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Singh S, Aw TG, Rose JB. Evaluation of an Automated Ultrafiltration System for Concentrating a Range of Viruses from Saline Waters. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09602-6. [PMID: 38951381 DOI: 10.1007/s12560-024-09602-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/30/2024] [Indexed: 07/03/2024]
Abstract
Pathogenic viruses in environmental water are usually present in levels too low for direct detection and thus, a concentration step is often required to increase the analytical sensitivity. The objective of this study was to evaluate an automated filtration device, the Innovaprep Concentrating Pipette Select (CP Select) for the rapid concentration of viruses in saline water samples, while considering duration of process and ease of use. Four bacteriophages (MS2, P22, Phi6, and PhiX174) and three animal viruses (adenovirus, coronavirus OC43, and canine distemper virus) were seeded in artificial seawater, aquarium water, and bay water samples, and processed using the CP Select. The recovery efficiencies of viruses were determined either using a plaque assay or droplet digital PCR (ddPCR). Using plaque assays, the average recovery efficiencies for bacteriophages ranged from 4.84 ± 3.8% to 82.73 ± 27.3%, with highest recovery for P22 phage. The average recovery efficiencies for the CP Select were 39.31 ± 26.6% for adenovirus, 19.04 ± 11.6% for coronavirus OC43, and 19.84 ± 13.6% for canine distemper virus, as determined by ddPCR. Overall, viral genome composition, not the size of the virus, affected the recovery efficiencies for the CP Select. The small sample volume size used for the ultrafilter pipette of the system hinders the use of this method as a primary concentration step for viruses in marine waters. However, the ease of use and rapid processing time of the CP Select are especially beneficial when rapid detection of viruses in highly contaminated water, such as wastewater or sewage-polluted surface water, is needed.
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Affiliation(s)
- Simran Singh
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA, 70112, USA.
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
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2
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Paracchini V, Petrillo M, Arcot Rajashekar A, Robuch P, Vincent U, Corbisier P, Tavazzi S, Raffael B, Suffredini E, La Rosa G, Gawlik BM, Marchini A. EU surveys insights: analytical tools, future directions, and the essential requirement for reference materials in wastewater monitoring of SARS-CoV-2, antimicrobial resistance and beyond. Hum Genomics 2024; 18:72. [PMID: 38937848 PMCID: PMC11210120 DOI: 10.1186/s40246-024-00641-5] [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: 03/13/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Wastewater surveillance (WWS) acts as a vigilant sentinel system for communities, analysing sewage to protect public health by detecting outbreaks and monitoring trends in pathogens and contaminants. To achieve a thorough comprehension of present and upcoming practices and to identify challenges and opportunities for standardisation and improvement in WWS methodologies, two EU surveys were conducted targeting over 750 WWS laboratories across Europe and other regions. The first survey explored a diverse range of activities currently undertaken or planned by laboratories. The second survey specifically targeted methods and quality controls utilised for SARS-CoV-2 surveillance. RESULTS The findings of the two surveys provide a comprehensive insight into the procedures and methodologies applied in WWS. In Europe, WWS primarily focuses on SARS-CoV-2 with 99% of the survey participants dedicated to this virus. However, the responses highlighted a lack of standardisation in the methodologies employed for monitoring SARS-CoV-2. The surveillance of other pathogens, including antimicrobial resistance, is currently fragmented and conducted by only a limited number of laboratories. Notably, these activities are anticipated to expand in the future. Survey replies emphasise the collective recognition of the need to enhance the accuracy of results in WWS practices, reflecting a shared commitment to advancing precision and effectiveness in WWS methodologies. CONCLUSIONS These surveys identified a lack of standardised common procedures in WWS practices and the need for quality standards and reference materials to enhance the accuracy and reliability of WWS methods in the future. In addition, it is important to broaden surveillance efforts beyond SARS-CoV-2 to include other emerging pathogens and antimicrobial resistance to ensure a comprehensive approach to protecting public health.
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Affiliation(s)
| | | | | | - Piotr Robuch
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | - Ursula Vincent
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | | | - Simona Tavazzi
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Barbara Raffael
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Giuseppina La Rosa
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità (ISS), Rome, Italy
| | | | - Antonio Marchini
- European Commission, Joint Research Centre (JRC), Geel, Belgium.
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3
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Robbins AA, Gallagher TL, Toledo DM, Hershberger KC, Salmela SM, Barney RE, Szczepiorkowski ZM, Tsongalis GJ, Martin IW, Hubbard JA, Lefferts JA. Analytical validation of a semi-automated methodology for quantitative measurement of SARS-CoV-2 RNA in wastewater collected in northern New England. Microbiol Spectr 2024; 12:e0112223. [PMID: 38747589 DOI: 10.1128/spectrum.01122-23] [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: 04/21/2023] [Accepted: 04/11/2024] [Indexed: 06/06/2024] Open
Abstract
Wastewater-based epidemiology (WBE) can be used to monitor the community presence of infectious disease pathogens of public health concern such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Viral nucleic acid has been detected in the stool of SARS-CoV-2-infected individuals. Asymptomatic SARS-CoV-2 infections make community monitoring difficult without extensive and continuous population screening. In this study, we validated a procedure that includes manual pre-processing, automated SARS-CoV-2 RNA extraction and detection workflows using both reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) and reverse transcriptase droplet digital PCR (RT-ddPCR). Genomic RNA and calibration materials were used to create known concentrations of viral material to determine the linearity, accuracy, and precision of the wastewater extraction and SARS-CoV-2 RNA detection. Both RT-qPCR and RT-ddPCR perform similarly in all the validation experiments, with a limit of detection of 50 copies/mL. A wastewater sample from a care facility with a known outbreak was assessed for viral content in replicate, and we showed consistent results across both assays. Finally, in a 2-week survey of two New Hampshire cities, we assessed the suitability of our methods for daily surveillance. This paper describes the technical validation of a molecular assay that can be used for long-term monitoring of SARS-CoV-2 in wastewater as a potential tool for community surveillance to assist with public health efforts.IMPORTANCEThis paper describes the technical validation of a molecular assay that can be used for the long-term monitoring of SARS-CoV-2 in wastewater as a potential tool for community surveillance to assist with public health efforts.
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Affiliation(s)
- Ashlee A Robbins
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Torrey L Gallagher
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Diana M Toledo
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- The Broad Institute at MIT and Harvard, Cambridge, Massachusetts, USA
| | - K Chase Hershberger
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Sabrina M Salmela
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Rachael E Barney
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Zbigniew M Szczepiorkowski
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Gregory J Tsongalis
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Isabella W Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Jacqueline A Hubbard
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Joel A Lefferts
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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Kantor RS, Jiang M. Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8161-8168. [PMID: 38691513 PMCID: PMC11097388 DOI: 10.1021/acs.est.4c02638] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Until recently, wastewater-based monitoring for pathogens of public health concern primarily used PCR-based quantification methods and targeted sequencing for specific pathogens (e.g., SARS-CoV-2). In the past three years, researchers have expanded sequencing to monitor a broad range of pathogens, applying probe capture enrichment to wastewater. The goals of those studies included (1) monitoring and expanding fundamental knowledge of disease dynamics for known pathogens and (2) evaluating the potential for early detection of emerging diseases resulting from zoonotic spillover or novel viral variants. Several studies using off-the-shelf probe panels designed for clinical and environmental surveillance reported that enrichment increased virus relative abundance but did not recover complete genomes for most nonenteric viruses. Based on our experience and recent results reported by others using these panels for wastewater, clinical, and synthetic samples, we discuss challenges and technical factors that affect the rates of false positive and false negative results. We identify trade-offs and opportunities throughout the workflow, including in wastewater sample processing, probe panel design, and bioinformatic analysis. We suggest tailored methods of virus concentration and background removal, carefully designed probe panels, and multithresholded bioinformatics analysis.
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Affiliation(s)
- Rose S. Kantor
- Department of Civil and Environmental
Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Minxi Jiang
- Department of Civil and Environmental
Engineering, University of California, Berkeley, Berkeley, California 94720, United States
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Mullins N, Alashraf AR, McDermott K, Brown RS, Payne SJ. Polyethylenimine mediated recovery of SARS-CoV-2 and total viral RNA: Impact of aqueous conditions on behaviour and recovery. WATER RESEARCH 2024; 253:121207. [PMID: 38401469 DOI: 10.1016/j.watres.2024.121207] [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: 07/03/2023] [Revised: 10/28/2023] [Accepted: 01/26/2024] [Indexed: 02/26/2024]
Abstract
Wastewater-based epidemiology (WBE) is an emerging, practical surveillance tool for monitoring community levels of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, SC2). However, a paucity of data exists regarding SARS-CoV-2 and viral biomarker behaviour in aqueous and wastewater environments. Therefore, there is a pressing need to develop efficient and robust methods that both improve method sensitivity and reduce time and cost. We present a novel method for SARS-CoV-2, Human Coronavirus 229E (229E), and Pepper Mild Mottle Virus (PMMoV) recovery utilizing surface charge-based attraction via the branched cationic polymer, polyethylenimine (PEI). Initially, dose-optimization experiments demonstrated that low concentrations of PEI (0.001% w/v) proved most effective at flocculating suspended viruses and viral material, including additional unbound SC2 viral fragments and/or RNA from raw wastewater. A design-of-experiments (DOE) approach was used to optimize virus and/or viral material aggregation behaviour and recovery across varying aqueous conditions, revealing pH as a major influence on recoverability in this system, combinatorially due to both a reduction in viral material surface charge and increased protonation of PEI-bound amine groups. Overall, this method has shown great promise in significantly improving quantitative viral recovery, providing a straightforward and effective augmentation to standard centrifugation techniques.
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Affiliation(s)
- Nathan Mullins
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; McMaster University, Department of Chemical Engineering, Hamilton, Ontario, L8S 4L7, Canada
| | - Abdul Rahman Alashraf
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada
| | | | - R Stephen Brown
- Queen's University, Department of Chemistry and School of Environmental Studies, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada.
| | - Sarah Jane Payne
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada.
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Li J, Liang X, Ma J, Cheng J, Wang H, Wang X, Wu JJ, An H. Photothermal-Based Multiplex Nested Digital PCR System for Rapid Detection of Foodborne Pathogens. MICROMACHINES 2024; 15:435. [PMID: 38675248 PMCID: PMC11052467 DOI: 10.3390/mi15040435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024]
Abstract
The rapid and sensitive detection of foodborne pathogens is crucial for ensuring food safety. Among virus testing methods, polymerase chain reaction (PCR) has served as the gold-standard technique in most food safety regulation organizations. However, to enhance the speed and efficiency of PCR, novel approaches are continually being explored. In this work, leveraging the photothermal effects and high thermal conductivity of gold nanoparticles, we have significantly improved the heating and cooling rates of thermal cycles, enabling ultra-fast PCR detection. Specifically, we present a pre-degassing multiplex digital PCR chip integrated with gold nanoparticles. We further developed a portable system with a light source for photothermal heating cycling, along with an optoelectronic sensor to analyze PCR amplification products after rapid thermal cycling. As proof of concept, the proposed chip and portable device was applied for the on-site detection of several types of foodborne pathogens, including Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, and Salmonella. The whole system could distinguish those pathogens within 20 min, showing good potential for the rapid detection of multiple types of foodborne pathogens.
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Affiliation(s)
- Junwei Li
- Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China; (J.L.); (H.W.)
| | - Xinyi Liang
- School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Jinsong Ma
- School of Mechanical Engineering, Hebei University of Technology, Tianjin 300401, China (J.C.)
| | - Jianye Cheng
- School of Mechanical Engineering, Hebei University of Technology, Tianjin 300401, China (J.C.)
| | - Hui Wang
- Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China; (J.L.); (H.W.)
- School of Science, Hebei University of Technology, Tianjin 300401, China
| | - Xuzhao Wang
- Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China; (J.L.); (H.W.)
| | - Jie Jayne Wu
- Department of Electrical Engineering and Computer Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Hailong An
- Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China; (J.L.); (H.W.)
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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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Malla B, Shrestha S, Haramoto E. Optimization of the 5-plex digital PCR workflow for simultaneous monitoring of SARS-CoV-2 and other pathogenic viruses in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169746. [PMID: 38159741 DOI: 10.1016/j.scitotenv.2023.169746] [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: 11/17/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Wastewater-based epidemiology is a valuable tool for monitoring pathogenic viruses in the environment, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). While quantitative polymerase chain reaction (qPCR) is widely used for pathogen surveillance in wastewater, it can be affected by inhibition and is limited to relative quantification. Digital PCR (dPCR) offers potential solutions to these limitations. In this study, a 5-plex dPCR workflow was optimized for the simultaneous detection of SARS-CoV-2, influenza A virus, enteroviruses (EnV), and noroviruses of genogroups I (NoV-GI) and GII (NoV-GII) in wastewater samples. Wastewater samples (n = 36) were collected from a wastewater treatment plant in Japan between August and October 2022. The optimization included the evaluation of singleplex and 5-plex dPCR assays, and two different concentration methods, extraction kits, and dPCR approaches. The performance of singleplex and 5-plex dPCR assays showed comparable linearity and reliability, with the 5-plex assays showing greater efficiency. The polyethylene glycol (PEG) precipitation method showed better performance over the centrifugation method, two-step reverse transcription (RT)-dPCR over the one-step RT-dPCR, and AllPrep PowerViral DNA/RNA Kit showed better performance than the QIAamp Viral RNA Mini Kit. The optimal workflow therefore included PEG precipitation, the AllPrep PowerViral DNA/RNA Kit, and two-step RT-dPCR. This workflow was selected to monitor the presence of SARS-CoV-2 and other pathogenic viruses in wastewater samples in a 5-plex dPCR approach, yielding promising results. SARS-CoV-2 RNA was detected in the majority of samples, with NoV-GI, NoV-GII, and EnV also being detected. The successful optimization and application of the 5-plex dPCR assay for pathogen surveillance in wastewater offers significant benefits, including enhanced community health assessment and more effective responses to public health threats.
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Affiliation(s)
- Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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Akter J, Smith WJ, Liu Y, Kim I, Simpson SL, Thai P, Korajkic A, Ahmed W. Comparison of adsorption-extraction (AE) workflows for improved measurements of viral and bacterial nucleic acid in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:167966. [PMID: 38476760 PMCID: PMC10927021 DOI: 10.1016/j.scitotenv.2023.167966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The lack of standardized methods and large differences in virus concentration and extraction workflows have hampered Severe Acute Respiratory Syndrome (SARS-CoV-2) wastewater surveillance and data reporting practices. Numerous studies have shown that adsorption-extraction (AE) method holds promise, yet several uncertainties remain regarding the optimal AE workflow. Several procedural components may influence the recovered concentrations of target nucleic acid, including membrane types, homogenization instruments, speed and duration, and lysis buffer. In this study, 42 different AE workflows that varied these components were compared to determine the optimal workflow by quantifying endogenous SARS-CoV-2, human adenovirus 40/41 (HAdV 40/41), and a bacterial marker gene of fecal contamination (Bacteroides HF183). Our findings suggest that the workflow chosen had a significant impact on SARS-CoV-2 concentrations, whereas it had minimal impact on HF183 and no effect on HAdV 40/41 concentrations. When comparing individual components in a workflow, such as membrane type (MF-Millipore™ 0.45 μm MCE vs. Isopore™ 0.40 μm), we found that they had no impact on SARS-CoV-2, HAdV 40/41, and HF183 concentrations. This suggests that at least some consumables and equipment are interchangeable. Buffer PM1 + TRIzol-based workflows yielded higher concentrations of SARS-CoV-2 than other workflows. HF183 concentrations were higher in workflows without chloroform. Similarly, higher homogenization speeds (5000-10,000 rpm) led to increased concentrations of SARS-CoV-2 and HF183 but had no effect on HAdV 40/41. Our findings indicate that minor enhancements to the AE workflow can improve the recovery of viruses and bacteria from the wastewater, leading to improved outcomes from wastewater surveillance efforts.
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Affiliation(s)
- Jesmin Akter
- Department of Civil and Environmental Engineering, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, Republic of Korea
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J.M. Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Ilho Kim
- Department of Civil and Environmental Engineering, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, Republic of Korea
| | | | - Phong Thai
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 4102 Brisbane, Australia
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
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de la Cruz Barron M, Kneis D, Geissler M, Dumke R, Dalpke A, Berendonk TU. Evaluating the sensitivity of droplet digital PCR for the quantification of SARS-CoV-2 in wastewater. Front Public Health 2023; 11:1271594. [PMID: 38425410 PMCID: PMC10903512 DOI: 10.3389/fpubh.2023.1271594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/27/2023] [Indexed: 03/02/2024] Open
Abstract
Wastewater surveillance for SARS-CoV-2 has been demonstrated to be a valuable tool in monitoring community-level virus circulation and assessing new outbreaks. It may become a useful tool in the early detection and response to future pandemics, enabling public health authorities to implement timely interventions and mitigate the spread of infectious diseases with the fecal excretion of their agents. It also offers a chance for cost-effective surveillance. Reverse transcription-quantitative polymerase chain reaction (RTqPCR) is the most commonly used method for viral RNA detection in wastewater due to its sensitivity, reliability, and widespread availability. However, recent studies have indicated that reverse transcription droplet digital PCR (RTddPCR) has the potential to offer improved sensitivity and accuracy for quantifying SARS-CoV-2 RNA in wastewater samples. In this study, we compared the performance of RTqPCR and RTddPCR approaches for SARS-CoV-2 detection and quantification on wastewater samples collected during the third epidemic wave in Saxony, Germany, characterized by low-incidence infection periods. The determined limits of detection (LOD) and quantification (LOQ) were within the same order of magnitude, and no significant differences were observed between the PCR approaches with respect to the number of positive or quantifiable samples. Our results indicate that both RTqPCR and RTddPCR are highly sensitive methods for detecting SARS-CoV-2. Consequently, the actual gain in sensitivity associated with ddPCR lags behind theoretical expectations. Hence, the choice between the two PCR methods in further environmental surveillance programs is rather a matter of available resources and throughput requirements.
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Affiliation(s)
| | - David Kneis
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Michael Geissler
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Roger Dumke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Alexander Dalpke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Heidelberg, Heidelberg, Germany
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11
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Wiesner-Friedman C, Brinkman NE, Wheaton E, Nagarkar M, Hart C, Keely SP, Varughese E, Garland J, Klaver P, Turner C, Barton J, Serre M, Jahne M. Characterizing Spatial Information Loss for Wastewater Surveillance Using crAssphage: Effect of Decay, Temperature, and Population Mobility. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:20802-20812. [PMID: 38015885 DOI: 10.1021/acs.est.3c05587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Populations contribute information about their health status to wastewater. Characterizing how that information degrades in transit to wastewater sampling locations (e.g., wastewater treatment plants and pumping stations) is critical to interpret wastewater responses. In this work, we statistically estimate the loss of information about fecal contributions to wastewater from spatially distributed populations at the census block group resolution. This was accomplished with a hydrologically and hydraulically influenced spatial statistical approach applied to crAssphage (Carjivirus communis) load measured from the influent of four wastewater treatment plants in Hamilton County, Ohio. We find that we would expect to observe a 90% loss of information about fecal contributions from a given census block group over a travel time of 10.3 h. This work demonstrates that a challenge to interpreting wastewater responses (e.g., during wastewater surveillance) is distinguishing between a distal but large cluster of contributions and a near but small contribution. This work demonstrates new modeling approaches to improve measurement interpretation depending on sewer network and wastewater characteristics (e.g., geospatial layout, temperature variability, population distribution, and mobility). This modeling can be integrated into standard wastewater surveillance methods and help to optimize sewer sampling locations to ensure that different populations (e.g., vulnerable and susceptible) are appropriately represented.
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Affiliation(s)
- Corinne Wiesner-Friedman
- Oak Ridge Institute for Science and Education, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Nichole E Brinkman
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Emily Wheaton
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Maitreyi Nagarkar
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Chloe Hart
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Scott P Keely
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Eunice Varughese
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Jay Garland
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Peter Klaver
- LimnoTech, 501 Avis Drive, Ann Arbor, Michigan 48108, United States
| | - Carrie Turner
- LimnoTech, 501 Avis Drive, Ann Arbor, Michigan 48108, United States
| | - John Barton
- Metropolitan Sewer District of Greater Cincinnati, 1081 Woodrow Street, Cincinnati, Ohio 45204, United States
| | - Marc Serre
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michael Jahne
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
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12
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Triggiano F, De Giglio O, Apollonio F, Brigida S, Fasano F, Mancini P, Bonanno Ferraro G, Veneri C, La Rosa G, Suffredini E, Lucentini L, Ungaro N, Di Vittorio G, Mongelli O, Albano N, Montagna MT. Wastewater-based Epidemiology and SARS-CoV-2: Variant Trends in the Apulia Region (Southern Italy) and Effect of Some Environmental Parameters. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:331-341. [PMID: 37735299 PMCID: PMC10654208 DOI: 10.1007/s12560-023-09565-0] [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: 07/10/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
During the COVID-19 pandemic, wastewater monitoring has been used to monitor the levels of SARS-CoV-2 RNA entering the sewerage system. In Italy, the Istituto Superiore di Sanità coordinated the SARI project (Sorveglianza Ambientale Reflue in Italia) to detect SARS-CoV-2 and its variants. In this study, the concentration of SARS-CoV-2 and its variants in raw wastewater against COVID-19 cases was evaluated together with the effect of temperature and precipitation on virus spread. We validated a predictive model, proposed by De Giglio et al., 2021, to establish the number of COVID-19 cases/100,000 inhabitants. A receiver operating characteristic curve model was applied to predict the number of COVID-19 cases and Poisson regression was applied to study the effect of temperature and rainfall on viral load. In Apulia, from October 2021 to December 2022, we analyzed 1041 samples, of which 985 (94.6%) tested positive for SARS-CoV-2. Median atmospheric temperature was inversely proportional to viral load in wastewater; no correlation was found with precipitation. The predictive model confirmed that at least 11 cases/100,000 inhabitants would occur in the 15 days following the detection of the virus in wastewater. Environmental surveillance of SARS-CoV-2 can be used to map the virus and its variants.
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Affiliation(s)
- Francesco Triggiano
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Osvalda De Giglio
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy.
| | - Francesca Apollonio
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Silvia Brigida
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Campus Ecotekne, Monteroni di Lecce, Lecce, 73047, Italy
| | - Fabrizio Fasano
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Giusy Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Carolina Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Luca Lucentini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Nicola Ungaro
- Agency for the Environmental Prevention and Protection (ARPA Puglia), Corso Trieste 27, Bari, 70126, Italy
| | | | - Onofrio Mongelli
- Department of Health Promotion and Animal Welfare, Apulia Region, Bari, Italy
| | - Nelhudoff Albano
- Department of Health Promotion and Animal Welfare, Apulia Region, Bari, Italy
| | - Maria Teresa Montagna
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
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13
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Babler KM, Sharkey ME, Amirali A, Boone MM, Comerford S, Currall BB, Grills GS, Laine J, Mason CE, Reding B, Schürer S, Stevenson M, Vidović D, Williams SL, Solo-Gabriele HM. Expanding a Wastewater-Based Surveillance Methodology for DNA Isolation from a Workflow Optimized for SARS-CoV-2 RNA Quantification. J Biomol Tech 2023; 34:3fc1f5fe.dfa8d906. [PMID: 38268997 PMCID: PMC10805363 DOI: 10.7171/3fc1f5fe.dfa8d906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Wastewater-based surveillance (WBS) is a noninvasive, epidemiological strategy for assessing the spread of COVID-19 in communities. This strategy was based upon wastewater RNA measurements of the viral target, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The utility of WBS for assessing the spread of COVID-19 has motivated research to measure targets beyond SARS-CoV-2, including pathogens containing DNA. The objective of this study was to establish the necessary steps for isolating DNA from wastewater by modifying a long-standing RNA-specific extraction workflow optimized for SARS-CoV-2 detection. Modifications were made to the sample concentration process and included an evaluation of bead bashing prior to the extraction of either DNA or RNA. Results showed that bead bashing reduced detection of RNA from wastewater but improved recovery of DNA as assessed by quantitative polymerase chain reaction (qPCR). Bead bashing is therefore not recommended for the quantification of RNA viruses using qPCR. Whereas for Mycobacterium bacterial DNA isolation, bead bashing was necessary for improving qPCR quantification. Overall, we recommend 2 separate workflows, one for RNA viruses that does not include bead bashing and one for other microbes that use bead bashing for DNA isolation. The experimentation done here shows that current-standing WBS program methodologies optimized for SARS-CoV-2 need to be modified and reoptimized to allow for alternative pathogens to be readily detected and monitored, expanding its utility as a tool for public health assessment.
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Affiliation(s)
- Kristina M. Babler
- Department of ChemicalEnvironmental and Materials
EngineeringUniversity of MiamiCoral GablesFlorida33124USA
| | - Mark E. Sharkey
- Department of MedicineUniversity of Miami Miller School
of MedicineMiamiFlorida33136USA
| | - Ayaaz Amirali
- Department of ChemicalEnvironmental and Materials
EngineeringUniversity of MiamiCoral GablesFlorida33124USA
| | - Melinda M. Boone
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - Samuel Comerford
- Department of MedicineUniversity of Miami Miller School
of MedicineMiamiFlorida33136USA
| | - Benjamin B. Currall
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - George S. Grills
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - Jennifer Laine
- Environmental Health and SafetyUniversity of MiamiMiamiFlorida33136USA
| | - Christopher E. Mason
- Department of Physiology and BiophysicsWeill Cornell
MedicineNew YorkNew York10065USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud
Institute for Computational BiomedicineWeill Cornell MedicineNew
YorkNew York10065USA
- The WorldQuant Initiative for Quantitative PredictionWeill Cornell MedicineNew YorkNew YorkUSA 10065USA
| | - Brian Reding
- Environmental Health and SafetyUniversity of MiamiMiamiFlorida33136USA
| | - Stephan Schürer
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
- Department of Molecular and Cellular PharmacologyUniversity of Miami Miller School of MedicineMiamiFlorida33136USA
- Institute for Data Science & Computing, University of
MiamiCoral GablesFlorida33146USA
| | - Mario Stevenson
- Department of MedicineUniversity of Miami Miller School
of MedicineMiamiFlorida33136USA
| | - Dušica Vidović
- Department of Molecular and Cellular PharmacologyUniversity of Miami Miller School of MedicineMiamiFlorida33136USA
| | - Sion L. Williams
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - Helena M. Solo-Gabriele
- Department of ChemicalEnvironmental and Materials
EngineeringUniversity of MiamiCoral GablesFlorida33124USA
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14
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Williams BB, Newborn A, Karamat A, Zamcho F, Salerno JL, Gillevet PM, Farris D, Wintermeyer SF, Van Aken B. Detection of SARS-CoV-2 RNA in wastewater from dormitory buildings in a university campus: comparison with individual testing results. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 88:2364-2377. [PMID: 37966188 PMCID: wst_2023_348 DOI: 10.2166/wst.2023.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Wastewater-based epidemiology (WBE) for monitoring COVID-19 has been largely used to detect the spread of the disease at the community level. From February to December 2022, we collected 24-h composite sewage samples from dormitory buildings in George Mason University (Fairfax, Virginia, USA) housing approximately 5,200 resident students. SARS-CoV-2 RNA extraction was achieved using an automated system based on magnetic nanoparticles. Analysis of SARS-CoV-2 RNA was performed using reverse transcription quantitative PCR based on the Centers for Disease Control and Prevention (CDC) N1 and N2 assays. From the 362 samples collected, 86% showed positive detection of SARS-CoV-2 RNA. Wastewater monitoring was able to detect SARS-CoV-2 RNA in 96% of the samples from buildings housing students with COVID-19. Over the period of study, we observed significant correlations between the SARS-CoV-2 concentration (copy number mL-1) in wastewater and the number of positive cases on campus based on individual saliva testing. Although several reports have been published on the wastewater monitoring of COVID-19 in university campuses, our study is one of the very few that provides results that were obtained during the last phase of the pandemic (roughly the year 2022), when the large majority of students were vaccinated and back on campus.
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Affiliation(s)
- Brandi B Williams
- Department of Chemistry & Biochemistry, George Mason University, Fairfax, Virginia, USA E-mail:
| | - Aaron Newborn
- Department of Chemistry & Biochemistry, George Mason University, Fairfax, Virginia, USA
| | - Ayesha Karamat
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Fanella Zamcho
- Department of Chemistry & Biochemistry, George Mason University, Fairfax, Virginia, USA
| | - Jennifer L Salerno
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | | | - David Farris
- Environmental Health and Safety, George Mason University, Fairfax, Virginia, USA
| | | | - Benoit Van Aken
- Department of Chemistry & Biochemistry, George Mason University, Fairfax, Virginia, USA
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15
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Oh C, Zhou A, O'Brien K, Schmidt AR, Geltz J, Shisler JL, Schmidt AR, Keefer L, Brown WM, Nguyen TH. Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance. Appl Environ Microbiol 2023; 89:e0033123. [PMID: 37791775 PMCID: PMC10654041 DOI: 10.1128/aem.00331-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/07/2023] [Indexed: 10/05/2023] Open
Abstract
Nucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of their genetic diversity. Here, we calculated the variability of nucleotides within the genomes of 10 human viral species in silico and found that endemic viruses exhibit a high percentage of variable nucleotides (e.g., 51.4% for norovirus genogroup II). This genetic diversity led to the variable probability of detection of PCR assays (the proportion of viral sequences that contain the assay's target sequences divided by the total number of viral sequences). We then experimentally confirmed that the probability of the target sequence detection is indicative of the number of mismatches between PCR assays and norovirus genomes. Next, we developed a degenerate PCR assay that detects 97% of known norovirus genogroup II genome sequences and recognized norovirus in eight clinical samples. By contrast, previously developed assays with 31% and 16% probability of detection had 1.1 and 2.5 mismatches on average, respectively, which negatively impacted RNA quantification. In addition, the two PCR assays with a lower probability of detection also resulted in false negatives for wastewater-based epidemiology. Our findings suggest that the probability of detection serves as a simple metric for evaluating nucleic acid-based assays for genetically diverse virus surveillance.IMPORTANCENucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are employed widely as a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of the rapid evolution and genetic variation of viruses. The study analyzed clinical and wastewater samples using multiple PCR assays and found significant performance variation among the PCR assays for genetically diverse norovirus surveillance. This finding suggests that some PCR assays may miss detecting certain virus strains, leading to a compromise in detection sensitivity. To address this issue, we propose a metric called the probability of detection, which can be simply calculated in silico using a code developed in this study, to evaluate nucleic acid-based assays for genetically diverse virus surveillance. This new approach can help improve the sensitivity and accuracy of virus detection, which is crucial for effective infectious disease surveillance and control.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kate O'Brien
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Arthur R. Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Joshua Geltz
- Division of Laboratories, Illinois Department of Public Health, Springfield, Illinois, USA
| | - Joanna L. Shisler
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Arthur R. Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Laura Keefer
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - William M. Brown
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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16
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Breadner PR, Dhiyebi HA, Fattahi A, Srikanthan N, Hayat S, Aucoin MG, Boegel SJ, Bragg LM, Craig PM, Xie Y, Giesy JP, Servos MR. A comparative analysis of the partitioning behaviour of SARS-CoV-2 RNA in liquid and solid fractions of wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165095. [PMID: 37355124 PMCID: PMC10287177 DOI: 10.1016/j.scitotenv.2023.165095] [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: 04/09/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
As fragments of SARS-CoV-2 RNA can be quantified and measured temporally in wastewater, surveillance of concentrations of SARS-CoV-2 in wastewater has become a vital resource for tracking the spread of COVID-19 in and among communities. However, the absence of standardized methods has affected the interpretation of data for public health efforts. In particular, analyzing either the liquid or solid fraction has implications for the interpretation of how viral RNA is quantified. Characterizing how SARS-CoV-2 or its RNA fragments partition in wastewater is a central part of understanding fate and behaviour in wastewater. In this study, partitioning of SARS-CoV-2 was investigated by use of centrifugation with varied durations of spin and centrifugal force, polyethylene glycol (PEG) precipitation followed by centrifugation, and ultrafiltration of wastewater. Partitioning of the endogenous pepper mild mottled virus (PMMoV), used to normalize the SARS-CoV-2 signal for fecal load in trend analysis, was also examined. Additionally, two surrogates for coronavirus, human coronavirus 229E and murine hepatitis virus, were analyzed as process controls. Even though SARS-CoV-2 has an affinity for solids, the total RNA copies of SARS-CoV-2 per wastewater sample, after centrifugation (12,000 g, 1.5 h, no brake), were partitioned evenly between the liquid and solid fractions. Centrifugation at greater speeds for longer durations resulted in a shift in partitioning for all viruses toward the solid fraction except for PMMoV, which remained mostly in the liquid fraction. The surrogates more closely reflected the partitioning of SARS-CoV-2 under high centrifugation speed and duration while PMMoV did not. Interestingly, ultrafiltration devices were inconsistent in estimating RNA copies in wastewater, which can influence the interpretation of partitioning. Developing a better understanding of the fate of SARS-CoV-2 in wastewater and creating a foundation of best practices is the key to supporting the current pandemic response and preparing for future potential infectious diseases.
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Affiliation(s)
- Patrick R Breadner
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Hadi A Dhiyebi
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Azar Fattahi
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Nivetha Srikanthan
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Samina Hayat
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Marc G Aucoin
- Department of Chemical Engineering, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Scott J Boegel
- Department of Chemical Engineering, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Leslie M Bragg
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Paul M Craig
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Yuwei Xie
- Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; Toxicology Centre, University of Saskatchewan, 44 Campus Dr, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, 44 Campus Dr, Saskatoon, Saskatchewan S7N 5B3, Canada; Department of Environmental Science, Baylor University, One Bear Place, Waco, TX 76798, USA
| | - Mark R Servos
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada.
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17
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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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18
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de Araújo Rolo C, Machado BAS, Dos Santos MC, Dos Santos RF, Fonseca MS, Hodel KVS, Silva JR, Nunes DDG, Dos Santos Almeida E, de Andrade JB. Long-term monitoring of COVID-19 prevalence in raw and treated wastewater in Salvador, the largest capital of the Brazilian Northeast. Sci Rep 2023; 13:15238. [PMID: 37709804 PMCID: PMC10502096 DOI: 10.1038/s41598-023-41060-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023] Open
Abstract
Wastewater-based epidemiology (WBE) becomes an interesting epidemiological approach to monitoring the prevalence of SARS-CoV-2 broadly and non-invasively. Herein, we employ for the first time WBE, associated or not with the PEG 8000 precipitation method, for the detection of SARS-CoV-2 in samples of raw or treated wastewater from 22 municipal wastewater treatment stations (WWTPs) located in Salvador, the fourth most populous city in Brazil. Our results demonstrate the success of the application of WBE for detecting SARS-CoV-2 in both types of evaluated samples, regardless of the usage of PEG 8000 concentration procedure. Further, an increase in SARS-CoV-2 positivity rate was observed in samples collected in months that presented the highest number of confirmed COVID-19 cases (May/2021, June/2021 and January/2022). While PEG 8000 concentration step was found to significantly increase the positivity rate in treated wastewater samples (p < 0.005), a strong positive correlation (r: 0.84; p < 0.002) between non-concentrated raw wastewater samples with the number of new cases of COVID-19 (April/2021-February/2022) was observed. In general, the present results reinforce the efficiency of WBE approach to monitoring the presence of SARS-CoV-2 in either low- or high-capacity WWTPs. The successful usage of WBE even in raw wastewater samples makes it an interesting low-cost tool for epidemiological surveillance.
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Affiliation(s)
- Carolina de Araújo Rolo
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Bruna Aparecida Souza Machado
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, 41650-010, Brazil
| | - Matheus Carmo Dos Santos
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Rosângela Fernandes Dos Santos
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Maísa Santos Fonseca
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Katharine Valéria Saraiva Hodel
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Jéssica Rebouças Silva
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Danielle Devequi Gomes Nunes
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Edna Dos Santos Almeida
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, 41650-010, Brazil
| | - Jailson Bittencourt de Andrade
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil.
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, 41650-010, Brazil.
- Centro Interdisciplinar de Energia e Ambiente - CIEnAm, Federal University of Bahia, Salvador, 40170-115, Brazil.
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19
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Panferov VG, Zherdev AV, Dzantiev BB. Post-Assay Chemical Enhancement for Highly Sensitive Lateral Flow Immunoassays: A Critical Review. BIOSENSORS 2023; 13:866. [PMID: 37754100 PMCID: PMC10526817 DOI: 10.3390/bios13090866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023]
Abstract
Lateral flow immunoassay (LFIA) has found a broad application for testing in point-of-care (POC) settings. LFIA is performed using test strips-fully integrated multimembrane assemblies containing all reagents for assay performance. Migration of liquid sample along the test strip initiates the formation of labeled immunocomplexes, which are detected visually or instrumentally. The tradeoff of LFIA's rapidity and user-friendliness is its relatively low sensitivity (high limit of detection), which restricts its applicability for detecting low-abundant targets. An increase in LFIA's sensitivity has attracted many efforts and is often considered one of the primary directions in developing immunochemical POC assays. Post-assay enhancements based on chemical reactions facilitate high sensitivity. In this critical review, we explain the performance of post-assay chemical enhancements, discuss their advantages, limitations, compared limit of detection (LOD) improvements, and required time for the enhancement procedures. We raise concerns about the performance of enhanced LFIA and discuss the bottlenecks in the existing experiments. Finally, we suggest the experimental workflow for step-by-step development and validation of enhanced LFIA. This review summarizes the state-of-art of LFIA with chemical enhancement, offers ways to overcome existing limitations, and discusses future outlooks for highly sensitive testing in POC conditions.
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Affiliation(s)
- Vasily G. Panferov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.G.P.); (A.V.Z.)
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.G.P.); (A.V.Z.)
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.G.P.); (A.V.Z.)
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20
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Kumblathan T, Liu Y, Qiu Y, Pang L, Hrudey SE, Le XC, Li XF. An efficient method to enhance recovery and detection of SARS-CoV-2 RNA in wastewater. J Environ Sci (China) 2023; 130:139-148. [PMID: 37032030 PMCID: PMC9554329 DOI: 10.1016/j.jes.2022.10.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 05/25/2023]
Abstract
Wastewater surveillance (WS) of SARS-CoV-2 currently requires multiple steps and suffers low recoveries and poor sensitivity. Here, we report an improved analytical method with high sensitivity and recovery to quantify SARS-CoV-2 RNA in wastewater. To improve the recovery, we concentrated SARS-CoV-2 viral particles and RNA from both the solid and aqueous phases of wastewater using an electronegative membrane (EM). The captured viral particles and RNA on the EM were incubated in our newly developed viral inactivation and RNA preservation (VIP) buffer. Subsequently, the RNA was concentrated on magnetic beads and inhibitors removed by washing. Without eluting, the RNA on the magnetic beads was directly detected using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Analysis of SARS-CoV-2 pseudovirus (SARS-CoV-2 RNA in a noninfectious viral coat) spiked to wastewater samples showed an improved recovery of 80%. Analysis of 120 wastewater samples collected twice weekly between May 2021 and February 2022 from two wastewater treatment plants showed 100% positive detection, which agreed with the results independently obtained by a provincial public health laboratory. The concentrations of SARS-CoV-2 RNA in these wastewater samples ranged from 2.4×102 to 2.9×106 copies per 100 mL of wastewater. Our method's capability of detecting trace and diverse concentrations of SARS-CoV-2 in complex wastewater samples is attributed to the enhanced recovery of SARS-CoV-2 RNA and efficient removal of PCR inhibitors. The improved method for the recovery and detection of viral RNA in wastewater is important for wastewater surveillance, complementing clinical diagnostic tests for public health protection.
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Affiliation(s)
- Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yuanyuan Qiu
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 2G3, Canada
| | - Lilly Pang
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 2G3, Canada; Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, T6G 2G3, Canada
| | - Steve E Hrudey
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
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21
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Zhao L, Geng Q, Corchis-Scott R, McKay RM, Norton J, Xagoraraki I. Targeting a free viral fraction enhances the early alert potential of wastewater surveillance for SARS-CoV-2: a methods comparison spanning the transition between delta and omicron variants in a large urban center. Front Public Health 2023; 11:1140441. [PMID: 37546328 PMCID: PMC10400354 DOI: 10.3389/fpubh.2023.1140441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction Wastewater surveillance has proven to be a valuable approach to monitoring the spread of SARS-CoV-2, the virus that causes Coronavirus disease 2019 (COVID-19). Recognizing the benefits of wastewater surveillance as a tool to support public health in tracking SARS-CoV-2 and other respiratory pathogens, numerous wastewater virus sampling and concentration methods have been tested for appropriate applications as well as their significance for actionability by public health practices. Methods Here, we present a 34-week long wastewater surveillance study that covers nearly 4 million residents of the Detroit (MI, United States) metropolitan area. Three primary concentration methods were compared with respect to recovery of SARS-CoV-2 from wastewater: Virus Adsorption-Elution (VIRADEL), polyethylene glycol precipitation (PEG), and polysulfone (PES) filtration. Wastewater viral concentrations were normalized using various parameters (flow rate, population, total suspended solids) to account for variations in flow. Three analytical approaches were implemented to compare wastewater viral concentrations across the three primary concentration methods to COVID-19 clinical data for both normalized and non-normalized data: Pearson and Spearman correlations, Dynamic Time Warping (DTW), and Time Lagged Cross Correlation (TLCC) and peak synchrony. Results It was found that VIRADEL, which captures free and suspended virus from supernatant wastewater, was a leading indicator of COVID-19 cases within the region, whereas PEG and PES filtration, which target particle-associated virus, each lagged behind the early alert potential of VIRADEL. PEG and PES methods may potentially capture previously shed and accumulated SARS-CoV-2 resuspended from sediments in the interceptors. Discussion These results indicate that the VIRADEL method can be used to enhance the early-warning potential of wastewater surveillance applications although drawbacks include the need to process large volumes of wastewater to concentrate sufficiently free and suspended virus for detection. While lagging the VIRADEL method for early-alert potential, both PEG and PES filtration can be used for routine COVID-19 wastewater monitoring since they allow a large number of samples to be processed concurrently while being more cost-effective and with rapid turn-around yielding results same day as collection.
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Affiliation(s)
- Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Robert Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - John Norton
- Great Lakes Water Authority, Detroit, MI, United States
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
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22
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Jiang G, Liu Y, Tang S, Kitajima M, Haramoto E, Arora S, Choi PM, Jackson G, D'Aoust PM, Delatolla R, Zhang S, Guo Y, Wu J, Chen Y, Sharma E, Prosun TA, Zhao J, Kumar M, Honda R, Ahmed W, Meiman J. Moving forward with COVID-19: Future research prospects of wastewater-based epidemiology methodologies and applications. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2023; 33:100458. [PMID: 37034453 PMCID: PMC10065412 DOI: 10.1016/j.coesh.2023.100458] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Wastewater-based epidemiology (WBE) has been demonstrated for its great potential in tracking of coronavirus disease 2019 (COVID-19) transmission among populations despite some inherent methodological limitations. These include non-optimized sampling approaches and analytical methods; stability of viruses in sewer systems; partitioning/retention in biofilms; and the singular and inaccurate back-calculation step to predict the number of infected individuals in the community. Future research is expected to (1) standardize best practices in wastewater sampling, analysis and data reporting protocols for the sensitive and reproducible detection of viruses in wastewater; (2) understand the in-sewer viral stability and partitioning under the impacts of dynamic wastewater flow, properties, chemicals, biofilms and sediments; and (3) achieve smart wastewater surveillance with artificial intelligence and big data models. Further specific research is essential in the monitoring of other viral pathogens with pandemic potential and subcatchment applications to maximize the benefits of WBE beyond COVID-19.
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Affiliation(s)
- Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Song Tang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Chaoyang District, Beijing 100021, China
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, 302017, India
| | - Phil M Choi
- Water Unit, Health Protection Branch, Queensland Public Health and Scientific Services, Queensland Health, Australia
| | - Greg Jackson
- Water Unit, Health Protection Branch, Queensland Public Health and Scientific Services, Queensland Health, Australia
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Shuxin Zhang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Ying Guo
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Jiangping Wu
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Yan Chen
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Elipsha Sharma
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Tanjila Alam Prosun
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Jiawei Zhao
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterey, Monterrey, 64849, Nuevo Leon, Mexico
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Japan
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Jon Meiman
- Wisconsin Department of Health Services, Madison, WI 53701, USA
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23
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Kim LH, Mikolaityte V, Kim S. Establishment of wastewater-based SARS-CoV-2 monitoring system over two years: Case studies in South Korea. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:110289. [PMID: 37292384 PMCID: PMC10240911 DOI: 10.1016/j.jece.2023.110289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/22/2023] [Accepted: 06/03/2023] [Indexed: 06/10/2023]
Abstract
With the global COVID-19 pandemic, wastewater surveillance has received a considerable attention as a method for the early identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater treatment plant (WWTP) and sewer systems. For the first time in Korea, this study utilized the wastewater surveillance technique to monitor the COVID-19 outbreak. Sampling efforts were carried out at the WWTPs in the capital city of Korea, Seoul, and Daegu the place where the first severe outbreak was reported. The RNA of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been extracted from the collected wastewater influent and primary sewage sludge samples. The outcomes were contrasted with the COVID-19 cases in the WWTPs served area. Additionally, whole transcriptome sequencing was used to compare the microbial community alterations before and after the COVID-19 outbreak and SARS-CoV-2 variations. The results demonstrated that the changes in SARS-CoV-2 RNA concentrations in the influent and sludge matched the trends of reported COVID-19 cases, especially sludge showed high-resolution data, which is well-matched when fewer COVID-19 cases (0-250) are reported. Interestingly, one month before the clinical report, we found that the SARS-CoV-2 Beta variant (South Africa, B.1.351) in the wastewater. In addition, the Aeromonas bacterial species was dominated (21.2%) among other bacterial species in wastewater after the COVID-19 outbreak, suggesting a potential indirect microbial indicator of the COVID-19 outbreak.
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Affiliation(s)
- Lan Hee Kim
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
| | - Viktorija Mikolaityte
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
| | - Sungpyo Kim
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
- Department of Environmental Systems Engineering, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
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24
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Rainey AL, Liang S, Bisesi JH, Sabo-Attwood T, Maurelli AT. A multistate assessment of population normalization factors for wastewater-based epidemiology of COVID-19. PLoS One 2023; 18:e0284370. [PMID: 37043469 PMCID: PMC10096268 DOI: 10.1371/journal.pone.0284370] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/29/2023] [Indexed: 04/13/2023] Open
Abstract
Wastewater-based epidemiology (WBE) has become a valuable tool for monitoring SARS-CoV-2 infection trends throughout the COVID-19 pandemic. Population biomarkers that measure the relative human fecal contribution to normalize SARS-CoV-2 wastewater concentrations are needed for improved analysis and interpretation of community infection trends. The Centers for Disease Control and Prevention National Wastewater Surveillance System (CDC NWSS) recommends using the wastewater flow rate or human fecal indicators as population normalization factors. However, there is no consensus on which normalization factor performs best. In this study, we provided the first multistate assessment of the effects of flow rate and human fecal indicators (crAssphage, F+ Coliphage, and PMMoV) on the correlation of SARS-CoV-2 wastewater concentrations and COVID-19 cases using the CDC NWSS dataset of 182 communities across six U.S. states. Flow normalized SARS-CoV-2 wastewater concentrations produced the strongest correlation with COVID-19 cases. The correlation from the three human fecal indicators were significantly lower than flow rate. Additionally, using reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) significantly improved correlation values over samples that were analyzed with real-time reverse transcription quantitative polymerase chain reaction (rRT-qPCR). Our assessment shows that utilizing flow normalization with RT-ddPCR generate the strongest correlation between SARS-CoV-2 wastewater concentrations and COVID-19 cases.
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Affiliation(s)
- Andrew L. Rainey
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Song Liang
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Joseph H. Bisesi
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - Tara Sabo-Attwood
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - Anthony T. Maurelli
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
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25
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Babler KM, Sharkey ME, Abelson S, Amirali A, Benitez A, Cosculluela GA, Grills GS, Kumar N, Laine J, Lamar W, Lamm ED, Lyu J, Mason CE, McCabe PM, Raghavender J, Reding BD, Roca MA, Schürer SC, Stevenson M, Szeto A, Tallon JJ, Vidović D, Zarnegarnia Y, Solo-Gabriele HM. Degradation rates influence the ability of composite samples to represent 24-hourly means of SARS-CoV-2 and other microbiological target measures in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161423. [PMID: 36623667 PMCID: PMC9817413 DOI: 10.1016/j.scitotenv.2023.161423] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/25/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
The utility of using severe-acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA for assessing the prevalence of COVID-19 within communities begins with the design of the sample collection program. The objective of this study was to assess the utility of 24-hour composites as representative samples for measuring multiple microbiological targets in wastewater, and whether normalization of SARS-CoV-2 by endogenous targets can be used to decrease hour to hour variability at different watershed scales. Two sets of experiments were conducted, in tandem with the same wastewater, with samples collected at the building, cluster, and community sewershed scales. The first set of experiments focused on evaluating degradation of microbiological targets: SARS-CoV-2, Simian Immunodeficiency Virus (SIV) - a surrogate spiked into the wastewater, plus human waste indicators of Pepper Mild Mottle Virus (PMMoV), Beta-2 microglobulin (B2M), and fecal coliform bacteria (FC). The second focused on the variability of these targets from samples, collected each hour on the hour. Results show that SARS-CoV-2, PMMoV, and B2M were relatively stable, with minimal degradation over 24-h. SIV, which was spiked-in prior to analysis, degraded significantly and FC increased significantly over the course of 24 h, emphasizing the possibility for decay and growth within wastewater. Hour-to-hour variability of the source wastewater was large between each hour of sampling relative to the variability of the SARS-CoV-2 levels calculated between sewershed scales; thus, differences in SARS-CoV-2 hourly variability were not statistically significant between sewershed scales. Results further provided that the quantified representativeness of 24-h composite samples (i.e., statistical equivalency compared against hourly collected grabs) was dependent upon the molecular target measured. Overall, improvements made by normalization were minimal within this study. Degradation and multiplication for other targets should be evaluated when deciding upon whether to collect composite or grab samples in future studies.
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Affiliation(s)
- Kristina M Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Mark E Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Samantha Abelson
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Aymara Benitez
- Miami-Dade Water and Sewer Department, Miami, FL 33149, USA
| | - Gabriella A Cosculluela
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Naresh Kumar
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Walter Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL 33136, USA
| | - Erik D Lamm
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Jiangnan Lyu
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Philip M McCabe
- Department of Psychology, University of Miami, Coral Gables, FL 33146, USA; Department of Biomedical Engineering, University of Miami, Coral Gables, FL 33146, USA
| | | | - Brian D Reding
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Matthew A Roca
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Stephan C Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL, USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Angela Szeto
- Department of Psychology, University of Miami, Coral Gables, FL 33146, USA
| | - John J Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL 33146, USA
| | - Dusica Vidović
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yalda Zarnegarnia
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA.
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26
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Le C. Sensitivity of wastewater surveillance: What is the minimum COVID-19 cases required in population for SARS-CoV-2 RNA to be detected in wastewater? J Environ Sci (China) 2023; 125:851-853. [PMID: 36375967 PMCID: PMC9392869 DOI: 10.1016/j.jes.2022.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Connie Le
- Li Ka Shing Institute of Virology, Department of Radiation Oncology, and Cross Cancer Institute, University of Alberta, Edmonton, Alberta T6G 2G3, Canada.
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27
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Helm B, Geissler M, Mayer R, Schubert S, Oertel R, Dumke R, Dalpke A, El-Armouche A, Renner B, Krebs P. Regional and temporal differences in the relation between SARS-CoV-2 biomarkers in wastewater and estimated infection prevalence - Insights from long-term surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159358. [PMID: 36240928 PMCID: PMC9554318 DOI: 10.1016/j.scitotenv.2022.159358] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Wastewater-based epidemiology provides a conceptual framework for the evaluation of the prevalence of public health related biomarkers. In the context of the Coronavirus disease-2019, wastewater monitoring emerged as a complementary tool for epidemic management. In this study, we evaluated data from six wastewater treatment plants in the region of Saxony, Germany. The study period lasted from February to December 2021 and covered the third and fourth regional epidemic waves. We collected 1065 daily composite samples and analyzed SARS-CoV-2 RNA concentrations using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Regression models quantify the relation between RNA concentrations and disease prevalence. We demonstrated that the relation is site and time specific. Median loads per diagnosed case differed by a factor of 3-4 among sites during both waves and were on average 45 % higher during the third wave. In most cases, log-log-transformed data achieved better regression performance than non-transformed data and local calibration outperformed global models for all sites. The inclusion of lag/lead time, discharge and detection probability improved model performance in all cases significantly, but the importance of these components was also site and time specific. In all cases, models with lag/lead time and log-log-transformed data obtained satisfactory goodness-of-fit with adjusted coefficients of determination higher than 0.5. Back-estimation of testing efficiency from wastewater data confirmed state-wide prevalence estimation from individual testing statistics, but revealed pronounced differences throughout the epidemic waves and among the different sites.
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Affiliation(s)
- Björn Helm
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany.
| | - Michael Geissler
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Robin Mayer
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany
| | - Sara Schubert
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; Institute of Hydrobiology, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany
| | - Reinhard Oertel
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Roger Dumke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Alexander Dalpke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; University Heidelberg, Institute of Medical Microbiology and Hygiene, Heidelberg, Germany
| | - Ali El-Armouche
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Bertold Renner
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Peter Krebs
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany
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28
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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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29
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Rainey AL, Buschang K, O’Connor A, Love D, Wormington AM, Messcher RL, Loeb JC, Robinson SE, Ponder H, Waldo S, Williams R, Shapiro J, McAlister EB, Lauzardo M, Lednicky JA, Maurelli AT, Sabo-Attwood T, Bisesi J. Retrospective Analysis of Wastewater-Based Epidemiology of SARS-CoV-2 in Residences on a Large College Campus: Relationships between Wastewater Outcomes and COVID-19 Cases across Two Semesters with Different COVID-19 Mitigation Policies. ACS ES&T WATER 2023; 3:16-29. [PMID: 37552720 PMCID: PMC9762499 DOI: 10.1021/acsestwater.2c00275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 06/18/2023]
Abstract
Wastewater-based epidemiology (WBE) has been utilized for outbreak monitoring and response efforts in university settings during the coronavirus disease 2019 (COVID-19) pandemic. However, few studies examined the impact of university policies on the effectiveness of WBE to identify cases and mitigate transmission. The objective of this study was to retrospectively assess relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) wastewater outcomes and COVID-19 cases in residential buildings of a large university campus across two academic semesters (August 2020-May 2021) under different COVID-19 mitigation policies. Clinical case surveillance data of student residents were obtained from the university COVID-19 response program. We collected and processed building-level wastewater for detection and quantification of SARS-CoV-2 RNA by RT-qPCR. The odds of obtaining a positive wastewater sample increased with COVID-19 clinical cases in the fall semester (OR = 1.50, P value = 0.02), with higher odds in the spring semester (OR = 2.63, P value < 0.0001). We observed linear associations between SARS-CoV-2 wastewater concentrations and COVID-19 clinical cases (parameter estimate = 1.2, P value = 0.006). Our study demonstrated the effectiveness of WBE in the university setting, though it may be limited under different COVID-19 mitigation policies. As a complementary surveillance tool, WBE should be accompanied by robust administrative and clinical testing efforts for the COVID-19 pandemic response.
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Affiliation(s)
- Andrew L. Rainey
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Emerging Pathogens Institute, University
of Florida, Gainesville, Florida32610, United
States
| | - Katherine Buschang
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Emerging Pathogens Institute, University
of Florida, Gainesville, Florida32610, United
States
- Center for Environmental and Human Toxicology,
University of Florida, Gainesville, Florida32611,
United States
| | - Amber O’Connor
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Center for Environmental and Human Toxicology,
University of Florida, Gainesville, Florida32611,
United States
| | - Deirdre Love
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Center for Environmental and Human Toxicology,
University of Florida, Gainesville, Florida32611,
United States
| | - Alexis M. Wormington
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Center for Environmental and Human Toxicology,
University of Florida, Gainesville, Florida32611,
United States
| | - Rebeccah L. Messcher
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Emerging Pathogens Institute, University
of Florida, Gainesville, Florida32610, United
States
| | - Julia C. Loeb
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Emerging Pathogens Institute, University
of Florida, Gainesville, Florida32610, United
States
| | - Sarah E. Robinson
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Emerging Pathogens Institute, University
of Florida, Gainesville, Florida32610, United
States
- Center for Environmental and Human Toxicology,
University of Florida, Gainesville, Florida32611,
United States
| | - Hunter Ponder
- UF Health Screen, Test, and Protect,
University of Florida, Gainesville, Florida32611,
United States
- Florida Department of
Health, Alachua County, Gainesville, Florida32641, United
States
| | - Sarah Waldo
- UF Health Screen, Test, and Protect,
University of Florida, Gainesville, Florida32611,
United States
- Florida Department of
Health, Alachua County, Gainesville, Florida32641, United
States
| | - Roy Williams
- UF Health Screen, Test, and Protect,
University of Florida, Gainesville, Florida32611,
United States
- Florida Department of
Health, Alachua County, Gainesville, Florida32641, United
States
| | - Jerne Shapiro
- UF Health Screen, Test, and Protect,
University of Florida, Gainesville, Florida32611,
United States
- Florida Department of
Health, Alachua County, Gainesville, Florida32641, United
States
- Department of Epidemiology, College of Public
Health and Health Professions and College of Medicine, Gainesville,
Florida32611, United States
| | | | - Michael Lauzardo
- Emerging Pathogens Institute, University
of Florida, Gainesville, Florida32610, United
States
- UF Health Screen, Test, and Protect,
University of Florida, Gainesville, Florida32611,
United States
- Department of Medicine, College of Medicine,
University of Florida, Gainesville, Florida32611,
United States
| | - John A. Lednicky
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Emerging Pathogens Institute, University
of Florida, Gainesville, Florida32610, United
States
| | - Anthony T. Maurelli
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Emerging Pathogens Institute, University
of Florida, Gainesville, Florida32610, United
States
| | - Tara Sabo-Attwood
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Emerging Pathogens Institute, University
of Florida, Gainesville, Florida32610, United
States
- Center for Environmental and Human Toxicology,
University of Florida, Gainesville, Florida32611,
United States
| | - Joseph
H. Bisesi
- Department of Environmental and Global Health, College
of Public Health and Health Professions, University of Florida,
Gainesville, Florida32610, United States
- Emerging Pathogens Institute, University
of Florida, Gainesville, Florida32610, United
States
- Center for Environmental and Human Toxicology,
University of Florida, Gainesville, Florida32611,
United States
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30
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Lott MEJ, Norfolk WA, Dailey CA, Foley AM, Melendez-Declet C, Robertson MJ, Rathbun SL, Lipp EK. Direct wastewater extraction as a simple and effective method for SARS-CoV-2 surveillance and COVID-19 community-level monitoring. FEMS MICROBES 2023; 4:xtad004. [PMID: 37333441 PMCID: PMC10117872 DOI: 10.1093/femsmc/xtad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/23/2022] [Accepted: 01/11/2023] [Indexed: 10/22/2023] Open
Abstract
Wastewater surveillance has proven to be an effective tool to monitor the transmission and emergence of infectious agents at a community scale. Workflows for wastewater surveillance generally rely on concentration steps to increase the probability of detection of low-abundance targets, but preconcentration can substantially increase the time and cost of analyses while also introducing additional loss of target during processing. To address some of these issues, we conducted a longitudinal study implementing a simplified workflow for SARS-CoV-2 detection from wastewater, using a direct column-based extraction approach. Composite influent wastewater samples were collected weekly for 1 year between June 2020 and June 2021 in Athens-Clarke County, Georgia, USA. Bypassing any concentration step, low volumes (280 µl) of influent wastewater were extracted using a commercial kit, and immediately analyzed by RT-qPCR for the SARS-CoV-2 N1 and N2 gene targets. SARS-CoV-2 viral RNA was detected in 76% (193/254) of influent samples, and the recovery of the surrogate bovine coronavirus was 42% (IQR: 28%, 59%). N1 and N2 assay positivity, viral concentration, and flow-adjusted daily viral load correlated significantly with per-capita case reports of COVID-19 at the county-level (ρ = 0.69-0.82). To compensate for the method's high limit of detection (approximately 106-107 copies l-1 in wastewater), we extracted multiple small-volume replicates of each wastewater sample. With this approach, we detected as few as five cases of COVID-19 per 100 000 individuals. These results indicate that a direct-extraction-based workflow for SARS-CoV-2 wastewater surveillance can provide informative and actionable results.
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Affiliation(s)
- Megan E J Lott
- Department of Environmental Health Science, University of Georgia, 150 East Green Street, Athens, GA 30602, United States
| | - William A Norfolk
- Department of Environmental Health Science, University of Georgia, 150 East Green Street, Athens, GA 30602, United States
| | - Cody A Dailey
- Department of Epidemiology and Biostatistics, University of Georgia, 101 Buck Road, Athens, GA 30606, United States
| | - Amelia M Foley
- Department of Environmental Health Science, University of Georgia, 150 East Green Street, Athens, GA 30602, United States
| | - Carolina Melendez-Declet
- Department of Environmental Health Science, University of Georgia, 150 East Green Street, Athens, GA 30602, United States
| | - Megan J Robertson
- Department of Environmental Health Science, University of Georgia, 150 East Green Street, Athens, GA 30602, United States
| | - Stephen L Rathbun
- Department of Epidemiology and Biostatistics, University of Georgia, 101 Buck Road, Athens, GA 30606, United States
| | - Erin K Lipp
- Department of Environmental Health Science, University of Georgia, 150 East Green Street, Athens, GA 30602, United States
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31
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Li X, Zhang S, Sherchan S, Orive G, Lertxundi U, Haramoto E, Honda R, Kumar M, Arora S, Kitajima M, Jiang G. Correlation between SARS-CoV-2 RNA concentration in wastewater and COVID-19 cases in community: A systematic review and meta-analysis. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129848. [PMID: 36067562 PMCID: PMC9420035 DOI: 10.1016/j.jhazmat.2022.129848] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 05/26/2023]
Abstract
Wastewater-based epidemiology (WBE) has been considered as a promising approach for population-wide surveillance of coronavirus disease 2019 (COVID-19). Many studies have successfully quantified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentration in wastewater (CRNA). However, the correlation between the CRNA and the COVID-19 clinically confirmed cases in the corresponding wastewater catchments varies and the impacts of environmental and other factors remain unclear. A systematic review and meta-analysis were conducted to identify the correlation between CRNA and various types of clinically confirmed case numbers, including prevalence and incidence rates. The impacts of environmental factors, WBE sampling design, and epidemiological conditions on the correlation were assessed for the same datasets. The systematic review identified 133 correlation coefficients, ranging from -0.38 to 0.99. The correlation between CRNA and new cases (either daily new, weekly new, or future cases) was stronger than that of active cases and cumulative cases. These correlation coefficients were potentially affected by environmental and epidemiological conditions and WBE sampling design. Larger variations of air temperature and clinical testing coverage, and the increase of catchment size showed strong negative impacts on the correlation between CRNA and COVID-19 case numbers. Interestingly, the sampling technique had negligible impact although increasing the sampling frequency improved the correlation. These findings highlight the importance of viral shedding dynamics, in-sewer decay, WBE sampling design and clinical testing on the accurate back-estimation of COVID-19 case numbers through the WBE approach.
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Affiliation(s)
- Xuan Li
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, Australia; Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Shuxin Zhang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, Australia
| | - Samendrdra Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA
| | - Gorka Orive
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, Vitoria-Gasteiz 01006, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Unax Lertxundi
- Bioaraba Health Research Institute; Osakidetza Basque Health Service, Araba Mental Health Network, Araba Psychiatric Hospital, Pharmacy Service, Vitoria-Gasteiz, Spain
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Kofu, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Japan
| | - Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, Jaipur, India
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Hokkaido, Japan
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia.
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32
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Maryam S, Ul Haq I, Yahya G, Ul Haq M, Algammal AM, Saber S, Cavalu S. COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2. Front Cell Infect Microbiol 2023; 12:978643. [PMID: 36683701 PMCID: PMC9854263 DOI: 10.3389/fcimb.2022.978643] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.
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Affiliation(s)
- Sajida Maryam
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Ihtisham Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
- Department of Physical Chemistry and Polymers Technology, Silesian University of Technology, Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Gliwice, Poland
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mehboob Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Abdelazeem M Algammal
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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33
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Clark JR, Terwilliger A, Avadhanula V, Tisza M, Cormier J, Javornik-Cregeen S, Ross MC, Hoffman KL, Troisi C, Hanson B, Petrosino J, Balliew J, Piedra PA, Rios J, Deegan J, Bauer C, Wu F, Mena KD, Boerwinkle E, Maresso AW. Wastewater pandemic preparedness: Toward an end-to-end pathogen monitoring program. Front Public Health 2023; 11:1137881. [PMID: 37026145 PMCID: PMC10070845 DOI: 10.3389/fpubh.2023.1137881] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/09/2023] [Indexed: 04/08/2023] Open
Abstract
Molecular analysis of public wastewater has great potential as a harbinger for community health and health threats. Long-used to monitor the presence of enteric viruses, in particular polio, recent successes of wastewater as a reliable lead indicator for trends in SARS-CoV-2 levels and hospital admissions has generated optimism and emerging evidence that similar science can be applied to other pathogens of pandemic potential (PPPs), especially respiratory viruses and their variants of concern (VOC). However, there are substantial challenges associated with implementation of this ideal, namely that multiple and distinct fields of inquiry must be bridged and coordinated. These include engineering, molecular sciences, temporal-geospatial analytics, epidemiology and medical, and governmental and public health messaging, all of which present their own caveats. Here, we outline a framework for an integrated, state-wide, end-to-end human pathogen monitoring program using wastewater to track viral PPPs.
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Affiliation(s)
- Justin R. Clark
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Austen Terwilliger
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Michael Tisza
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Juwan Cormier
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Sara Javornik-Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Matthew Clayton Ross
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Kristi Louise Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Catherine Troisi
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Blake Hanson
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - John Balliew
- El Paso Water Utility, El Paso, TX, United States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Pediatrics Department, Baylor College of Medicine, Houston, TX, United States
| | - Janelle Rios
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Jennifer Deegan
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Cici Bauer
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Department of Biostatistics and Data Science, UTHealth School of Public Health, Houston, TX, United States
| | - Fuqing Wu
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Kristina D. Mena
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Eric Boerwinkle
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Anthony W. Maresso
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Anthony W. Maresso
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Oh C, Zhou A, O'Brien K, Jamal Y, Wennerdahl H, Schmidt AR, Shisler JL, Jutla A, Schmidt AR, Keefer L, Brown WM, Nguyen TH. Application of neighborhood-scale wastewater-based epidemiology in low COVID-19 incidence situations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158448. [PMID: 36063927 PMCID: PMC9436825 DOI: 10.1016/j.scitotenv.2022.158448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/08/2022] [Accepted: 08/28/2022] [Indexed: 05/17/2023]
Abstract
Wastewater-based epidemiology (WBE), an emerging approach for community-wide COVID-19 surveillance, was primarily characterized at large sewersheds such as wastewater treatment plants serving a large population. Although informed public health measures can be better implemented for a small population, WBE for neighborhood-scale sewersheds is less studied and not fully understood. This study applied WBE to seven neighborhood-scale sewersheds (average population of 1471) from January to November 2021. Community testing data showed an average of 0.004 % incidence rate in these sewersheds (97 % of monitoring periods reported two or fewer daily infections). In 92 % of sewage samples, SARS-CoV-2 N gene fragments were below the limit of quantification. We statistically determined 10-2.6 as the threshold of the SARS-CoV-2 N gene concentration normalized to pepper mild mottle virus (N/PMMOV) to alert high COVID-19 incidence rate in the studied sewershed. This threshold of N/PMMOV identified neighborhood-scale outbreaks (COVID-19 incidence rate higher than 0.2 %) with 82 % sensitivity and 51 % specificity. Importantly, neighborhood-scale WBE can discern local outbreaks that would not otherwise be identified by city-scale WBE. Our findings suggest that neighborhood-scale WBE is an effective community-wide disease surveillance tool when COVID-19 incidence is maintained at a low level.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States.
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States
| | - Kate O'Brien
- School of Integrative Biology, University of Illinois Urbana-Champaign, United States
| | - Yusuf Jamal
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, United States
| | - Hayden Wennerdahl
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, United States
| | - Arthur R Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States
| | - Joanna L Shisler
- Department of Microbiology, University of Illinois Urbana-Champaign, United States
| | - Antarpreet Jutla
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, United States
| | - Arthur R Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States
| | - Laura Keefer
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, United States
| | - William M Brown
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, United States
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States; Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
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35
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Zhang X, Zhang L, Wang Y, Zhang M, Zhou J, Liu X, Wang Y, Qu C, Han W, Hou M, Deng F, Luo Y, Mao Y, Gu W, Dong Z, Pan Y, Zhang D, Tang S, Zhang L. Detection of the SARS-CoV-2 Delta Variant in the Transboundary Rivers of Yunnan, China. ACS ES&T WATER 2022; 2:2367-2377. [PMID: 37552741 PMCID: PMC9631342 DOI: 10.1021/acsestwater.2c00224] [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: 05/17/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 05/30/2023]
Abstract
Ruili and Longchuan, two border counties in southwestern China, are facing epidemic control challenges due to the high rate of COVID-19 infections originating from neighboring Myanmar. Here, we aimed to establish the applicability of wastewater and environmental water surveillance of SARS-CoV-2 and conduct whole-genome sequencing (WGS) to trace the possible infection origin. In August 2021, total 72 wastewater and river water samples were collected from 32 sampling sites. SARS-CoV-2 ORF1ab and N genes were measured by RT-qPCR. We found that 19 samples (26.39%) were positive, and the viral loads of ORF1ab and N genes were 6.62 × 102-2.55×105 and 1.86 × 103-2.32 × 105 copies/L, respectively. WGS further indicated the sequences in two transboundary river samples, and one hospital wastewater sample belonged to the delta variant, suggesting that the infection source might be areas with high COVID-19 delta variant incidence in Southeast Asia (e.g., Myanmar). We reported for the first time the detection and quantification of SARS-CoV-2 RNA in the transboundary rivers of Myanmar-China. Our findings demonstrate that wastewater and environmental water may provide independent and nonintrusive surveillance points to monitor the global spread of emerging COVID-19 variants of concern, particularly in high-risk regions or border areas with considerable epidemic challenges and poor wastewater treatment facilities.
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Affiliation(s)
- Xiao Zhang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Liang Zhang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Yuanyuan Wang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Meiling Zhang
- Acute Infectious Disease Prevention and Control
Institute, Yunnan Center for Disease Control and Prevention,
Kunming, Yunnan650022, China
| | - Jienan Zhou
- Acute Infectious Disease Prevention and Control
Institute, Yunnan Center for Disease Control and Prevention,
Kunming, Yunnan650022, China
| | - Xin Liu
- Ruili Center for Disease Control and
Prevention, Ruili, Yunnan678599, China
| | - Yan Wang
- Ruili Center for Disease Control and
Prevention, Ruili, Yunnan678599, China
| | - Changsheng Qu
- Longchuan Center for Disease Control and
Prevention, Longchuan, Yunnan678799, China
| | - Wenxiang Han
- Longchuan Center for Disease Control and
Prevention, Longchuan, Yunnan678799, China
| | - Min Hou
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Fuchang Deng
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Yueyun Luo
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Yixin Mao
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Wen Gu
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Zhaomin Dong
- School of Space and Environment, Beihang
University, Beijing100191, China
| | - Yang Pan
- Institute for Infectious Disease and Endemic Disease Control,
Beijing Center for Disease Prevention and Control,
Beijing100013, China
| | - Daitao Zhang
- Institute for Infectious Disease and Endemic Disease Control,
Beijing Center for Disease Prevention and Control,
Beijing100013, China
| | - Song Tang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Lan Zhang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
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36
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Hoar C, McClary-Gutierrez J, Wolfe MK, Bivins A, Bibby K, Silverman AI, McLellan SL. Looking Forward: The Role of Academic Researchers in Building Sustainable Wastewater Surveillance Programs. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:125002. [PMID: 36580023 PMCID: PMC9799055 DOI: 10.1289/ehp11519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND In just over 2 years, tracking the COVID-19 pandemic through wastewater surveillance advanced from early reports of successful SARS-CoV-2 RNA detection in untreated wastewater to implementation of programs in at least 60 countries. Early wastewater monitoring efforts primarily originated in research laboratories and are now transitioning into more formal surveillance programs run in commercial and public health laboratories. A major challenge in this progression has been to simultaneously optimize methods and build scientific consensus while implementing surveillance programs, particularly during the rapidly changing landscape of the pandemic. Translating wastewater surveillance results for effective use by public health agencies also remains a key objective for the field. OBJECTIVES We examined the evolution of wastewater surveillance to identify model collaborations and effective partnerships that have created rapid and sustained success. We propose needed areas of research and key roles academic researchers can play in the framework of wastewater surveillance to aid in the transition from early monitoring efforts to more formalized programs within the public health system. DISCUSSION Although wastewater surveillance has rapidly developed as a useful public health tool for tracking COVID-19, there remain technical challenges and open scientific questions that academic researchers are equipped to address. This includes validating methodology and backfilling important knowledge gaps, such as fate and transport of surveillance targets and epidemiological links to wastewater concentrations. Our experience in initiating and implementing wastewater surveillance programs in the United States has allowed us to reflect on key barriers and draw useful lessons on how to promote synergy between different areas of expertise. As wastewater surveillance programs are formalized, the working relationships developed between academic researchers, commercial and public health laboratories, and data users should promote knowledge co-development. We believe active involvement of academic researchers will contribute to building robust surveillance programs that will ultimately provide new insights into population health. https://doi.org/10.1289/EHP11519.
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Affiliation(s)
- Catherine Hoar
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, New York, USA
| | - Jill McClary-Gutierrez
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marlene K. Wolfe
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Indiana, USA
| | - Andrea I. Silverman
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, New York, USA
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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37
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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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38
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Silva CS, Tryndyak VP, Camacho L, Orloff MS, Porter A, Garner K, Mullis L, Azevedo M. Temporal dynamics of SARS-CoV-2 genome and detection of variants of concern in wastewater influent from two metropolitan areas in Arkansas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157546. [PMID: 35914602 PMCID: PMC9338166 DOI: 10.1016/j.scitotenv.2022.157546] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
Although SARS-CoV-2 can cause severe illness and death, a percentage of the infected population is asymptomatic. This, along with other factors, such as insufficient diagnostic testing and underreporting due to self-testing, contributes to the silent transmission of SARS-CoV-2 and highlights the importance of implementing additional surveillance tools. The fecal shedding of the virus from infected individuals enables its detection in community wastewater, and this has become a valuable public health tool worldwide as it allows the monitoring of the disease on a populational scale. Here, we monitored the presence of SARS-CoV-2 and its dynamic genomic changes in wastewater sampled from two metropolitan areas in Arkansas during major surges of COVID-19 cases and assessed how the viral titers in these samples related to the clinical case counts between late April 2020 and January 2022. The levels of SARS-CoV-2 RNA were quantified by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) using a set of TaqMan assays targeting three different viral genes (encoding ORF1ab polyprotein, surface glycoprotein, and nucleocapsid phosphoprotein). An allele-specific RT-qPCR approach was used to screen the samples for SARS-CoV-2 mutations. The identity and genetic diversity of the virus were further investigated through amplicon-based RNA sequencing, and SARS-CoV-2 variants of concern were detected in wastewater samples throughout the duration of this study. Our data show how changes in the virus genome can affect the sensitivity of specific RT-qPCR assays used in COVID-19 testing with the surge of new variants. A significant association was observed between viral titers in wastewater and recorded number of COVID-19 cases in the areas studied, except when assays failed to detect targets due to the presence of particular variants. These findings support the use of wastewater surveillance as a reliable complementary tool for monitoring SARS-CoV-2 and its genetic variants at the community level.
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Affiliation(s)
- Camila S Silva
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
| | - Volodymyr P Tryndyak
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Luísa Camacho
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Mohammed S Orloff
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Center for the Studies of Tobacco, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Austin Porter
- Department of Health Policy and Management, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Arkansas Department of Health, Little Rock, AR, USA
| | - Kelley Garner
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Arkansas Department of Health, Little Rock, AR, USA
| | - Lisa Mullis
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Marli Azevedo
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
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39
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Mendoza Grijalva L, Brown B, Cauble A, Tarpeh WA. Diurnal Variability of SARS-CoV-2 RNA Concentrations in Hourly Grab Samples of Wastewater Influent during Low COVID-19 Incidence. ACS ES&T WATER 2022; 2:2125-2133. [PMID: 37552729 PMCID: PMC9063989 DOI: 10.1021/acsestwater.2c00061] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/31/2022] [Accepted: 04/06/2022] [Indexed: 06/17/2023]
Abstract
Wastewater-based epidemiology (WBE) has been widely deployed during the COVID-19 pandemic, but with limited evaluation of the utility of discrete sampling for large sewersheds and low COVID-19 incidence. In this study, SARS-CoV-2 RNA was measured in 72 consecutive hourly influent grab samples collected at a wastewater treatment plant serving nearly 500 000 residents when incidence was low (approximately 20 cases per 100 000). We characterized diurnal variability and relationships between SARS-CoV-2 RNA detection and physicochemical covariates [flow rate, total ammonia nitrogen (TAN), and total solids (TS)]. The highest detection rate observed was 82% during the first peak flow, which occurred in the early afternoon (14:00). Higher detection rates were also observed when sampling above median TAN concentrations (71%; p < 0.01; median = 40.26 mg of NH4/L). SARS-CoV-2 RNA concentrations were weakly correlated with flow rate (Kendall's τ = 0.16; p < 0.01), TAN (τ = 0.19; p < 0.05), and TS (τ = 0.18; p < 0.01), suggesting generally low RNA sewer discharges as expected at low incidence. Our results elucidated sensible adjustments to maximize detection rates, including using multiple gene targets, collecting duplicate samples, and sampling during higher flow and TAN discharges. Optimizing the lower-incidence bounds of WBE can help assess its suitability for verifying COVID-19 reemergence or eradication.
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Affiliation(s)
- Lorelay Mendoza Grijalva
- Department of Civil and Environmental Engineering,
Stanford University, Stanford, California 94305,
United States
| | - Blake Brown
- Central Contra Costa Sanitary
District, Martinez, California 94553, United
States
| | - Amanda Cauble
- Central Contra Costa Sanitary
District, Martinez, California 94553, United
States
| | - William A. Tarpeh
- Department of Civil and Environmental Engineering,
Stanford University, Stanford, California 94305,
United States
- Department of Chemical Engineering,
Stanford University, Stanford, California 94305,
United States
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40
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Holm RH, Brick JM, Amraotkar AR, Hart JL, Mukherjee A, Zeigler J, Bushau-Sprinkle AM, Anderson LB, Walker KL, Talley D, Keith RJ, Rai SN, Palmer KE, Bhatnagar A, Smith T. Public Awareness of and Support for the Use of Wastewater for SARS-CoV-2 Monitoring: A Community Survey in Louisville, Kentucky. ACS ES&T WATER 2022; 2:1891-1898. [PMID: 37552721 PMCID: PMC9063986 DOI: 10.1021/acsestwater.1c00405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 05/16/2023]
Abstract
The majority of sewer systems in the United States and other countries are operated by public utilities. In the absence of any regulation, the public perception of wastewater monitoring for population health biomarkers is an important consideration for a public utility commission when allocating resources for this purpose. We conducted a survey in August 2021 as part of an ongoing COVID-19 community prevalence study in Louisville/Jefferson County, KY, US. The survey comprised seven questions about wastewater awareness and privacy concerns and was sent to approximately 35 000 households randomly distributed within the county. A total of 1220 adults were involved in the probability sample, and data from 981 respondents were used in the analysis. A total of 2444 adults additionally responded to the convenience sample, and data from 1751 respondents were used in the analysis. The samples were weighted to obtain estimates representative of all adults in the county. Public awareness of tracking the virus that causes COVID-19 in sewers was low. Opinions strongly support the public disclosure of monitoring results. Responses showed that people more strongly supported measurements in the largest areas (>50 000 households), typically representing population levels found in a large community wastewater treatment plant. Those with a history of COVID-19 infection were more likely to support highly localized monitoring. Understanding wastewater surveillance strategies and privacy concern thresholds requires an in-depth and comprehensive analysis of public opinion for continued success and effective public health monitoring.
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Affiliation(s)
- Rochelle H. Holm
- Christina Lee Brown Envirome Institute, School of
Medicine, University of Louisville, 302 East Muhammad Ali
Boulevard, Louisville, Kentucky 40202, United States
| | - J. Michael Brick
- Westat, Incorporated, 1600
Research Boulevard, Rockville, Maryland 20850, United States
| | - Alok R. Amraotkar
- Christina Lee Brown Envirome Institute, School of
Medicine, University of Louisville, 302 East Muhammad Ali
Boulevard, Louisville, Kentucky 40202, United States
| | - Joy L. Hart
- Christina Lee Brown Envirome Institute, School of
Medicine, University of Louisville, 302 East Muhammad Ali
Boulevard, Louisville, Kentucky 40202, United States
- Department of Communication, College of Arts and
Sciences, University of Louisville, 2010 South Avery Court
Walk, Louisville, Kentucky 40208, United States
| | - Anish Mukherjee
- Department of Bioinformatics and Biostatistics, School
of Public Health and Information Science, University of
Louisville, 505 South Hancock Street, Louisville, Kentucky 40202,
United States
| | - Jacob Zeigler
- Christina Lee Brown Envirome Institute, School of
Medicine, University of Louisville, 302 East Muhammad Ali
Boulevard, Louisville, Kentucky 40202, United States
| | - Adrienne M. Bushau-Sprinkle
- Center for Predictive Medicine for Biodefense and
Emerging Infectious Diseases, University of Louisville, 505
South Hancock Street, Louisville, Kentucky 40202, United States
| | - Lauren B. Anderson
- Christina Lee Brown Envirome Institute, School of
Medicine, University of Louisville, 302 East Muhammad Ali
Boulevard, Louisville, Kentucky 40202, United States
- Center for Healthy Air, Water and Soil,
University of Louisville, 302 East Muhammad Ali Boulevard,
Louisville, Kentucky 40202, United States
| | - Kandi L. Walker
- Christina Lee Brown Envirome Institute, School of
Medicine, University of Louisville, 302 East Muhammad Ali
Boulevard, Louisville, Kentucky 40202, United States
- Department of Communication, College of Arts and
Sciences, University of Louisville, 2010 South Avery Court
Walk, Louisville, Kentucky 40208, United States
| | - Daymond Talley
- Louisville/Jefferson County Metropolitan
Sewer District, Morris Forman Water Quality Treatment Center, 4522
Algonquin Parkway, Louisville, Kentucky 40211, United States
| | - Rachel J. Keith
- Christina Lee Brown Envirome Institute, School of
Medicine, University of Louisville, 302 East Muhammad Ali
Boulevard, Louisville, Kentucky 40202, United States
| | - Shesh N. Rai
- Christina Lee Brown Envirome Institute, School of
Medicine, University of Louisville, 302 East Muhammad Ali
Boulevard, Louisville, Kentucky 40202, United States
- Department of Bioinformatics and Biostatistics, School
of Public Health and Information Science, University of
Louisville, 505 South Hancock Street, Louisville, Kentucky 40202,
United States
- Brown Cancer Center, School of Medicine,
University of Louisville, 505 South Hancock Street,
Louisville, Kentucky 40202, United States
- Center for Integrative Environmental
Health Sciences, 500 South Preston Street, Louisville, Kentucky 40202,
United States
| | - Kenneth E. Palmer
- Center for Predictive Medicine for Biodefense and
Emerging Infectious Diseases, University of Louisville, 505
South Hancock Street, Louisville, Kentucky 40202, United States
- Department of Pharmacology and Toxicology, School of
Medicine, University of Louisville, 323 East Chestnut Street,
Louisville, Kentucky 40202, United States
| | - Aruni Bhatnagar
- Christina Lee Brown Envirome Institute, School of
Medicine, University of Louisville, 302 East Muhammad Ali
Boulevard, Louisville, Kentucky 40202, United States
| | - Ted Smith
- Christina Lee Brown Envirome Institute, School of
Medicine, University of Louisville, 302 East Muhammad Ali
Boulevard, Louisville, Kentucky 40202, United States
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41
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Ahmed W, Smith WJM, Metcalfe S, Jackson G, Choi PM, Morrison M, Field D, Gyawali P, Bivins A, Bibby K, Simpson SL. Comparison of RT-qPCR and RT-dPCR Platforms for the Trace Detection of SARS-CoV-2 RNA in Wastewater. ACS ES&T WATER 2022; 2:1871-1880. [PMID: 36380768 PMCID: PMC8848507 DOI: 10.1021/acsestwater.1c00387] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We compared reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and RT digital PCR (RT-dPCR) platforms for the trace detection of SARS-CoV-2 RNA in low-prevalence COVID-19 locations in Queensland, Australia, using CDC N1 and CDC N2 assays. The assay limit of detection (ALOD), PCR inhibition rates, and performance characteristics of each assay, along with the positivity rates with the RT-qPCR and RT-dPCR platforms, were evaluated by seeding known concentrations of exogenous SARS-CoV-2 in wastewater. The ALODs using RT-dPCR were approximately 2-5 times lower than those using RT-qPCR. During sample processing, the endogenous (n = 96) and exogenous (n = 24) SARS-CoV-2 wastewater samples were separated, and RNA was extracted from both wastewater eluates and pellets (solids). The RT-dPCR platform demonstrated a detection rate significantly greater than that of RT-qPCR for the CDC N1 and CDC N2 assays in the eluate (N1, p = 0.0029; N2, p = 0.0003) and pellet (N1, p = 0.0015; N2, p = 0.0067) samples. The positivity results also indicated that for the analysis of SARS-CoV-2 RNA in wastewater, including the eluate and pellet samples may further increase the detection sensitivity using RT-dPCR.
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Affiliation(s)
- Warish Ahmed
- CSIRO
Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J. M. Smith
- CSIRO
Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Suzanne Metcalfe
- CSIRO
Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Greg Jackson
- Water
Unit, Health Protection Branch, Prevention Division, Queensland Health, Brisbane, QLD 4001, Australia
| | - Phil M. Choi
- Water
Unit, Health Protection Branch, Prevention Division, Queensland Health, Brisbane, QLD 4001, Australia
| | - Mary Morrison
- Water
Unit, Health Protection Branch, Prevention Division, Queensland Health, Brisbane, QLD 4001, Australia
| | - Daniel Field
- Water
Unit, Health Protection Branch, Prevention Division, Queensland Health, Brisbane, QLD 4001, Australia
| | - Pradip Gyawali
- Institute
of Environmental Science and Research Ltd. (ESR), Porirua 5240, New Zealand
| | - Aaron Bivins
- Department
of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kyle Bibby
- Department
of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
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42
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Babler KM, Amirali A, Sharkey ME, Williams SL, Boone MM, Cosculluela GA, Currall BB, Grills GS, Laine J, Mason CE, Reding BD, Schürer SC, Stevenson M, Vidovic D, Solo-Gabriele HM. Comparison of Electronegative Filtration to Magnetic Bead-Based Concentration and V2G-qPCR to RT-qPCR for Quantifying Viral SARS-CoV-2 RNA from Wastewater. ACS ES&T WATER 2022; 2:2004-2013. [PMID: 37601294 PMCID: PMC10438908 DOI: 10.1021/acsestwater.2c00047] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Methods of wastewater concentration (electronegative filtration (ENF) versus magnetic bead-based concentration (MBC)) were compared for the analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), beta-2 microglobulin, and human-coronavirus OC43. Using ENF as the concentration method, two quantitative Polymerase Chain Reaction (qPCR) analytical methods were also compared: Volcano 2nd Generation (V2G)-qPCR and reverse transcriptase (RT)-qPCR measuring three different targets of the virus responsible for the COVID-19 illness (N1, modified N3, and ORF1ab). Correlations between concentration methods were strong and statistically significant for SARS-CoV-2 (r=0.77, p<0.001) and B2M (r=0.77, p<0.001). Comparison of qPCR analytical methods indicate that, on average, each method provided equivalent results with average ratios of 0.96, 0.96 and 1.02 for N3 to N1, N3 to ORF1ab, and N1 to ORF1ab and were supported by significant (p<0.001) correlation coefficients (r =0.67 for V2G (N3) to RT (N1), r =0.74 for V2G (N3) to RT (ORF1ab), r = 0.81 for RT (N1) to RT (ORF1ab)). Overall results suggest that the two concentration methods and qPCR methods provide equivalent results, although variability is observed for individual measurements. Given the equivalency of results, additional advantages and disadvantages, as described in the discussion, are to be considered when choosing an appropriate method.
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Affiliation(s)
- Kristina M. Babler
- Department of Chemical, Environmental and Materials Engineering, Coral Gables, FL USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental and Materials Engineering, Coral Gables, FL USA
| | - Mark E. Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL USA
| | - Sion L. Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - Melinda M. Boone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | | | - Benjamin B. Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - Jennifer Laine
- Department of Physiology and Biophysics and the WorldQuant Initiative, Weill Cornell Medicine, New York City, NY USA
| | | | - Brian D. Reding
- Department of Physiology and Biophysics and the WorldQuant Initiative, Weill Cornell Medicine, New York City, NY USA
| | - Stephan C. Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL USA
- Institute for Data Science & Computing, University of Miami, Coral Gables, FL USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL USA
| | - Dusica Vidovic
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL USA
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43
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Holst MM, Person J, Jennings W, Welsh RM, Focazio MJ, Bradley PM, Schill WB, Kirby AE, Marsh ZA. Rapid Implementation of High-Frequency Wastewater Surveillance of SARS-CoV-2. ACS ES&T WATER 2022; 2:2201-2210. [PMID: 37552727 PMCID: PMC9291391 DOI: 10.1021/acsestwater.2c00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 08/10/2023]
Abstract
There have been over 507 million cases of COVID-19, the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in 6 million deaths globally. Wastewater surveillance has emerged as a valuable tool in understanding SARS-CoV-2 burden in communities. The National Wastewater Surveillance System (NWSS) partnered with the United States Geological Survey (USGS) to implement a high-frequency sampling program. This report describes basic surveillance and sampling statistics as well as a comparison of SARS-CoV-2 trends between high-frequency sampling 3-5 times per week, referred to as USGS samples, and routine sampling 1-2 times per week, referred to as NWSS samples. USGS samples provided a more nuanced impression of the changes in wastewater trends, which could be important in emergency response situations. Despite the rapid implementation time frame, USGS samples had similar data quality and testing turnaround times as NWSS samples. Ensuring there is a reliable sample collection and testing plan before an emergency arises will aid in the rapid implementation of a high-frequency sampling approach. High-frequency sampling requires a constant flow of information and supplies throughout sample collection, testing, analysis, and data sharing. High-frequency sampling may be a useful approach for increased resolution of disease trends in emergency response.
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Affiliation(s)
- Meghan M. Holst
- Centers for Disease Control and Prevention,
National Center for Emerging and Zoonotic Infectious
Diseases, 1600 Clifton Road, Atlanta, Georgia 30333, United
States
| | - John Person
- Centers for Disease Control and Prevention,
National Center for Emerging and Zoonotic Infectious
Diseases, 1600 Clifton Road, Atlanta, Georgia 30333, United
States
| | - Wiley Jennings
- Centers for Disease Control and Prevention,
National Center for Emerging and Zoonotic Infectious
Diseases, 1600 Clifton Road, Atlanta, Georgia 30333, United
States
| | - Rory M. Welsh
- Centers for Disease Control and Prevention,
National Center for Emerging and Zoonotic Infectious
Diseases, 1600 Clifton Road, Atlanta, Georgia 30333, United
States
| | - Michael J. Focazio
- United States Geological
Survey, 12201 Sunrise Valley Drive, Reston, Virginia 20192,
United States
| | - Paul M. Bradley
- United States Geological
Survey, Columbia, South Carolina 29210, United
States
| | - William B. Schill
- United States Geological
Survey, Kearneysville, West Virginia 25430, United
States
| | - Amy E. Kirby
- Centers for Disease Control and Prevention,
National Center for Emerging and Zoonotic Infectious
Diseases, 1600 Clifton Road, Atlanta, Georgia 30333, United
States
| | - Zachary A. Marsh
- Centers for Disease Control and Prevention,
National Center for Emerging and Zoonotic Infectious
Diseases, 1600 Clifton Road, Atlanta, Georgia 30333, United
States
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44
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Hoar C, Li Y, Silverman AI. Assessment of Commonly Measured Wastewater Parameters to Estimate Sewershed Populations for Use in Wastewater-Based Epidemiology: Insights into Population Dynamics in New York City during the COVID-19 Pandemic. ACS ES&T WATER 2022; 2:2014-2024. [PMID: 37552716 PMCID: PMC9063991 DOI: 10.1021/acsestwater.2c00052] [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: 01/31/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 06/18/2023]
Abstract
Understanding per capita rates of disease incidence or prevalence from wastewater surveillance data requires an estimate of the population contributing to wastewater samples, given that populations in large urban areas are dynamic, especially if major events, such as the onset of the COVID-19 pandemic, cause large population shifts. To assess whether commonly measured wastewater parameters can be used to estimate sewershed populations, we used wastewater data collected from New York City's (NYC) 14 wastewater treatment facilities to evaluate the relationship between influent loads of four wastewater parameters-ammonia, total Kjeldahl nitrogen, total suspended solids, and five-day carbonaceous biochemical oxygen demand-and census-based population estimates of the corresponding sewersheds during 2019, when populations were assumed to be relatively stable. Ammonia mass load had the most consistent relationship with sewershed population, regardless of wet weather contributions to NYC's predominantly combined sewer system. Changes in ammonia loads due to COVID-19 restrictions enacted in March 2020 generally reflected population shifts in sewersheds serving areas of Manhattan and Brooklyn, for which previous studies report decreased commuter mobility and residential populations. Our findings highlight the utility of ammonia mass load in influent wastewater as a population indicator to normalize wastewater-based epidemiology data and track sewershed population dynamics.
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Affiliation(s)
| | | | - Andrea I. Silverman
- Department of Civil and Urban Engineering, Tandon School of Engineering,
New York University, Brooklyn, New York 11201,
United States
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45
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Safford H, Zuniga-Montanez RE, Kim M, Wu X, Wei L, Sharpnack J, Shapiro K, Bischel HN. Wastewater-Based Epidemiology for COVID-19: Handling qPCR Nondetects and Comparing Spatially Granular Wastewater and Clinical Data Trends. ACS ES&T WATER 2022; 2:2114-2124. [PMID: 37552742 PMCID: PMC9397567 DOI: 10.1021/acsestwater.2c00053] [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: 01/31/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 05/28/2023]
Abstract
Wastewater-based epidemiology (WBE) is a useful complement to clinical testing for managing COVID-19. While community-scale wastewater and clinical data frequently correlate, less is known about subcommunity relationships between the two data types. Moreover, nondetects in qPCR wastewater data are typically handled through methods known to bias results, overlooking perhaps better alternatives. We address these knowledge gaps using data collected from September 2020-June 2021 in Davis, California (USA). We hypothesize that coupling the expectation maximization (EM) algorithm with the Markov Chain Monte Carlo (MCMC) method could improve estimation of "missing" values in wastewater qPCR data. We test this hypothesis by applying EM-MCMC to city wastewater treatment plant data and comparing output to more conventional nondetect handling methods. Dissimilarities in results (i) underscore the importance of specifying nondetect handling method in reporting and (ii) suggest that using EM-MCMC may yield better agreement between community-scale clinical and wastewater data. We also present a novel framework for spatially aligning clinical data with wastewater data collected upstream of a treatment plant (i.e., distributed across a sewershed). Applying the framework to data from Davis reveals reasonable agreement between wastewater and clinical data at highly granular spatial scales-further underscoring the public-health value of WBE.
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Affiliation(s)
- Hannah Safford
- Department of Civil and Environmental Engineering,
University of California Davis, 3109 Ghausi Hall, 480 Bainer
Hall Drive, Davis, California 95616, United States
| | - Rogelio E. Zuniga-Montanez
- Department of Civil and Environmental Engineering,
University of California Davis, 3109 Ghausi Hall, 480 Bainer
Hall Drive, Davis, California 95616, United States
| | - Minji Kim
- School of Veterinary Medicine, University
of California Davis, Davis, California 95616, United
States
| | - Xiaoliu Wu
- Department of Statistics, University of
California Davis, Davis, California 95616, United
States
| | - Lifeng Wei
- Department of Statistics, University of
California Davis, Davis, California 95616, United
States
| | - James Sharpnack
- Department of Statistics, University of
California Davis, Davis, California 95616, United
States
| | - Karen Shapiro
- School of Veterinary Medicine, University
of California Davis, Davis, California 95616, United
States
| | - Heather N. Bischel
- Department of Civil and Environmental Engineering,
University of California Davis, 3109 Ghausi Hall, 480 Bainer
Hall Drive, Davis, California 95616, United States
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46
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Xie Y, Challis JK, Oloye FF, Asadi M, Cantin J, Brinkmann M, McPhedran KN, Hogan N, Sadowski M, Jones PD, Landgraff C, Mangat C, Servos MR, Giesy JP. RNA in Municipal Wastewater Reveals Magnitudes of COVID-19 Outbreaks across Four Waves Driven by SARS-CoV-2 Variants of Concern. ACS ES&T WATER 2022; 2:1852-1862. [PMID: 37552734 PMCID: PMC8887651 DOI: 10.1021/acsestwater.1c00349] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 05/07/2023]
Abstract
There are no standardized protocols for quantifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater to date, especially for population normalization. Here, a pipeline was developed, applied, and assessed to quantify SARS-CoV-2 and key variants of concern (VOCs) RNA in wastewater at Saskatoon, Canada. Normalization approaches using recovery ratio and extraction efficiency, wastewater parameters, or population indicators were assessed by comparing to daily numbers of new cases. Viral load was positively correlated with daily new cases reported in the sewershed. Wastewater surveillance (WS) had a lead time of approximately 7 days, which indicated surges in the number of new cases. WS revealed the variant α and δ driving the third and fourth wave, respectively. The adjustment with the recovery ratio and extraction efficiency improved the correlation between viral load and daily new cases. Normalization of viral concentration to concentrations of the artificial sweetener acesulfame K improved the trend of viral load during the Christmas and New Year holidays when populations were dynamic and variable. Acesulfame K performed better than pepper mild mottle virus, creatinine, and ammonia for population normalization. Hence, quality controls to characterize recovery ratios and extraction efficiencies and population normalization with acesulfame are promising for precise WS programs supporting decision-making in public health.
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Affiliation(s)
- Yuwei Xie
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Jonathan K. Challis
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Femi F. Oloye
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental
Engineering, College of Engineering, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5A9,
Canada
| | - Jenna Cantin
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Markus Brinkmann
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- School of Environment and Sustainability,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- Global Institute for Water Security,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5,
Canada
| | - Kerry N. McPhedran
- Department of Civil, Geological and Environmental
Engineering, College of Engineering, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5A9,
Canada
- Global Institute for Water Security,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5,
Canada
| | - Natacha Hogan
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- College of Agriculture and Bioresources, Department of
Animal and Poultry Sciences, University of Saskatchewan,
Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department,
City of Saskatoon, Saskatoon, Saskatchewan S7M 1X5,
Canada
| | - Paul D. Jones
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- School of Environment and Sustainability,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology
Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
R3E 3R2, Canada
- Food Science Department, University of
Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Chand Mangat
- Antimicrobial Resistance and Nosocomial Infections,
National Microbiology Laboratory, Public Health Agency of
Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Mark R. Servos
- Department of Biology, University of
Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - John P. Giesy
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- Department of Veterinary Biomedical Sciences,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4,
Canada
- Department of Environmental Sciences,
Baylor University, Waco, Texas 76706, United
States
- Department of Zoology and Center for Integrative
Toxicology, Michigan State University, East Lansing, Michigan
48824, United States
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47
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Langan LM, O’Brien M, Rundell ZC, Back JA, Ryan BJ, Chambliss CK, Norman RS, Brooks BW. Comparative Analysis of RNA-Extraction Approaches and Associated Influences on RT-qPCR of the SARS-CoV-2 RNA in a University Residence Hall and Quarantine Location. ACS ES&T WATER 2022; 2:1929-1943. [PMID: 37552714 PMCID: PMC9063990 DOI: 10.1021/acsestwater.1c00476] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 05/09/2023]
Abstract
Wastewater-based epidemiology (WBE) provides an early warning and trend analysis approach for determining the presence of COVID-19 in a community and complements clinical testing in assessing the population level, even as viral loads fluctuate. Here, we evaluate combinations of two wastewater concentration methods (i.e., ultrafiltration and composite supernatant-solid), four pre-RNA extraction modifications, and three nucleic acid extraction kits using two different wastewater sampling locations. These consisted of a quarantine facility containing clinically confirmed COVID-19-positive inhabitants and a university residence hall. Of the combinations examined, composite supernatant-solid with pre-RNA extraction consisting of water concentration and RNA/DNA shield performed the best in terms of speed and sensitivity. Further, of the three nucleic acid extraction kits examined, the most variability was associated with the Qiagen kit. Focusing on the quarantine facility, viral concentrations measured in wastewater were generally significantly related to positive clinical cases, with the relationship dependent on method, modification, kit, target, and normalization, although results were variable-dependent on individual time points (Kendall's Tau-b (τ) = 0.17 to 0.6) or cumulatively (Kendall's Tau-b (τ) = -0.048 to 1). These observations can support laboratories establishing protocols to perform wastewater surveillance and monitoring efforts for COVID-19.
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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
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Zach C. Rundell
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Jeffrey A. Back
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Benjamin J. Ryan
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
| | - C. Kevin Chambliss
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Chemistry and Biochemistry,
Baylor University, One Bear Place #97348, Waco, Texas 76798,
United States
| | - R. Sean Norman
- Environmental Health Sciences, Arnold
School of Public Health, South Carolina, 921 Assembly Street, Columbia,
South Carolina 29208, 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
- Institute of Biomedical Studies, Baylor
University, One Bear Place #97224, Waco, Texas 76798, United
States
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48
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Vadde KK, Al-Duroobi H, Phan DC, Jafarzadeh A, Moghadam SV, Matta A, Kapoor V. Assessment of Concentration, Recovery, and Normalization of SARS-CoV-2 RNA from Two Wastewater Treatment Plants in Texas and Correlation with COVID-19 Cases in the Community. ACS ES&T WATER 2022; 2:2060-2069. [PMID: 37552728 PMCID: PMC9128005 DOI: 10.1021/acsestwater.2c00054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/12/2022] [Accepted: 05/04/2022] [Indexed: 05/18/2023]
Abstract
The purpose of this study was to conduct a correlative assessment of SARS-CoV-2 RNA concentrations in wastewater with COVID-19 cases and a systematic evaluation of the effect of using different virus concentration methods and recovery and normalization approaches. We measured SARS-CoV-2 RNA concentrations at two different wastewater treatment plants (WWTPs) in the Bexar County of Texas from October 2020 to May 2021 (32 weeks) using reverse transcription droplet digital PCR (RT-ddPCR). We evaluated three different adsorption-extraction (AE) based virus concentration methods (acidification, addition of MgCl2, or without any pretreatment) using bovine coronavirus (BCoV) as surrogate virus and observed that the direct AE method showed the highest mean recovery. COVID-19 cases were correlated significantly with SARS-CoV-2 N1 concentrations in Salitrillo (ρ = 0.75, p < 0.001) and Martinez II (ρ = 0.68, p < 0.001) WWTPs, but normalizing to a spiked recovery control (BCoV) or a fecal marker (HF183) reduced correlations for both treatment plants. The results generated in this 32-week monitoring study will enable researchers to prioritize the virus recovery method and subsequent correlation studies for wastewater surveillance.
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Affiliation(s)
- Kiran Kumar Vadde
- School of Civil & Environmental Engineering, and
Construction Management, University of Texas at San Antonio,
San Antonio, Texas 78249, United States
| | - Haya Al-Duroobi
- School of Civil & Environmental Engineering, and
Construction Management, University of Texas at San Antonio,
San Antonio, Texas 78249, United States
| | - Duc C. Phan
- School of Civil & Environmental Engineering, and
Construction Management, University of Texas at San Antonio,
San Antonio, Texas 78249, United States
| | - Arash Jafarzadeh
- School of Civil & Environmental Engineering, and
Construction Management, University of Texas at San Antonio,
San Antonio, Texas 78249, United States
| | - Sina V. Moghadam
- School of Civil & Environmental Engineering, and
Construction Management, University of Texas at San Antonio,
San Antonio, Texas 78249, United States
| | - Akanksha Matta
- Department of Chemistry, University of
Texas at San Antonio, San Antonio, Texas 78249, United
States
| | - Vikram Kapoor
- School of Civil & Environmental Engineering, and
Construction Management, University of Texas at San Antonio,
San Antonio, Texas 78249, United States
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49
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The Detection of Periodic Reemergence Events of SARS-CoV-2 Delta Strain in Communities Dominated by Omicron. Pathogens 2022; 11:pathogens11111249. [PMID: 36365000 PMCID: PMC9697103 DOI: 10.3390/pathogens11111249] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/14/2022] [Accepted: 10/24/2022] [Indexed: 12/01/2022] Open
Abstract
Despite entering an endemic phase, SARS-CoV-2 remains a significant burden to public health across the global community. Wastewater sampling has consistently proven utility to understanding SARS-CoV-2 prevalence trends and genetic variation as it represents a less biased assessment of the corresponding communities. Here, we report that ongoing monitoring of SARS-CoV-2 genetic variation in samples obtained from the wastewatersheds of the city of Louisville in Jefferson county Kentucky has revealed the periodic reemergence of the Delta strain in the presence of the presumed dominant Omicron strain. Unlike previous SARS-CoV-2 waves/emergence events, the Delta reemergence events were geographically restricted in the community and failed to spread into other areas as determined by wastewater analyses. Moreover, the reemergence of the Delta strain did not correlate with vaccination rates as communities with lower relative vaccination have been, to date, not affected. Importantly, Delta reemergence events correlate with increased public health burdens, as indicated by increased daily case rates and mortality relative to non-Delta wastewatershed communities. While the underlying reasons for the reemergence of the Delta variant remain unclear, these data reaffirm the ongoing importance of wastewater genomic analyses towards understanding SARS-CoV-2 as it enters the endemic phase.
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50
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Jakariya M, Ahmed F, Islam MA, Al Marzan A, Hasan MN, Hossain M, Ahmed T, Hossain A, Reza HM, Hossen F, Nahla T, Rahman MM, Bahadur NM, Islam MT, Didar-Ul-Alam M, Mow N, Jahan H, Barceló D, Bibby K, Bhattacharya P. Wastewater-based epidemiological surveillance to monitor the prevalence of SARS-CoV-2 in developing countries with onsite sanitation facilities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 311:119679. [PMID: 35753547 PMCID: PMC9225114 DOI: 10.1016/j.envpol.2022.119679] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 05/23/2023]
Abstract
Wastewater-based epidemiology (WBE) has emerged as a valuable approach for forecasting disease outbreaks in developed countries with a centralized sewage infrastructure. On the other hand, due to the absence of well-defined and systematic sewage networks, WBE is challenging to implement in developing countries like Bangladesh where most people live in rural areas. Identification of appropriate locations for rural Hotspot Based Sampling (HBS) and urban Drain Based Sampling (DBS) are critical to enable WBE based monitoring system. We investigated the best sampling locations from both urban and rural areas in Bangladesh after evaluating the sanitation infrastructure for forecasting COVID-19 prevalence. A total of 168 wastewater samples were collected from 14 districts of Bangladesh during each of the two peak pandemic seasons. RT-qPCR commercial kits were used to target ORF1ab and N genes. The presence of SARS-CoV-2 genetic materials was found in 98% (165/168) and 95% (160/168) wastewater samples in the first and second round sampling, respectively. Although wastewater effluents from both the marketplace and isolation center drains were found with the highest amount of genetic materials according to the mixed model, quantifiable SARS-CoV-2 RNAs were also identified in the other four sampling sites. Hence, wastewater samples of the marketplace in rural areas and isolation centers in urban areas can be considered the appropriate sampling sites to detect contagion hotspots. This is the first complete study to detect SARS-CoV-2 genetic components in wastewater samples collected from rural and urban areas for monitoring the COVID-19 pandemic. The results based on the study revealed a correlation between viral copy numbers in wastewater samples and SARS-CoV-2 positive cases reported by the Directorate General of Health Services (DGHS) as part of the national surveillance program for COVID-19 prevention. The findings of this study will help in setting strategies and guidelines for the selection of appropriate sampling sites, which will facilitate in development of comprehensive wastewater-based epidemiological systems for surveillance of rural and urban areas of low-income countries with inadequate sewage infrastructure.
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Affiliation(s)
- Md Jakariya
- Department of Environmental Science and Management, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Firoz Ahmed
- COVID-19 Diagnostic Laboratory, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Aminul Islam
- COVID-19 Diagnostic Laboratory, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh; Advanced Molecular Laboratory, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, Bangladesh
| | - Abdullah Al Marzan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Mohammad Nayeem Hasan
- Department of Statistics, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Maqsud Hossain
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Tanvir Ahmed
- Department of Civil Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Ahmed Hossain
- Department of Public Health, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Hasan Mahmud Reza
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Foysal Hossen
- COVID-19 Diagnostic Laboratory, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Turasa Nahla
- Department of Environmental Science and Management, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Mohammad Moshiur Rahman
- Department of Environmental Science and Management, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Tahmidul Islam
- WaterAid Bangladesh, Dhaka, 1213, Bangladesh; COVID-19 Research@KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-10044, Stockholm, Sweden
| | - Md Didar-Ul-Alam
- Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Nowrin Mow
- WaterAid Bangladesh, Dhaka, 1213, Bangladesh
| | - Hasin Jahan
- WaterAid Bangladesh, Dhaka, 1213, Bangladesh
| | - Damiá Barceló
- Water, Environmental and Food Chemistry Unit (ENFOCHEM), Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Spanish National Research Council (CSIC), C. Jordi Giron 18-26, 08034, Barcelona, Spain
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Prosun Bhattacharya
- COVID-19 Research@KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-10044, Stockholm, Sweden.
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