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Fondriest M, Vaccari L, Aldrovandi F, De Lellis L, Ferretti F, Fiorentino C, Mari E, Mascolo MG, Minelli L, Perlangeli V, Bortone G, Pandolfi P, Colacci A, Ranzi A. Wastewater-Based Epidemiology for SARS-CoV-2 in Northern Italy: A Spatiotemporal Model. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2024; 21:741. [PMID: 38928987 PMCID: PMC11203876 DOI: 10.3390/ijerph21060741] [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: 04/04/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
The study investigated the application of Wastewater-Based Epidemiology (WBE) as a tool for monitoring the SARS-CoV-2 prevalence in a city in northern Italy from October 2021 to May 2023. Based on a previously used deterministic model, this study proposed a variation to account for the population characteristics and virus biodegradation in the sewer network. The model calculated virus loads and corresponding COVID-19 cases over time in different areas of the city and was validated using healthcare data while considering viral mutations, vaccinations, and testing variability. The correlation between the predicted and reported cases was high across the three waves that occurred during the period considered, demonstrating the ability of the model to predict the relevant fluctuations in the number of cases. The population characteristics did not substantially influence the predicted and reported infection rates. Conversely, biodegradation significantly reduced the virus load reaching the wastewater treatment plant, resulting in a 30% reduction in the total virus load produced in the study area. This approach can be applied to compare the virus load values across cities with different population demographics and sewer network structures, improving the comparability of the WBE data for effective surveillance and intervention strategies.
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Affiliation(s)
- Matilde Fondriest
- Regional Agency for Prevention, Environment and Energy of Emilia-Romagna, 40139 Bologna, Italy; (L.V.); (E.M.); (M.G.M.); (G.B.); (A.C.); (A.R.)
| | - Lorenzo Vaccari
- Regional Agency for Prevention, Environment and Energy of Emilia-Romagna, 40139 Bologna, Italy; (L.V.); (E.M.); (M.G.M.); (G.B.); (A.C.); (A.R.)
| | - Federico Aldrovandi
- Alma Mater Institute on Healthy Planet, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40138 Bologna, Italy;
| | | | - Filippo Ferretti
- Local Health Authority of Bologna, Department of Public Health, 40124 Bologna, Italy; (F.F.); (C.F.); (V.P.); (P.P.)
| | - Carmine Fiorentino
- Local Health Authority of Bologna, Department of Public Health, 40124 Bologna, Italy; (F.F.); (C.F.); (V.P.); (P.P.)
| | - Erica Mari
- Regional Agency for Prevention, Environment and Energy of Emilia-Romagna, 40139 Bologna, Italy; (L.V.); (E.M.); (M.G.M.); (G.B.); (A.C.); (A.R.)
- Local Health Authority of Bologna, Department of Public Health, 40124 Bologna, Italy; (F.F.); (C.F.); (V.P.); (P.P.)
| | - Maria Grazia Mascolo
- Regional Agency for Prevention, Environment and Energy of Emilia-Romagna, 40139 Bologna, Italy; (L.V.); (E.M.); (M.G.M.); (G.B.); (A.C.); (A.R.)
| | | | - Vincenza Perlangeli
- Local Health Authority of Bologna, Department of Public Health, 40124 Bologna, Italy; (F.F.); (C.F.); (V.P.); (P.P.)
| | - Giuseppe Bortone
- Regional Agency for Prevention, Environment and Energy of Emilia-Romagna, 40139 Bologna, Italy; (L.V.); (E.M.); (M.G.M.); (G.B.); (A.C.); (A.R.)
| | - Paolo Pandolfi
- Local Health Authority of Bologna, Department of Public Health, 40124 Bologna, Italy; (F.F.); (C.F.); (V.P.); (P.P.)
| | - Annamaria Colacci
- Regional Agency for Prevention, Environment and Energy of Emilia-Romagna, 40139 Bologna, Italy; (L.V.); (E.M.); (M.G.M.); (G.B.); (A.C.); (A.R.)
| | - Andrea Ranzi
- Regional Agency for Prevention, Environment and Energy of Emilia-Romagna, 40139 Bologna, Italy; (L.V.); (E.M.); (M.G.M.); (G.B.); (A.C.); (A.R.)
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2
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Pasha ABT, Kotlarz N, Holcomb D, Reckling S, Kays J, Bailey E, Guidry V, Christensen A, Berkowitz S, Engel LS, de Los Reyes F, Harris A. Monitoring SARS-CoV-2 RNA in wastewater from a shared septic system and sub-sewershed sites to expand COVID-19 disease surveillance. JOURNAL OF WATER AND HEALTH 2024; 22:978-992. [PMID: 38935450 DOI: 10.2166/wh.2024.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/21/2024] [Indexed: 06/29/2024]
Abstract
Wastewater-based epidemiology has expanded as a tool for collecting COVID-19 surveillance data, but there is limited information on the feasibility of this form of surveillance within decentralized wastewater systems (e.g., septic systems). This study assessed SARS-CoV-2 RNA concentrations in wastewater samples from a septic system servicing a mobile home park (66 households) and from two pumping stations serving a similarly sized (71 households) and a larger (1,000 households) neighborhood within a nearby sewershed over 35 weeks in 2020. Also, raw wastewater from a hospital in the same sewershed was sampled. The mobile home park samples had the highest detection frequency (39/39 days) and mean concentration of SARS-CoV-2 RNA (2.7 × 107 gene copies/person/day for the N1) among the four sampling sites. N1 gene and N2 gene copies were highly correlated across mobile home park samples (Pearson's r = 0.93, p < 0.0001). In the larger neighborhood, new COVID-19 cases were reported every week during the sampling period; however, we detected SARS-CoV-2 RNA in 12% of the corresponding wastewater samples. The results of this study suggest that sampling from decentralized wastewater infrastructure can be used for continuous monitoring of SARS-CoV-2 infections.
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Affiliation(s)
- A B Tanvir Pasha
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA
| | - Nadine Kotlarz
- Center for Human Health and the Environment, NC State, Raleigh, NC, USA
| | - David Holcomb
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Stacie Reckling
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Judith Kays
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA
| | | | - Virginia Guidry
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Ariel Christensen
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Steven Berkowitz
- Division of Public Health, North Carolina Department of Health and Human Services, Raleigh, NC, USA
| | - Lawrence S Engel
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Francis de Los Reyes
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA
| | - Angela Harris
- Department of Civil, Construction and Environmental Engineering, North Carolina State University (NC State), 915 Partners Way, Raleigh, NC 27606, USA E-mail:
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3
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Holm RH, Pocock G, Severson MA, Huber VC, Smith T, McFadden LM. Using wastewater to overcome health disparities among rural residents. GEOFORUM; JOURNAL OF PHYSICAL, HUMAN, AND REGIONAL GEOSCIENCES 2023; 144:103816. [PMID: 37396346 PMCID: PMC10292026 DOI: 10.1016/j.geoforum.2023.103816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023]
Abstract
The SARS-CoV-2 pandemic highlighted the need for novel tools to promote health equity. There has been a historical legacy around the location and allocation of public facilities (such as health care) focused on efficiency, which is not attainable in rural, low-density, United States areas. Differences in the spread of the disease and outcomes of infections have been observed between urban and rural populations throughout the COVID-19 pandemic. The purpose of this article was to review rural health disparities related to the SARS-CoV-2 pandemic while using evidence to support wastewater surveillance as a potentially innovative tool to address these disparities more widely. The successful implementation of wastewater surveillance in resource-limited settings in South Africa demonstrates the ability to monitor disease in underserved areas. A better surveillance model of disease detection among rural residents will overcome issues around the interactions of a disease and social determinants of health. Wastewater surveillance can be used to promote health equity, particularly in rural and resource-limited areas, and has the potential to identify future global outbreaks of endemic and pandemic viruses.
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Affiliation(s)
- Rochelle H Holm
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, United States
| | - Gina Pocock
- Waterlab, 23B De Havilland Crescent, 0020 Persequor Technopark, South Africa
| | - Marie A Severson
- Division of Basic Biomedical Sciences, University of South Dakota, 414 E. Clark St., Vermillion, SD 57069, United States
| | - Victor C Huber
- Division of Basic Biomedical Sciences, University of South Dakota, 414 E. Clark St., Vermillion, SD 57069, United States
| | - Ted Smith
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, United States
| | - Lisa M McFadden
- Division of Basic Biomedical Sciences, University of South Dakota, 414 E. Clark St., Vermillion, SD 57069, United States
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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5
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Assoum M, Lau CL, Thai PK, Ahmed W, Mueller JF, Thomas KV, Choi PM, Jackson G, Selvey LA. Wastewater Surveillance Can Function as an Early Warning System for COVID-19 in Low-Incidence Settings. Trop Med Infect Dis 2023; 8:tropicalmed8040211. [PMID: 37104337 PMCID: PMC10143724 DOI: 10.3390/tropicalmed8040211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Introduction: During the first two years of the COVID-19 pandemic, Australia implemented a series of international and interstate border restrictions. The state of Queensland experienced limited COVID-19 transmission and relied on lockdowns to stem any emerging COVID-19 outbreaks. However, early detection of new outbreaks was difficult. In this paper, we describe the wastewater surveillance program for SARS-CoV-2 in Queensland, Australia, and report two case studies in which we aimed to assess the potential for this program to provide early warning of new community transmission of COVID-19. Both case studies involved clusters of localised transmission, one originating in a Brisbane suburb (Brisbane Inner West) in July–August 2021, and the other originating in Cairns, North Queensland in February–March 2021. Materials and Methods: Publicly available COVID-19 case data derived from the notifiable conditions (NoCs) registry from the Queensland Health data portal were cleaned and merged spatially with the wastewater surveillance data using statistical area 2 (SA2) codes. The positive predictive value and negative predictive value of wastewater detection for predicting the presence of COVID-19 reported cases were calculated for the two case study sites. Results: Early warnings for local transmission of SARS-CoV-2 through wastewater surveillance were noted in both the Brisbane Inner West cluster and the Cairns cluster. The positive predictive value of wastewater detection for the presence of notified cases of COVID-19 in Brisbane Inner West and Cairns were 71.4% and 50%, respectively. The negative predictive value for Brisbane Inner West and Cairns were 94.7% and 100%, respectively. Conclusions: Our findings highlight the utility of wastewater surveillance as an early warning tool in low COVID-19 transmission settings.
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Affiliation(s)
- Mohamad Assoum
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Colleen L. Lau
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Phong K. Thai
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Jochen F. Mueller
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Kevin V. Thomas
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Phil Min Choi
- Health Protection Branch, Queensland Health, Brisbane, QLD 4006, Australia
| | - Greg Jackson
- Health Protection Branch, Queensland Health, Brisbane, QLD 4006, Australia
| | - Linda A. Selvey
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
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6
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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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7
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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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8
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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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9
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Amman F, Markt R, Endler L, Hupfauf S, Agerer B, Schedl A, Richter L, Zechmeister M, Bicher M, Heiler G, Triska P, Thornton M, Penz T, Senekowitsch M, Laine J, Keszei Z, Klimek P, Nägele F, Mayr M, Daleiden B, Steinlechner M, Niederstätter H, Heidinger P, Rauch W, Scheffknecht C, Vogl G, Weichlinger G, Wagner AO, Slipko K, Masseron A, Radu E, Allerberger F, Popper N, Bock C, Schmid D, Oberacher H, Kreuzinger N, Insam H, Bergthaler A. Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale. Nat Biotechnol 2022; 40:1814-1822. [PMID: 35851376 DOI: 10.1038/s41587-022-01387-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/07/2022] [Indexed: 01/14/2023]
Abstract
SARS-CoV-2 surveillance by wastewater-based epidemiology is poised to provide a complementary approach to sequencing individual cases. However, robust quantification of variants and de novo detection of emerging variants remains challenging for existing strategies. We deep sequenced 3,413 wastewater samples representing 94 municipal catchments, covering >59% of the population of Austria, from December 2020 to February 2022. Our system of variant quantification in sewage pipeline designed for robustness (termed VaQuERo) enabled us to deduce the spatiotemporal abundance of predefined variants from complex wastewater samples. These results were validated against epidemiological records of >311,000 individual cases. Furthermore, we describe elevated viral genetic diversity during the Delta variant period, provide a framework to predict emerging variants and measure the reproductive advantage of variants of concern by calculating variant-specific reproduction numbers from wastewater. Together, this study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without extensive individual monitoring.
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Affiliation(s)
- Fabian Amman
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Rudolf Markt
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Sebastian Hupfauf
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Schedl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Lukas Richter
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | | | - Martin Bicher
- dwh GmbH, Vienna, Austria.,Institute for Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Georg Heiler
- Complexity Science Hub, Vienna, Austria.,Institute of Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Petr Triska
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Matthew Thornton
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Martin Senekowitsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jan Laine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Zsofia Keszei
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Peter Klimek
- Complexity Science Hub, Vienna, Austria.,Section for Science of Complex Systems, Medical University of Vienna, Vienna, Austria
| | - Fabiana Nägele
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Markus Mayr
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Beatrice Daleiden
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Steinlechner
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Harald Niederstätter
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Petra Heidinger
- Austrian Centre of Industrial Biotechnology GmbH, Graz, Austria
| | - Wolfgang Rauch
- Department of Infrastructure, Universität Innsbruck, Innsbruck, Austria
| | | | - Gunther Vogl
- Institut für Lebensmittelsicherheit, Veterinärmedizin und Umwelt des Landes Kärnten, Klagenfurt am Wörthersee, Austria
| | - Günther Weichlinger
- Abteilung 12 - Wasserwirtschaft, Amt der Kärntner Landesregierung, Klagenfurt am Wörthersee, Austria
| | | | - Katarzyna Slipko
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Amandine Masseron
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Elena Radu
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria.,Ştefan S. Nicolau Institute of Virology, Bucharest, Romania
| | | | - Niki Popper
- dwh GmbH, Vienna, Austria.,Institute for Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Daniela Schmid
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Heribert Insam
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
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10
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Martins RM, Carvalho T, Bittar C, Quevedo DM, Miceli RN, Nogueira ML, Ferreira HL, Costa PI, Araújo JP, Spilki FR, Rahal P, Calmon MF. Long-Term Wastewater Surveillance for SARS-CoV-2: One-Year Study in Brazil. Viruses 2022; 14:v14112333. [PMID: 36366431 PMCID: PMC9692902 DOI: 10.3390/v14112333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/26/2022] [Accepted: 10/05/2022] [Indexed: 02/01/2023] Open
Abstract
Wastewater-based epidemiology (WBE) is a tool involving the analysis of wastewater for chemicals and pathogens at the community level. WBE has been shown to be an effective surveillance system for SARS-CoV-2, providing an early-warning-detection system for disease prevalence in the community via the detection of genetic materials in the wastewater. In numerous nation-states, studies have indicated the presence of SARS-CoV-2 in wastewater. Herein, we report the primary time-course monitoring of SARS-CoV-2 RNA in wastewater samples in São José do Rio Preto-SP/Brazil in order to explain the dynamics of the presence of SARS-CoV-2 RNA during one year of the SARS-CoV-2 pandemic and analyze possible relationships with other environmental parameters. We performed RNA quantification of SARS-CoV-2 by RT-qPCR using N1 and N2 targets. The proportion of positive samples for every target resulted in 100% and 96.6% for N1 and N2, respectively. A mean lag of -5 days is observed between the wastewater signal and the new SARS-CoV-2-positive cases reported. A correlation was found between the air and wastewater temperatures and therefore between the SARS-CoV-2 viral titers for N1 and N2 targets. We also observed a correlation between SARS-CoV-2 viral titers and media wastewater flow for the N1 target. In addition, we observed higher viral genome copies within the wastewater samples collected on non-rainy days for the N1 target. Thus, we propose that, based on our results, monitoring raw wastewater may be a broadly applicable strategy that might contribute to resolving the pressing problem of insufficient diagnostic testing; it may represent an inexpensive and early-warning method for future COVID-19 outbreaks, mainly in lower- and middle-income countries.
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Affiliation(s)
- Renan Moura Martins
- Laboratory of Genomic Studies, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Tamara Carvalho
- Laboratory of Genomic Studies, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Cintia Bittar
- Laboratory of Genomic Studies, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Daniela Muller Quevedo
- Institute of Exact and Technological Sciences (ICET), University Feevale, Novo Hamburgo 93525-075, RS, Brazil
| | - Rafael Nava Miceli
- SeMAE-Autonomous Municipal Water and Sewage Service, São José do Rio Preto 15048-000, SP, Brazil
| | - Mauricio Lacerda Nogueira
- Virology Research Laboratory (LPV), Faculty of Medicine of São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil
| | - Helena Lage Ferreira
- Applied Preventive Veterinary Medicine Laboratory, Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil
| | - Paulo Inácio Costa
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14801-360, SP, Brazil
| | - João Pessoa Araújo
- Biotechnology Institute, São Paulo State University (UNESP), Botucatu 18607-440, SP, Brazil
| | - Fernando Rosado Spilki
- Molecular Microbiology Laboratory, University Feevale, Novo Hamburgo 93525-075, RS, Brazil
| | - Paula Rahal
- Laboratory of Genomic Studies, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Marilia Freitas Calmon
- Laboratory of Genomic Studies, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto 15054-000, SP, Brazil
- Correspondence:
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11
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Robins K, Leonard AFC, Farkas K, Graham DW, Jones DL, Kasprzyk-Hordern B, Bunce JT, Grimsley JMS, Wade MJ, Zealand AM, McIntyre-Nolan S. Research needs for optimising wastewater-based epidemiology monitoring for public health protection. JOURNAL OF WATER AND HEALTH 2022; 20:1284-1313. [PMID: 36170187 DOI: 10.2166/wh.2022.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Wastewater-based epidemiology (WBE) is an unobtrusive method used to observe patterns in illicit drug use, poliovirus, and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The pandemic and need for surveillance measures have led to the rapid acceleration of WBE research and development globally. With the infrastructure available to monitor SARS-CoV-2 from wastewater in 58 countries globally, there is potential to expand targets and applications for public health protection, such as other viral pathogens, antimicrobial resistance (AMR), pharmaceutical consumption, or exposure to chemical pollutants. Some applications have been explored in academic research but are not used to inform public health decision-making. We reflect on the current knowledge of WBE for these applications and identify barriers and opportunities for expanding beyond SARS-CoV-2. This paper critically reviews the applications of WBE for public health and identifies the important research gaps for WBE to be a useful tool in public health. It considers possible uses for pathogenic viruses, AMR, and chemicals. It summarises the current evidence on the following: (1) the presence of markers in stool and urine; (2) environmental factors influencing persistence of markers in wastewater; (3) methods for sample collection and storage; (4) prospective methods for detection and quantification; (5) reducing uncertainties; and (6) further considerations for public health use.
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Affiliation(s)
- Katie Robins
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail: ; School of Engineering, Newcastle University, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Anne F C Leonard
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail: ; University of Exeter Medical School, European Centre for Environment and Human Health, University of Exeter, Cornwall TR10 9FE, UK
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - David W Graham
- School of Engineering, Newcastle University, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - David L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA 6105, Australia
| | | | - Joshua T Bunce
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail: ; School of Engineering, Newcastle University, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Jasmine M S Grimsley
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail:
| | - Matthew J Wade
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail: ; School of Engineering, Newcastle University, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Andrew M Zealand
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail:
| | - Shannon McIntyre-Nolan
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK E-mail: ; Her Majesty's Prison and Probation Service, Ministry of Justice, London, SW1H 9AJ, UK
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12
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Welling CM, Singleton DR, Haase SB, Browning CH, Stoner BR, Gunsch CK, Grego S. Predictive values of time-dense SARS-CoV-2 wastewater analysis in university campus buildings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155401. [PMID: 35469858 PMCID: PMC9026951 DOI: 10.1016/j.scitotenv.2022.155401] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 05/14/2023]
Abstract
Wastewater-based SARS-CoV-2 surveillance on college campuses has the ability to detect individual clinical COVID-19 cases at the building-level. High concordance of wastewater results and clinical cases has been observed when calculated over a time window of four days or longer and in settings with high incidence of infection. At Duke University, twice a week clinical surveillance of all resident undergraduates was carried out in the spring 2021 semester. We conducted simultaneous wastewater surveillance with daily frequency on selected residence halls to assess wastewater as an early warning tool during times of low transmission with the hope of scaling down clinical test frequency. We evaluated the temporal relationship of the two time-dense data sets, wastewater and clinical, and sought a strategy to achieve the highest wastewater predictive values using the shortest time window to enable timely intervention. There were 11 days with clinical cases in the residence halls (80-120 occupants) under wastewater surveillance with 5 instances of a single clinical case and 3 instances of two clinical cases which also corresponded to a positive wastewater SARS-CoV-2 signal. While the majority (71%) of our wastewater samples were negative for SARS-CoV-2, 29% resulted in at least one positive PCR signal, some of which did not correlate with an identified clinical case. Using a criteria of two consecutive days of positive wastewater signals, we obtained a positive predictive value (PPV) of 75% and a negative predictive value of 87% using a short 2 day time window for agreement. A conventional concordance over a much longer 4 day time window resulted in PPV of only 60%. Our data indicated that daily wastewater collection and using a criteria of two consecutive days of positive wastewater signals was the most predictive approach to timely early warning of COVID-19 cases at the building level.
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Affiliation(s)
- Claire M Welling
- Center for Water, Sanitation, Hygiene and Infectious Disease (WASH-AID), Department of Electrical and Computer Engineering, Duke University, Durham, NC, United States of America
| | - David R Singleton
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, United States of America
| | - Steven B Haase
- Departments of Biology and Medicine, Duke University, Durham, NC, United States of America
| | - Christian H Browning
- Office of Information Technology, Duke University, Durham, NC, United States of America
| | - Brian R Stoner
- Center for Water, Sanitation, Hygiene and Infectious Disease (WASH-AID), Department of Electrical and Computer Engineering, Duke University, Durham, NC, United States of America
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, United States of America
| | - Sonia Grego
- Center for Water, Sanitation, Hygiene and Infectious Disease (WASH-AID), Department of Electrical and Computer Engineering, Duke University, Durham, NC, United States of America.
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High Sensitivity and Specificity of Dormitory-Level Wastewater Surveillance for COVID-19 during Fall Semester 2020 at Syracuse University, New York. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084851. [PMID: 35457720 PMCID: PMC9030442 DOI: 10.3390/ijerph19084851] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 01/27/2023]
Abstract
A residential building’s wastewater presents a potential non-invasive method of surveilling numerous infectious diseases, including SARS-CoV-2. We analyzed wastewater from 16 different residential locations at Syracuse University (Syracuse, NY, USA) during fall semester 2020, testing for SARS-CoV-2 RNA twice weekly and compared the presence of clinical COVID-19 cases to detection of the viral RNA in wastewater. The sensitivity of wastewater surveillance to correctly identify dormitories with a case of COVID-19 ranged from 95% (95% confidence interval [CI] = 76–100%) on the same day as the case was diagnosed to 73% (95% CI = 53–92%), with 7 days lead time of wastewater. The positive predictive value ranged from 20% (95% CI = 13–30%) on the same day as the case was diagnosed to 50% (95% CI = 40–60%) with 7 days lead time. The specificity of wastewater surveillance to correctly identify dormitories without a case of COVID-19 ranged from 60% (95% CI = 52–67%) on the day of the wastewater sample to 67% (95% CI = 58–74%) with 7 days lead time. The negative predictive value ranged from 99% (95% CI = 95–100%) on the day of the wastewater sample to 84% (95% CI = 77–91%) with 7 days lead time. Wastewater surveillance for SARS-CoV-2 at the building level is highly accurate in determining if residents have a COVID-19 infection. Particular benefit is derived from negative wastewater results that can confirm a building is COVID-19 free.
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14
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Inferring SARS-CoV-2 RNA shedding into wastewater relative to the time of infection - CORRIGENDUM. Epidemiol Infect 2022; 150:e49. [PMID: 35241199 PMCID: PMC8914130 DOI: 10.1017/s0950268822000322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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