reliable system for monitoring the spread of SARS-CoV-2, a causative agent of COVID-19, in an urban population. As this monitoring enables the identification of the prevalence of spreading variants of SARS-CoV-2, it could provide a critical tool in the fight against this viral disease. In this study, we evaluated the presence of variants and subvariants of SARS-CoV-2 in Prague wastewater using nanopore-based sequencing. During August 2021, the data clearly showed that the number of identified SARS-CoV-2 RNA copies increased in the wastewater earlier than in clinical samples indicating the upcoming wave of the Delta variant. New SARS-CoV-2 variants consistently prevailed in wastewater samples around a month after they already prevailed in clinical samples. We also analyzed wastewater samples from smaller sub-sewersheds of Prague and detected significant differences in SARS-CoV-2 lineage progression dynamics among individual localities studied, e.g., suggesting faster prevalence of new variants among the sites with highest population density and mobility.
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Affiliation(s)
- Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology Prague, Czech Republic; National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Kamila Zdeňková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic.
| | - Jana Bartáčková
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
| | - Eliška Čermáková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Marina Kapisheva
- National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Marco A Lopez Marin
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Vojtěch Kouba
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
| | - Petr Sýkora
- PVK a.s., Prague Water Supply and Sewerage Company, Czech Republic
| | - Martin Chmel
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic; Military Health Institute, Military Medical Agency, Czech Republic
| | - Oldřich Bartoš
- Military Health Institute, Military Medical Agency, Czech Republic
| | - Jiří Dresler
- Military Health Institute, Military Medical Agency, Czech Republic
| | - Kateřina Demnerová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology Prague, Czech Republic; National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Jan Bartáček
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
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Guérin-Rechdaoui S, Bize A, Levesque-Ninio C, Janvier A, Lacroix C, Le Brizoual F, Barbier J, Amsaleg CR, Azimi S, Rocher V. Fate of SARS-CoV-2 coronavirus in wastewater treatment sludge during storage and thermophilic anaerobic digestion. ENVIRONMENTAL RESEARCH 2022; 214:114057. [PMID: 35995225 PMCID: PMC9391084 DOI: 10.1016/j.envres.2022.114057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/31/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Since the COVID-19 outbreak has started in late 2019, SARS-CoV-2 has been widely detected in human stools and in urban wastewater. No infectious SARS-CoV-2 particles have been detected in raw wastewater until now, but it has been reported occasionally in human stools. This has raised questions on the fate of SARS-CoV-2 during wastewater treatment and notably in its end-product, wastewater treatment sludge, which is classically valorized by land spreading for agricultural amendment. In the present work, we focused on SARS-CoV-2 stability in wastewater treatment sludge, either during storage (4 °C, room temperature) or thermophilic anaerobic digestion (50 °C). Anaerobic digestion is one of the possible processes for sludge valorization. Experiments were conducted in laboratory pilots; SARS-CoV-2 detection was based on RT-quantitative PCR or RT-digital droplet PCR. In addition to SARS-CoV-2, Bovine Coronavirus (BCoV) particles were used as surrogate virus. The RNA from SARS-CoV-2 particles, inactivated or not, was close to the detection limit but stable in wastewater treatment sludge, over the whole duration of the assays at 4 °C (55 days) and at ambient temperature (∼20 °C, 25 days). By contrast, the RNA levels of BCoV and inactivated SARS-CoV-2 particles decreased rapidly during the thermophilic anaerobic digestion of wastewater treatment sludge lasting for 5 days, with final levels that were close to the detection limit. Although the particles' infectivity was not assessed, these results suggest that thermophilic anaerobic digestion is a suitable process for sludge sanitation, consistent with previous knowledge on other coronaviruses.
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Affiliation(s)
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PROSE, Antony, 92160, France
| | - Camille Levesque-Ninio
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Alice Janvier
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Carlyne Lacroix
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
| | - Florence Le Brizoual
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Jérôme Barbier
- ID Solutions, Development Department, Grabels, 34790, France
| | | | - Sam Azimi
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
| | - Vincent Rocher
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
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Reynolds LJ, Gonzalez G, Sala-Comorera L, Martin NA, Byrne A, Fennema S, Holohan N, Kuntamukkula SR, Sarwar N, Nolan TM, Stephens JH, Whitty M, Bennett C, Luu Q, Morley U, Yandle Z, Dean J, Joyce E, O'Sullivan JJ, Cuddihy JM, McIntyre AM, Robinson EP, Dahly D, Fletcher NF, Carr M, De Gascun C, Meijer WG. SARS-CoV-2 variant trends in Ireland: Wastewater-based epidemiology and clinical surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155828. [PMID: 35588817 PMCID: PMC9110007 DOI: 10.1016/j.scitotenv.2022.155828] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 05/21/2023]
Abstract
SARS-CoV-2 RNA quantification in wastewater is an important tool for monitoring the prevalence of COVID-19 disease on a community scale which complements case-based surveillance systems. As novel variants of concern (VOCs) emerge there is also a need to identify the primary circulating variants in a community, accomplished to date by sequencing clinical samples. Quantifying variants in wastewater offers a cost-effective means to augment these sequencing efforts. In this study, SARS-CoV-2 N1 RNA concentrations and daily loadings were determined and compared to case-based data collected as part of a national surveillance programme to determine the validity of wastewater surveillance to monitor infection spread in the greater Dublin area. Further, sequencing of clinical samples was conducted to determine the primary SARS-CoV-2 lineages circulating in Dublin. Finally, digital PCR was employed to determine whether SARS-CoV-2 VOCs, Alpha and Delta, were quantifiable from wastewater. No lead or lag time was observed between SARS-CoV-2 wastewater and case-based data and SARS-CoV-2 trends in Dublin wastewater significantly correlated with the notification of confirmed cases through case-based surveillance preceding collection with a 5-day average. This demonstrates that viral RNA in Dublin's wastewater mirrors the spread of infection in the community. Clinical sequence data demonstrated that increased COVID-19 cases during Ireland's third wave coincided with the introduction of the Alpha variant, while the fourth wave coincided with increased prevalence of the Delta variant. Interestingly, the Alpha variant was detected in Dublin wastewater prior to the first genome being sequenced from clinical samples, while the Delta variant was identified at the same time in clinical and wastewater samples. This work demonstrates the validity of wastewater surveillance for monitoring SARS-CoV-2 infections and also highlights its effectiveness in identifying circulating variants which may prove useful when sequencing capacity is limited.
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Affiliation(s)
- Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Gabriel Gonzalez
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10 Kita-ku, Sapporo 001-0020, Japan
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Alannah Byrne
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Sanne Fennema
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Niamh Holohan
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Sailusha Ratnam Kuntamukkula
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Natasha Sarwar
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Tristan M Nolan
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Jayne H Stephens
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Megan Whitty
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Charlene Bennett
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Quynh Luu
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Ursula Morley
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Zoe Yandle
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Jonathan Dean
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Eadaoin Joyce
- Irish Water, Colvill House, 24-26 Talbot Street, Dublin 1, Ireland
| | - John J O'Sullivan
- UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin, Dublin 4, Ireland
| | - John M Cuddihy
- HSE - Health Protection Surveillance Centre, Dublin, Ireland
| | | | - Eve P Robinson
- HSE - Health Protection Surveillance Centre, Dublin, Ireland
| | - Darren Dahly
- Health Research Board Clinical Research Facility, University College Cork, Cork, Ireland
| | - Nicola F Fletcher
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Michael Carr
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland; International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10 Kita-ku, Sapporo 001-0020, Japan
| | - Cillian De Gascun
- National Virus Reference Laboratory (NVRL), School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
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