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Chai X, Liu S, Liu C, Bai J, Meng J, Tian H, Han X, Han G, Xu X, Li Q. Surveillance of SARS-CoV-2 in wastewater by quantitative PCR and digital PCR: a case study in Shijiazhuang city, Hebei province, China. Emerg Microbes Infect 2024; 13:2324502. [PMID: 38465692 DOI: 10.1080/22221751.2024.2324502] [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: 12/13/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024]
Abstract
In this study, we reported the first long-term monitoring of SARS-CoV-2 in wastewater in Mainland China from November 2021 to October 2023. The city of Shijiazhuang was employed for this case study. We developed a triple reverse transcription droplet digital PCR (RT-ddPCR) method using triple primer-probes for simultaneous detection of the N1 gene, E gene, and Pepper mild mottle virus (PMMoV) to achieve accurate quantification of SARS-CoV-2 RNA in wastewater. Both the RT-ddPCR method and the commercial multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) method were implemented for the detection of SARS-CoV-2 in wastewater in Shijiazhuang City over a 24-month period. Results showed that SARS-CoV-2 was detected for the first time in the wastewater of Shijiazhuang City on 10 November 2022. The peak of COVID-19 cases occurred in the middle of December 2022, when the concentration of SARS-CoV-2 in the wastewater was highest. The trend of virus concentration increases and decreases forming a "long-tailed" shape in the COVID-19 outbreak and recession cycle. The results indicated that both multiplex RT-ddPCR and RT-qPCR are effective in detecting SARS-CoV-2 in wastewater, but RT-ddPCR is capable of detecting low concentrations of SARS-CoV-2 in wastewater which is more efficient. The SARS-CoV-2 abundance in wastewater is correlated to clinical data, outlining the public health utility of this work.HighlightsFirst long-term monitoring of SARS-CoV-2 in wastewater in Mainland ChinaCOVID-19 outbreak was tracked in Shijiazhuang City from outbreak to containmentWastewater was monitored simultaneously using RT-ddPCR and RT-qPCR methodsTriple primer-probe RT-ddPCR detects N1 and E genes of SARS-CoV-2 and PMMoV.
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Affiliation(s)
- Xiaoru Chai
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Shiyou Liu
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Chao Liu
- Shijiazhuang Qiaodong Sewage Treatment Plant, Shijiazhuang, People's Republic of China
| | - Jiaxuan Bai
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Juntao Meng
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Hong Tian
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Xu Han
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Guangyue Han
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Xiangdong Xu
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, People's Republic of China
| | - Qi Li
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
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Tang L, Guo Z, Lu X, Zhao J, Li Y, Yang K. Wastewater multiplex PCR amplicon sequencing revealed community transmission of SARS-CoV-2 lineages during the outbreak of infection in Chinese Mainland. Heliyon 2024; 10:e35332. [PMID: 39166043 PMCID: PMC11334792 DOI: 10.1016/j.heliyon.2024.e35332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/22/2024] Open
Abstract
During the COVID-19, wastewater-based epidemiology (WBE) has become a powerful epidemic surveillance tool widely used worldwide. However, the development and application of this technology in Chinese Mainland are relatively lagging. Herein, we for the first time monitored the community circulation of SARS-CoV-2 lineages using WBE methods in Chinese Mainland. During the peak period of infection outbreak at the end of 2022, six precious sewage samples were collected from the manhole in the student dormitory area on Wangjiang Campus of Sichuan University. RT-qPCR revealed that the six sewage samples were all positive for SARS-CoV-2 RNA. Multiplex PCR amplicon sequencing of the sewage samples reflected the local transmission of SARS-CoV-2 variants. The results of two deconvolution methods indicate that the main virus lineages have clear evolutionary genetic correlations. Furthermore, the sampling time is consistent with the timeline of concern for these virus lineages, as well as the timeline of uploading the nucleic acid sequences from the corresponding lineages in Sichuan to the database. These results demonstrate the reliability of the sewage sequencing results. Multiplex PCR amplicon sequencing is by far the most powerful analytical tool of WBE, enabling quantitative detection of virus lineages transmission and evolution at the community level.
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Affiliation(s)
| | | | - Xiaoyi Lu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Junqiao Zhao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Yonghong Li
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
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Corchis-Scott R, Beach M, Geng Q, Podadera A, Corchis-Scott O, Norton J, Busch A, Faust RA, McFarlane S, Withington S, Irwin B, Aloosh M, Ng KKS, McKay RM. Wastewater Surveillance to Confirm Differences in Influenza A Infection between Michigan, USA, and Ontario, Canada, September 2022-March 2023. Emerg Infect Dis 2024; 30:1580-1588. [PMID: 39043398 PMCID: PMC11286066 DOI: 10.3201/eid3008.240225] [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] [Indexed: 07/25/2024] Open
Abstract
Wastewater surveillance is an effective way to track the prevalence of infectious agents within a community and, potentially, the spread of pathogens between jurisdictions. We conducted a retrospective wastewater surveillance study of the 2022-23 influenza season in 2 communities, Detroit, Michigan, USA, and Windsor-Essex, Ontario, Canada, that form North America's largest cross-border conurbation. We observed a positive relationship between influenza-related hospitalizations and the influenza A virus (IAV) wastewater signal in Windsor-Essex (ρ = 0.785; p<0.001) and an association between influenza-related hospitalizations in Michigan and the IAV wastewater signal for Detroit (ρ = 0.769; p<0.001). Time-lagged cross correlation and qualitative examination of wastewater signal in the monitored sewersheds showed the peak of the IAV season in Detroit was delayed behind Windsor-Essex by 3 weeks. Wastewater surveillance for IAV reflects regional differences in infection dynamics which may be influenced by many factors, including the timing of vaccine administration between jurisdictions.
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D'Aoust PM, Hegazy N, Ramsay NT, Yang MI, Dhiyebi HA, Edwards E, Servos MR, Ybazeta G, Habash M, Goodridge L, Poon A, Arts E, Brown RS, Payne SJ, Kirkwood A, Simmons D, Desaulniers JP, Ormeci B, Kyle C, Bulir D, Charles T, McKay RM, Gilbride K, Oswald C, Peng H, Pileggi V, Wang ML, Tong A, Orellano D, DeGroot CT, Delatolla R. SARS-CoV-2 viral titer measurements in Ontario, Canada wastewaters throughout the COVID-19 pandemic. Sci Data 2024; 11:656. [PMID: 38906875 PMCID: PMC11192951 DOI: 10.1038/s41597-024-03414-w] [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: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 06/23/2024] Open
Abstract
During the COVID-19 pandemic, the Province of Ontario, Canada, launched a wastewater surveillance program to monitor SARS-CoV-2, inspired by the early work and successful forecasts of COVID-19 waves in the city of Ottawa, Ontario. This manuscript presents a dataset from January 1, 2021, to March 31, 2023, with RT-qPCR results for SARS-CoV-2 genes and PMMoV from 107 sites across all 34 public health units in Ontario, covering 72% of the province's and 26.2% of Canada's population. Sampling occurred 2-7 times weekly, including geographical coordinates, serviced populations, physico-chemical water characteristics, and flowrates. In doing so, this manuscript ensures data availability and metadata preservation to support future research and epidemic preparedness through detailed analyses and modeling. The dataset has been crucial for public health in tracking disease locally, especially with the rise of the Omicron variant and the decline in clinical testing, highlighting wastewater-based surveillance's role in estimating disease incidence in Ontario.
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Affiliation(s)
| | | | | | | | | | | | | | - Gustavo Ybazeta
- Health Sciences North Research Institute, Sudbury, ON, Canada
| | | | | | - Art Poon
- Western University, London, ON, Canada
| | - Eric Arts
- Western University, London, ON, Canada
| | | | | | | | | | | | | | | | | | | | | | | | - Claire Oswald
- Toronto Metropolitan University, Toronto, ON, Canada
| | - Hui Peng
- University of Toronto, Toronto, ON, Canada
| | - Vince Pileggi
- Ontario Ministry of the Environment, Conservation and Parks, Toronto, ON, Canada
| | - Menglu L Wang
- Toronto Metropolitan University, Toronto, ON, Canada
| | - Arthur Tong
- Toronto Metropolitan University, Toronto, ON, Canada
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Lee CS, Wang M, Nanjappa D, Lu YT, Meliker J, Clouston S, Gobler CJ, Venkatesan AK. Monitoring of over-the-counter (OTC) and COVID-19 treatment drugs complement wastewater surveillance of SARS-CoV-2. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2024; 34:448-456. [PMID: 38052940 PMCID: PMC11222153 DOI: 10.1038/s41370-023-00613-2] [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: 04/24/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND The application of wastewater-based epidemiology to track the outbreak and prevalence of coronavirus disease (COVID-19) in communities has been tested and validated by several researchers across the globe. However, the RNA-based surveillance has its inherent limitations and uncertainties. OBJECTIVE This study aims to complement the ongoing wastewater surveillance efforts by analyzing other chemical biomarkers in wastewater to help assess community response (hospitalization and treatment) during the pandemic (2020-2021). METHODS Wastewater samples (n = 183) were collected from the largest wastewater treatment facility in Suffolk County, NY, USA and analyzed for COVID-19 treatment drugs (remdesivir, chloroquine, and hydroxychloroquine (HCQ)) and their human metabolites. We additionally monitored 26 pharmaceuticals including common over-the-counter (OTC) drugs. Lastly, we developed a Bayesian model that uses viral RNA, COVID-19 treatment drugs, and pharmaceuticals data to predict the confirmed COVID-19 cases within the catchment area. RESULTS The viral RNA levels in wastewater tracked the actual COVID-19 case numbers well as expected. COVID-19 treatment drugs were detected with varying frequency (9-100%) partly due to their instability in wastewater. We observed a significant correlation (R = 0.30, p < 0.01) between the SARS-CoV-2 genes and desethylhydroxychloroquine (DHCQ, metabolite of HCQ). Remdesivir levels peaked immediately after the Emergency Use Authorization approved by the FDA. Although, 13 out of 26 pharmaceuticals assessed were consistently detected (DF = 100%, n = 111), only acetaminophen was significantly correlated with viral loads, especially when the Omicron variant was dominant. The Bayesian models were capable of reproducing the temporal trend of the confirmed cases. IMPACT In this study, for the first time, we measured COVID-19 treatment and pharmaceutical drugs and their metabolites in wastewater to complement ongoing COVID-19 viral RNA surveillance efforts. Our results highlighted that, although the COVID-19 treatment drugs were not very stable in wastewater, their detection matched with usage trends in the community. Acetaminophen, an OTC drug, was significantly correlated with viral loads and confirmed cases, especially when the Omicron variant was dominant. A Bayesian model was developed which could predict COVID-19 cases more accurately when incorporating other drugs data along with viral RNA levels in wastewater.
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Affiliation(s)
- Cheng-Shiuan Lee
- New York State Center for Clean Water Technology, Stony Brook University, Stony Brook, NY, 11794, USA
- Research Center for Environmental Changes, Academia Sinica, Taipei, 11529, Taiwan
| | - Mian Wang
- New York State Center for Clean Water Technology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Deepak Nanjappa
- New York State Center for Clean Water Technology, Stony Brook University, Stony Brook, NY, 11794, USA
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Yi-Ta Lu
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Jaymie Meliker
- Program in Public Health, Department of Family, Population & Preventive Medicine, Stony Brook University Medical Center, Stony Brook, NY, 11794, USA
| | - Sean Clouston
- Program in Public Health, Department of Family, Population & Preventive Medicine, Stony Brook University Medical Center, Stony Brook, NY, 11794, USA
| | - Christopher J Gobler
- New York State Center for Clean Water Technology, Stony Brook University, Stony Brook, NY, 11794, USA
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Arjun K Venkatesan
- New York State Center for Clean Water Technology, Stony Brook University, Stony Brook, NY, 11794, USA.
- Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
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Chen C, Kaur G, Adiga A, Espinoza B, Venkatramanan S, Warren A, Lewis B, Crow J, Singh R, Lorentz A, Toney D, Marathe M. Wastewater-based Epidemiology for COVID-19 Surveillance: A Survey. ARXIV 2024:arXiv:2403.15291v1. [PMID: 38562450 PMCID: PMC10984000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The pandemic of COVID-19 has imposed tremendous pressure on public health systems and social economic ecosystems over the past years. To alleviate its social impact, it is important to proactively track the prevalence of COVID-19 within communities. The traditional way to estimate the disease prevalence is to estimate from reported clinical test data or surveys. However, the coverage of clinical tests is often limited and the tests can be labor-intensive, requires reliable and timely results, and consistent diagnostic and reporting criteria. Recent studies revealed that patients who are diagnosed with COVID-19 often undergo fecal shedding of SARS-CoV-2 virus into wastewater, which makes wastewater-based epidemiology (WBE) for COVID-19 surveillance a promising approach to complement traditional clinical testing. In this paper, we survey the existing literature regarding WBE for COVID-19 surveillance and summarize the current advances in the area. Specifically, we have covered the key aspects of wastewater sampling, sample testing, and presented a comprehensive and organized summary of wastewater data analytical methods. Finally, we provide the open challenges on current wastewater-based COVID-19 surveillance studies, aiming to encourage new ideas to advance the development of effective wastewater-based surveillance systems for general infectious diseases.
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Affiliation(s)
- Chen Chen
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Gursharn Kaur
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Aniruddha Adiga
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Baltazar Espinoza
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Srinivasan Venkatramanan
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Andrew Warren
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Bryan Lewis
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Justin Crow
- Virginia Department of Health, Richmond, 23219, United States
| | - Rekha Singh
- Virginia Department of Health, Richmond, 23219, United States
| | - Alexandra Lorentz
- Division of Consolidated Laboratory Services, Department of General Services, Richmond, 23219, United States
| | - Denise Toney
- Division of Consolidated Laboratory Services, Department of General Services, Richmond, 23219, United States
| | - Madhav Marathe
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
- Department of Computer Science, University of Virginia, Charlottesville, 22904, United States
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Carducci A, Federigi I, Lauretani G, Muzio S, Pagani A, Atomsa NT, Verani M. Critical Needs for Integrated Surveillance: Wastewater-Based and Clinical Epidemiology in Evolving Scenarios with Lessons Learned from SARS-CoV-2. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:38-49. [PMID: 38168848 DOI: 10.1007/s12560-023-09573-0] [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: 07/19/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024]
Abstract
During the COVID-19 pandemic, wastewater-based epidemiology (WBE) and clinical surveillance have been used as tools for analyzing the circulation of SARS-CoV-2 in the community, but both approaches can be strongly influenced by some sources of variability. From the challenging perspective of integrating environmental and clinical data, we performed a correlation analysis between SARS-CoV-2 concentrations in raw sewage and incident COVID-19 cases in areas served by medium-size wastewater treatment plants (WWTPs) from 2021 to 2023. To this aim, both datasets were adjusted for several sources of variability: WBE data were adjusted for factors including the analytical protocol, sewage flow, and population size, while clinical data adjustments considered the demographic composition of the served population. Then, we addressed the impact on the correlation of differences among sewerage networks and variations in the frequency and type of swab tests due to changes in political and regulatory scenarios. Wastewater and clinical data were significantly correlated when restrictive containment measures and limited movements were in effect (ρ = 0.50) and when COVID-19 cases were confirmed exclusively through molecular testing (ρ = 0.49). Moreover, a positive (although weak) correlation arose for WWTPs located in densely populated areas (ρ = 0.37) and with shorter sewerage lengths (ρ = 0.28). This study provides methodological approaches for interpreting WBE and clinical surveillance data, which could also be useful for other infections. Data adjustments and evaluation of possible sources of bias need to be carefully considered from the perspective of integrated environmental and clinical surveillance of infections.
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Affiliation(s)
- Annalaura Carducci
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
| | - Ileana Federigi
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy.
| | - Giulia Lauretani
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
| | - Sara Muzio
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
| | - Alessandra Pagani
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
| | - Nebiyu Tariku Atomsa
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
| | - Marco Verani
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
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Thakali O, Mercier É, Eid W, Wellman M, Brasset-Gorny J, Overton AK, Knapp JJ, Manuel D, Charles TC, Goodridge L, Arts EJ, Poon AFY, Brown RS, Graber TE, Delatolla R, DeGroot CT. Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation. Sci Rep 2024; 14:3728. [PMID: 38355869 PMCID: PMC10866965 DOI: 10.1038/s41598-024-54319-y] [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: 08/02/2023] [Accepted: 02/11/2024] [Indexed: 02/16/2024] Open
Abstract
Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity of RT-qPCR has been achieved, in part, by monitoring two or more genomic loci of SARS-CoV-2. In Ontario, Canada, the provincial Wastewater Surveillance Initiative reports the average copies of the CDC N1 and N2 loci normalized to the fecal biomarker pepper mild mottle virus. In November 2021, the emergence of the Omicron variant of concern, harboring a C28311T mutation within the CDC N1 probe region, challenged the accuracy of the consensus between the RT-qPCR measurements of the N1 and N2 loci of SARS-CoV-2. In this study, we developed and applied a novel real-time dual loci quality assurance and control framework based on the relative difference between the loci measurements to the City of Ottawa dataset to identify a loss of sensitivity of the N1 assay in the period from July 10, 2022 to January 31, 2023. Further analysis via sequencing and allele-specific RT-qPCR revealed a high proportion of mutations C28312T and A28330G during the study period, both in the City of Ottawa and across the province. It is hypothesized that nucleotide mutations in the probe region, especially A28330G, led to inefficient annealing, resulting in reduction in sensitivity and accuracy of the N1 assay. This study highlights the importance of implementing quality assurance and control criteria to continually evaluate, in near real-time, the accuracy of the signal produced in wastewater surveillance applications that rely on detection of pathogens whose genomes undergo high rates of mutation.
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Affiliation(s)
- Ocean Thakali
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Martin Wellman
- The Ottawa Hospital Research Institute, 1053 Carling Ave, Ottawa, ON, K1Y 4E9, Canada
| | - Julia Brasset-Gorny
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Alyssa K Overton
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Jennifer J Knapp
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Douglas Manuel
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
- Department of Family Medicine, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON, K1N 6N5, Canada
- School of Epidemiology and Public Health, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON, K1N 6N5, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Lawrence Goodridge
- Department of Food Science, Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Art F Y Poon
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - R Stephen Brown
- School of Environmental Studies and Department of Chemistry, Queen's University, Kingston, ON, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher T DeGroot
- Department of Mechanical and Materials Engineering, Western University, London, ON, N6A 5B9, Canada.
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Therrien JD, Thomson M, Sion ES, Lee I, Maere T, Nicolaï N, Manuel DG, Vanrolleghem PA. A comprehensive, open-source data model for wastewater-based epidemiology. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 89:1-19. [PMID: 38214983 PMCID: wst_2023_409 DOI: 10.2166/wst.2023.409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
The recent SARS-COV-2 pandemic has sparked the adoption of wastewater-based epidemiology (WBE) as a low-cost way to monitor the health of populations. In parallel, the pandemic has encouraged researchers to openly share their data to serve the public better and accelerate science. However, environmental surveillance data are highly dependent on context and are difficult to interpret meaningfully across sites. This paper presents the second iteration of the Public Health Environmental Surveillance Open Data Model (PHES-ODM), an open-source dictionary and set of data tools to enhance the interoperability of environmental surveillance data and enable the storage of contextual (meta)data. The data model describes how to store environmental surveillance program data, metadata about measurements taken on various specimens (water, air, surfaces, sites, populations) and data about measurement protocols. The model provides software tools that support the collection and use of PHES-ODM formatted data, including performing PCR calculations and data validation, recording data into input templates, generating wide tables for analysis, and producing SQL database definitions. Fully open-source and already adopted by institutions in Canada, the European Union, and other countries, the PHES-ODM provides a path forward for creating robust, interoperable, open datasets for environmental public health surveillance for SARS-CoV-2 and beyond.
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Affiliation(s)
| | - Mathew Thomson
- Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Eugen-Sorin Sion
- European Commission, European Research Council, Joint Research Centre, Ispra, Italy
| | - Ivan Lee
- Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Thomas Maere
- modelEAU, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Niels Nicolaï
- modelEAU, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Douglas G Manuel
- Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
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10
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Brighton K, Fisch S, Wu H, Vigil K, Aw TG. Targeted community wastewater surveillance for SARS-CoV-2 and Mpox virus during a festival mass-gathering event. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167443. [PMID: 37793442 DOI: 10.1016/j.scitotenv.2023.167443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023]
Abstract
Wastewater surveillance has emerged recently as a powerful approach to understanding infectious disease dynamics in densely populated zones. Wastewater surveillance, while promising as a public health tool, is often hampered by slow turn-around times, complex analytical protocols, and resource-intensive techniques. In this study, we evaluated an affinity capture method and microfluidic digital PCR as a rapid approach to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mpox (formerly known as monkeypox) virus, and fecal indicator, pepper mild mottle virus (PMMoV) in wastewater during a mass-gathering event. Wastewater samples (n = 131) were collected from residential and commercial manholes, pump stations, and a city's wastewater treatment plant. The use of Nanotrap® Microbiome Particles and microfluidic digital PCR produced comparable results to other established methodologies, with reduced process complexity and analytical times, providing same day results for public health preparedness and response. Using indigenous SARS-CoV-2 and PMMoV in wastewater, the average viral recovery efficiency was estimated at 10.1 %. Both SARS-CoV-2 N1 and N2 genes were consistently detected throughout the sampling period, with increased RNA concentrations mainly in wastewater samples collected from commercial area after festival mass gatherings. The mpox virus was sporadically detected in wastewater samples during the surveillance period, without distinct temporal trends. SARS-CoV-2 RNA concentrations in the city's wastewater mirrored the city's COVID-19 cases, confirming the predictive properties of wastewater surveillance. Wastewater surveillance continues to be beneficial for tracking diseases that display gastrointestinal symptoms, including SARS-CoV-2, and can be a powerful tool for sentinel surveillance. However, careful site selection and a thorough understanding of community dynamics are necessary when performing targeted surveillance during temporary mass-gathering events as potential confirmation bias may occur.
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Affiliation(s)
- Keegan Brighton
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Samuel Fisch
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Huiyun Wu
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Katie Vigil
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA.
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11
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Hegazy N, Tian X, D'Aoust PM, Pisharody L, Towhid ST, Mercier É, Zhang Z, Wan S, Thakali O, Kabir MP, Fang W, Nguyen TB, Ramsay NT, MacKenzie AE, Graber TE, Guilherme S, Delatolla R. Impact of coagulation on SARS-CoV-2 and PMMoV viral signal in wastewater solids. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:5242-5253. [PMID: 38112868 DOI: 10.1007/s11356-023-31444-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
Wastewater surveillance (WWS) of SARS-CoV-2 has become a crucial tool for monitoring COVID-19 cases and outbreaks. Previous studies have indicated that SARS-CoV-2 RNA measurement from testing solid-rich primary sludge yields better sensitivity compared to testing wastewater influent. Furthermore, measurement of pepper mild mottle virus (PMMoV) signal in wastewater allows for precise normalization of SARS-CoV-2 viral signal based on solid content, enhancing disease prevalence tracking. However, despite the widespread adoption of WWS, a knowledge gap remains regarding the impact of ferric sulfate coagulation, commonly used in enhanced primary clarification, the initial stage of wastewater treatment where solids are sedimented and removed, on SARS-CoV-2 and PMMoV quantification in wastewater-based epidemiology. This study examines the effects of ferric sulfate addition, along with the associated pH reduction, on the measurement of SARS-CoV-2 and PMMoV viral measurements in wastewater primary clarified sludge through jar testing. Results show that the addition of Fe3+ concentrations in the conventional 0 to 60 mg/L range caused no effect on SARS-CoV-2 N1 and N2 gene region measurements in wastewater solids. However, elevated Fe3+ concentrations were shown to be associated with a statistically significant increase in PMMoV viral measurements in wastewater solids, which consequently resulted in the underestimation of PMMoV-normalized SARS-CoV-2 viral signal measurements (N1 and N2 copies/copies of PMMoV). The observed pH reduction from coagulant addition did not contribute to the increased PMMoV measurements, suggesting that this phenomenon arises from the partitioning of PMMoV viral particles into wastewater solids.
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Affiliation(s)
- Nada Hegazy
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Xin Tian
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Lakshmi Pisharody
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | | | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Zhihao Zhang
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Shen Wan
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Ocean Thakali
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Md Pervez Kabir
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Wanting Fang
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Tram B Nguyen
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Nathan T Ramsay
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | | | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada.
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12
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Hasing ME, Lee BE, Gao T, Li Q, Qiu Y, Ellehoj E, Graber TE, Fuzzen M, Servos M, Landgraff C, Delatolla R, Tipples G, Zelyas N, Hinshaw D, Maal-Bared R, Sikora C, Parkins M, Hubert CRJ, Frankowski K, Hrudey SE, Pang XL. Wastewater surveillance monitoring of SARS-CoV-2 variants of concern and dynamics of transmission and community burden of COVID-19. Emerg Microbes Infect 2023; 12:2233638. [PMID: 37409382 PMCID: PMC10408568 DOI: 10.1080/22221751.2023.2233638] [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: 11/21/2022] [Revised: 06/04/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Wastewater-based surveillance is a valuable approach for monitoring COVID-19 at community level. Monitoring SARS-CoV-2 variants of concern (VOC) in wastewater has become increasingly relevant when clinical testing capacity and case-based surveillance are limited. In this study, we ascertained the turnover of six VOC in Alberta wastewater from May 2020 to May 2022. Wastewater samples from nine wastewater treatment plants across Alberta were analysed using VOC-specific RT-qPCR assays. The performance of the RT-qPCR assays in identifying VOC in wastewater was evaluated against next generation sequencing. The relative abundance of each VOC in wastewater was compared to positivity rate in COVID-19 testing. VOC-specific RT-qPCR assays performed comparatively well against next generation sequencing; concordance rates ranged from 89% to 98% for detection of Alpha, Beta, Gamma, Omicron BA.1 and Omicron BA.2, with a slightly lower rate of 85% for Delta (p < 0.01). Elevated relative abundance of Alpha, Delta, Omicron BA.1 and BA.2 were each associated with increased COVID-19 positivity rate. Alpha, Delta and Omicron BA.2 reached 90% relative abundance in wastewater within 80, 111 and 62 days after their initial detection, respectively. Omicron BA.1 increased more rapidly, reaching a 90% relative abundance in wastewater after 35 days. Our results from VOC surveillance in wastewater correspond with clinical observations that Omicron is the VOC with highest disease burden over the shortest period in Alberta to date. The findings suggest that changes in relative abundance of a VOC in wastewater can be used as a supplementary indicator to track and perhaps predict COVID-19 burden in a population.
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Affiliation(s)
- Maria E. Hasing
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Bonita E. Lee
- Department of Paediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Tiejun Gao
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Qiaozhi Li
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Erik Ellehoj
- Ellehoj Redmond Consulting, Edmonton, Alberta, Canada
| | - Tyson E. Graber
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mark Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Graham Tipples
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Nathan Zelyas
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Deena Hinshaw
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Christopher Sikora
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaoli L. Pang
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
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13
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Bohrerova Z, Brinkman NE, Chakravarti R, Chattopadhyay S, Faith SA, Garland J, Herrin J, Hull N, Jahne M, Kang DW, Keely SP, Lee J, Lemeshow S, Lenhart J, Lytmer E, Malgave D, Miao L, Minard-Smith A, Mou X, Nagarkar M, Quintero A, Savona FDR, Senko J, Slonczewski JL, Spurbeck RR, Sovic MG, Taylor RT, Weavers LK, Weir M. Ohio Coronavirus Wastewater Monitoring Network: Implementation of Statewide Monitoring for Protecting Public Health. JOURNAL OF PUBLIC HEALTH MANAGEMENT AND PRACTICE 2023; 29:845-853. [PMID: 37738597 PMCID: PMC10539008 DOI: 10.1097/phh.0000000000001783] [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] [Indexed: 09/24/2023]
Abstract
CONTEXT Prior to the COVID-19 pandemic, wastewater influent monitoring for tracking disease burden in sewered communities was not performed in Ohio, and this field was only on the periphery of the state academic research community. PROGRAM Because of the urgency of the pandemic and extensive state-level support for this new technology to detect levels of community infection to aid in public health response, the Ohio Water Resources Center established relationships and support of various stakeholders. This enabled Ohio to develop a statewide wastewater SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) monitoring network in 2 months starting in July 2020. IMPLEMENTATION The current Ohio Coronavirus Wastewater Monitoring Network (OCWMN) monitors more than 70 unique locations twice per week, and publicly available data are updated weekly on the public dashboard. EVALUATION This article describes the process and decisions that were made during network initiation, the network progression, and data applications, which can inform ongoing and future pandemic response and wastewater monitoring. DISCUSSION Overall, the OCWMN established wastewater monitoring infrastructure and provided a useful tool for public health professionals responding to the pandemic.
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Affiliation(s)
- Zuzana Bohrerova
- Ohio Water Resources Center (Drs Bohrerova, Lenhart, and Weavers), Civil, Environmental and Geodetic Engineering (Drs Bohrerova, Hull, Lenhart, and Weavers), Infectious Diseases Institute (Drs Faith and Lee and Ms Savona), Sustainability Institute (Dr Hull), Department of Food Science & Technology (Dr Lee), and Center for Applied Plant Sciences (Dr Sovic), The Ohio State University, Columbus, Ohio; Office of Research and Development, US Environmental Protection Agency, Washington, District of Columbia (Drs Brinkman, Garland, Jahne, Keely, and Nagarkar); Departments of Physiology and Pharmacology (Dr Chakravarti) and Medical Microbiology and Immunology (Drs Chattopadhyay and Taylor), University of Toledo College of Medicine and Life Sciences, Toledo, Ohio; LuminUltra Technologies Inc, Hialeah, Florida (Mr Herrin and Dr Quintero); Department of Civil and Environmental Engineering, University of Toledo, Toledo, Ohio (Dr Kang); Divisions of Environmental Health Sciences (Drs Lee and Weir) and Biostatistics (Drs Lemeshow and Malgave and Ms Miao), The Ohio State University College of Public Health, Columbus, Ohio; Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio (Ms Lytmer); Health Outcomes and Biotechnology Solutions, Battelle Memorial Institute, Columbus, Ohio (Ms Minard-Smith and Dr Spurbeck); Department of Biological Sciences, Kent State University, Kent, Ohio (Dr Mou); Department of Geosciences and Department of Biology, The University of Akron, Akron, Ohio (Dr Senko); and Department of Biology, Kenyon College, Gambier, Ohio (Dr Slonczewski)
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14
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Marques Dos Santos M, Caixia L, Snyder SA. Evaluation of wastewater-based epidemiology of COVID-19 approaches in Singapore's 'closed-system' scenario: A long-term country-wide assessment. WATER RESEARCH 2023; 244:120406. [PMID: 37542765 DOI: 10.1016/j.watres.2023.120406] [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: 07/23/2022] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/07/2023]
Abstract
With the COVID-19 pandemic the use of WBE to track diseases spread has rapidly evolved into a widely applied strategy worldwide. However, many of the current studies lack the necessary systematic approach and supporting quality of epidemiological data to fully evaluate the effectiveness and usefulness of such methods. Use of WBE in a very low disease prevalence setting and for long-term monitoring has yet to be validated and it is critical for its intended use as an early warning system. In this study we seek to evaluate the sensitivity of WBE approaches under low prevalence of disease and ability to provide early warning. Two monitoring scenarios were used: (i) city wide monitoring (population 5,700,000) and (ii) community/localized monitoring (population 24,000 to 240,000). Prediction of active cases by WBE using multiple linear regression shows that a multiplexed qPCR approach with three gene targets has a significant advantage over single-gene monitoring approaches, with R2 = 0.832 (RMSE 0.053) for an analysis using N, ORF1ab and S genes (R2 = 0.677 to 0.793 for single gene strategies). A predicted disease prevalence of 0.001% (1 in 100,000) for a city-wide monitoring was estimated by the multiplexed RT-qPCR approach and was corroborated by epidemiological data evidence in three 'waves'. Localized monitoring setting shows an estimated detectable disease prevalence of ∼0.002% (1 in 56,000) and is supported by the geospatial distribution of active cases and local population dynamics data. Data analysis also shows that this approach has a limitation in sensitivity, or hit rate, of 62.5 % and an associated high miss rate (false negative rate) of 37.5 % when compared to available epidemiological data. Nevertheless, our study shows that, with enough sampling resolution, WBE at a community level can achieve high precision and accuracies for case detection (96 % and 95 %, respectively) with low false omission rate (4.5 %) even at low disease prevalence levels.
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Affiliation(s)
- Mauricius Marques Dos Santos
- Nanyang Technological University, Nanyang Environment & Water Research Institute (NEWRI), 1 Cleantech Loop, CleanTech One, #06-08, Singapore 637141
| | - Li Caixia
- Nanyang Technological University, Nanyang Environment & Water Research Institute (NEWRI), 1 Cleantech Loop, CleanTech One, #06-08, Singapore 637141
| | - Shane Allen Snyder
- Nanyang Technological University, Nanyang Environment & Water Research Institute (NEWRI), 1 Cleantech Loop, CleanTech One, #06-08, Singapore 637141; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
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15
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Peng KK, Renouf EM, Dean CB, Hu XJ, Delatolla R, Manuel DG. An exploration of the relationship between wastewater viral signals and COVID-19 hospitalizations in Ottawa, Canada. Infect Dis Model 2023; 8:617-631. [PMID: 37342365 PMCID: PMC10245285 DOI: 10.1016/j.idm.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/15/2023] [Accepted: 05/28/2023] [Indexed: 06/22/2023] Open
Abstract
Monitoring of viral signal in wastewater is considered a useful tool for monitoring the burden of COVID-19, especially during times of limited availability in testing. Studies have shown that COVID-19 hospitalizations are highly correlated with wastewater viral signals and the increases in wastewater viral signals can provide an early warning for increasing hospital admissions. The association is likely nonlinear and time-varying. This project employs a distributed lag nonlinear model (DLNM) (Gasparrini et al., 2010) to study the nonlinear exposure-response delayed association of the COVID-19 hospitalizations and SARS-CoV-2 wastewater viral signals using relevant data from Ottawa, Canada. We consider up to a 15-day time lag from the average of SARS-CoV N1 and N2 gene concentrations to COVID-19 hospitalizations. The expected reduction in hospitalization is adjusted for vaccination efforts. A correlation analysis of the data verifies that COVID-19 hospitalizations are highly correlated with wastewater viral signals with a time-varying relationship. Our DLNM based analysis yields a reasonable estimate of COVID-19 hospitalizations and enhances our understanding of the association of COVID-19 hospitalizations with wastewater viral signals.
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Affiliation(s)
- K. Ken Peng
- Department of Statistics and Actuarial Science, Simon Fraser University, 8888 University Dr, Burnaby, V5A 1S6, BC, Canada
| | - Elizabeth M. Renouf
- Department of Statistics and Actuarial Science, University of Waterloo, 200 University Ave W, Waterloo, N2L 3G1, ON, Canada
| | - Charmaine B. Dean
- Department of Statistics and Actuarial Science, University of Waterloo, 200 University Ave W, Waterloo, N2L 3G1, ON, Canada
| | - X. Joan Hu
- Department of Statistics and Actuarial Science, Simon Fraser University, 8888 University Dr, Burnaby, V5A 1S6, BC, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, 75 Laurier Ave. E, Ottawa, K1N 6N5, ON, Canada
| | - Douglas G. Manuel
- The Ottawa Hospital Research Institute, 1053 Carling Ave, Ottawa, K1Y 4E9, ON, Canada
- Department of Family Medicine, University of Ottawa, 75 Laurier Ave. E, Ottawa, K1N 6N5, ON, Canada
- School of Epidemiology and Public Health, University of Ottawa, 75 Laurier Ave. E, Ottawa, K1N 6N5, ON, Canada
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16
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Phan T, Brozak S, Pell B, Oghuan J, Gitter A, Hu T, Ribeiro RM, Ke R, Mena KD, Perelson AS, Kuang Y, Wu F. Making waves: Integrating wastewater surveillance with dynamic modeling to track and predict viral outbreaks. WATER RESEARCH 2023; 243:120372. [PMID: 37494742 DOI: 10.1016/j.watres.2023.120372] [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: 03/26/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 07/28/2023]
Abstract
Wastewater surveillance has proved to be a valuable tool to track the COVID-19 pandemic. However, most studies using wastewater surveillance data revolve around establishing correlations and lead time relative to reported case data. In this perspective, we advocate for the integration of wastewater surveillance data with dynamic within-host and between-host models to better understand, monitor, and predict viral disease outbreaks. Dynamic models overcome emblematic difficulties of using wastewater surveillance data such as establishing the temporal viral shedding profile. Complementarily, wastewater surveillance data bypasses the issues of time lag and underreporting in clinical case report data, thus enhancing the utility and applicability of dynamic models. The integration of wastewater surveillance data with dynamic models can enhance real-time tracking and prevalence estimation, forecast viral transmission and intervention effectiveness, and most importantly, provide a mechanistic understanding of infectious disease dynamics and the driving factors. Dynamic modeling of wastewater surveillance data will advance the development of a predictive and responsive monitoring system to improve pandemic preparedness and population health.
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Affiliation(s)
- Tin Phan
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Samantha Brozak
- School of Mathematical and Statistical Sciences, Arizona State University, AZ 85281, USA
| | - Bruce Pell
- Department of Mathematics and Computer Science, Lawrence Technological University, MI 48075, USA
| | - Jeremiah Oghuan
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Anna Gitter
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Tao Hu
- Department of Geography, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Kristina D Mena
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Texas Epidemic Public Health Institute, Houston, TX 77030, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, AZ 85281, USA
| | - Fuqing Wu
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Texas Epidemic Public Health Institute, Houston, TX 77030, USA.
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17
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Arts PJ, Kelly JD, Midgley CM, Anglin K, Lu S, Abedi GR, Andino R, Bakker KM, Banman B, Boehm AB, Briggs-Hagen M, Brouwer AF, Davidson MC, Eisenberg MC, Garcia-Knight M, Knight S, Peluso MJ, Pineda-Ramirez J, Diaz Sanchez R, Saydah S, Tassetto M, Martin JN, Wigginton KR. Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage. mSphere 2023; 8:e0013223. [PMID: 37338211 PMCID: PMC10506459 DOI: 10.1128/msphere.00132-23] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/03/2023] [Indexed: 06/21/2023] Open
Abstract
Wastewater-based epidemiology (WBE) emerged during the coronavirus disease 2019 (COVID-19) pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden. The lack of high-resolution fecal shedding data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) limits our ability to link WBE measurements to disease burden. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as for the commonly used fecal indicators pepper mild mottle virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. The shedding trajectories from 48 SARS-CoV-2-infected individuals suggest a highly individualized, dynamic course of SARS-CoV-2 RNA fecal shedding. Of the individuals that provided at least three stool samples spanning more than 14 days, 77% had one or more samples that tested positive for SARS-CoV-2 RNA. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall. CrAssphage DNA was detected in at least one sample from 80% (38/48) of individuals and was detected in 48% (179/371) of all samples. The geometric mean concentrations of PMMoV and crAssphage in stool across all individuals were 8.7 × 104 and 1.4 × 104 gene copies/milligram-dry weight, respectively, and crAssphage shedding was more consistent for individuals than PMMoV shedding. These results provide us with a missing link needed to connect laboratory WBE results with mechanistic models, and this will aid in more accurate estimates of COVID-19 burden in sewersheds. Additionally, the PMMoV and crAssphage data are critical for evaluating their utility as fecal strength normalizing measures and for source-tracking applications. IMPORTANCE This research represents a critical step in the advancement of wastewater monitoring for public health. To date, mechanistic materials balance modeling of wastewater-based epidemiology has relied on SARS-CoV-2 fecal shedding estimates from small-scale clinical reports or meta-analyses of research using a wide range of analytical methodologies. Additionally, previous SARS-CoV-2 fecal shedding data have not contained sufficient methodological information for building accurate materials balance models. Like SARS-CoV-2, fecal shedding of PMMoV and crAssphage has been understudied to date. The data presented here provide externally valid and longitudinal fecal shedding data for SARS-CoV-2, PMMoV, and crAssphage which can be directly applied to WBE models and ultimately increase the utility of WBE.
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Affiliation(s)
- Peter J. Arts
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Division of Hospital Medicine, UCSF, San Francisco, California, USA
- F.I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Claire M. Midgley
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Khamal Anglin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Glen R. Abedi
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Raul Andino
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
| | - Kevin M. Bakker
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Bryon Banman
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandria B. Boehm
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California, USA
| | - Melissa Briggs-Hagen
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrew F. Brouwer
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marisa C. Eisenberg
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Sterling Knight
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael J. Peluso
- Division of HIV, Infectious Disease, and Global Medicine, UCSF, San Francisco, California, USA
| | - Jesus Pineda-Ramirez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Ruth Diaz Sanchez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Sharon Saydah
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Krista R. Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
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18
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Wadi VS, Daou M, Zayed N, AlJabri M, Alsheraifi HH, Aldhaheri SS, Abuoudah M, Alhammadi M, Aldhuhoori M, Lopes A, Alalawi A, Yousef AF, Hasan SW, Alsafar H. Long-term study on wastewater SARS-CoV-2 surveillance across United Arab Emirates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 887:163785. [PMID: 37149161 PMCID: PMC10156646 DOI: 10.1016/j.scitotenv.2023.163785] [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] [Received: 02/21/2023] [Revised: 04/18/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Wastewater-based epidemiology (WBE) demonstrates an efficient tool to monitor and predict SARS-CoV-2 community distribution. Many countries across the world have adopted the technique, however, most of these studies were conducted for a short duration with a limited sampling size. In this study, long-term reliability and quantification of wastewater SARS-CoV-2 surveillance is reported via analyzing 16,858 samples collected from 453 different locations across the United Arab Emirates (UAE) from May 2020 to June 2022. The collected composite samples were first incubated at 60 °C followed by filtration, concentration, and then RNA extraction using commercially available kits. The extracted RNA was then analyzed by one-step RT-qPCR and RT-ddPCR, and the data was compared to the reported clinical cases. The average positivity rate in the wastewater samples was found to be 60.61 % (8.41-96.77 %), however, the positivity rate obtained from the RT-ddPCR was significantly higher than the RT-qPCR suggesting higher sensitivity of RT-ddPCR. Time-lagged correlation analysis indicated an increase in positive cases in the wastewater samples when the clinical positive cases declined suggesting that wastewater data are highly affected by the unreported asymptomatic, pre-symptomatic and recovering individuals. The weekly SARS-CoV-2 viral count in the wastewater samples are positively correlated with the diagnosed new clinical cases throughout the studied period and the studied locations. Viral count in wastewater peaked approximately one to two weeks prior to the peaks appearing in active clinical cases indicating that wastewater viral concentrations are effective in predicting clinical cases. Overall, this study further confirms the long-term sensitivity and robust approach of WBE to detect trends in SARS-CoV-2 spread and helps contribute to pandemic management.
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Affiliation(s)
- Vijay S Wadi
- Center for Membranes and Advanced Water Technology (CMAT), Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Mariane Daou
- Department of Biology, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Noora Zayed
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Maryam AlJabri
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Hamad H Alsheraifi
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Saeed S Aldhaheri
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Miral Abuoudah
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Mohammad Alhammadi
- Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
| | - Malika Aldhuhoori
- Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
| | - Alvaro Lopes
- Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
| | - Abdulrahman Alalawi
- Department of Health, Safety and Environment, Department of Energy, Abu Dhabi, United Arab Emirates
| | - Ahmed F Yousef
- Center for Membranes and Advanced Water Technology (CMAT), Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates; Department of Biology, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Shadi W Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates; Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates; Department of Biomedical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates.
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19
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de Melo T, Islam G, Simmons DBD, Desaulniers JP, Kirkwood AE. An alternative method for monitoring and interpreting influenza A in communities using wastewater surveillance. Front Public Health 2023; 11:1141136. [PMID: 37575124 PMCID: PMC10413874 DOI: 10.3389/fpubh.2023.1141136] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Seasonal influenza is an annual public health challenge that strains healthcare systems, yet population-level prevalence remains under-reported using standard clinical surveillance methods. Wastewater surveillance (WWS) of influenza A can allow for reliable flu surveillance within a community by leveraging existing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) WWS networks regardless of the sample type (primary sludge vs. primary influent) using an RT-qPCR-based viral RNA detection method for both targets. Additionally, current influenza A outbreaks disproportionately affect the pediatric population. In this study, we show the utility of interpreting influenza A WWS data with elementary student absenteeism due to illness to selectively interpret disease spread in the pediatric population. Our results show that the highest statistically significant correlation (Rs = 0.96, p = 0.011) occurred between influenza A WWS data and elementary school absences due to illness. This correlation coefficient is notably higher than the correlations observed between influenza A WWS data and influenza A clinical case data (Rs = 0.79, p = 0.036). This method can be combined with a suite of pathogen data from wastewater to provide a robust system for determining the causative agents of diseases that are strongly symptomatic in children to infer pediatric outbreaks within communities.
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Affiliation(s)
| | - Golam Islam
- Faculty of Science, Ontario Tech University, Oshawa, ON, Canada
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20
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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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21
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Fuzzen M, Harper NBJ, Dhiyebi HA, Srikanthan N, Hayat S, Bragg LM, Peterson SW, Yang I, Sun JX, Edwards EA, Giesy JP, Mangat CS, Graber TE, Delatolla R, Servos MR. An improved method for determining frequency of multiple variants of SARS-CoV-2 in wastewater using qPCR assays. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163292. [PMID: 37030387 PMCID: PMC10079313 DOI: 10.1016/j.scitotenv.2023.163292] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 06/01/2023]
Abstract
Wastewater-based surveillance has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Variants of Concern (VOCs) have been detected in wastewater by use of reverse transcription polymerase chain reaction (RT-PCR) or whole genome sequencing (WGS). Rapid, reliable RT-PCR assays continue to be needed to determine the relative frequencies of VOCs and sub-lineages in wastewater-based surveillance programs. The presence of multiple mutations in a single region of the N-gene allowed for the design of a single amplicon, multiple probe assay, that can distinguish among several VOCs in wastewater RNA extracts. This approach which multiplexes probes designed to target mutations associated with specific VOC's along with an intra-amplicon universal probe (non-mutated region) was validated in singleplex and multiplex. The prevalence of each mutation (i.e. VOC) is estimated by comparing the abundance of the targeted mutation with a non-mutated and highly conserved region within the same amplicon. This is advantageous for the accurate and rapid estimation of variant frequencies in wastewater. The N200 assay was applied to monitor frequencies of VOCs in wastewater extracts from several communities in Ontario, Canada in near real time from November 28, 2021 to January 4, 2022. This includes the period of the rapid replacement of the Delta variant with the introduction of the Omicron variant in these Ontario communities in early December 2021. The frequency estimates using this assay were highly reflective of clinical WGS estimates for the same communities. This style of qPCR assay, which simultaneously measures signal from a non-mutated comparator probe and multiple mutation-specific probes contained within a single qPCR amplicon, can be applied to future assay development for rapid and accurate estimations of variant frequencies.
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Affiliation(s)
- Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
| | | | - Hadi A Dhiyebi
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Nivetha Srikanthan
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Samina Hayat
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Leslie M Bragg
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Shelley W Peterson
- One-Health Division, Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3M4, Canada
| | - Ivy Yang
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - J X Sun
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Elizabeth A Edwards
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - John P Giesy
- Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
| | - Chand S Mangat
- One-Health Division, Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3M4, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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22
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Gupta P, Liao S, Ezekiel M, Novak N, Rossi A, LaCross N, Oakeson K, Rohrwasser A. Wastewater Genomic Surveillance Captures Early Detection of Omicron in Utah. Microbiol Spectr 2023; 11:e0039123. [PMID: 37154725 PMCID: PMC10269515 DOI: 10.1128/spectrum.00391-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
Wastewater-based epidemiology has emerged as a powerful public health tool to trace new outbreaks, detect trends in infection, and provide an early warning of COVID-19 community spread. Here, we investigated the spread of SARS-CoV-2 infections across Utah by characterizing lineages and mutations detected in wastewater samples. We sequenced over 1,200 samples from 32 sewersheds collected between November 2021 and March 2022. Wastewater sequencing confirmed the presence of Omicron (B.1.1.529) in Utah in samples collected on November 19, 2021, up to 10 days before its corresponding detection via clinical sequencing. Analysis of diversity of SARS-CoV-2 lineages revealed Delta as the most frequently detected lineage during November 2021 (67.71%), but it started declining in December 2021 with the onset of Omicron (B.1.1529) and its sublineage BA.1 (6.79%). The proportion of Omicron increased to ~58% by January 4, 2022, and completely displaced Delta by February 7, 2022. Wastewater genomic surveillance revealed the presence of Omicron sublineage BA.3, a lineage that was not identified from Utah's clinical surveillance. Interestingly, several Omicron-defining mutations began to appear in early November 2021 and increased in prevalence across sewersheds from December to January, aligning with the surge in clinical cases. Our study highlights the importance of tracking epidemiologically relevant mutations in detecting emerging lineages in the early stages of an outbreak. Wastewater genomic epidemiology provides an unbiased representation of community-wide infection dynamics and is an excellent complementary tool to SARS-CoV-2 clinical surveillance, with the potential of guiding public health action and policy decisions. IMPORTANCE SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has had a significant impact on public health. Global emergence of novel SARS-CoV-2 variants, shift to at-home tests, and reduction in clinical tests demonstrate the need for a reliable and effective surveillance strategy to contain COVID-19 spread. Monitoring of SARS-CoV-2 viruses in wastewater is an effective way to trace new outbreaks, establish baseline levels of infection, and complement clinical surveillance efforts. Wastewater genomic surveillance, in particular, can provide valuable insights into the evolution and spread of SARS-CoV-2 variants. We characterized the diversity of SARS-CoV-2 mutations and lineages using whole-genome sequencing to trace the introduction of lineage B.1.1.519 (Omicron) in Utah. Our data showed that Omicron appeared in Utah on November 19, 2021, up to 10 days prior to its detection in patient samples, indicating that wastewater surveillance provides an early warning signal. Our findings are important from a public health perspective as timely identification of communities with high COVID-19 transmission could help guide public health interventions.
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Affiliation(s)
- Pooja Gupta
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Stefan Liao
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Maleea Ezekiel
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Nicolle Novak
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Alessandro Rossi
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Nathan LaCross
- Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Kelly Oakeson
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Andreas Rohrwasser
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
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23
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Maida CM, Tramuto F, Giammanco GM, Palermo R, Priano W, De Grazia S, Purpari G, La Rosa G, Suffredini E, Lucentini L, Palermo M, Pollina Addario W, Graziano G, Immordino P, Vitale F, Mazzucco W. Wastewater-Based Epidemiology as a Tool to Detect SARS-CoV-2 Circulation at the Community Level: Findings from a One-Year Wastewater Investigation Conducted in Sicily, Italy. Pathogens 2023; 12:748. [PMID: 37375438 PMCID: PMC10305655 DOI: 10.3390/pathogens12060748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Wastewater-based epidemiology is a well-established tool for detecting and monitoring the spread of enteric pathogens and the use of illegal drugs in communities in real time. Since only a few studies in Italy have investigated the correlation between SARS-CoV-2 in wastewater and the prevalence of COVID-19 cases from clinical testing, we conducted a one-year wastewater surveillance study in Sicily to correlate the load of SARS-CoV-2 RNA in wastewater and the reported cumulative prevalence of COVID-19 in 14 cities from October 2021 to September 2022. Furthermore, we investigated the role of SARS-CoV-2 variants and subvariants in the increase in the number of SARS-CoV-2 infections. Our findings showed a significant correlation between SARS-CoV-2 RNA load in wastewater and the number of active cases reported by syndromic surveillance in the population. Moreover, the correlation between SARS-CoV-2 in wastewater and the active cases remained high when a lag of 7 or 14 days was considered. Finally, we attributed the epidemic waves observed to the rapid emergence of the Omicron variant and the BA.4 and BA.5 subvariants. We confirmed the effectiveness of wastewater monitoring as a powerful epidemiological proxy for viral variant spread and an efficient complementary method for surveillance.
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Affiliation(s)
- Carmelo Massimo Maida
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
- Clinical Epidemiology Unit, Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital “P. Giaccone”, Via del Vespro 133, 90127 Palermo, Italy
| | - Fabio Tramuto
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
- Clinical Epidemiology Unit, Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital “P. Giaccone”, Via del Vespro 133, 90127 Palermo, Italy
| | - Giovanni Maurizio Giammanco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
| | - Roberta Palermo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
| | - Walter Priano
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
| | - Simona De Grazia
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
| | - Giuseppa Purpari
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Marinuzzi, 90129 Palermo, Italy;
| | - Giuseppina La Rosa
- Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, 00161 Rome, Italy; (G.L.R.)
| | - Elisabetta Suffredini
- Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, 00161 Rome, Italy; (G.L.R.)
| | - Luca Lucentini
- Istituto Superiore di Sanità (ISS), Viale Regina Elena 299, 00161 Rome, Italy; (G.L.R.)
| | - Mario Palermo
- Regional Health Authority of Sicily, Via Vaccaro 5, 90145 Palermo, Italy
| | | | - Giorgio Graziano
- Clinical Epidemiology Unit, Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital “P. Giaccone”, Via del Vespro 133, 90127 Palermo, Italy
| | - Palmira Immordino
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
| | - Francesco Vitale
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
- Clinical Epidemiology Unit, Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital “P. Giaccone”, Via del Vespro 133, 90127 Palermo, Italy
| | | | - Walter Mazzucco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
- Clinical Epidemiology Unit, Regional Reference Laboratory of Western Sicily for the Emergence of COVID-19, University Hospital “P. Giaccone”, Via del Vespro 133, 90127 Palermo, Italy
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24
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Corchis-Scott R, Geng Q, Al Riahi AM, Labak A, Podadera A, Ng KKS, Porter LA, Tong Y, Dixon JC, Menard SL, Seth R, McKay RM. Actionable wastewater surveillance: application to a university residence hall during the transition between Delta and Omicron resurgences of COVID-19. Front Public Health 2023; 11:1139423. [PMID: 37265515 PMCID: PMC10230041 DOI: 10.3389/fpubh.2023.1139423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Wastewater surveillance has gained traction during the COVID-19 pandemic as an effective and non-biased means to track community infection. While most surveillance relies on samples collected at municipal wastewater treatment plants, surveillance is more actionable when samples are collected "upstream" where mitigation of transmission is tractable. This report describes the results of wastewater surveillance for SARS-CoV-2 at residence halls on a university campus aimed at preventing outbreak escalation by mitigating community spread. Another goal was to estimate fecal shedding rates of SARS-CoV-2 in a non-clinical setting. Passive sampling devices were deployed in sewer laterals originating from residence halls at a frequency of twice weekly during fall 2021 as the Delta variant of concern continued to circulate across North America. A positive detection as part of routine sampling in late November 2021 triggered daily monitoring and further isolated the signal to a single wing of one residence hall. Detection of SARS-CoV-2 within the wastewater over a period of 3 consecutive days led to a coordinated rapid antigen testing campaign targeting the residence hall occupants and the identification and isolation of infected individuals. With knowledge of the number of individuals testing positive for COVID-19, fecal shedding rates were estimated to range from 3.70 log10 gc ‧ g feces-1 to 5.94 log10 gc ‧ g feces-1. These results reinforce the efficacy of wastewater surveillance as an early indicator of infection in congregate living settings. Detections can trigger public health measures ranging from enhanced communications to targeted coordinated testing and quarantine.
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Affiliation(s)
- Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Abdul Monem Al Riahi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Amr Labak
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ana Podadera
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Lisa A. Porter
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Jess C. Dixon
- Department of Kinesiology, University of Windsor, Windsor, ON, Canada
| | | | - Rajesh Seth
- Civil and Environmental Engineering, University of Windsor, Windsor, ON, Canada
| | - R. Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
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25
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Harris-Lovett S, Nelson KL, Kantor R, Korfmacher KS. Wastewater Surveillance to Inform Public Health Decision Making in Residential Institutions. JOURNAL OF PUBLIC HEALTH MANAGEMENT AND PRACTICE 2023; 29:317-321. [PMID: 36214654 PMCID: PMC10038809 DOI: 10.1097/phh.0000000000001636] [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] [Indexed: 11/07/2022]
Abstract
Testing sewage (wastewater-based surveillance, or WBS) for pathogens is an increasingly important tool for monitoring the health of populations. During the COVID-19 pandemic, some residential institutions including colleges, prisons, and skilled nursing facilities used facility-level wastewater data to inform their pandemic responses. To understand how these early adopters used WBS data in decision making, we conducted in-depth, semistructured interviews with multiple decision makers at 6 residential institutions in the United States (universities, prisons, and nursing homes) encompassing a total of more than 70 000 residents and staff about interpretation, uses, and limitations of these data. We found that WBS data were used in extremely diverse ways. WBS combined with clinical surveillance informed a wide range of public health actions at residential institutions, including transmission reduction measures, public health communications, and allocation of resources. WBS also served other institutional purposes, such as maintaining relationships with external stakeholders and helping alleviate decision makers' pervasive stress. Recognizing these diverse ways of using WBS data can inform expansion of this practice among institutions as well as development of community-scale systems.
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Affiliation(s)
- Sasha Harris-Lovett
- Berkeley Water Center (Dr Harris-Lovett) and Department of Civil and Environmental Engineering (Drs Nelson and Kantor), University of California Berkeley, Berkeley, California; and Department of Environmental Medicine, University of Rochester, Rochester, New York (Dr Korfmacher)
| | - Kara L. Nelson
- Berkeley Water Center (Dr Harris-Lovett) and Department of Civil and Environmental Engineering (Drs Nelson and Kantor), University of California Berkeley, Berkeley, California; and Department of Environmental Medicine, University of Rochester, Rochester, New York (Dr Korfmacher)
| | - Rose Kantor
- Berkeley Water Center (Dr Harris-Lovett) and Department of Civil and Environmental Engineering (Drs Nelson and Kantor), University of California Berkeley, Berkeley, California; and Department of Environmental Medicine, University of Rochester, Rochester, New York (Dr Korfmacher)
| | - Katrina Smith Korfmacher
- Berkeley Water Center (Dr Harris-Lovett) and Department of Civil and Environmental Engineering (Drs Nelson and Kantor), University of California Berkeley, Berkeley, California; and Department of Environmental Medicine, University of Rochester, Rochester, New York (Dr Korfmacher)
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Tang L, Wu J, Liu R, Feng Z, Zhang Y, Zhao Y, Li Y, Yang K. Exploration on wastewater-based epidemiology of SARS-CoV-2: Mimic relative quantification with endogenous biomarkers as internal reference. Heliyon 2023; 9:e15705. [PMID: 37124340 PMCID: PMC10122556 DOI: 10.1016/j.heliyon.2023.e15705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023] Open
Abstract
Wastewater-based epidemiology has become a powerful surveillance tool for monitoring the pandemic of COVID-19. Although it is promising to quantitatively correlate the SARS-CoV-2 RNA concentration in wastewater with the incidence of community infection, there is still no consensus on whether the viral nucleic acid concentration in sewage should be normalized against the abundance of endogenous biomarkers and which biomarker should be used as a reference for the normalization. Here, several candidate endogenous reference biomarkers for normalization of SARS-CoV-2 signal in municipal sewage were evaluated. The human fecal indicator virus (crAssphage) is a promising candidate of endogenous reference biomarker for data normalization of both DNA and RNA viruses for its intrinsic viral nature and high and stable content in sewage. Without constructing standard curves, the relative quantification of sewage viral nucleic acid against the abundance of the reference biomarker can be used to correlate with community COVID-19 incidence, which was proved via mimic experiments by spiking pseudovirus of different concentrations in sewage samples. Dilution of pseudovirus-seeded wastewater did not affect the relative abundance of viral nucleic acid, demonstrating that relative quantification can overcome the sewage dilution effects caused by the greywater input, precipitation and/or groundwater infiltration. The process of concentration, recovery and detection of the endogenous biomarker was consistent with that of SARS-CoV-2 RNA. Thus, it is necessary to co-quantify the endogenous biomarker because it can be not only an internal reference for data normalization, but also a process control.
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Affiliation(s)
- Langjun Tang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Jinyong Wu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Rui Liu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Zhongxi Feng
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yanan Zhang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yingzhe Zhao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yonghong Li
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
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Saingam P, Li B, Nguyen Quoc B, Jain T, Bryan A, Winkler MKH. Wastewater surveillance of SARS-CoV-2 at intra-city level demonstrated high resolution in tracking COVID-19 and calibration using chemical indicators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161467. [PMID: 36626989 PMCID: PMC9825140 DOI: 10.1016/j.scitotenv.2023.161467] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/17/2022] [Accepted: 01/04/2023] [Indexed: 05/12/2023]
Abstract
Wastewater-based epidemiology has proven to be a supportive tool to better comprehend the dynamics of the COVID-19 pandemic. As the disease moves into endemic stage, the surveillance at wastewater sub-catchments such as pump station and manholes is providing a novel mechanism to examine the reemergence and to take measures that can prevent the spread. However, there is still a lack of understanding when it comes to wastewater-based epidemiology implementation at the smaller intra-city level for better granularity in data, and dilution effect of rain precipitation at pump stations. For this study, grab samples were collected from six areas of Seattle between March-October 2021. These sampling sites comprised five manholes and one pump station with population ranging from 2580 to 39,502 per manhole/pump station. The wastewater samples were analyzed for SARS-CoV-2 RNA concentrations, and we also obtained the daily COVID-19 cases (from individual clinical testing) for each corresponding sewershed, which ranged from 1 to 12 and the daily incidence varied between 3 and 64 per 100,000 of population. Rain precipitation lowered viral RNA levels and sensitivity of viral detection but wastewater total ammonia (NH4+-N) and phosphate (PO43--P) were shown as potential chemical indicators to calibrate/level out the dilution effect. These chemicals showed the potential in improving the wastewater surveillance capacity of COVID-19.
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Affiliation(s)
- Prakit Saingam
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA.
| | - Bo Li
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Bao Nguyen Quoc
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Tanisha Jain
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Andrew Bryan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Mari K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA.
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Wolken M, Sun T, McCall C, Schneider R, Caton K, Hundley C, Hopkins L, Ensor K, Domakonda K, Kalvapalle P, Persse D, Williams S, Stadler LB. Wastewater surveillance of SARS-CoV-2 and influenza in preK-12 schools shows school, community, and citywide infections. WATER RESEARCH 2023; 231:119648. [PMID: 36702023 PMCID: PMC9858235 DOI: 10.1016/j.watres.2023.119648] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/16/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Wastewater surveillance is a passive and efficient way to monitor the spread of infectious diseases in large populations and high transmission areas such as preK-12 schools. Infections caused by respiratory viruses in school-aged children are likely underreported, particularly because many children may be asymptomatic or mildly symptomatic. Wastewater monitoring of SARS-CoV-2 has been studied extensively and primarily by sampling at centralized wastewater treatment plants, and there are limited studies on SARS-CoV-2 in preK-12 school wastewater. Similarly, wastewater detections of influenza have only been reported in wastewater treatment plant and university manhole samples. Here, we present the results of a 17-month wastewater monitoring program for SARS-CoV-2 (n = 2176 samples) and influenza A and B (n = 1217 samples) in 51 preK-12 schools. We show that school wastewater concentrations of SARS-CoV-2 RNA were strongly associated with COVID-19 cases in schools and community positivity rates, and that influenza detections in school wastewater were significantly associated with citywide influenza diagnosis rates. Results were communicated back to schools and local communities to enable mitigation strategies to stop the spread, and direct resources such as testing and vaccination clinics. This study demonstrates that school wastewater surveillance is reflective of local infections at several population levels and plays a crucial role in the detection and mitigation of outbreaks.
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Affiliation(s)
- Madeline Wolken
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS-519, Houston, TX, USA; Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Science Center, 1200 Pressler Street, Houston, TX, USA
| | - Thomas Sun
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX, USA
| | - Camille McCall
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS-519, Houston, TX, USA
| | | | - Kelsey Caton
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX, USA
| | - Courtney Hundley
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX, USA
| | - Loren Hopkins
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX, USA; Houston Health Department, 8000 N. Stadium Dr., Houston, TX, USA
| | - Katherine Ensor
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX, USA
| | - Kaavya Domakonda
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX, USA
| | | | - David Persse
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX, USA; Department of Medicine and Surgery, Baylor College of Medicine, Houston, TX, USA; City of Houston Emergency Medical Services, Houston, TX, USA
| | - Stephen Williams
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX, USA
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS-519, Houston, TX, USA.
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Othman I, Helmi A, Slama I, Hamdi R, Mastouri M, Aouni M. Evaluation of three viral concentration methods for detection and quantification of SARS-CoV-2 in wastewater. JOURNAL OF WATER AND HEALTH 2023; 21:354-360. [PMID: 37338315 PMCID: wh_2023_264 DOI: 10.2166/wh.2023.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Wastewater-based epidemiology (WBE) could be useful as an early warning system for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic spread. Viruses are highly diluted in wastewater. Therefore, a virus concentration step is needed for SARS-CoV-2 wastewater detection. We tested the efficiency of three wastewater viral concentration methods: ultrafiltration (UF), electronegative membrane filtration and aluminum hydroxide adsorption-elution. We spiked wastewater with inactivated SARS-CoV-2 and we collected 20 other wastewater samples from five sites in Tunisia. Samples were concentrated by the three methods and SARS-CoV-2 was quantified by reverse transcription digital PCR (RT-dPCR). The most efficient method was UF with a mean SARS-CoV-2 recovery of 54.03 ± 8.25. Moreover, this method provided significantly greater mean concentration and virus detection ability (95%) than the two other methods. The second-most efficient method used electronegative membrane filtration with a mean SARS-CoV-2 recovery of 25.59 ± 5.04% and the least efficient method was aluminum hydroxide adsorption-elution. This study suggests that the UF method provides rapid and straightforward recovery of SARS-CoV-2 in wastewater.
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Affiliation(s)
- Ines Othman
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia E-mail:
| | - Amna Helmi
- Directorate of Milieu Hygiene and Environmental Protection at the Health Ministry, Tunis, Tunisia
| | - Ichrak Slama
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia E-mail:
| | - Rawand Hamdi
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia E-mail:
| | - Maha Mastouri
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia E-mail: ; Fattouma Bourguiba University Hospital, Laboratory of Microbiology, Monastir, Tunisia
| | - Mahjoub Aouni
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia E-mail:
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30
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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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31
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de Araújo JC, Madeira CL, Bressani T, Leal C, Leroy D, Machado EC, Fernandes LA, Espinosa MF, Freitas GTO, Leão T, Mota VT, Pereira AD, Perdigão C, Tröger F, Ayrimoraes S, de Melo MC, Laguardia F, Reis MTP, Mota C, Chernicharo CAL. Quantification of SARS-CoV-2 in wastewater samples from hospitals treating COVID-19 patients during the first wave of the pandemic in Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160498. [PMID: 36436622 PMCID: PMC9691275 DOI: 10.1016/j.scitotenv.2022.160498] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/04/2023]
Abstract
The COVID-19 pandemic has caused a global health crisis, and wastewater-based epidemiology (WBE) has emerged as an important tool to assist public health decision-making. Recent studies have shown that the SARS-CoV-2 RNA concentration in wastewater samples is a reliable indicator of the severity of the pandemic for large populations. However, few studies have established a strong correlation between the number of infected people and the viral concentration in wastewater due to variations in viral shedding over time, viral decay, infiltration, and inflow. Herein we present the relationship between the number of COVID-19-positive patients and the viral concentration in wastewater samples from three different hospitals (A, B, and C) in the city of Belo Horizonte, Minas Gerais, Brazil. A positive and strong correlation between wastewater SARS-CoV-2 concentration and the number of confirmed cases was observed for Hospital B for both regions of the N gene (R = 0.89 and 0.77 for N1 and N2, respectively), while samples from Hospitals A and C showed low and moderate correlations, respectively. Even though the effects of viral decay and infiltration were minimized in our study, the variability of viral shedding throughout the infection period and feces dilution due to water usage for different activities in the hospitals could have affected the viral concentrations. These effects were prominent in Hospital A, which had the smallest sewershed population size, and where no correlation between the number of defecations from COVID-19 patients and viral concentration in wastewater was observed. Although we could not determine trends in the number of infected patients through SARS-CoV-2 concentrations in hospitals' wastewater samples, our results suggest that wastewater monitoring can be efficient for the detection of infected individuals at a local level, complementing clinical data.
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Affiliation(s)
- Juliana Calábria de Araújo
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil.
| | - Camila L Madeira
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Thiago Bressani
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Cíntia Leal
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Deborah Leroy
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Elayne C Machado
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Luyara A Fernandes
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Maria Fernanda Espinosa
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Gabriel Tadeu O Freitas
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Thiago Leão
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Vera Tainá Mota
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Alyne Duarte Pereira
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | | | - Flávio Tröger
- National Agency for Water and Sanitation (ANA), Brazil
| | | | | | | | | | - César Mota
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Carlos A L Chernicharo
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
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32
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Câmara AB, Bonfante J, da Penha MG, Cassini STA, de Pinho Keller R. Detecting SARS-CoV-2 in sludge samples: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160012. [PMID: 36368397 PMCID: PMC9643039 DOI: 10.1016/j.scitotenv.2022.160012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
AIMS This paper aims to review the main sludge concentration methods used for SARS-CoV-2 detection in sewage sludge samples, discussing the main methods and sample volume related to increased viral load. In addition, we aim to evaluate the countries associated with increased positivity rates for SARS-CoV-2 in sludge samples. METHODS This systematic methodology was registered in PROSPERO and followed the PRISMA guidelines. The search was carried out in the SciELO, PubMed/MEDLINE, Lilacs, and Google Scholar databases in January-March 2022. Quantitative studies with conclusive results were included in this review. Concentration methods (polyethylene glycol (PEG), PEG + NaCl, gravity thickening, skimmed milk flocculation, ultrafiltration, filtration using charged filters, primary sedimentation, and anaerobic digestion), as well as detection methods (RTqPCR and reverse transcription droplet digital PCR assay) were evaluated in this review. The SPSS v23 software program was used for statistical analysis. RESULTS PEG (with or without NaCl addition) and gravity thickening were the most used sludge concentration methods to detect SARS-CoV-2. The main method associated with increased viral load (>2,02 × 10^4 copies/mL) was PEG + NaCl (p < 0.05, Mann-Whitney test). The average positivity rate for SARS-CoV-2 in sludge samples was 61 %, and a correlation was found between the sludge volume and the viral load (ro 0.559, p = 0.03, Spearman correlation). CONCLUSION The sludge volume may influence the SARS-CoV-2 load since the virus can adhere to solid particles in these samples. Other factors may be associated with SARS-CoV-2 load, including the methods used; especially PEG + NaCl may result in a high viral load detected in sludge, and may provide a suitable pH for SARS-CoV-2 recovery.
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Affiliation(s)
- Alice Barros Câmara
- Sanitation Laboratory, Department of Environmental Engineering, Universidade Federal do Espírito Santo, Ave. Fernando Ferrari, 515, Goiabeiras, 29075051 Vitória, ES, Brazil.
| | - Júlia Bonfante
- Sanitation Laboratory, Department of Environmental Engineering, Universidade Federal do Espírito Santo, Ave. Fernando Ferrari, 515, Goiabeiras, 29075051 Vitória, ES, Brazil
| | - Marília Gueler da Penha
- Sanitation Laboratory, Department of Environmental Engineering, Universidade Federal do Espírito Santo, Ave. Fernando Ferrari, 515, Goiabeiras, 29075051 Vitória, ES, Brazil
| | - Sérvio Túlio Alves Cassini
- Sanitation Laboratory, Department of Environmental Engineering, Universidade Federal do Espírito Santo, Ave. Fernando Ferrari, 515, Goiabeiras, 29075051 Vitória, ES, Brazil
| | - Regina de Pinho Keller
- Sanitation Laboratory, Department of Environmental Engineering, Universidade Federal do Espírito Santo, Ave. Fernando Ferrari, 515, Goiabeiras, 29075051 Vitória, ES, Brazil
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Acosta N, Bautista MA, Waddell BJ, Du K, McCalder J, Pradhan P, Sedaghat N, Papparis C, Beaudet AB, Chen J, Van Doorn J, Xiang K, Chan L, Vivas L, Low K, Lu X, Lee J, Westlund P, Chekouo T, Dai X, Cabaj J, Bhatnagar S, Ruecker N, Achari G, Clark RG, Pearce C, Harrison JJ, Meddings J, Leal J, Ellison J, Missaghi B, Kanji JN, Larios O, Rennert‐May E, Kim J, Hrudey SE, Lee BE, Pang X, Frankowski K, Conly J, Hubert CRJ, Parkins MD. Surveillance for SARS-CoV-2 and its variants in wastewater of tertiary care hospitals correlates with increasing case burden and outbreaks. J Med Virol 2023; 95:e28442. [PMID: 36579780 PMCID: PMC9880705 DOI: 10.1002/jmv.28442] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022]
Abstract
Wastewater-based SARS-CoV-2 surveillance enables unbiased and comprehensive monitoring of defined sewersheds. We performed real-time monitoring of hospital wastewater that differentiated Delta and Omicron variants within total SARS-CoV-2-RNA, enabling correlation to COVID-19 cases from three tertiary-care facilities with >2100 inpatient beds in Calgary, Canada. RNA was extracted from hospital wastewater between August/2021 and January/2022, and SARS-CoV-2 quantified using RT-qPCR. Assays targeting R203M and R203K/G204R established the proportional abundance of Delta and Omicron, respectively. Total and variant-specific SARS-CoV-2 in wastewater was compared to data for variant specific COVID-19 hospitalizations, hospital-acquired infections, and outbreaks. Ninety-six percent (188/196) of wastewater samples were SARS-CoV-2 positive. Total SARS-CoV-2 RNA levels in wastewater increased in tandem with total prevalent cases (Delta plus Omicron). Variant-specific assessments showed this increase to be mainly driven by Omicron. Hospital-acquired cases of COVID-19 were associated with large spikes in wastewater SARS-CoV-2 and levels were significantly increased during outbreaks relative to nonoutbreak periods for total SARS-CoV2, Delta and Omicron. SARS-CoV-2 in hospital wastewater was significantly higher during the Omicron-wave irrespective of outbreaks. Wastewater-based monitoring of SARS-CoV-2 and its variants represents a novel tool for passive COVID-19 infection surveillance, case identification, containment, and potentially to mitigate viral spread in hospitals.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | | | - Barbara J. Waddell
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Kristine Du
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Janine McCalder
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Puja Pradhan
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Navid Sedaghat
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Chloe Papparis
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | | | - Jianwei Chen
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | | | - Kevin Xiang
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Leslie Chan
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Laura Vivas
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Kashtin Low
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Xuewen Lu
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
| | - Jangwoo Lee
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | | | - Thierry Chekouo
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
- Division of Biostatistics, School of Public HealthUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Xiaotian Dai
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
| | - Jason Cabaj
- Department of Community Health SciencesUniversity of CalgaryCalgaryCanada
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Provincial Population & Public HealthAlberta Health ServicesCalgaryCanada
- O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
| | - Srijak Bhatnagar
- Faculty of Science and TechnologyAthabasca UniversityAthabascaAlbertaCanada
| | | | - Gopal Achari
- Department of Civil EngineeringUniversity of CalgaryCalgaryCanada
| | - Rhonda G. Clark
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Craig Pearce
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Joe J. Harrison
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Jon Meddings
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Jenine Leal
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Community Health SciencesUniversity of CalgaryCalgaryCanada
- O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Jennifer Ellison
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Bayan Missaghi
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Jamil N. Kanji
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada
- Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada
- Department of Pathology and Laboratory MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Oscar Larios
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
- Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada
| | - Elissa Rennert‐May
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of Community Health SciencesUniversity of CalgaryCalgaryCanada
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Joseph Kim
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada
- Department of Analytical and Environmental ToxicologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Bonita E. Lee
- Department of PediatricsUniversity of AlbertaEdmontonAlbertaCanada
- Women & Children's Health Research InstituteEdmontonAlbertaCanada
- Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Xiaoli Pang
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada
- Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada
- Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin Frankowski
- Advancing Canadian Water AssetsUniversity of CalgaryCalgaryCanada
| | - John Conly
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Department of Pathology and Laboratory MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | | | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
- Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
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Islam MA, Rahman MA, Jakariya M, Bahadur NM, Hossen F, Mukharjee SK, Hossain MS, Tasneem A, Haque MA, Sera F, Jahid IK, Ahmed T, Hasan MN, Islam MT, Hossain A, Amin R, Tiwari A, Didar-Ul-Alam M, Dhama K, Bhattacharya P, Ahmed F. A 30-day follow-up study on the prevalence of SARS-COV-2 genetic markers in wastewater from the residence of COVID-19 patient and comparison with clinical positivity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159350. [PMID: 36265620 PMCID: PMC9576909 DOI: 10.1016/j.scitotenv.2022.159350] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 10/07/2022] [Accepted: 10/07/2022] [Indexed: 05/07/2023]
Abstract
Wastewater based epidemiology (WBE) is an important tool to fight against COVID-19 as it provides insights into the health status of the targeted population from a small single house to a large municipality in a cost-effective, rapid, and non-invasive way. The implementation of wastewater based surveillance (WBS) could reduce the burden on the public health system, management of pandemics, help to make informed decisions, and protect public health. In this study, a house with COVID-19 patients was targeted for monitoring the prevalence of SARS-CoV-2 genetic markers in wastewater samples (WS) with clinical specimens (CS) for a period of 30 days. RT-qPCR technique was employed to target nonstructural (ORF1ab) and structural-nucleocapsid (N) protein genes of SARS-CoV-2, according to a validated experimental protocol. Physiological, environmental, and biological parameters were also measured following the American Public Health Association (APHA) standard protocols. SARS-CoV-2 viral shedding in wastewater peaked when the highest number of COVID-19 cases were clinically diagnosed. Throughout the study period, 7450 to 23,000 gene copies/1000 mL were detected, where we identified 47 % (57/120) positive samples from WS and 35 % (128/360) from CS. When the COVID-19 patient number was the lowest (2), the highest CT value (39.4; i.e., lowest copy number) was identified from WS. On the other hand, when the COVID-19 patients were the highest (6), the lowest CT value (25.2 i.e., highest copy numbers) was obtained from WS. An advance signal of increased SARS-CoV-2 viral load from the COVID-19 patient was found in WS earlier than in the CS. Using customized primer sets in a traditional PCR approach, we confirmed that all SARS-CoV-2 variants identified in both CS and WS were Delta variants (B.1.617.2). To our knowledge, this is the first follow-up study to determine a temporal relationship between COVID-19 patients and their discharge of SARS-CoV-2 RNA genetic markers in wastewater from a single house including all family members for clinical sampling from a developing country (Bangladesh), where a proper sewage system is lacking. The salient findings of the study indicate that monitoring the genetic markers of the SARS-CoV-2 virus in wastewater could identify COVID-19 cases, which reduces the burden on the public health system during COVID-19 pandemics.
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Affiliation(s)
- Md Aminul Islam
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh; Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, Bangladesh
| | - Md Arifur Rahman
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Md Jakariya
- 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
| | - Foysal Hossen
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Sanjoy Kumar Mukharjee
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Mohammad Salim Hossain
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Atkeeya Tasneem
- Department of Environmental Science and Disaster Management, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Md Atiqul Haque
- Key Lab of Animal Epidemiology and Zoonoses of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China; Department of Microbiology, Faculty of Veterinary and Animal Science, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Francesco Sera
- Department of Statistics, Informatics, Applications, University of Florence, Florence, Italy; Department of Public Health, Environments and Society, London School of Hygiene & Tropical Medicine, London, UK
| | - Iqbal Kabir Jahid
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Tanvir Ahmed
- Department of Civil Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Mohammad Nayeem Hasan
- Department of Statistics, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | | | - Amzad Hossain
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Ruhul Amin
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Ananda Tiwari
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland; Department of Health Security, Expert Microbiology Research Unit, Finnish Institute for Health and Welfare, Finland
| | - Md Didar-Ul-Alam
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - 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.
| | - Firoz Ahmed
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
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Gagliano E, Biondi D, Roccaro P. Wastewater-based epidemiology approach: The learning lessons from COVID-19 pandemic and the development of novel guidelines for future pandemics. CHEMOSPHERE 2023; 313:137361. [PMID: 36427570 PMCID: PMC9678975 DOI: 10.1016/j.chemosphere.2022.137361] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) provides a comprehensive real-time framework of population attitude and health status. This approach is attracting the interest of medical community and health authorities to monitor the prevalence of a virus (such as the severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) among a community. Indeed, WBE is currently fine-tuning as environmental surveillance tool for coronavirus disease 2019 (COVID-19) pandemic. After a bibliometric analysis conducted to discover the research trends in WBE field, this work aimed to side-by-side compare the conventional method based on clinical testing with WBE approach. Furthermore, novel guidelines were developed to apply the WBE approach to a pandemic. The growing interest on WBE approach for COVID-19 pandemic is demonstrated by looking at the sharp increase in scientific papers published in the last years and at the ongoing studies on viral quantification methods and analytical procedures. The side-by-side comparison highlighted the ability of WBE to identify the hot-spot areas faster than the conventional approach, reducing the costs (e.g., rational use of available resources) and the gatherings at medical centers. Contrary to clinical testing, WBE has the surveillance capacity for preventing the virus resurgence, including asymptomatic contribution, and ensuring the preservation of medical staff health by avoiding the exposure to the virus infection during clinical testing. As extensively reported, the time in collecting epidemiological data is crucial for establishing the prevention and mitigation measures that are essential for curbing a pandemic. The developed guidelines can help to build a WBE system useful to control any future pandemic.
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Affiliation(s)
- Erica Gagliano
- Department of Civil Engineering and Architecture, University of Catania, Catania, Italy; Department of Civil, Chemical and Environmental Engineering, University of Genoa, Genoa, Italy
| | - Deborah Biondi
- Department of Civil Engineering and Architecture, University of Catania, Catania, Italy
| | - Paolo Roccaro
- Department of Civil Engineering and Architecture, University of Catania, Catania, Italy.
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36
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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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Maal-Bared R, Qiu Y, Li Q, Gao T, Hrudey SE, Bhavanam S, Ruecker NJ, Ellehoj E, Lee BE, Pang X. Does normalization of SARS-CoV-2 concentrations by Pepper Mild Mottle Virus improve correlations and lead time between wastewater surveillance and clinical data in Alberta (Canada): comparing twelve SARS-CoV-2 normalization approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158964. [PMID: 36167131 PMCID: PMC9508694 DOI: 10.1016/j.scitotenv.2022.158964] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 05/02/2023]
Abstract
Wastewater-based surveillance (WBS) data normalization is an analyte measurement correction that addresses variations resulting from dilution of fecal discharge by non-sanitary sewage, stormwater or groundwater infiltration. No consensus exists on what WBS normalization parameters result in the strongest correlations and lead time between SARS-CoV-2 WBS data and COVID-19 cases. This study compared flow, population size and biomarker normalization impacts on the correlations and lead times for ten communities in twelve sewersheds in Alberta (Canada) between September 2020 and October 2021 (n = 1024) to determine if normalization by Pepper Mild Mottle Virus (PMMoV) provides any advantages compared to other normalization parameters (e.g., flow, reported and dynamic population sizes, BOD, TSS, NH3, TP). PMMoV concentrations (GC/mL) corresponded with plant influent flows and were highest in the urban centres. SARS-CoV-2 target genes E, N1 and N2 were all negatively associated with wastewater influent pH, while PMMoV was positively associated with temperature. Pooled data analysis showed that normalization increased ρ-values by almost 0.1 and was highest for ammonia, TKN and TP followed by PMMoV. Normalization by other parameters weakened associations. None of the differences were statistically significant. Site-specific correlations showed that normalization of SARS-CoV-2 data by PMMoV only improved correlations significantly in two of the twelve systems; neither were large sewersheds or combined sewer systems. In five systems, normalization by traditional wastewater strength parameters and dynamic population estimates improved correlations. Lead time ranged between 1 and 4 days in both pooled and site-specific comparisons. We recommend that WBS researchers and health departments: a) Investigate WWTP influent properties (e.g., pH) in the WBS planning phase and use at least two parallel approaches for normalization only if shown to provide value; b) Explore normalization by wastewater strength parameters and dynamic population size estimates further; and c) Evaluate purchasing an influent flow meter in small communities to support long-term WBS efforts and WWTP management.
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Affiliation(s)
- Rasha Maal-Bared
- Quality Assurance and Environment, EPCOR Water, Edmonton, Alberta, Canada.
| | - Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Qiaozhi Li
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Tiejun Gao
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Steve E Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sudha Bhavanam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Norma J Ruecker
- Water Quality Services, City of Calgary, Calgary, Alberta, Canada
| | - Erik Ellehoj
- Ellehoj Redmond Consulting, Edmonton, Alberta, Canada
| | - Bonita E Lee
- Department of Paediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, Alberta, Canada
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38
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Hopkins L, Persse D, Caton K, Ensor K, Schneider R, McCall C, Stadler LB. Citywide wastewater SARS-CoV-2 levels strongly correlated with multiple disease surveillance indicators and outcomes over three COVID-19 waves. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:158967. [PMID: 36162580 PMCID: PMC9507781 DOI: 10.1016/j.scitotenv.2022.158967] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Public health surveillance systems for COVID-19 are multifaceted and include multiple indicators reflective of different aspects of the burden and spread of the disease in a community. With the emergence of wastewater disease surveillance as a powerful tool to track infection dynamics of SARS-CoV-2, there is a need to integrate and validate wastewater information with existing disease surveillance systems and demonstrate how it can be used as a routine surveillance tool. A first step toward integration is showing how it relates to other disease surveillance indicators and outcomes, such as case positivity rates, syndromic surveillance data, and hospital bed use rates. Here, we present an 86-week long surveillance study that covers three major COVID-19 surges. City-wide SARS-CoV-2 RNA viral loads in wastewater were measured across 39 wastewater treatment plants and compared to other disease metrics for the city of Houston, TX. We show that wastewater levels are strongly correlated with positivity rate, syndromic surveillance rates of COVID-19 visits, and COVID-19-related general bed use rates at hospitals. We show that the relative timing of wastewater relative to each indicator shifted across the pandemic, likely due to a multitude of factors including testing availability, health-seeking behavior, and changes in viral variants. Next, we show that individual WWTPs led city-wide changes in SARS-CoV-2 viral loads, indicating a distributed monitoring system could be used to enhance the early-warning capability of a wastewater monitoring system. Finally, we describe how the results were used in real-time to inform public health response and resource allocation.
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Affiliation(s)
- Loren Hopkins
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX, United States of America; Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX, United States of America
| | - David Persse
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX, United States of America; Department of Medicine and Surgery, Baylor College of Medicine, Houston, TX, United States of America; City of Houston Emergency Medical Services, Houston, TX, United States of America
| | - Kelsey Caton
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX, United States of America
| | - Katherine Ensor
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX, United States of America
| | - Rebecca Schneider
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX, United States of America
| | - Camille McCall
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS-519, Houston, TX, United States of America
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street MS-519, Houston, TX, United States of America.
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39
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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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40
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Kotlarz N, Holcomb DA, Tanvir Pasha ABM, Reckling S, Kays J, Lai YC, Daly S, Palani S, Bailey E, Guidry VT, Christensen A, Berkowitz S, Hoppin JA, Mitasova H, Engel LS, Reyes FLDL, Harris A. Timing and Trends for Municipal Wastewater, Lab-Confirmed Case, and Syndromic Case Surveillance of COVID-19 in Raleigh, North Carolina. Am J Public Health 2023; 113:79-88. [PMID: 36356280 PMCID: PMC9755929 DOI: 10.2105/ajph.2022.307108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2022] [Indexed: 11/12/2022]
Abstract
Objectives. To compare 4 COVID-19 surveillance metrics in a major metropolitan area. Methods. We analyzed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater influent and primary solids in Raleigh, North Carolina, from April 10 through December 13, 2020. We compared wastewater results with lab-confirmed COVID-19 cases and syndromic COVID-like illness (CLI) cases to answer 3 questions: (1) Did they correlate? (2) What was the temporal alignment of the different surveillance systems? (3) Did periods of significant change (i.e., trends) align? Results. In the Raleigh sewershed, wastewater influent, wastewater primary solids, lab-confirmed cases, and CLI were strongly or moderately correlated. Trends in lab-confirmed cases and wastewater influent were observed earlier, followed by CLI and, lastly, wastewater primary solids. All 4 metrics showed sustained increases in COVID-19 in June, July, and November 2020 and sustained decreases in August and September 2020. Conclusions. In a major metropolitan area in 2020, the timing of and trends in municipal wastewater, lab-confirmed case, and syndromic case surveillance of COVID-19 were in general agreement. Public Health Implications. Our results provide evidence for investment in SARS-CoV-2 wastewater and CLI surveillance to complement information provided through lab-confirmed cases. (Am J Public Health. 2023;113(1):79-88. https://doi.org/10.2105/AJPH.2022.307108).
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Affiliation(s)
- Nadine Kotlarz
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - David A Holcomb
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - A B M Tanvir Pasha
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Stacie Reckling
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Judith Kays
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Yi-Chun Lai
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Sean Daly
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Sivaranjani Palani
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Erika Bailey
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Virginia T Guidry
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Ariel Christensen
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Steven Berkowitz
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Jane A Hoppin
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Helena Mitasova
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Lawrence S Engel
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Francis L de Los Reyes
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
| | - Angela Harris
- Nadine Kotlarz and Jane A. Hoppin are with the Department of Biological Sciences, North Carolina State University, Raleigh. David A. Holcomb and Lawrence S. Engel are with the Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill. A. B. M. Tanvir Pasha, Judith Kays, Yi-Chun Lai, Sean Daly, Francis L. de los Reyes III, and Angela Harris are with the Department of Civil, Construction, and Environmental Engineering, North Carolina State University. Stacie Reckling and Helena Mitasova are with the Center for Geospatial Analytics, North Carolina State University. Sivaranjani Palani is with the Department of Plant and Microbial Biology, North Carolina State University. Erika Bailey is with Raleigh Water, Raleigh, NC. Virginia T. Guidry, Ariel Christensen, and Steven Berkowitz are with the Division of Public Health, North Carolina Department of Health and Human Services, Raleigh
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41
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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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42
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Prajapati B, Rathore D, Joshi C, Joshi M. Digital PCR: A Partitioning-Based Application for Detection and Surveillance of SARS-CoV-2 from Sewage Samples. Methods Mol Biol 2023; 2967:1-16. [PMID: 37608098 DOI: 10.1007/978-1-0716-3358-8_1] [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] [Indexed: 08/24/2023]
Abstract
The wastewater-based surveillance of SARS-CoV-2 has emerged as a potential tool for cost-effective, simple, and long-term monitoring of the pandemic. Since the COVID-19 pandemic, several developed countries have incorporated the national wastewater surveillance program into their national policies related to pandemic management. Various research groups have utilized the approach of real-time quantitative reverse transcription PCR (RT-qPCR) for the quantification of SARS-CoV-2 from environmental samples like sewage water. However, detection and quantification using RT-qPCR relies on standards and is known to have lesser tolerance to inhibitors present in the sample. Unlike RT-qPCR, digital PCR (dPCR) offers an absolute and sensitive quantification without a need reference and offers higher tolerance to inhibitors present in the wastewater samples. Additionally, the accuracy of detection increases with the presence of rare target copies in the sample. The methodology herein presented comprises the detection and quantification of SARS-CoV-2 from sewer shed samples using the dPCR approach. The main features of the process include virus concentration and absolute quantification of the virus surpassing the substantial presence of inhibitors in the sample. This chapter presents the optimized PEG and NaCl-based protocol for virus concentration followed by nucleic acid extraction and quantification using CDC-approved N1 + N2 assay. The protocol uses MS2 bacteriophage as a process recovery or internal control.The methodology herein described highlights the importance of digital PCR technologies for environmental surveillance of important emerging pathogens or pandemics.
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Affiliation(s)
- Bhumika Prajapati
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Dalipsingh Rathore
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India.
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43
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Hegazy N, Cowan A, D'Aoust PM, Mercier É, Towhid ST, Jia JJ, Wan S, Zhang Z, Kabir MP, Fang W, Graber TE, MacKenzie AE, Guilherme S, Delatolla R. Understanding the dynamic relation between wastewater SARS-CoV-2 signal and clinical metrics throughout the pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158458. [PMID: 36075428 PMCID: PMC9444583 DOI: 10.1016/j.scitotenv.2022.158458] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 05/27/2023]
Abstract
Wastewater surveillance (WWS) of SARS-CoV-2 was proven to be a reliable and complementary tool for population-wide monitoring of COVID-19 disease incidence but was not as rigorously explored as an indicator for disease burden throughout the pandemic. Prior to global mass immunization campaigns and during the spread of the wildtype COVID-19 and the Alpha variant of concern (VOC), viral measurement of SARS-CoV-2 in wastewater was a leading indicator for both COVID-19 incidence and disease burden in communities. As the two-dose vaccination rates escalated during the spread of the Delta VOC in Jul. 2021 through Dec. 2021, relations weakened between wastewater signal and community COVID-19 disease incidence and maintained a strong relationship with clinical metrics indicative of disease burden (new hospital admissions, ICU admissions, and deaths). Further, with the onset of the vaccine-resistant Omicron BA.1 VOC in Dec. 2021 through Mar. 2022, wastewater again became a strong indicator of both disease incidence and burden during a period of limited natural immunization (no recent infection), vaccine escape, and waned vaccine effectiveness. Lastly, with the populations regaining enhanced natural and vaccination immunization shortly prior to the onset of the Omicron BA.2 VOC in mid-Mar 2022, wastewater is shown to be a strong indicator for both disease incidence and burden. Hospitalization-to-wastewater ratio is further shown to be a good indicator of VOC virulence when widespread clinical testing is limited. In the future, WWS is expected to show moderate indication of incidence and strong indication of disease burden in the community during future potential seasonal vaccination campaigns.
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Affiliation(s)
- Nada Hegazy
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Aaron Cowan
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Shen Wan
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Zhihao Zhang
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Md Pervez Kabir
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Wanting Fang
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Stéphanie Guilherme
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada.
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44
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D'Aoust PM, Tian X, Towhid ST, Xiao A, Mercier E, Hegazy N, Jia JJ, Wan S, Kabir MP, Fang W, Fuzzen M, Hasing M, Yang MI, Sun J, Plaza-Diaz J, Zhang Z, Cowan A, Eid W, Stephenson S, Servos MR, Wade MJ, MacKenzie AE, Peng H, Edwards EA, Pang XL, Alm EJ, Graber TE, Delatolla R. Wastewater to clinical case (WC) ratio of COVID-19 identifies insufficient clinical testing, onset of new variants of concern and population immunity in urban communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158547. [PMID: 36067855 PMCID: PMC9444156 DOI: 10.1016/j.scitotenv.2022.158547] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/10/2022] [Accepted: 09/01/2022] [Indexed: 05/14/2023]
Abstract
Clinical testing has been the cornerstone of public health monitoring and infection control efforts in communities throughout the COVID-19 pandemic. With the anticipated reduction of clinical testing as the disease moves into an endemic state, SARS-CoV-2 wastewater surveillance (WWS) will have greater value as an important diagnostic tool. An in-depth analysis and understanding of the metrics derived from WWS is required to interpret and utilize WWS-acquired data effectively (McClary-Gutierrez et al., 2021; O'Keeffe, 2021). In this study, the SARS-CoV-2 wastewater signal to clinical cases (WC) ratio was investigated across seven cities in Canada over periods ranging from 8 to 21 months. This work demonstrates that significant increases in the WC ratio occurred when clinical testing eligibility was modified to appointment-only testing, identifying a period of insufficient clinical testing (resulting in a reduction to testing access and a reduction in the number of daily tests) in these communities, despite increases in the wastewater signal. Furthermore, the WC ratio decreased significantly in 6 of the 7 studied locations, serving as a potential signal of the emergence of the Alpha variant of concern (VOC) in a relatively non-immunized community (40-60 % allelic proportion), while a more muted decrease in the WC ratio signaled the emergence of the Delta VOC in a relatively well-immunized community (40-60 % allelic proportion). Finally, a significant decrease in the WC ratio signaled the emergence of the Omicron VOC, likely because of the variant's greater effectiveness at evading immunity, leading to a significant number of new reported clinical cases, even when community immunity was high. The WC ratio, used as an additional monitoring metric, could complement clinical case counts and wastewater signals as individual metrics in its potential ability to identify important epidemiological occurrences, adding value to WWS as a diagnostic technology during the COVID-19 pandemic and likely for future pandemics.
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Affiliation(s)
- Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Xin Tian
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | | | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Elisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Nada Hegazy
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Shen Wan
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Md Pervez Kabir
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Wanting Fang
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Maria Hasing
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Minqing Ivy Yang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Jianxian Sun
- Department of Chemistry, University of Toronto, Toronto, Canada
| | - Julio Plaza-Diaz
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Zhihao Zhang
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Aaron Cowan
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Sean Stephenson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Matthew J Wade
- Data, Analytics and Surveillance Group, UK Health Security Agency, London, United Kingdom
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Hui Peng
- Department of Chemistry, University of Toronto, Toronto, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada.
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45
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Jain N, Hamilton D, Mital S, Ilias A, Brinkmann M, McPhedran K. Long-term passive wastewater surveillance of SARS-CoV-2 for seven university dormitories in comparison to municipal surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158421. [PMID: 36058330 PMCID: PMC9433341 DOI: 10.1016/j.scitotenv.2022.158421] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 05/28/2023]
Abstract
Wastewater-based surveillance (WBS) has been an effective tool for monitoring and understanding potential SARS-CoV-2 transmission across small and large-scale communities. In this study at the University of Saskatchewan, the assessment of SARS-CoV-2 was done over eight months during the 2021-2022 academic year. Wastewater samples were collected using passive samplers that were deployed in domestic sewer lines near adjacent campus residences and extracted for viral RNA, followed by Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR). The results showed similar trends for SARS-CoV-2 detection frequencies and viral loads across university residences, the whole campus, and from related WBS at Saskatoon Wastewater Treatment Plant. The maximum daily detection frequency for seven dormitories considered was about 75 %, while maximum daily case numbers for the residences and campus-wide were about 11 and 75 people, respectively. In addition, self-reported rates of infection on campus peaked during similar time frames as increases in viral load were detected at the Saskatoon wastewater treatment plant. These similarities indicate the usefulness and cost-effectiveness of monitoring the spread of COVID-19 in small-scale communities using WBS.
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Affiliation(s)
- N Jain
- Department of Civil, Geological, and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - D Hamilton
- Department of Civil, Geological, and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - S Mital
- Department of Civil, Geological, and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - A Ilias
- Department of Civil, Geological, and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - M Brinkmann
- Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Centre for Hydrology, University of Saskatchewan, Saskatoon, SK, Canada.
| | - K McPhedran
- Department of Civil, Geological, and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
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46
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Bonanno Ferraro G, Veneri C, Mancini P, Iaconelli M, Suffredini E, Bonadonna L, Lucentini L, Bowo-Ngandji A, Kengne-Nde C, Mbaga DS, Mahamat G, Tazokong HR, Ebogo-Belobo JT, Njouom R, Kenmoe S, La Rosa G. A State-of-the-Art Scoping Review on SARS-CoV-2 in Sewage Focusing on the Potential of Wastewater Surveillance for the Monitoring of the COVID-19 Pandemic. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:315-354. [PMID: 34727334 PMCID: PMC8561373 DOI: 10.1007/s12560-021-09498-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/21/2021] [Indexed: 05/07/2023]
Abstract
The outbreak of coronavirus infectious disease-2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has rapidly spread throughout the world. Several studies have shown that detecting SARS-CoV-2 in untreated wastewater can be a useful tool to identify new outbreaks, establish outbreak trends, and assess the prevalence of infections. On 06 May 2021, over a year into the pandemic, we conducted a scoping review aiming to summarize research data on SARS-CoV-2 in sewage. Papers dealing with raw sewage collected at wastewater treatment plants, sewer networks, septic tanks, and sludge treatment facilities were included in this review. We also reviewed studies on sewage collected in community settings such as private or municipal hospitals, healthcare facilities, nursing homes, dormitories, campuses, airports, aircraft, and cruise ships. The literature search was conducted using the electronic databases PubMed, EMBASE, and Web Science Core Collection. This comprehensive research yielded 1090 results, 66 of which met the inclusion criteria and are discussed in this review. Studies from 26 countries worldwide have investigated the occurrence of SARS-CoV-2 in sewage of different origin. The percentage of positive samples in sewage ranged from 11.6 to 100%, with viral concentrations ranging from ˂LOD to 4.6 × 108 genome copies/L. This review outlines the evidence currently available on wastewater surveillance: (i) as an early warning system capable of predicting COVID-19 outbreaks days or weeks before clinical cases; (ii) as a tool capable of establishing trends in current outbreaks; (iii) estimating the prevalence of infections; and (iv) studying SARS-CoV-2 genetic diversity. In conclusion, as a cost-effective, rapid, and reliable source of information on the spread of SARS-CoV-2 and its variants in the population, wastewater surveillance can enhance genomic and epidemiological surveillance with independent and complementary data to inform public health decision-making during the ongoing pandemic.
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Affiliation(s)
- G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - P Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Bonadonna
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Lucentini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - A Bowo-Ngandji
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - C Kengne-Nde
- Research Monitoring and Planning Unit, National Aids Control Committee, Douala, Cameroon
| | - D S Mbaga
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - G Mahamat
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - H R Tazokong
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - J T Ebogo-Belobo
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - R Njouom
- Virology Department, Centre Pasteur of Cameroon, Yaounde, Cameroon
| | - S Kenmoe
- Virology Department, Centre Pasteur of Cameroon, Yaounde, Cameroon
| | - G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy.
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47
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Kumar M. Spectrum of environmental surveillance of SARS-CoV-2 fragments: Questions, quests, and conquest. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2022; 30:100401. [PMID: 36339883 PMCID: PMC9617644 DOI: 10.1016/j.coesh.2022.100401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This works examines the entire spectrum of 'Environmental Surveillance (EnvSurv)' of SARS-CoV-2 fragments i.e. the questions, quests, and conquests of the technology since early year 2020. The prime focus of the present work to document the journey with achieved objectives and remaining ambitions associated with the technology. Despite the EnvSurv may be regarded as the techniques, which rather achieved more than expected, will it win the struggle for its existence or lose its way once the pandemic and fear associated with it completely fades. Pertaining to this discussions, major researched topics were investigated, followed by enlisting of ten bullets of the past experiences along with corresponding challenges, and finally key targets for the techniques are enlisted. The article targets to be a simple guide of the journey of EnvSur in terms of its effectiveness for treatment, infectivity, monitoring & estimation (TIME) till date.
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Affiliation(s)
- Manish Kumar
- Sustainability Cluster, School of Engineering, Enery Agcres, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India
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48
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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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49
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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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50
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Ma D, Straathof J, Liu Y, Hull NM. Monitoring SARS-CoV-2 RNA in Wastewater with RT-qPCR and Chip-Based RT-dPCR: Sewershed-Level Trends and Relationships to COVID-19. ACS ES&T WATER 2022; 2:2084-2093. [PMID: 37552751 PMCID: PMC9173673 DOI: 10.1021/acsestwater.2c00055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 08/10/2023]
Abstract
We evaluated the performance of reverse transcription quantitative PCR (uniplex and duplex RT-qPCR) and chip-based digital PCR (duplex RT-dPCR) using CDC N1 and CDC N2 assays for longitudinal monitoring of SARS-CoV-2 RNA in influent wastewater samples (n = 281) from three wastewater plants in Ohio from January 2021 to January 2022. Human fecal virus (PMMoV) and wastewater flow rate were used to normalize SARS-CoV-2 concentrations. SARS-CoV-2 measurements and COVID-19 cases were strongly correlated, but normalization effects on correlations varied between sewersheds. SARS-CoV-2 measurements by RT-qPCR were strongly correlated with 7-day moving average COVID-19 cases (average Spearman's ρ = 0.58, p < 0.05). SARS-CoV-2 was detected more frequently in samples with duplex RT-dPCR than with duplex RT-qPCR during periods of low COVID-19 cases. Duplex and uniplex RT-qPCR N1 concentrations were more strongly correlated with cases (ρ = 0.62) than N2 (ρ = 0.52). RT-dPCR correlations (average ρ = 0.21) were weaker than those of RT-qPCR (average ρ = 0.58). We also share practical experience from establishing wastewater surveillance. Per sample, RT-qPCR had a lower cost ($6 vs $18) and sample turnaround time (3-4 h vs 7-9 h) than RT-dPCR. These findings reinforce selection and use of PCR-based wastewater surveillance tools.
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Affiliation(s)
- Daniel Ma
- Department of Civil, Environmental and Geodetic
Engineering, The Ohio State University, Columbus, Ohio 43210,
United States
| | - Judith Straathof
- Department of Civil, Environmental and Geodetic
Engineering, The Ohio State University, Columbus, Ohio 43210,
United States
| | - Yijing Liu
- Department of Civil, Environmental and Geodetic
Engineering, The Ohio State University, Columbus, Ohio 43210,
United States
| | - Natalie Marie Hull
- Department of Civil, Environmental and Geodetic
Engineering, The Ohio State University, Columbus, Ohio 43210,
United States
- The Sustainability Institute, The Ohio
State University, Columbus, Ohio 43210, United
States
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