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D'Souza N, Porter AM, Rose JB, Dreelin E, Peters SE, Nowlin PJ, Carbonell S, Cissell K, Wang Y, Flood MT, Rachmadi AT, Xi C, Song P, Briggs S. Public health use and lessons learned from a statewide SARS-CoV-2 wastewater monitoring program (MiNET). Heliyon 2024; 10:e35790. [PMID: 39220928 PMCID: PMC11363850 DOI: 10.1016/j.heliyon.2024.e35790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/27/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
The global SARS-CoV-2 monitoring effort has been extensive, resulting in many states and countries establishing wastewater-based epidemiology programs to address the spread of the virus during the pandemic. Challenges for programs include concurrently optimizing methods, training new laboratories, and implementing successful surveillance programs that can rapidly translate results for public health, and policy making. Surveillance in Michigan early in the pandemic in 2020 highlights the importance of quality-controlled data and explores correlations with wastewater and clinical case data aggregated at the state level. The lessons learned and potential measures to improve public utilization of results are discussed. The Michigan Network for Environmental Health and Technology (MiNET) established a network of laboratories that partnered with local health departments, universities, wastewater treatment plants (WWTPs) and other stakeholders to monitor SARS-CoV-2 in wastewater at 214 sites in Michigan. MiNET consisted of nineteen laboratories, twenty-nine local health departments, 6 Native American tribes, and 60 WWTPs monitoring sites representing 45 % of Michigan's population from April 6 and December 29, 2020. Three result datasets were created based on quality control criteria. Wastewater results that met all quality assurance criteria (Dataset Mp) produced strongest correlations with reported clinical cases at 16 days lag (rho = 0.866, p < 0.05). The project demonstrated the ability to successfully track SARS-CoV-2 on a large, state-wide scale, particularly data that met the outlined quality criteria and provided an early warning of increasing COVID-19 cases. MiNET is currently poised to leverage its competency to complement public health surveillance networks through environmental monitoring for new and emerging pathogens of concern and provides a valuable resource to state and federal agencies to support future responses.
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Affiliation(s)
- Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Alexis M. Porter
- Annis Water Resources Insititute, Grand Valley State University, Muskegon, MI, USA
| | - Joan B. Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Erin Dreelin
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Susan E. Peters
- Michigan Department of Health and Human Services, Lansing, MI, USA
| | | | - Samantha Carbonell
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | | | - Yili Wang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew T. Flood
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | | | - Chuanwu Xi
- University of Michigan, Ann Arbor, Michigan, USA
| | - Peter Song
- University of Michigan, Ann Arbor, Michigan, USA
| | - Shannon Briggs
- Michigan Department of Environment, Great Lakes, and Energy, Lansing, MI, USA
| | - the Michigan Network for Environmental Health and Technology (MiNET) consortium
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
- Annis Water Resources Insititute, Grand Valley State University, Muskegon, MI, USA
- Michigan Department of Health and Human Services, Lansing, MI, USA
- Northern Michigan Regional Laboratory, Gaylord, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Saginaw Valley State University, Michigan, USA
- University of Michigan, Ann Arbor, Michigan, USA
- Institute of Environmental Science and Research (ESR), New Zealand
- Michigan Department of Environment, Great Lakes, and Energy, Lansing, MI, USA
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Williams RC, Perry WB, Lambert-Slosarska K, Futcher B, Pellett C, Richardson-O'Neill I, Paterson S, Grimsley JMS, Wade MJ, Weightman AJ, Farkas K, Jones DL. Examining the stability of viral RNA and DNA in wastewater: Effects of storage time, temperature, and freeze-thaw cycles. WATER RESEARCH 2024; 259:121879. [PMID: 38865915 DOI: 10.1016/j.watres.2024.121879] [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: 12/19/2023] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024]
Abstract
Wastewater-based epidemiology (WBE) has been demonstrably successful as a relatively unbiased tool for monitoring levels of SARS-CoV-2 virus circulating in communities during the COVID-19 pandemic. Accumulated biobanks of wastewater samples allow retrospective exploration of spatial and temporal trends for public health indicators such as chemicals, viruses, antimicrobial resistance genes, and the possible emergence of novel human or zoonotic pathogens. We investigated virus resilience to time, temperature, and freeze-thaw cycles, plus the optimal storage conditions to maintain the stability of genetic material (RNA/DNA) of viral +ssRNA (Envelope - E, Nucleocapsid - N and Spike protein - S genes of SARS-CoV-2), dsRNA (Phi6 phage) and circular dsDNA (crAssphage) in wastewater. Samples consisted of (i) processed and extracted wastewater samples, (ii) processed and extracted distilled water samples, and (iii) raw, unprocessed wastewater samples. Samples were stored at -80 °C, -20 °C, 4 °C, or 20 °C for 10 days, going through up to 10 freeze-thaw cycles (once per day). Sample stability was measured using reverse transcription quantitative PCR, quantitative PCR, automated electrophoresis, and short-read whole genome sequencing. Exploring different areas of the SARS-CoV-2 genome demonstrated that the S gene in processed and extracted samples showed greater sensitivity to freeze-thaw cycles than the E or N genes. Investigating surrogate and normalisation viruses showed that Phi6 remains a stable comparison for SARS-CoV-2 in a laboratory setting and crAssphage was relatively resilient to temperature variation. Recovery of SARS-CoV-2 in raw unprocessed samples was significantly greater when stored at 4 °C, which was supported by the sequencing data for all viruses - both time and freeze-thaw cycles negatively impacted sequencing metrics. Historical extracts stored at -80 °C that were re-quantified 12, 14 and 16 months after original quantification showed no major changes. This study highlights the importance of the fast processing and extraction of wastewater samples, following which viruses are relatively robust to storage at a range of temperatures.
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Affiliation(s)
- Rachel C Williams
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
| | - William B Perry
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | | | - Ben Futcher
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK; Department of Oncology, Medical Sciences Division, University of Oxford, Old Road Campus Research Building, Headington, Oxford, OX3 7DQ, UK
| | - Cameron Pellett
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | | | - Steve Paterson
- Centre for Genomic Research, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jasmine M S Grimsley
- UK Health Security Agency, Data Analytics & Surveillance Group, 10 South Colonnade, Canary Wharf, London, E14 4PU, UK; The London Data Company, London, EC2N 2AT, UK
| | - Matthew J Wade
- UK Health Security Agency, Data Analytics & Surveillance Group, 10 South Colonnade, Canary Wharf, London, E14 4PU, UK
| | - Andrew J Weightman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Kata Farkas
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Davey L Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
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3
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Pasha ABT, Kotlarz N, Holcomb D, Reckling S, Kays J, Bailey E, Guidry V, Christensen A, Berkowitz S, Engel LS, de Los Reyes F, Harris A. Monitoring SARS-CoV-2 RNA in wastewater from a shared septic system and sub-sewershed sites to expand COVID-19 disease surveillance. JOURNAL OF WATER AND HEALTH 2024; 22:978-992. [PMID: 38935450 DOI: 10.2166/wh.2024.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/21/2024] [Indexed: 06/29/2024]
Abstract
Wastewater-based epidemiology has expanded as a tool for collecting COVID-19 surveillance data, but there is limited information on the feasibility of this form of surveillance within decentralized wastewater systems (e.g., septic systems). This study assessed SARS-CoV-2 RNA concentrations in wastewater samples from a septic system servicing a mobile home park (66 households) and from two pumping stations serving a similarly sized (71 households) and a larger (1,000 households) neighborhood within a nearby sewershed over 35 weeks in 2020. Also, raw wastewater from a hospital in the same sewershed was sampled. The mobile home park samples had the highest detection frequency (39/39 days) and mean concentration of SARS-CoV-2 RNA (2.7 × 107 gene copies/person/day for the N1) among the four sampling sites. N1 gene and N2 gene copies were highly correlated across mobile home park samples (Pearson's r = 0.93, p < 0.0001). In the larger neighborhood, new COVID-19 cases were reported every week during the sampling period; however, we detected SARS-CoV-2 RNA in 12% of the corresponding wastewater samples. The results of this study suggest that sampling from decentralized wastewater infrastructure can be used for continuous monitoring of SARS-CoV-2 infections.
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Affiliation(s)
- A B Tanvir Pasha
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA
| | - Nadine Kotlarz
- Center for Human Health and the Environment, NC State, Raleigh, NC, USA
| | - David Holcomb
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Stacie Reckling
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Judith Kays
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA
| | | | - Virginia Guidry
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Ariel Christensen
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Steven Berkowitz
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Lawrence S Engel
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Francis de Los Reyes
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA
| | - Angela Harris
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA E-mail:
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4
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Rauch W, Schenk H, Rauch N, Harders M, Oberacher H, Insam H, Markt R, Kreuzinger N. Estimating actual SARS-CoV-2 infections from secondary data. Sci Rep 2024; 14:6732. [PMID: 38509181 PMCID: PMC10954653 DOI: 10.1038/s41598-024-57238-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
Eminent in pandemic management is accurate information on infection dynamics to plan for timely installation of control measures and vaccination campaigns. Despite huge efforts in diagnostic testing of individuals, the underestimation of the actual number of SARS-CoV-2 infections remains significant due to the large number of undocumented cases. In this paper we demonstrate and compare three methods to estimate the dynamics of true infections based on secondary data i.e., (a) test positivity, (b) infection fatality and (c) wastewater monitoring. The concept is tested with Austrian data on a national basis for the period of April 2020 to December 2022. Further, we use the results of prevalence studies from the same period to generate (upper and lower bounds of) credible intervals for true infections for four data points. Model parameters are subsequently estimated by applying Approximate Bayesian Computation-rejection sampling and Genetic Algorithms. The method is then validated for the case study Vienna. We find that all three methods yield fairly similar results for estimating the true number of infections, which supports the idea that all three datasets contain similar baseline information. None of them is considered superior, as their advantages and shortcomings depend on the specific case study at hand.
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Affiliation(s)
- Wolfgang Rauch
- Unit of Environmental Engineering, Department of Infrastructure, University of Innsbruck, Technikerstrasse 13, 6020, Innsbruck, Austria.
| | - Hannes Schenk
- Unit of Environmental Engineering, Department of Infrastructure, University of Innsbruck, Technikerstrasse 13, 6020, Innsbruck, Austria
| | - Nikolaus Rauch
- Interactive Graphics and Simulation Group, University of Innsbruck, Innsbruck, Austria
| | - Matthias Harders
- Interactive Graphics and Simulation Group, University of Innsbruck, Innsbruck, Austria
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Rudolf Markt
- Department of Health Sciences and Social Work, Carinthia University of Applied Sciences, Villach, Austria
| | - Norbert Kreuzinger
- Institute of Water Quality and Resource Management, Technical University Vienna, Vienna, Austria
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5
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Parkins MD, Lee BE, Acosta N, Bautista M, Hubert CRJ, Hrudey SE, Frankowski K, Pang XL. Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond. Clin Microbiol Rev 2024; 37:e0010322. [PMID: 38095438 PMCID: PMC10938902 DOI: 10.1128/cmr.00103-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024] Open
Abstract
Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.
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Affiliation(s)
- Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O’Brien Institute of Public Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole Acosta
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maria Bautista
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Provincial Health Laboratory, Alberta Health Services, Calgary, Alberta, Canada
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6
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Barrantes K, Chacón-Jiménez L, Rivera-Montero L, Segura-Villalta A, Badilla-Aguilar A, Alfaro-Arrieta E, Rivera-Navarro P, Méndez-Chacón E, Santamaría-Ulloa C. Challenges detecting SARS-CoV-2 in Costa Rican domestic wastewater and river water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165393. [PMID: 37433341 DOI: 10.1016/j.scitotenv.2023.165393] [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: 03/31/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/13/2023]
Abstract
This study presents the development of a SARS-CoV-2 detection method for domestic wastewater and river water in Costa Rica, a middle-income country in Central America. Over a three-year period (November to December 2020, July to November 2021, and June to October 2022), 80 composite wastewater samples (43 influent and 37 effluent) were collected from a Wastewater Treatment Plant (SJ-WWTP) located in San José, Costa Rica. Additionally, 36 river water samples were collected from the Torres River near the SJ-WWTP discharge site. A total of three protocols for SARS-CoV-2 viral concentration and RNA detection and quantification were analyzed. Two protocols using adsorption-elution with PEG precipitation (Protocol A and B, differing in the RNA extraction kit; n = 82) were used on wastewater samples frozen prior to concentration, while wastewater (n = 34) collected in 2022 were immediately concentrated using PEG precipitation. The percent recovery of Bovine coronavirus (BCoV) was highest using the Zymo Environ Water RNA (ZEW) kit with PEG precipitation executed on the same day as collection (mean 6.06 % ± 1.37 %). It was lowest when samples were frozen and thawed, and viruses were concentrated using adsorption-elution and PEG concentration methods using the PureLink™ Viral RNA/DNA Mini (PLV) kit (protocol A; mean 0.48 % ± 0.23 %). Pepper mild mottle virus and Bovine coronavirus were used as process controls to understand the suitability and potential impact of viral recovery on the detection/quantification of SARS-CoV-2 RNA. Overall, SARS-CoV-2 RNA was detected in influent and effluent wastewater samples collected in 2022 but not in earlier years when the method was not optimized. The burden of SARS-CoV-2 at the SJ-WWTP decreased from week 36 to week 43 of 2022, coinciding with a decline in the national COVID-19 prevalence rate. Developing comprehensive nationwide surveillance programs for wastewater-based epidemiology in low-middle-income countries involves significant technical and logistical challenges.
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Affiliation(s)
- Kenia Barrantes
- Health Research Institute, University of Costa Rica, P.O. Box: 11501-2060, San José, Costa Rica.
| | - Luz Chacón-Jiménez
- Health Research Institute, University of Costa Rica, P.O. Box: 11501-2060, San José, Costa Rica.
| | - Luis Rivera-Montero
- Health Research Institute, University of Costa Rica, P.O. Box: 11501-2060, San José, Costa Rica.
| | | | - Andrei Badilla-Aguilar
- National Water Laboratory of the Costa Rican Institute of Aqueducts and Sewerage, P.O.Box 1097-1200, Cartago, Costa Rica.
| | - Ernesto Alfaro-Arrieta
- National Water Laboratory of the Costa Rican Institute of Aqueducts and Sewerage, P.O.Box 1097-1200, Cartago, Costa Rica.
| | - Pablo Rivera-Navarro
- National Water Laboratory of the Costa Rican Institute of Aqueducts and Sewerage, P.O.Box 1097-1200, Cartago, Costa Rica.
| | - Ericka Méndez-Chacón
- School of Statistics, University of Costa Rica, P.O. Box 11501-2060, San José, Costa Rica.
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7
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Thapar I, Langan LM, Davis H, Norman RS, Bojes HK, Brooks BW. Influence of storage conditions and multiple freeze-thaw cycles on N1 SARS-CoV-2, PMMoV, and BCoV signal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165098. [PMID: 37392884 PMCID: PMC10307669 DOI: 10.1016/j.scitotenv.2023.165098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
Wastewater-based epidemiology/wastewater-based surveillance (WBE/WBS) continues to serve as an effective means of monitoring various diseases, including COVID-19 and the emergence of SARS-CoV-2 variants, at the population level. As the use of WBE expands, storage conditions of wastewater samples will play a critical role in ensuring the accuracy and reproducibility of results. In this study, the impacts of water concentration buffer (WCB), storage temperature, and freeze-thaw cycles on the detection of SARS-CoV-2 and other WBE-related gene targets were examined. Freeze-thawing of concentrated samples did not significantly affect (p > 0.05) crossing/cycle threshold (Ct) value for any of the gene targets studied (SARS-CoV-2 N1, PMMoV, and BCoV). However, use of WCB during concentration resulted in a significant (p < 0.05) decrease in Ct for all targets, and storage at -80 °C (in contrast to -20 °C) appeared preferable for wastewater storage signal stability based on decreased Ct values, although this was only significantly different (p < 0.05) for the BCoV target. Interestingly, when Ct values were converted to gene copies per influent sample, no significant differences (p > 0.05) were observed in any of the targets examined. Stability of RNA targets in concentrated wastewater against freeze-thaw degradation supports archiving of concentrated samples for use in retrospective examination of COVID-19 trends and tracing SARS-CoV-2 variants and potentially other viruses, and provides a starting point for establishing a consistent procedure for specimen collection and storage for the WBE/WBS community.
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Affiliation(s)
- Isha Thapar
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA
| | - Laura M Langan
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA.
| | - Haley Davis
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US-1, Fort Pierce, FL 34946, USA
| | - R Sean Norman
- Department of Environmental Health Sciences, Arnold School of Public Health, South Carolina, 921 Assembly St., Columbia, SC 29208, USA
| | - Heidi K Bojes
- Environmental Epidemiology and Disease Registries Section, Texas Department of State Health Services, Austin, TX 78756, USA
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA; Institute of Biomedical Studies, Baylor University, One Bear Place #97224, Waco, TX 76798, USA
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8
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Cutrupi F, Rossi M, Cadonna M, Poznanski E, Manara S, Postinghel M, Palumbi G, Bellisomi M, Nicosia E, Allaria G, Dondero L, Veneri C, Mancini P, Ferraro GB, Rosa G, Suffredini E, Foladori P, Grasselli E. Evaluation of concentration procedures, sample pre-treatment, and storage condition for the detection of SARS-CoV-2 in wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:106660-106670. [PMID: 37733200 PMCID: PMC10579110 DOI: 10.1007/s11356-023-29696-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
Crucial information on the pandemic's spread has been gathered by monitoring the trend of SARS-CoV-2 in wastewater. This surveillance has highlighted that the initial concentration is a critical step of the analytical procedure due to the low viral titer that may be present in this matrix. This paper presents the results of the evaluation of two different wastewater concentration protocols to determine the most efficient and cost-effective. The two methods tested were the following: (a) a biphasic separation system with PEG-dextran and (b) a PEG/NaCl precipitation protocol. Other aspects of the detection method were also investigated including the influence of storage temperature on virus recovery and the heat treatment of pasteurization, which aims to make samples safer for operators and the environment. The PEG/NaCl precipitation method was found to perform better than the biphasic separation system, allowing for more sensitive identification of the presence of the virus and the detection of a higher viral titer than that identified with the biphasic separation in all results. Storage of the samples at 4.3±0.2°C for up to 3 weeks did not adversely affect the virus titer and the pasteurization pre-treatment increases operator safety and maintains the identification of the viral concentration.
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Affiliation(s)
- Francesca Cutrupi
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, via Mesiano 77, 38123, Trento, Italy.
| | - Michele Rossi
- Department of Biosciences, University of Milano, Via Celoria 26, 20134, Milano, Italy
| | - Maria Cadonna
- ADEP, Agenzia per la Depurazione (Wastewater Treatment Agency), Autonomous Province of Trento, via Gilli 3, 38121, Trento, Italy
| | | | - Serena Manara
- Department of Cellular Computational and Integrative Biology-CIBIO, Via Sommarive 9, 38123, Trento, Italy
| | - Mattia Postinghel
- ADEP, Agenzia per la Depurazione (Wastewater Treatment Agency), Autonomous Province of Trento, via Gilli 3, 38121, Trento, Italy
| | - Giulia Palumbi
- ARPAL Virology and enviromental biotecnological laboratory, Genova, Liguria, Italy
| | - Marta Bellisomi
- ARPAL Virology and enviromental biotecnological laboratory, Genova, Liguria, Italy
| | - Elena Nicosia
- ARPAL Virology and enviromental biotecnological laboratory, Genova, Liguria, Italy
- Department of Health and Social Services, Liguria Region Administration, Piazza della Vittoria 119, 16121, Genova, Italy
| | - Giorgia Allaria
- Department of Earth Sciences of the Environment and Life, University of Genova, Corso Europa 26, 16132, Genova, Italy
| | - Lorenzo Dondero
- Department of Earth Sciences of the Environment and Life, University of Genova, Corso Europa 26, 16132, Genova, Italy
| | - Carolina Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Giuseppina Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Foladori
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, via Mesiano 77, 38123, Trento, Italy
| | - Elena Grasselli
- Department of Earth Sciences of the Environment and Life, University of Genova, Corso Europa 26, 16132, Genova, Italy
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9
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Schenk H, Heidinger P, Insam H, Kreuzinger N, Markt R, Nägele F, Oberacher H, Scheffknecht C, Steinlechner M, Vogl G, Wagner AO, Rauch W. Prediction of hospitalisations based on wastewater-based SARS-CoV-2 epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162149. [PMID: 36773921 PMCID: PMC9911153 DOI: 10.1016/j.scitotenv.2023.162149] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 05/03/2023]
Abstract
Wastewater-based epidemiology is widely applied in Austria since April 2020 to monitor the SARS-CoV-2 pandemic. With a steadily increasing number of monitored wastewater facilities, 123 plants covering roughly 70 % of the 9 million population were monitored as of August 2022. In this study, the SARS-CoV-2 viral concentrations in raw sewage were analysed to infer short-term hospitalisation occupancy. The temporal lead of wastewater-based epidemiological time series over hospitalisation occupancy levels facilitates the construction of forecast models. Data pre-processing techniques are presented, including the approach of comparing multiple decentralised wastewater signals with aggregated and centralised clinical data. Time‑lead quantification was performed using cross-correlation analysis and coefficient of determination optimisation approaches. Multivariate regression models were successfully applied to infer hospitalisation bed occupancy. The results show a predictive potential of viral loads in sewage towards Covid-19 hospitalisation occupancy, with an average lead time towards ICU and non-ICU bed occupancy between 14.8-17.7 days and 8.6-11.6 days, respectively. The presented procedure provides access to the trend and tipping point behaviour of pandemic dynamics and allows the prediction of short-term demand for public health services. The results showed an increase in forecast accuracy with an increase in the number of monitored wastewater treatment plants. Trained models are sensitive to changing variant types and require recalibration of model parameters, likely caused by immunity by vaccination and/or infection. The utilised approach displays a practical and rapidly implementable application of wastewater-based epidemiology to infer hospitalisation occupancy.
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Affiliation(s)
- Hannes Schenk
- Unit of Environmental Engineering, University of Innsbruck, Technikerstraße 13, Innsbruck 6020, Austria.
| | - Petra Heidinger
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz 8010, Austria.
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria.
| | - Norbert Kreuzinger
- Institute of Water Quality and Resource Management at TU Wien, Karlsplatz 13, Vienna 1040, Austria.
| | - Rudolf Markt
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria; Department of Health Sciences and Social Work, Carinthia University of Applied Sciences, St. Veiter Straße, 47, Klagenfurt 9020, Austria.
| | - Fabiana Nägele
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria.
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Müllerstraße, 44, Innsbruck 6020, Austria.
| | - Christoph Scheffknecht
- Institut für Umwelt und Lebensmittelsicherheit des Landes Vorarlberg, Montfortstraße 4, Bregenz 6900, Austria.
| | - Martin Steinlechner
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Müllerstraße, 44, Innsbruck 6020, Austria.
| | - Gunther Vogl
- Institut f¨ur Lebensmittelsicherheit, Veterinärmedizin und Umwelt, Kirchengasse 43, Klagenfurt 9020, Austria.
| | - Andreas Otto Wagner
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria.
| | - Wolfgang Rauch
- Unit of Environmental Engineering, University of Innsbruck, Technikerstraße 13, Innsbruck 6020, Austria.
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10
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Hart JJ, Jamison MN, McNair JN, Szlag DC. Frequency and degradation of SARS-CoV-2 markers N1, N2, and E in sewage. JOURNAL OF WATER AND HEALTH 2023; 21:514-524. [PMID: 37119151 DOI: 10.2166/wh.2023.314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease that is mainly spread through aerosolized droplets containing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is excreted in feces by infected individuals. Sewage surveillance has been applied widely to obtain data on the prevalence of COVID-19 in whole communities. We used SARS-CoV-2 gene targets N1, N2, and E to determine the prevalence of COVID-19 at both municipal and building levels. Frequency analysis of wastewater testing indicated that single markers detected only 85% or less of samples that were detected as positive for SARS-CoV-2 with the three markers combined, indicating the necessity of pairing markers to lower the false-negative rate. The best pair of markers in both municipal and building level monitoring was N1 and N2, which correctly identified 98% of positive samples detected with the three markers combined. The degradation rates of all three targets were assessed at two different temperatures (25 and 35 °C) as a possible explanation for observed differences between markers in frequency. Results indicated that all three RNA targets degrade at nearly the same rate, indicating that differences in degradation rate are not responsible for the observed differences in marker frequency.
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Affiliation(s)
- John J Hart
- Oakland University, Department of Chemistry, 146 Library Dr, Rochester, MI 48309, USA E-mail: ; Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI 49441, USA
| | - Megan N Jamison
- Oakland University, Department of Chemistry, 146 Library Dr, Rochester, MI 48309, USA E-mail: ; The Ohio State University, 281 W Lane Ave, Columbus, OH 43210, USA
| | - James N McNair
- Robert B. Annis Water Resources Institute, 740 West Shoreline Dr, Muskegon, MI 49441, USA
| | - David C Szlag
- Oakland University, Department of Chemistry, 146 Library Dr, Rochester, MI 48309, USA E-mail:
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11
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Tavazzi S, Cacciatori C, Comero S, Fatta-Kassinos D, Karaolia P, Iakovides IC, Loutsiou P, Gutierrez-Aguirre I, Lengar Z, Bajde I, Tenson T, Kisand V, Laas P, Panksep K, Tammert H, Mariani G, Skejo H, Gawlik BM. Short-term stability of wastewater samples for storage and shipment in the context of the EU Sewage Sentinel System for SARS-CoV-2. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:109623. [PMID: 36890876 PMCID: PMC9979635 DOI: 10.1016/j.jece.2023.109623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
In the context of an EU-wide surveillance system for SARS-CoV-2 in wastewater, recommended by the European Commission, this study aims to provide scientific support to the adequacy of transport and storage conditions of samples both in terms of duration and samples temperature. Three laboratories in Slovenia, Cyprus and Estonia investigated the short-term, one-week, isochronous stability of wastewater samples by RT-qPCR based detection of SARS-CoV-2 genes. The results were tested for statistical significance to determine uncertainty of quantification and shelf-life, at testing temperatures of + 20 °C and - 20 °C, relative to reference at + 4 °C. Samples were collected from three urban wastewater treatment plant influents and analysed respectively for SARS-CoV-2 genes N1, N2 (Laboratory 1), N2, E (Laboratory 2) and N3 (Laboratory 3), with various analytical methods. For a period of 7/8 days at + 20 °C, decreasing trends of measured concentrations were observed for all genes resulting in instability according to the statistical analysis, while at - 20 °C the trend of variation was stable only for N1, N2 (Laboratory 1) and N3 (Laboratory 3). Trends for gene E concentrations at - 20 °C (Laboratory 2) could not be tested statistically for stability because of lack of data. Over a period of just 3 days at + 20 °C, the variation was statistically non-significant indicating stability for genes N1, E and N3 for laboratories 1, 2 and 3, respectively. Nonetheless, the outcome of the study presents evidence to support the choice of the selected temperature at which samples shall be preserved during storage before analysis or transport to the laboratory. The conditions (+4 °C, ∼ few days) chosen for EU wastewater surveillance are in accordance with these results, highlighting the importance of stability testing of environmental samples to determine the short-term analytical uncertainty.
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Affiliation(s)
- S Tavazzi
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - C Cacciatori
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - S Comero
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - D Fatta-Kassinos
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - P Karaolia
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - I C Iakovides
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - P Loutsiou
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | | | - Z Lengar
- National Institute of Biology, Vecna Pot 111, SI-1000 Ljubljana, Slovenia
| | - I Bajde
- National Institute of Biology, Vecna Pot 111, SI-1000 Ljubljana, Slovenia
| | - T Tenson
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - V Kisand
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - P Laas
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - K Panksep
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - H Tammert
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - G Mariani
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - H Skejo
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - B M Gawlik
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
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12
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Burnet JB, Cauchie HM, Walczak C, Goeders N, Ogorzaly L. Persistence of endogenous RNA biomarkers of SARS-CoV-2 and PMMoV in raw wastewater: Impact of temperature and implications for wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159401. [PMID: 36240930 PMCID: PMC9554201 DOI: 10.1016/j.scitotenv.2022.159401] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/21/2022] [Accepted: 10/08/2022] [Indexed: 05/28/2023]
Abstract
Understanding the persistence of SARS-CoV-2 biomarkers in wastewater should guide wastewater-based epidemiology users in selecting best RNA biomarkers for reliable detection of the virus during current and future waves of the pandemic. In the present study, the persistence of endogenous SARS-CoV-2 were assessed during one month for six different RNA biomarkers and for the pepper mild mottle virus (PMMoV) at three different temperatures (4, 12 and 20 °C) in one wastewater sample. All SARS-CoV-2 RNA biomarkers were consistently detected during 6 days at 4° and differences in signal persistence among RNA biomarkers were mostly observed at 20 °C with N biomarkers being globally more persistent than RdRP, E and ORF1ab ones. SARS-CoV-2 signal persistence further decreased in a temperature dependent manner. At 12 and 20 °C, RNA biomarker losses of 1-log10 occurred on average after 6 and 4 days, and led to a complete signal loss after 13 and 6 days, respectively. Besides the effect of temperature, SARS-CoV-2 RNA signals were more persistent in the particulate phase compared to the aqueous one. Finally, PMMoV RNA signal was highly persistent in both phases and significantly differed from that of SARS-CoV-2 biomarkers. We further provide a detailed overview of the latest literature on SARS-CoV-2 and PMMoV decay rates in sewage matrices.
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Affiliation(s)
- Jean-Baptiste Burnet
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation Department, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Henry-Michel Cauchie
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation Department, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Cécile Walczak
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation Department, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Nathalie Goeders
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation Department, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Leslie Ogorzaly
- Luxembourg Institute of Science and Technology (LIST), Environmental Research & Innovation Department, 41 rue du Brill, L-4422 Belvaux, Luxembourg.
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13
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Maksimovic Carvalho Ferreira O, Lengar Ž, Kogej Z, Bačnik K, Bajde I, Milavec M, Županič A, Mehle N, Kutnjak D, Ravnikar M, Gutierrez-Aguirre I. Evaluation of Methods and Processes for Robust Monitoring of SARS-CoV-2 in Wastewater. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:384-400. [PMID: 35999429 PMCID: PMC9398038 DOI: 10.1007/s12560-022-09533-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/01/2022] [Indexed: 05/15/2023]
Abstract
The SARS-CoV-2 pandemic has accelerated the development of virus concentration and molecular-based virus detection methods, monitoring systems and overall approach to epidemiology. Early into the pandemic, wastewater-based epidemiology started to be employed as a tool for tracking the virus transmission dynamics in a given area. The complexity of wastewater coupled with a lack of standardized methods led us to evaluate each step of the analysis individually and see which approach gave the most robust results for SARS-CoV-2 monitoring in wastewater. In this article, we present a step-by-step, retrospective view on the method development and implementation for the case of a pilot monitoring performed in Slovenia. We specifically address points regarding the thermal stability of the samples during storage, screening for the appropriate sample concentration and RNA extraction procedures and real-time PCR assay selection. Here, we show that the temperature and duration of the storage of the wastewater sample can have a varying impact on the detection depending on the structural form in which the SARS-CoV-2 target is present. We found that concentration and RNA extraction using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using semi-automated kit from Promega give the most optimal results out of the seven methods tested. Lastly, we confirm the use of N1 and N2 assays developed by the CDC (USA) as the best performing assays among four tested in combination with Fast Virus 1-mastermix. Data show a realistic overall process for method implementation as well as provide valuable information in regards to how different approaches in the analysis compare to one another under the specific conditions present in Slovenia during a pilot monitoring running from the beginning of the pandemic.
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Affiliation(s)
- Olivera Maksimovic Carvalho Ferreira
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
- International Postgraduate School Jožef Stefan, Jamova cesta 39, 1000, Ljubljana, Slovenia.
| | - Živa Lengar
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Zala Kogej
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
- International Postgraduate School Jožef Stefan, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Katarina Bačnik
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Irena Bajde
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Mojca Milavec
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Anže Županič
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Dvorec Lanthieri, Glavni trg 8, 5271, Vipava, Slovenia
| | - Denis Kutnjak
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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14
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Freitas ÍN, Dourado AV, da Silva Matos SG, de Souza SS, da Luz TM, Rodrigues ASDL, Guimarães ATB, Mubarak NM, Rahman MM, Arias AH, Malafaia G. Short-term exposure of the mayfly larvae (Cloeon dipterum, Ephemeroptera: Baetidae) to SARS-CoV-2-derived peptides and other emerging pollutants: A new threat for the aquatic environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157813. [PMID: 35931160 PMCID: PMC9345649 DOI: 10.1016/j.scitotenv.2022.157813] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 05/09/2023]
Abstract
The input of SARS-CoV-2 or its fragments into freshwater ecosystems (via domestic or hospital sewage) has raised concerns about its possible impacts on aquatic organisms. Thus, using mayfly larvae [Cloeon dipterum (L.), Ephemeroptera: Baetidae] as a model system, we aimed to evaluate the possible effects of the combined short exposure of SARS-CoV-2-derived peptides (named PSPD-2001, PSPD-2002, and PSPD-2003 - at 266.2 ng/L) with multiple emerging pollutants at ambient concentrations. After six days of exposure, we observed higher mortality of larvae exposed to SARS-CoV-2-derived peptides (alone or in combination with the pollutant mix) and a lower-body condition index than those unexposed larvae. In the "PSPD" and "Mix+PSPD" groups, the activity of superoxide dismutase, catalase, DPPH radical scavenging activity, and the total thiol levels were also lower than in the "control" group. In addition, we evidenced the induction of nitrosative stress (inferred by increased nitrite production) and reduced acetylcholinesterase activity by SARS-CoV-2-derived peptides. On the other hand, malondialdehyde levels in larvae exposed to treatments were significantly lower than in unexposed larvae. The values of the integrated biomarker response index and the principal component analysis (PCA) results confirmed the similarity between the responses of animals exposed to SARS-CoV-2-derived peptides (alone and in combination with the pollutant mix). Although viral peptides did not intensify the effects of the pollutant mix, our study sheds light on the potential ecotoxicological risk associated with the spread of the new coronavirus in aquatic environments. Therefore, we recommend exploring this topic in other organisms and experimental contexts.
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Affiliation(s)
- Ítalo Nascimento Freitas
- Laboratory of Toxicology Applied to the Environment, Goiano Federal Institute, Urutaí, GO, Brazil; Post-Graduation Program in Conservation of Cerrado Natural Resources, Goiano Federal Institute, Urutaí, GO, Brazil
| | - Amanda Vieira Dourado
- Laboratory of Toxicology Applied to the Environment, Goiano Federal Institute, Urutaí, GO, Brazil
| | | | - Sindoval Silva de Souza
- Post-Graduation Program in Biotechnology and Biodiversity, Federal University of Goiás, Goiânia, GO, Brazil
| | - Thiarlen Marinho da Luz
- Laboratory of Toxicology Applied to the Environment, Goiano Federal Institute, Urutaí, GO, Brazil; Post-Graduation Program in Conservation of Cerrado Natural Resources, Goiano Federal Institute, Urutaí, GO, Brazil
| | | | | | - Nabisab Mujawar Mubarak
- Petroleum and Chemical Engineering, Faculty of Engineering, Universiti Teknologi Brunei, Bandar Seri Begawan BE1410, Brunei Darussalam
| | - Md Mostafizur Rahman
- Laboratory of Environmental Health and Ecotoxicology, Department of Environmental Sciences, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Andrés Hugo Arias
- Instituto Argentino de Oceanografía (IADO), Universidad Nacional del Sur (UNS)-CONICET, Florida 8000, Complejo CCT CONICET Bahía Blanca, Bahía Blanca, Argentina
| | - Guilherme Malafaia
- Laboratory of Toxicology Applied to the Environment, Goiano Federal Institute, Urutaí, GO, Brazil; Post-Graduation Program in Conservation of Cerrado Natural Resources, Goiano Federal Institute, Urutaí, GO, Brazil; Petroleum and Chemical Engineering, Faculty of Engineering, Universiti Teknologi Brunei, Bandar Seri Begawan BE1410, Brunei Darussalam; Post-Graduation Program in Ecology, Conservation, and Biodiversity, Federal University of Uberlândia, Uberlândia, MG, Brazil.
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15
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Hayes EK, Sweeney CL, Fuller M, Erjavec GB, Stoddart AK, Gagnon GA. Operational Constraints of Detecting SARS-CoV-2 on Passive Samplers using Electronegative Filters: A Kinetic and Equilibrium Analysis. ACS ES&T WATER 2022; 2:1910-1920. [PMID: 37566371 PMCID: PMC8805996 DOI: 10.1021/acsestwater.1c00441] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 05/05/2023]
Abstract
In developing an effective monitoring program for the wastewater surveillance of SARS-CoV-2 ribonucleic acid (RNA), the importance of sampling methodology is paramount. Passive sampling has been shown to be an effective tool to detect SARS-CoV-2 RNA in wastewater. However, the adsorption characteristics of SARS-CoV-2 RNA on passive sampling material are not well-understood, which further obscures the relationship between wastewater surveillance and community infection. In this work, adsorption kinetics and equilibrium characteristics were evaluated using batch-adsorption experiments for heat-inactivated SARS-CoV-2 (HI-SCV-2) adsorption to electronegative filters. Equilibrium isotherms were assessed or a range of total suspended solids (TSS) concentrations (118, 265, and 497 mg L-1) in wastewater, and a modeled qmax of 7 × 103 GU cm-2 was found. Surrogate adsorption kinetics followed a pseudo-first-order model in wastewater with maximum concentrations achieved within 24 h. In both field and isotherm experiments, equilibrium behavior and viral recovery were found to be associated with wastewater and eluate TSS. On the basis of the results of this study, we recommend a standard deployment duration of 24-48 h and the inclusion of eluate TSS measurement to assess the likelihood of solids inhibition during analysis.
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Affiliation(s)
- Emalie K. Hayes
- Centre for Water Resources Studies, Faculty of
Engineering, Dalhousie University, Halifax, NS B3H 4R2,
Canada
| | - Crystal L. Sweeney
- Centre for Water Resources Studies, Faculty of
Engineering, Dalhousie University, Halifax, NS B3H 4R2,
Canada
| | - Megan Fuller
- Centre for Water Resources Studies, Faculty of
Engineering, Dalhousie University, Halifax, NS B3H 4R2,
Canada
| | - Genevieve B. Erjavec
- Centre for Water Resources Studies, Faculty of
Engineering, Dalhousie University, Halifax, NS B3H 4R2,
Canada
| | - Amina K. Stoddart
- Centre for Water Resources Studies, Faculty of
Engineering, Dalhousie University, Halifax, NS B3H 4R2,
Canada
| | - Graham A. Gagnon
- Centre for Water Resources Studies, Faculty of
Engineering, Dalhousie University, Halifax, NS B3H 4R2,
Canada
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16
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Langan LM, O’Brien M, Lovin LM, Scarlett KR, Davis H, Henke AN, Seidel SE, Archer N, Lawrence E, Norman RS, Bojes HK, Brooks BW. Quantitative Reverse Transcription PCR Surveillance of SARS-CoV-2 Variants of Concern in Wastewater of Two Counties in Texas, United States. ACS ES&T WATER 2022; 2:2211-2224. [PMID: 37552718 PMCID: PMC9291321 DOI: 10.1021/acsestwater.2c00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 06/02/2023]
Abstract
After its emergence in late November/December 2019, the severe acute respiratory syndrome coronavirus 2 virus (SARS-CoV-2) rapidly spread globally. Recognizing that this virus is shed in feces of individuals and that viral RNA is detectable in wastewater, testing for SARS-CoV-2 in sewage collections systems has allowed for the monitoring of a community's viral burden. Over a 9 month period, the influents of two regional wastewater treatment facilities were concurrently examined for wild-type SARS-CoV-2 along with variants B.1.1.7 and B.1.617.2 incorporated as they emerged. Epidemiological data including new confirmed COVID-19 cases and associated hospitalizations and fatalities were tabulated within each location. RNA from SARS-CoV-2 was detectable in 100% of the wastewater samples, while variant detection was more variable. Quantitative reverse transcription PCR (RT-qPCR) results align with clinical trends for COVID-19 cases, and increases in COVID-19 cases were positively related with increases in SARS-CoV-2 RNA load in wastewater, although the strength of this relationship was location specific. Our observations demonstrate that clinical and wastewater surveillance of SARS-CoV-2 wild type and constantly emerging variants of concern can be combined using RT-qPCR to characterize population infection dynamics. This may provide an early warning for at-risk communities and increases in COVID-19 related hospitalizations.
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Affiliation(s)
- Laura M. Langan
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Megan O’Brien
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Public Health, Baylor
University, One Bear Place #97343, Waco, Texas 76798, United
States
| | - Lea M. Lovin
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Kendall R. Scarlett
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Haley Davis
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Abigail N. Henke
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Biology, Baylor
University, One Bear Place #97388, Waco, Texas 76798, United
States
| | - Sarah E. Seidel
- Center for Health
Statistics, Texas Department of State Health Services, Austin, Texas
78756, United States
| | - Natalie Archer
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - Eric Lawrence
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - R. Sean Norman
- Department of Environmental Health Sciences, Arnold School of
Public Health, University of South Carolina, 921 Assembly
Street Columbia, South Carolina 29208, United States
| | - Heidi K. Bojes
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - Bryan W. Brooks
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Public Health, Baylor
University, One Bear Place #97343, Waco, Texas 76798, United
States
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17
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Beattie RE, Blackwood AD, Clerkin T, Dinga C, Noble RT. Evaluating the impact of sample storage, handling, and technical ability on the decay and recovery of SARS-CoV-2 in wastewater. PLoS One 2022; 17:e0270659. [PMID: 35749532 PMCID: PMC9232146 DOI: 10.1371/journal.pone.0270659] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022] Open
Abstract
Wastewater based epidemiology (WBE) is useful for tracking and monitoring the level of disease prevalence in a community and has been used extensively to complement clinical testing during the current COVID-19 pandemic. Despite the numerous benefits, sources of variability in sample storage, handling, and processing methods can make WBE data difficult to generalize. We performed an experiment to determine sources of variability in WBE data including the impact of storage time, handling, and processing techniques on the concentration of SARS-CoV-2 in wastewater influent from three wastewater treatment plants (WWTP) in North Carolina over 19 days. The SARS-CoV-2 concentration in influent samples held at 4°C did not degrade significantly over the 19-day experiment. Heat pasteurization did not significantly impact the concentration of SARS-CoV-2 at two of the three WWTP but did reduce viral recovery at the WWTP with the smallest population size served. On each processing date, one filter from each sample was processed immediately while a replicate filter was frozen at -80°C. Once processed, filters previously frozen were found to contain slightly higher concentrations (<0.2 log copies/L) than their immediately processed counterparts, indicating freezing filters is a viable method for delayed quantification and may even improve recovery at WWTP with low viral concentrations. Investigation of factors contributing to variability during sample processing indicated that analyst experience level contributed significantly (p<0.001) to accepted droplet generation while extraction efficiency and reverse transcription efficiency contributed significantly (p<0.05) to day-to-day SARS-CoV-2 variability. This study provides valuable practical information for minimizing decay and/or loss of SARS CoV-2 in wastewater influent while adhering to safety procedures, promoting efficient laboratory workflows, and accounting for sources of variability.
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Affiliation(s)
- Rachelle E. Beattie
- Department of Earth, Marine, and Environmental Sciences, Institute of Marine Science, University of North Carolina at Chapel Hill, Morehead City, North Carolina, United States of America
| | - A. Denene Blackwood
- Department of Earth, Marine, and Environmental Sciences, Institute of Marine Science, University of North Carolina at Chapel Hill, Morehead City, North Carolina, United States of America
| | - Thomas Clerkin
- Department of Earth, Marine, and Environmental Sciences, Institute of Marine Science, University of North Carolina at Chapel Hill, Morehead City, North Carolina, United States of America
| | - Carly Dinga
- Department of Earth, Marine, and Environmental Sciences, Institute of Marine Science, University of North Carolina at Chapel Hill, Morehead City, North Carolina, United States of America
| | - Rachel T. Noble
- Department of Earth, Marine, and Environmental Sciences, Institute of Marine Science, University of North Carolina at Chapel Hill, Morehead City, North Carolina, United States of America
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18
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Yanaç K, Adegoke A, Wang L, Uyaguari M, Yuan Q. Detection of SARS-CoV-2 RNA throughout wastewater treatment plants and a modeling approach to understand COVID-19 infection dynamics in Winnipeg, Canada. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153906. [PMID: 35218826 PMCID: PMC8864809 DOI: 10.1016/j.scitotenv.2022.153906] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 05/07/2023]
Abstract
Although numerous studies have detected SARS-CoV-2 RNA in wastewater and attempted to find correlations between the concentration of SARS-CoV-2 RNA and the number of cases, no consensus has been reached on sample collection and processing, and data analysis. Moreover, the fate of SARS-CoV-2 in wastewater treatment plants is another issue, specifically regarding the discharge of the virus into environmental settings and the water cycle. The current study monitored SARS-CoV-2 RNA in influent and effluent wastewater samples with three different concentration methods and sludge samples over six months (July to December 2020) to compare different virus concentration methods, assess the fate of SARS-CoV-2 RNA in wastewater treatment plants, and describe the potential relationship between SARS-CoV-2 RNA concentrations in influent and infection dynamics. Skimmed milk flocculation (SMF) resulted in 15.27 ± 3.32% recovery of an internal positive control, Armored RNA, and a high positivity rate of SARS-CoV-2 RNA in stored wastewater samples compared to ultrafiltration methods employing a prefiltration step to eliminate solids in fresh wastewater samples. Our results suggested that SARS-CoV-2 RNA may predominate in solids, and therefore, concentration methods focusing on both supernatant and solid fractions may result in better recovery. SARS-CoV-2 RNA was detected in influent and primary sludge samples but not in secondary and final effluent samples, indicating a significant reduction during primary and secondary treatments. SARS-CoV-2 RNA was first detected in influent on September 30th, 2020. A decay-rate formula was applied to estimate initial concentrations of late-processed samples with SMF. A model based on shedding rate and new cases was applied to estimate SARS-CoV-2 RNA concentrations and the number of active shedders. Inferred sensitivity of observed and modeled concentrations to the fluctuations in new cases and test-positivity rates indicated a potential contribution of newly infected individuals to SARS-CoV-2 RNA loads in wastewater.
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Affiliation(s)
- Kadir Yanaç
- Department of Civil Engineering, University of Manitoba, Winnipeg, Canada
| | - Adeola Adegoke
- Department of Statistics, University of Manitoba, Winnipeg, Canada
| | - Liqun Wang
- Department of Statistics, University of Manitoba, Winnipeg, Canada
| | - Miguel Uyaguari
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Qiuyan Yuan
- Department of Civil Engineering, University of Manitoba, Winnipeg, Canada.
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