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Korajkic A, McMinn BR, Pemberton AC, Kelleher J, Ahmed W. The comparison of decay rates of infectious SARS-CoV-2 and viral RNA in environmental waters and wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174379. [PMID: 38955270 PMCID: PMC11290430 DOI: 10.1016/j.scitotenv.2024.174379] [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: 05/17/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
Understanding the decay characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater and ambient waters is important for multiple applications including assessment of risk of exposure associated with handling wastewater samples, public health risk associated with recreation in wastewater polluted ambient waters and better understanding and interpretation of wastewater-based epidemiology (WBE) results. We evaluated the decay rates of infectious SARS-CoV-2 and viral RNA in wastewater and ambient waters under temperature regimes representative of seasonal fluctuations. Infectious virus was seeded in autoclaved primary wastewater effluent, final dechlorinated wastewater effluent, lake water, and marine water at a final concentration of 6.26 ± 0.07 log10 plaque forming units per milliliter. Each suspension was incubated at either 4°, 25°, and 37 °C. Samples were initially collected on an hourly basis, then approximately every other day for 15 days. All samples were analyzed for infectious virus via a plaque assay using the Vero E6 cell line, and viral gene copy levels were quantified with the US CDC's N1 and N2 reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assays. The infectious virus decayed significantly faster (p ≤ 0.0214) compared to viral RNA, which persisted for the duration of the study irrespective of the incubation conditions. The initial loss (within 15 min of seeding) as well as decay of infectious SARS-CoV-2 was significantly faster (p ≤ 0.0387) in primary treated wastewater compared to other water types, but viral RNA did not degrade appreciably in this matrix until day 15. Overall, temperature was the most important driver of decay, and after 24 h, no infectious SARS-CoV-2 was detected at 37 °C in any water type. Moreover, the CDC N2 gene assay target decayed significantly (p ≤ 0.0174) faster at elevated temperatures compared to CDC N1, which has important implications for RT-qPCR assay selection for WBE approach.
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Affiliation(s)
- Asja Korajkic
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States.
| | - Brian R McMinn
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Adin C Pemberton
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Julie Kelleher
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct 41 Boggo Road, Qld 4102, Australia
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2
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Zhao L, Guzman HP, Xagoraraki I. Comparative analyses of SARS-CoV-2 RNA concentrations in Detroit wastewater quantified with CDC N1, N2, and SC2 assays reveal optimal target for predicting COVID-19 cases. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:174140. [PMID: 38906283 DOI: 10.1016/j.scitotenv.2024.174140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
To monitor COVID-19 through wastewater surveillance, global researchers dedicated significant endeavors and resources to develop and implement diverse RT-qPCR or RT-ddPCR assays targeting different genes of SARS-CoV-2. Effective wastewater surveillance hinges on the appropriate selection of the most suitable assay, especially for resource-constrained regions where scant technical and socioeconomic resources restrict the options for testing with multiple assays. Further research is imperative to evaluate the existing assays through comprehensive comparative analyses. Such analyses are crucial for health agencies and wastewater surveillance practitioners in the selection of appropriate methods for monitoring COVID-19. In this study, untreated wastewater samples were collected weekly from the Detroit wastewater treatment plant, Michigan, USA, between January and December 2023. Polyethylene glycol precipitation (PEG) was applied to concentrate the samples followed by RNA extraction and RT-ddPCR. Three assays including N1, N2 (US CDC Real-Time Reverse Transcription PCR Panel for Detection of SARS-CoV-2), and SC2 assay (US CDC Influenza SARS-CoV-2 Multiplex Assay) were implemented to detect SARS-CoV-2 in wastewater. The limit of blank and limit of detection for the three assays were experimentally determined. SARS-CoV-2 RNA concentrations were evaluated and compared through three statistical approaches, including Pearson and Spearman's rank correlations, Dynamic Time Warping, and vector autoregressive models. N1 and N2 demonstrated the highest correlation and most similar time series patterns. Conversely, N2 and SC2 assay demonstrated the lowest correlation and least similar time series patterns. N2 was identified as the optimal target to predict COVID-19 cases. This study presents a rigorous effort in evaluating and comparing SARS-CoV-2 RNA concentrations quantified with N1, N2, and SC2 assays and their interrelations and correlations with clinical cases. This study provides valuable insights into identifying the optimal target for monitoring COVID-19 through wastewater surveillance.
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Affiliation(s)
- Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, MI 48823, USA
| | - Heidy Peidro Guzman
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, MI 48823, USA
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct., East Lansing, MI 48823, USA.
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3
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Purves K, Reynolds LJ, Sala-Comorera L, Martin NA, Dahly DL, Meijer WG, Fletcher NF. Decay of RNA and infectious SARS-CoV-2 and murine hepatitis virus in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173877. [PMID: 38871327 DOI: 10.1016/j.scitotenv.2024.173877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
Wastewater-based epidemiology (WBE) has been an important tool for population surveillance during the COVID-19 pandemic and continues to play a key role in monitoring SARS-CoV-2 infection levels following reductions in national clinical testing schemes. Studies measuring decay profiles of SARS-CoV-2 in wastewater have underscored the value of WBE, however investigations have been hampered by high biosafety requirements for SARS-CoV-2 infection studies. Therefore, surrogate viruses with lower biosafety standards have been used for SARS-CoV-2 decay studies, such as murine hepatitis virus (MHV), but few studies have directly compared decay rates of both viruses. We compared the persistence of SARS-CoV-2 and MHV in wastewater, using 50 % tissue culture infectious dose (TCID50) and reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays to assess infectious virus titre and viral gene markers, respectively. Infectious SARS-CoV-2 and MHV indicate similar endpoints, however observed early decay characteristics differed, with infectious SARS-CoV-2 decaying more rapidly than MHV. We find that MHV is an appropriate infectious virus surrogate for viable SARS-CoV-2, however inconsistencies exist in viral RNA decay parameters, indicating MHV may not be a suitable nucleic acid surrogate across certain temperature regimes. This study highlights the importance of sample preparation and the potential for decay rate overestimation in wastewater surveillance for SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Kevin Purves
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Ireland
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Ireland
| | - Laura Sala-Comorera
- Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Ireland
| | - Darren L Dahly
- Health Research Board Clinical Research Facility, University College Cork, Ireland; School of Public Health, University College Cork, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Ireland
| | - Nicola F Fletcher
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Ireland.
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Shrestha S, Malla B, Haramoto E. High-throughput microfluidic quantitative PCR system for the simultaneous detection of antibiotic resistance genes and bacterial and viral pathogens in wastewater. ENVIRONMENTAL RESEARCH 2024; 255:119156. [PMID: 38759773 DOI: 10.1016/j.envres.2024.119156] [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: 04/12/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Comprehensive data on bacterial and viral pathogens of diarrhea and studies applying culture-independent methods for examining antibiotic resistance in wastewater are lacking. This study aimed to simultaneously quantify antibiotic resistance genes (ARGs), class 1 integron-integrase (int1), bacterial and viral pathogens of diarrhea, 16S rRNA, and other indicators using a high-throughput quantitative PCR (HT-qPCR) system. Thirty-six grab wastewater samples from a wastewater treatment plant in Japan, collected three times a month between August 2022 and July 2023, were centrifuged, followed by nucleic acid extraction, reverse transcription, and HT-qPCR. Fourteen targets were included, and HT-qPCR was performed on the Biomark X9™ System (Standard BioTools). For all qPCR assays, R2 was ≥0.978 and the efficiencies ranged from 90.5% to 117.7%, exhibiting high performance. Of the 36 samples, 20 (56%) were positive for Norovirus genogroup II (NoV-GII), whereas Salmonella spp. and Campylobacter jejuni were detected in 24 (67%) and Campylobacter coli in 13 (36%) samples, with mean concentrations ranging from 3.2 ± 0.8 to 4.7 ± 0.3 log10 copies/L. NoV-GII detection ratios and concentrations were higher in winter and spring. None of the pathogens of diarrhea correlated with acute gastroenteritis cases, except for NoV-GII, suggesting the need for data on specific bacterial infections to validate bacterial wastewater-based epidemiology (WBE). All samples tested positive for sul1, int1, and blaCTX-M, irrespective of season. The less explored blaNDM-1 showed a wide prevalence (>83%) and consistent abundance ranging from 4.3 ± 1.0 to 4.9 ± 0.2 log10 copies/L in all seasons. sul1 was the predominant ARG, whereas absolute abundances of 16S rRNA, int1, and blaCTX-M varied seasonally. int1 was significantly correlated with blaCTX-M in autumn and spring, whereas it showed no correlation with blaNDM-1, questioning the applicability of int1 as a sole indicator of overall resistance determinants. This study exhibited that the HT-qPCR system is pivotal for WBE.
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Affiliation(s)
- Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi, 400-8511, Japan.
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi, 400-8511, Japan.
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi, 400-8511, Japan.
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Murni IK, Oktaria V, McCarthy DT, Supriyati E, Nuryastuti T, Handley A, Donato CM, Wiratama BS, Dinari R, Laksono IS, Thobari JA, Bines JE. Wastewater-based epidemiology surveillance as an early warning system for SARS-CoV-2 in Indonesia. PLoS One 2024; 19:e0307364. [PMID: 39024238 PMCID: PMC11257287 DOI: 10.1371/journal.pone.0307364] [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] [Received: 02/23/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Wastewater-based epidemiology (WBE) surveillance has been proposed as an early warning system (EWS) for community SARS-CoV-2 transmission. However, there is limited data from low-and middle-income countries (LMICs). This study aimed to assess the ability of WBE surveillance to detect SARS-CoV-2 in formal and informal environments in Indonesia using different methods of sample collection, to compare WBE data with patterns of clinical cases of COVID-19 within the relevant communities, and to assess the WBE potential to be used as an EWS for SARS-CoV-2 outbreaks within a community. MATERIALS AND METHODS We conducted WBE surveillance in three districts in Yogyakarta province, Indonesia, over eleven months (27 July 2021 to 7 January 2022 [Delta wave]; 18 January to 3 June 2022 [Omicron wave]). Water samples using grab, and/or passive sampling methods and soil samples were collected either weekly or fortnightly. RNA was extracted from membrane filters from processed water samples and directly from soil. Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the SARS-CoV-2 N and ORF1ab genes. RESULTS A total of 1,582 samples were collected. Detection rates of SARS-CoV-2 in wastewater reflected the incidence of community cases, with rates of 85% at the peak to 2% at the end of the Delta wave and from 94% to 11% during the Omicron wave. A 2-week lag time was observed between the detection of SARS-CoV-2 in wastewater and increasing cases in the corresponding community. CONCLUSION WBE surveillance for SARS-CoV-2 in Indonesia was effective in monitoring patterns of cases of COVID-19 and served as an early warning system, predicting the increasing incidence of COVID-19 cases in the community.
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Affiliation(s)
- Indah Kartika Murni
- Center for Child Health – Pediatric Research Office, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Child Health Department, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Vicka Oktaria
- Center for Child Health – Pediatric Research Office, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Biostatistics, Epidemiology, and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - David T. McCarthy
- Department of Civil Engineering, Environmental and Public Health Microbiology Lab (EPHM Lab), Monash University, Clayton, Victoria Australia
- School of Civil and Environmental Engineering, Faculty of Engineering, Queensland University of Technology, Queensland, Australia
| | - Endah Supriyati
- Center for Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Amanda Handley
- Medicines Development for Global Health, Southbank, Victoria Australia
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Celeste M. Donato
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Bayu Satria Wiratama
- Department of Biostatistics, Epidemiology, and Population Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rizka Dinari
- Center for Child Health – Pediatric Research Office, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ida Safitri Laksono
- Center for Child Health – Pediatric Research Office, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Child Health Department, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Jarir At Thobari
- Center for Child Health – Pediatric Research Office, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Julie E Bines
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Department of Gastroenterology and Clinical Nutrition, Royal Children’s Hospital Melbourne, Victoria, Australia
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6
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Geiwitz M, Page OR, Marello T, Nichols ME, Kumar N, Hummel S, Belosevich V, Ma Q, van Opijnen T, Batten B, Meyer MM, Burch KS. Graphene Multiplexed Sensor for Point-of-Need Viral Wastewater-Based Epidemiology. ACS APPLIED BIO MATERIALS 2024; 7:4622-4632. [PMID: 38954405 DOI: 10.1021/acsabm.4c00484] [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: 07/04/2024]
Abstract
Wastewater-based epidemiology (WBE) can help mitigate the spread of respiratory infections through the early detection of viruses, pathogens, and other biomarkers in human waste. The need for sample collection, shipping, and testing facilities drives up the cost of WBE and hinders its use for rapid detection and isolation in environments with small populations and in low-resource settings. Given the ubiquitousness and regular outbreaks of respiratory syncytial virus, SARS-CoV-2, and various influenza strains, there is a rising need for a low-cost and easy-to-use biosensing platform to detect these viruses locally before outbreaks can occur and monitor their progression. To this end, we have developed an easy-to-use, cost-effective, multiplexed platform able to detect viral loads in wastewater with several orders of magnitude lower limit of detection than that of mass spectrometry. This is enabled by wafer-scale production and aptamers preattached with linker molecules, producing 44 chips at once. Each chip can simultaneously detect four target analytes using 20 transistors segregated into four sets of five for each analyte to allow for immediate statistical analysis. We show our platform's ability to rapidly detect three virus proteins (SARS-CoV-2, RSV, and Influenza A) and a population normalization molecule (caffeine) in wastewater. Going forward, turning these devices into hand-held systems would enable wastewater epidemiology in low-resource settings and be instrumental for rapid, local outbreak prevention.
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Affiliation(s)
- Michael Geiwitz
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Owen Rivers Page
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Tio Marello
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Marina E Nichols
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Narendra Kumar
- GRIP Molecular Technologies, Inc., 1000 Westgate Drive, Saint Paul, Minnesota 55114, United States
| | - Stephen Hummel
- Department of Chemistry and Life Science, United States Military Academy, West Point, New York 10996, United States
| | - Vsevolod Belosevich
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Qiong Ma
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Bruce Batten
- GRIP Molecular Technologies, Inc., 1000 Westgate Drive, Saint Paul, Minnesota 55114, United States
| | - Michelle M Meyer
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Kenneth S Burch
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
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Yigci D, Bonventre J, Ozcan A, Tasoglu S. Repurposing Sewage and Toilet Systems: Environmental, Public Health, and Person-Centered Healthcare Applications. GLOBAL CHALLENGES (HOBOKEN, NJ) 2024; 8:2300358. [PMID: 39006062 PMCID: PMC11237177 DOI: 10.1002/gch2.202300358] [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: 11/22/2023] [Revised: 01/27/2024] [Indexed: 07/16/2024]
Abstract
Global terrestrial water supplies are rapidly depleting due to the consequences of climate change. Water scarcity results in an inevitable compromise of safe hygiene and sanitation practices, leading to the transmission of water-borne infectious diseases, and the preventable deaths of over 800.000 people each year. Moreover, almost 500 million people lack access to toilets and sanitation systems. Ecosystems are estimated to be contaminated by 6.2 million tons of nitrogenous products from human wastewater management practices. It is therefore imperative to transform toilet and sewage systems to promote equitable access to water and sanitation, improve public health, conserve water, and protect ecosystems. Here, the integration of emerging technologies in toilet and sewage networks to repurpose toilet and wastewater systems is reviewed. Potential applications of these systems to develop sustainable solutions to environmental challenges, promote public health, and advance person-centered healthcare are discussed.
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Affiliation(s)
- Defne Yigci
- School of MedicineKoç UniversityIstanbul34450Türkiye
| | - Joseph Bonventre
- Division of Renal MedicineDepartment of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering DepartmentUniversity of CaliforniaLos AngelesCA90095USA
- Bioengineering DepartmentUniversity of CaliforniaLos AngelesCA90095USA
- California NanoSystems Institute (CNSI)University of CaliforniaLos AngelesCA90095USA
- Computer Science DepartmentUniversity of CaliforniaLos AngelesCA90095USA
- Department of SurgeryDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCA90095USA
| | - Savas Tasoglu
- Department of Mechanical EngineeringKoç UniversitySariyerIstanbul34450Türkiye
- Koç University Translational Medicine Research Center (KUTTAM)Koç UniversityIstanbul34450Türkiye
- Boğaziçi Institute of Biomedical EngineeringBoğaziçi UniversityIstanbul34684Turkey
- Koç University Arçelik Research Center for Creative Industries (KUAR)Koç UniversityIstanbul34450Turkey
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Shrestha S, Malla B, Haramoto E. Group A Streptococcus pyogenes in wastewater: Applicability of wastewater-based epidemiology for monitoring the prevalence of GAS pharyngitis during the late COVID-19 pandemic phase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172447. [PMID: 38621526 DOI: 10.1016/j.scitotenv.2024.172447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Streptococcus pyogenes, Group A Streptococcus (GAS), is a human pathogen that causes a spectrum of diseases from mild to severe, including GAS pharyngitis, a common acute respiratory disease in developed countries. Although wastewater-based epidemiology (WBE) has been extensively used to monitor viral pathogens such as severe acute respiratory syndrome coronavirus 2, its applicability to S. pyogenes remains unexplored. This study was conducted to investigate the feasibility of detecting and quantifying S. pyogenes in wastewater by quantitative polymerase chain reaction (qPCR) and evaluate the applicability of WBE for monitoring the prevalence of GAS pharyngitis. A total of 52 grab influent samples were collected from a wastewater treatment plant in Japan once a week between March 2023 and February 2024. The samples were centrifuged, followed by nucleic acid extraction and qPCR for the S. pyogenes-specific genes speB and spy1258. Of the 52 samples, 90 % and 81 % were positive for speB and spy1258 genes, respectively, indicating the feasibility of S. pyogenes for wastewater surveillance. However, the percentage of quantifiable samples for speB gene was significantly higher in winter than in spring and summer. Similarly, the concentrations of both genes in wastewater samples were significantly higher in winter (speB, 4.1 ± 0.27 log10 copies/L; spy1258, 4.1 ± 0.28 log10 copies/L; One-way ANOVA, p < 0.01) than in spring and summer. Higher concentrations and detection ratios of S. pyogenes genes were observed during increased GAS pharyngitis cases in the catchment. Significant moderate correlations were observed between target gene concentrations and reported GAS pharyngitis cases. This study enhances the understanding role of WBE in monitoring and managing infectious diseases within communities.
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Affiliation(s)
- Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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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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Ruzi II, Ishak AR, Abdullah MA, Zain NNM, Tualeka AR, Adriyani R, Mohamed R, Edinur HA, Aziz MY. Heavy metal contamination in Sungai Petani, Malaysia: a wastewater-based epidemiology study. JOURNAL OF WATER AND HEALTH 2024; 22:953-966. [PMID: 38935448 DOI: 10.2166/wh.2024.241] [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: 08/11/2023] [Accepted: 05/09/2024] [Indexed: 06/29/2024]
Abstract
The aim of this study was to investigate the use of wastewater-based epidemiology (WBE) to estimate heavy metal exposure in Sungai Petani, Malaysia. Atomic absorption spectroscopy was used to detect copper (Cu), nickel (Ni), zinc (Zn), iron (Fe), and cadmium (Cd) in wastewater from eight sewage treatment facilities in Sungai Petani in January 2022. The heavy metal concentrations were measured in both influent and effluent, and the mean concentrations in the wastewater were found to be in the following order: Fe > Ni > Zn > Cd > Cu, with a 100% detection frequency. The results of WBE estimation showed that Fe, Ni, and Zn had the highest estimated per population exposure levels, while Cd had the lowest. Compared to a similar study conducted in Penang, Malaysia, all metals except Cu were found to have higher concentrations in Sungai Petani, even though it is a non-industrial district. These findings highlight the importance of addressing heavy metal contamination in Sungai Petani and implementing effective risk management and prevention strategies.
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Affiliation(s)
- Iqbal Iman Ruzi
- Department of Toxicology, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Bertam, Kepala Batas, Penang, Malaysia
| | - Ahmad Razali Ishak
- Center of Environmental Health & Safety, Faculty of Health Sciences, Universiti Teknologi MARA, Puncak Alam 42300, Selangor, Malaysia
| | - Muhamad Azwat Abdullah
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Puncak Alam, Selangor 42300, Malaysia
| | - Nur Nadhirah Mohamad Zain
- Department of Toxicology, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Bertam, Kepala Batas, Penang, Malaysia
| | - Abdul Rohim Tualeka
- Department of Occupational Health and Safety, Public Health Faculty, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Retno Adriyani
- Department of Environmental Health, Faculty of Public Health, Airlangga University, Surabaya 60115, East Java, Indonesia
| | - Rafeezul Mohamed
- Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Bertam, Kepala Batas, Penang, Malaysia
| | - Hisham Atan Edinur
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Mohd Yusmaidie Aziz
- Department of Toxicology, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Bertam, Kepala Batas, Penang, Malaysia; Department of Occupational Health and Safety, Public Health Faculty, Universitas Airlangga, Surabaya, East Java 60115, Indonesia E-mail:
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11
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Starke JC, Bell NS, Martinez CM, Friberg IK, Lawley C, Sriskantharajah V, Hirschberg DL. Measuring SARS-CoV-2 RNA concentrations in neighborhood wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172021. [PMID: 38552966 DOI: 10.1016/j.scitotenv.2024.172021] [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: 09/27/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
Longitudinal wastewater sampling during the COVID-19 pandemic was an important aspect of disease surveillance, adding to a more complete understanding of infection dynamics and providing important data for community public health monitoring and intervention planning. This was largely accomplished by testing SARS-CoV-2 RNA concentrations in samples from municipal wastewater treatment plants (WWTPs). We evaluated the utility of testing for virus levels upstream from WWTP within the residential neighborhoods that feed into the WWTP. We propose that monitoring virus dynamics across residential neighborhoods could reveal important public health-relevant information about community sub-group heterogeneity in virus concentrations. PRINCIPAL RESULTS: Virus concentration patterns display heterogeneity within neighborhoods and between neighborhoods over time. Sewage SARS-CoV-2 RNA concentrations as measured by RT-qPCR also corresponded closely to verified COVID-19 infection counts within individual neighborhoods. More importantly, our data suggest the loss of disease-relevant public health information when sampling occurs only at the level of WWTP instead of upstream in neighborhoods. Spikes in SARS-CoV-2 RNA concentrations in neighborhoods are often masked by dilution from other neighborhoods in the WWTP samples. MAJOR CONCLUSIONS: Wastewater-based epidemiology (WBE) employed at WWTP reliably detects SARS-CoV-2 in a city-sized population but provides less actionable public health information about neighborhoods experiencing greater viral infection and disease. Neighborhood sewershed sampling reveals important population-based information about local virus dynamics and improves opportunities for public health intervention. Longitudinally employed, neighborhood sewershed surveillance may provide a 3-6 day early warning of SARS-CoV-2 infection spikes and, importantly, highly specific information on subpopulations in a community particularly at higher risk at different points in time. Sampling in neighborhoods may thus provide timely and cost-saving information for targeted interventions within communities.
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Affiliation(s)
| | - Nicole S Bell
- RAIN Incubator, Tacoma, WA, USA; Squally Creek, LLC, Tacoma, WA, USA
| | - Chloe Mae Martinez
- RAIN Incubator, Tacoma, WA, USA; University of Washington-Tacoma, Tacoma, WA, USA
| | | | | | | | - David L Hirschberg
- RAIN Incubator, Tacoma, WA, USA; School of Engineering and Technology, University of Washington-Tacoma, Tacoma, WA, USA
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12
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Combe M, Cherif E, Deremarque T, Rivera-Ingraham G, Seck-Thiam F, Justy F, Doudou JC, Carod JF, Carage T, Procureur A, Gozlan RE. Wastewater sequencing as a powerful tool to reveal SARS-CoV-2 variant introduction and spread in French Guiana, South America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171645. [PMID: 38479523 DOI: 10.1016/j.scitotenv.2024.171645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/19/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
The origin of introduction of a new pathogen in a country, the evolutionary dynamics of an epidemic within a country, and the role of cross-border areas on pathogen dynamics remain complex to disentangle and are often poorly understood. For instance, cross-border areas represent the ideal location for the sharing of viral variants between countries, with international air travel, land travel and waterways playing an important role in the cross-border spread of infectious diseases. Unfortunately, monitoring the point of entry and the evolutionary dynamics of viruses in space and time within local populations remain challenging. Here we tested the efficiency of wastewater-based epidemiology and genotyping in monitoring Covid-19 epidemiology and SARS-CoV-2 variant dynamics in French Guiana, a tropical country located in South America. Our results suggest that wastewater-based epidemiology and genotyping are powerful tools to monitor variant introduction and disease evolution within a tropical country but the inclusion of both clinical and wastewater samples could still improve our understanding of genetic diversity co-circulating. Wastewater sequencing also revealed the cryptic transmission of SARS-CoV-2 variants within the country. Interestingly, we found some amino acid changes specific to the variants co-circulating in French Guiana, suggesting a local evolution of the SARS-CoV-2 variants after their introduction. More importantly, our results showed that the proximity to bordering countries was not the origin of the emergence of the French Guianese B.1.160.25 variant, but rather that this variant emerged from an ancestor B.1.160 variant introduced by European air plane travelers, suggesting thus that air travel remains a significant risk for cross-border spread of infectious diseases. Overall, we suggest that wastewater-based epidemiology and genotyping provides a cost effective and non-invasive approach for pathogen monitoring and an early-warning tool for disease emergence and spread within a tropical country.
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Affiliation(s)
- Marine Combe
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France.
| | - Emira Cherif
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France
| | | | - Georgina Rivera-Ingraham
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France; Centre IRD de Cayenne, Guyane Française, France
| | | | | | | | - Jean-François Carod
- Laboratoire et Pôle Appui aux Fonctions Cliniques, Centre Hospitalier de l'Ouest Guyanais (CHOG), 97320 Saint-Laurent du Maroni, Guyane Française, France
| | - Thierry Carage
- Laboratoire de Biologie Médicale Carage de Kourou, 6 avenue Leopold Heder, 97310 Kourou, Guyane Française, France
| | - Angélique Procureur
- Laboratoire de Biologie Médicale Carage de Kourou, 6 avenue Leopold Heder, 97310 Kourou, Guyane Française, France
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13
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Folkes M, Castro-Gutierrez V, Lundy L, Bajón-Fernández Y, Soares A, Jeffrey P, Hassard F. Campus source to sink wastewater surveillance of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100240. [PMID: 38774836 PMCID: PMC11106825 DOI: 10.1016/j.crmicr.2024.100240] [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] [Indexed: 05/24/2024] Open
Abstract
Wastewater-based surveillance (WBS) offers an aggregate, and cost-effective approach for tracking infectious disease outbreak prevalence within communities, that provides data on community health complementary to individual clinical testing. This study reports on a 16-month WBS initiative on a university campus in England, UK, assessing the presence of SARS-CoV-2 in sewers from large buildings, downstream sewer locations, raw wastewater, partially treated and treated effluents. Key findings include the detection of the Alpha (B.1.1.7) variant in wastewater, with 70 % of confirmed campus cases correlating with positive wastewater samples. Notably, ammonium nitrogen (NH4-N) levels showed a positive correlation (ρ = 0.543, p < 0.01) with virus levels at the large building scale, a relationship not observed at the sewer or wastewater treatment works (WWTW) levels due to dilution. The WWTW was compliant to wastewater standards, but the secondary treatment processes were not efficient for virus removal as SARS-CoV-2 was consistently detected in treated discharges. Tools developed through WBS can also be used to enhance traditional environmental monitoring of aquatic systems. This study provides a detailed source-to-sink evaluation, emphasizing the critical need for the widespread application and improvement of WBS. It showcases WBS utility and reinforces the ongoing challenges posed by viruses to receiving water quality.
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Affiliation(s)
- M. Folkes
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - V.M. Castro-Gutierrez
- Center for Research on Environmental Pollution (CICA), Universidad de Costa Rica, Montes de Oca, 11501, Costa Rica
| | - L. Lundy
- Department of Natural Sciences, Middlesex University, NW4 4BT, UK
| | - Y. Bajón-Fernández
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - A. Soares
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - P. Jeffrey
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - F. Hassard
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
- Institute for Nanotechnology and Water Sustainability, College of Science, Engineering and Technology, University of South Africa, Johannesburg, South Africa
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14
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Sovová K, Vašíčková P, Valášek V, Výravský D, Očenášková V, Juranová E, Bušová M, Tuček M, Bencko V, Mlejnková HZ. SARS-CoV-2 wastewater surveillance in the Czech Republic: Spatial and temporal differences in SARS-CoV-2 RNA concentrations and relationship to clinical data and wastewater parameters. WATER RESEARCH X 2024; 23:100220. [PMID: 38628304 PMCID: PMC11017050 DOI: 10.1016/j.wroa.2024.100220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
This study presents the results of systematic wastewater monitoring of SARS-CoV-2 RNA and basic wastewater parameters from four different wastewater treatment plants (WWTPs) in the Czech Republic over the 2020-2022 epidemic. Two-step reverse-transcription quantitative PCR targeting genes encoding the N and Nsp12 proteins was employed to detect SARS-CoV-2 RNA loading in 420 wastewater samples. The results obtained were used to evaluate the potential of wastewater analysis for describing the epidemiological situation in cities of different sizes and determining temporal differences based on the prevailing SARS-CoV-2 variant. Strong correlations between the number of active and hospitalised COVID-19 cases in each WWTP catchment area and the concentration of SARS-CoV-2 RNA detected in the wastewater clearly demonstrated the suitability of this wastewater-based epidemiological approach for WWTPs of different sizes and characteristics, despite differences in SARS-CoV-2 variant waves, with some WWTPs showing high predictive potential. This study demonstrated on the data from the Czech Republic that targeted systematic monitoring of wastewater provides sufficiently robust data for surveillance of viral loads in sample populations, and thus contributes to preventing the spread of infection and subsequent introduction of appropriate measures.
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Affiliation(s)
- Kateřina Sovová
- T. G. Masaryk Water Research Institute p.r.i., Brno Branch, Mojmírovo náměstí 16, 612 00 Brno, Czech Republic
| | - Petra Vašíčková
- Masaryk University, Faculty of Science, Kotlářská 267/2, 611 37 Brno, Czech Republic
| | - Vojtěch Valášek
- T. G. Masaryk Water Research Institute, Podbabská 30, 160 00 Prague, Czech Republic
| | - David Výravský
- T. G. Masaryk Water Research Institute p.r.i., Brno Branch, Mojmírovo náměstí 16, 612 00 Brno, Czech Republic
| | - Věra Očenášková
- T. G. Masaryk Water Research Institute, Podbabská 30, 160 00 Prague, Czech Republic
| | - Eva Juranová
- T. G. Masaryk Water Research Institute, Podbabská 30, 160 00 Prague, Czech Republic
| | - Milena Bušová
- Charles University, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Studničkova 7, 128 00 Prague, Czech Republic
| | - Milan Tuček
- Charles University, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Studničkova 7, 128 00 Prague, Czech Republic
| | - Vladimír Bencko
- Charles University, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Studničkova 7, 128 00 Prague, Czech Republic
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15
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Sutcliffe SG, Kraemer SA, Ellmen I, Knapp JJ, Overton AK, Nash D, Nissimov JI, Charles TC, Dreifuss D, Topolsky I, Baykal PI, Fuhrmann L, Jablonski KP, Beerenwinkel N, Levy JI, Olabode AS, Becker DG, Gugan G, Brintnell E, Poon AF, Valieris R, Drummond RD, Defelicibus A, Dias-Neto E, Rosales RA, Tojal da Silva I, Orfanou A, Psomopoulos F, Pechlivanis N, Pipes L, Chen Z, Baaijens JA, Baym M, Shapiro BJ. Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data. Microb Genom 2024; 10:001249. [PMID: 38785221 PMCID: PMC11165662 DOI: 10.1099/mgen.0.001249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic 'novel' lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1 % frequency, results were more reliable above a 5 % threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of error or bias in wastewater sequencing analysis and to appreciate the commonalities and differences across methods.
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Affiliation(s)
- Steven G. Sutcliffe
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Susanne A. Kraemer
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Environment and Climate Change Canada, Montreal, QC, Canada
| | - Isaac Ellmen
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | | | - Delaney Nash
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | | | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Pelin I. Baykal
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Kim P. Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Abayomi S. Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Devan G. Becker
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Gopi Gugan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erin Brintnell
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Art F.Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Renan Valieris
- Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | | | | | | | | | | | - Aspasia Orfanou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Nikolaos Pechlivanis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Lenore Pipes
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Zihao Chen
- School of Mathematical Sciences, Peking University, Beijing, BJ, PR China
| | - Jasmijn A. Baaijens
- Delft University of Technology, Delft, ZH, Netherlands
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
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16
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Zhuang X, Vo V, Moshi MA, Dhede K, Ghani N, Akbar S, Chang CL, Young AK, Buttery E, Bendik W, Zhang H, Afzal S, Moser D, Cordes D, Lockett C, Gerrity D, Kan HY, Oh EC. Early Detection of Novel SARS-CoV-2 Variants from Urban and Rural Wastewater through Genome Sequencing and Machine Learning. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.18.24306052. [PMID: 38699326 PMCID: PMC11065002 DOI: 10.1101/2024.04.18.24306052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Genome sequencing from wastewater has emerged as an accurate and cost-effective tool for identifying SARS-CoV-2 variants. However, existing methods for analyzing wastewater sequencing data are not designed to detect novel variants that have not been characterized in humans. Here, we present an unsupervised learning approach that clusters co-varying and time-evolving mutation patterns leading to the identification of SARS-CoV-2 variants. To build our model, we sequenced 3,659 wastewater samples collected over a span of more than two years from urban and rural locations in Southern Nevada. We then developed a multivariate independent component analysis (ICA)-based pipeline to transform mutation frequencies into independent sources with co-varying and time-evolving patterns and compared variant predictions to >5,000 SARS-CoV-2 clinical genomes isolated from Nevadans. Using the source patterns as data-driven reference "barcodes", we demonstrated the model's accuracy by successfully detecting the Delta variant in late 2021, Omicron variants in 2022, and emerging recombinant XBB variants in 2023. Our approach revealed the spatial and temporal dynamics of variants in both urban and rural regions; achieved earlier detection of most variants compared to other computational tools; and uncovered unique co-varying mutation patterns not associated with any known variant. The multivariate nature of our pipeline boosts statistical power and can support accurate and early detection of SARS-CoV-2 variants. This feature offers a unique opportunity for novel variant and pathogen detection, even in the absence of clinical testing.
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17
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Gwenzi W, Adelodun B, Kumar P, Ajibade FO, Silva LFO, Choi KS, Selvarajan R, Abia ALK, Gholipour S, Mohammadi F, Nikaeen M. Human viral pathogens in the wastewater-source water-drinking water continuum: Evidence, health risks, and lessons for future outbreaks in low-income settings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170214. [PMID: 38278242 DOI: 10.1016/j.scitotenv.2024.170214] [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: 09/01/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
Human viral pathogens, including SARS-CoV-2 continue to attract public and research attention due to their disruption of society, global health, and the economy. Several earlier reviews have investigated the occurrence and fate of SARS-CoV-2 in wastewater, and the potential to use such data in wastewater-based epidemiology. However, comprehensive reviews tracking SARS-CoV-2 and other viral pathogens in the wastewater-water-drinking water continuum and the associated risk assessment are still lacking. Therefore, to address this gap, the present paper makes the following contributions: (1) critically examines the early empirical results to highlight the occurrence and stability of SARS-CoV-2 in the wastewater-source water-drinking water continuum, (2) discusses the anthropogenic and hydro(geo)logical processes controlling the circulation of SARS-CoV-2 in the wastewater-source water-drinking water continuum, (3) discusses the risky behaviour, drivers and high-risk settings in the wastewater-source water-drinking water continuum, (4) uses the available empirical data on SARS-CoV-2 occurrence in the wastewater-source water-drinking water continuum to discuss human health risks from multiple exposure pathways, gendered aspects of SARS-CoV-2 transmission via shared on-site sanitation systems, and (5) develops and risk mitigation strategy based on the available empirical evidence and quantitative human risk assessment data. Finally, it presents a comprehensive research agenda on SARS-CoV-2/COVID-19 to guide the mitigation of future similar outbreaks in low-income settings.
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Affiliation(s)
- Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, 380 New Adylin, Westgate, Harare, Zimbabwe; Currently Alexander von Humboldt Fellow and Guest/Visiting Professor at: Grassland Science and Renewable Plant Resources, Faculty of Organic Agricultural Sciences, Universität Kassel, Steinstraße 19, D-37213 Witzenhausen, Germany; Leibniz-Institut für Agrartechnik und Bioökonomie e.V. (ATB), Max-Eyth-Allee 100, D-14469, Potsdam, Germany.
| | - Bashir Adelodun
- Department of Agricultural Civil Engineering, Kyungpook National University, Daegu 41566, Republic of Korea; Department of Agricultural and Biosystems Engineering, University of Ilorin, PMB 1515, Ilorin 240003, Nigeria; Institute of Agricultural Science & Technology, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Pankaj Kumar
- Agro-Ecology and Pollution Research Laboratory, Department of Zoology and Environmental Science, Gurukula Kangri (Deemed to Be University), Haridwar 249404, India; Research and Development Division, Society for AgroEnvironmental Sustainability, Dehradun 248007, India.
| | - Fidelis Odedishemi Ajibade
- Department of Civil and Environmental Engineering, Federal University of Technology, PMB 704, Akure, 340001, Nigeria.
| | - Luis F O Silva
- Department of Civil and Environmental Engineering, Universidad de la Costa, Calle 58 #55-66, 080002 Barranquilla, Atlàntico, Colombia.
| | - Kyung Sook Choi
- Department of Agricultural Civil Engineering, Kyungpook National University, Daegu 41566, Republic of Korea; Institute of Agricultural Science & Technology, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida branch, Johannesburg, South Africa
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Environmental Research Foundation, Westville 3630, Kwazulu-Natal, South Africa
| | - Sahar Gholipour
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farzaneh Mohammadi
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahnaz Nikaeen
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran; Environment Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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18
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Duker EO, Obodai E, Addo SO, Kwasah L, Mensah ES, Gberbi E, Anane A, Attiku KO, Boakye J, Agbotse GD, Dickson AE, Quarcoo JA, Darko PA, Larbi YA, Ntim NAA, Dzudzor B, Odoom JK. First Molecular Detection of SARS-CoV-2 in Sewage and Wastewater in Ghana. BIOMED RESEARCH INTERNATIONAL 2024; 2024:9975781. [PMID: 38595329 PMCID: PMC11003379 DOI: 10.1155/2024/9975781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/26/2024] [Accepted: 02/28/2024] [Indexed: 04/11/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is shed in the stool of infected individuals and can be detected in sewage and wastewater contaminated with infected stool. This study is aimed at detecting the virus and its potential survival in sewage and wastewater in Ghana. The cross-sectional study included samples from 16 validated environmental surveillance sites in 7 regions of Ghana. A total of 354 samples composed of wastewater (280) and sewage (74) were collected from November 2020 to November 2022. Overall, 17% of the samples were positive for SARS-CoV-2 by real-time PCR, with 6% in sewage and 11% in wastewater. The highest number of positive samples was collected from the Greater Accra Region (7.3%) with the least recorded in the Bono East Region (0.6%). Further characterization of the positive samples using the next-generation sequencing (NGS) approach yielded two variants: Alpha (B.1.1.7) and Delta (AY.36). Attempts to isolate SARS-CoV-2 in the Vero cell line were not successful probably due to the low viral load concentrations (Ct values > 35) or prolonged exposure to high temperatures rendering the virus noninfectious. Our findings suggest that SARS-CoV-2 RNA in sewage and wastewater may not be infectious, but the prevalence shows that the virus persists in the communities within Ghana.
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Affiliation(s)
- Ewurabena Oduma Duker
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Evangeline Obodai
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Seth Offei Addo
- Parasitology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Lorreta Kwasah
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Edna Serwah Mensah
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Emmanuel Gberbi
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Abraham Anane
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Keren O. Attiku
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Jessica Boakye
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Gayheart Deladem Agbotse
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Angelina Evelyn Dickson
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Joseph Ahia Quarcoo
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Patience Akosua Darko
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Yaw Awuku Larbi
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Nana Afia Asante Ntim
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Bartholomew Dzudzor
- Department of Medical Biochemistry, University of Ghana Medical School, University of Ghana, Legon, Accra, Ghana
| | - John Kofi Odoom
- Virology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
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19
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Ryon MG, Langan LM, Brennan C, O'Brien ME, Bain FL, Miller AE, Snow CC, Salinas V, Norman RS, Bojes HK, Brooks BW. Influences of 23 different equations used to calculate gene copies of SARS-CoV-2 during wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170345. [PMID: 38272099 DOI: 10.1016/j.scitotenv.2024.170345] [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: 10/01/2023] [Revised: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
Following the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the use of wastewater-based surveillance (WBS) has increased dramatically along with associated infrastructure globally. However, due to the global nature of its application, and various workflow adaptations (e.g., sample collection, water concentration, RNA extraction kits), numerous methods for back-calculation of gene copies per volume (gc/L) of sewage have also emerged. Many studies have considered the comparability of processing methods (e.g., water concentration, RNA extraction); however, for equations used to calculate gene copies in a wastewater sample and subsequent influences on monitoring viral trends in a community and its association with epidemiological data, less is known. Due to limited information on how many formulas exist for the calculation of SARS-CoV-2 gene copies in wastewater, we initially attempted to quantify how many equations existed in the referred literature. We identified 23 unique equations, which were subsequently applied to an existing wastewater dataset. We observed a range of gene copies based on use of different equations, along with variability of AUC curve values, and results from correlation and regression analyses. Though a number of individual laboratories appear to have independently converged on a similar formula for back-calculation of viral load in wastewater, and share similar relationships with epidemiological data, differential influences of various equations were observed for variation in PCR volumes, RNA extraction volumes, or PCR assay parameters. Such observations highlight challenges when performing comparisons among WBS studies when numerous methodologies and back-calculation methods exist. To facilitate reproducibility among studies, the different gc/L equations were packaged as an R Shiny app, which provides end users the ability to investigate variability within their datasets and support comparisons among studies.
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Affiliation(s)
- Mia G Ryon
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Laura M Langan
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA.
| | - Christopher Brennan
- Department of Entomology, Texas A&M University, TAMU 2475, College Station, TX 77843-2475, USA
| | - Megan E O'Brien
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Fallon L Bain
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Aubree E Miller
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Christine C Snow
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Victoria Salinas
- Environmental Epidemiology and Disease Registries, Texas Department of State Health Services, Austin, TX 78756, USA
| | - R Sean Norman
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, 921 Assembly St., Columbia, SC 28208, USA
| | - Heidi K Bojes
- Environmental Epidemiology and Disease Registries, Texas Department of State Health Services, Austin, TX 78756, USA
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA; Department of Public Health, Baylor University, One Bear Place #97343, Waco, TX 76798, USA.
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20
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Leisman KP, Owen C, Warns MM, Tiwari A, Bian GZ, Owens SM, Catlett C, Shrestha A, Poretsky R, Packman AI, Mangan NM. A modeling pipeline to relate municipal wastewater surveillance and regional public health data. WATER RESEARCH 2024; 252:121178. [PMID: 38309063 DOI: 10.1016/j.watres.2024.121178] [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: 09/05/2023] [Revised: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
As COVID-19 becomes endemic, public health departments benefit from improved passive indicators, which are independent of voluntary testing data, to estimate the prevalence of COVID-19 in local communities. Quantification of SARS-CoV-2 RNA from wastewater has the potential to be a powerful passive indicator. However, connecting measured SARS-CoV-2 RNA to community prevalence is challenging due to the high noise typical of environmental samples. We have developed a generalized pipeline using in- and out-of-sample model selection to test the ability of different correction models to reduce the variance in wastewater measurements and applied it to data collected from treatment plants in the Chicago area. We built and compared a set of multi-linear regression models, which incorporate pepper mild mottle virus (PMMoV) as a population biomarker, Bovine coronavirus (BCoV) as a recovery control, and wastewater system flow rate into a corrected estimate for SARS-CoV-2 RNA concentration. For our data, models with BCoV performed better than those with PMMoV, but the pipeline should be used to reevaluate any new data set as the sources of variance may change across locations, lab methods, and disease states. Using our best-fit model, we investigated the utility of RNA measurements in wastewater as a leading indicator of COVID-19 trends. We did this in a rolling manner for corrected wastewater data and for other prevalence indicators and statistically compared the temporal relationship between new increases in the wastewater data and those in other prevalence indicators. We found that wastewater trends often lead other COVID-19 indicators in predicting new surges.
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Affiliation(s)
- Katelyn Plaisier Leisman
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Christopher Owen
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Maria M Warns
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Anuj Tiwari
- Discovery Partners Institute, University of Illinois Chicago, Chicago, IL, USA
| | - George Zhixin Bian
- Department of Computer Science, Northwestern University, Evanston, IL, USA
| | - Sarah M Owens
- Biosciences, Argonne National Laboratory, Lemont, IL, USA
| | - Charlie Catlett
- Discovery Partners Institute, University of Illinois Chicago, Chicago, IL, USA; Computing, Environment, and Life Sciences, Argonne National Laboratory, Lemont, IL, USA
| | - Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois Chicago, Chicago, IL, USA
| | - Rachel Poretsky
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Aaron I Packman
- Center for Water Research, Northwestern University, Evanston, IL, USA; Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Niall M Mangan
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA; Center for Water Research, Northwestern University, Evanston, IL, USA.
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21
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Bognich G, Howell N, Butler E. Fate-and-transport modeling of SARS-CoV-2 for rural wastewater-based epidemiology application benefit. Heliyon 2024; 10:e25927. [PMID: 38434294 PMCID: PMC10904236 DOI: 10.1016/j.heliyon.2024.e25927] [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: 07/26/2023] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/05/2024] Open
Abstract
Wastewater-based epidemiology (WBE) for the detection of agents of concern such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been prevalent in literature since 2020. The majority of reported research focuses on large urban centers with few references to rural communities. In this research the EPA-Storm Water Management Model (EPA-SWMM) software was used to describe a small sewershed and identify the effects of temperature, temperature-affected decay rate, flow rate, flush time, fecal shedding rate, and historical infection rates during the spread of the Omicron variant of the SARS-CoV-2 virus within the sewershed. Due to the sewershed's relative isolation from the rest of the city, its wastewater quality behavior is similar to a rural sewershed. The model was used to assess city wastewater sampling campaigns to best appropriate field and or lab equipment when sampling wastewater. An important aspect of the assessment was the comparison of SARS-CoV-2 quantification methods with specifically between a traditional microbiological lab (practical quantitation limit, PQL, 1 GC/mL) versus what can be known from a field method (PQL 10 GC/mL). Understanding these monitoring choices will help rural communities make decisions on how to best implement the collection and testing for WBE agents of concern. An important outcome of this work is the knowledge that it is possible to simulate a WBE agent of concern with reasonable precision, if uncertainties are incorporated into model sensitivity. These ideas could form the basis for future mixed monitoring-modeling studies that will enhance its application and therefore adoption of WBE techniques in communities of many sizes and financial means.
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Affiliation(s)
- Gabrielle Bognich
- Holland School of Sciences and Mathematics, Hardin-Simmons University, Abilene, TX, USA
| | - Nathan Howell
- College of Engineering, West Texas A&M University, Canyon, TX, USA
| | - Erick Butler
- College of Engineering, West Texas A&M University, Canyon, TX, USA
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22
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Parkins MD, Lee BE, Acosta N, Bautista M, Hubert CRJ, Hrudey SE, Frankowski K, Pang XL. Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond. Clin Microbiol Rev 2024; 37:e0010322. [PMID: 38095438 PMCID: PMC10938902 DOI: 10.1128/cmr.00103-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024] Open
Abstract
Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.
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Affiliation(s)
- Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O’Brien Institute of Public Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole Acosta
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maria Bautista
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Provincial Health Laboratory, Alberta Health Services, Calgary, Alberta, Canada
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23
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Rezaeitavabe F, Rezaie M, Modayil M, Pham T, Ice G, Riefler G, Coschigano KT. Beyond linear regression: Modeling COVID-19 clinical cases with wastewater surveillance of SARS-CoV-2 for the city of Athens and Ohio University campus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169028. [PMID: 38061656 DOI: 10.1016/j.scitotenv.2023.169028] [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: 05/05/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 01/18/2024]
Abstract
Wastewater-based surveillance has emerged as a detection tool for population-wide infectious diseases, including coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infected individuals shed the virus, which can be detected in wastewater using molecular techniques such as reverse transcription-digital polymerase chain reaction (RT-dPCR). This study examined the association between the number of clinical cases and the concentration of SARS-CoV-2 in wastewater beyond linear regression and for various normalizations of viral loads. Viral loads were measured in a total of 446 wastewater samples during the period from August 2021 to April 2022. These samples were collected from nine different locations, with 220 samples taken from four specific sites within the city of Athens and 226 samples from five sites within Ohio University. The correlation between COVID-19 cases and wastewater viral concentrations, which was estimated using the Pearson correlation coefficient, was statistically significant and ranged from 0.6 to 0.9. In addition, time-lagged cross correlation was applied to identify the lag time between clinical and wastewater data, estimated 4 to 7 days. While we also explored the effect on the correlation coefficients of various normalizations of viral loads accounting for procedural loss or amount of fecal material and of estimated lag times, these alternative specifications did not change our substantive conclusions. Additionally, several linear and non-linear regression models were applied to predict the COVID-19 cases given wastewater data as input. The non-linear approach was found to yield the highest R-squared and Pearson correlation and lowest Mean Absolute Error values between the predicted and actual number of COVID-19 cases for both aggregated OHIO Campus and city data. Our results provide support for previous studies on correlation and time lag and new evidence that non-linear models, approximated with artificial neural networks, should be implemented for WBS of contagious diseases.
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Affiliation(s)
- Fatemeh Rezaeitavabe
- Ohio University, Russ College of Engineering, Department of Civil and Environmental Engineering, Athens, OH 45701, USA
| | - Mehdi Rezaie
- Kansas State University, Department of Physics, Manhattan, KS 66506, USA
| | - Maria Modayil
- Ohio University, Division of Diversity and Inclusion, Athens, OH 45701, USA; Ohio University, College of Health Sciences and Professions, Department of Interdisciplinary Health Studies, Athens, OH 45701, USA
| | - Tuyen Pham
- Ohio University, Voinovich School of Leadership and Public Service, Athens, OH 45701, USA
| | - Gillian Ice
- Ohio University, College of Health Sciences and Professions, Department of Interdisciplinary Health Studies, Athens, OH 45701, USA; Ohio University, Heritage College of Osteopathic Medicine, Department of Social Medicine, Athens, OH 45701, USA
| | - Guy Riefler
- Ohio University, Russ College of Engineering, Department of Civil and Environmental Engineering, Athens, OH 45701, USA
| | - Karen T Coschigano
- Ohio University, Heritage College of Osteopathic Medicine, Department of Biomedical Sciences, Athens, OH 45701, USA.
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24
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Dorevitch S, Shrestha A. Priority setting for global WASH challenges in the age of wastewater-based epidemiological surveillance. JOURNAL OF WATER AND HEALTH 2024; 22:367-371. [PMID: 38421630 PMCID: wh_2024_298 DOI: 10.2166/wh.2024.298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
HIGHLIGHTS
Mortality due to inadequate WASH facilities exceeded that of COVID-19 in the regions of South-East Asia and Africa. The costs and benefits of wastewater-based surveillance are not known; however, the benefits of WASH interventions greatly exceed the costs. The dedication of effort and resources to wastewater-based surveillance and WASH in low- and middle-income countries should reflect disease burdens and cost/benefit assessments.
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Affiliation(s)
- Samuel Dorevitch
- University of Illinois Chicago School of Public Health, 1603 W. Taylor St., Chicago, IL 60612, USA E-mail:
| | - Abhilasha Shrestha
- University of Illinois Chicago School of Public Health, 1603 W. Taylor St., Chicago, IL 60612, USA
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25
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Gogoi G, Singh SD, Kalyan E, Koch D, Gogoi P, Kshattry S, Mahanta HJ, Imran M, Pandey R, Bharali P. An interpretative review of the wastewater-based surveillance of the SARS-CoV-2: where do we stand on its presence and concern? Front Microbiol 2024; 15:1338100. [PMID: 38318336 PMCID: PMC10839012 DOI: 10.3389/fmicb.2024.1338100] [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: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has been used for monitoring infectious diseases like polio, hepatitis, etc. since the 1940s. It is also being used for tracking the SARS-CoV-2 at the population level. This article aims to compile and assess the information for the qualitative and quantitative detection of the SARS-CoV-2 in wastewater. Based on the globally published studies, we highlight the importance of monitoring SARS-CoV-2 presence/detection in the wastewater and concurrently emphasize the development of early surveillance techniques. SARS-CoV-2 RNA sheds in the human feces, saliva, sputum and mucus that ultimately reaches to the wastewater and brings viral RNA into it. For the detection of the virus in the wastewater, different detection techniques have been optimized and are in use. These are based on serological, biosensor, targeted PCR, and next generation sequencing for whole genome sequencing or targeted amplicon sequencing. The presence of the SARS-CoV-2 RNA in wastewater could be used as a potential tool for early detection and devising the strategies for eradication of the virus before it is spread in the community. Additionally, with the right and timely understanding of viral behavior in the environment, an accurate and instructive model that leverages WBE-derived data may be created. This might help with the creation of technological tools and doable plans of action to lessen the negative effects of current viral epidemics or future potential outbreaks on public health and the economy. Further work toward whether presence of viral load correlates with its ability to induce infection, still needs evidence. The current increasing incidences of JN.1 variant is a case in point for continued early detection and surveillance, including wastewater.
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Affiliation(s)
- Gayatri Gogoi
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sarangthem Dinamani Singh
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Emon Kalyan
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Devpratim Koch
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pronami Gogoi
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Suman Kshattry
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Hridoy Jyoti Mahanta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Md Imran
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Rajesh Pandey
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Pankaj Bharali
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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26
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Clark EC, Neumann S, Hopkins S, Kostopoulos A, Hagerman L, Dobbins M. Changes to Public Health Surveillance Methods Due to the COVID-19 Pandemic: Scoping Review. JMIR Public Health Surveill 2024; 10:e49185. [PMID: 38241067 PMCID: PMC10837764 DOI: 10.2196/49185] [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: 05/23/2023] [Revised: 09/06/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Public health surveillance plays a vital role in informing public health decision-making. The onset of the COVID-19 pandemic in early 2020 caused a widespread shift in public health priorities. Global efforts focused on COVID-19 monitoring and contact tracing. Existing public health programs were interrupted due to physical distancing measures and reallocation of resources. The onset of the COVID-19 pandemic intersected with advancements in technologies that have the potential to support public health surveillance efforts. OBJECTIVE This scoping review aims to explore emergent public health surveillance methods during the early COVID-19 pandemic to characterize the impact of the pandemic on surveillance methods. METHODS A scoping search was conducted in multiple databases and by scanning key government and public health organization websites from March 2020 to January 2022. Published papers and gray literature that described the application of new or revised approaches to public health surveillance were included. Papers that discussed the implications of novel public health surveillance approaches from ethical, legal, security, and equity perspectives were also included. The surveillance subject, method, location, and setting were extracted from each paper to identify trends in surveillance practices. Two public health epidemiologists were invited to provide their perspectives as peer reviewers. RESULTS Of the 14,238 unique papers, a total of 241 papers describing novel surveillance methods and changes to surveillance methods are included. Eighty papers were review papers and 161 were single studies. Overall, the literature heavily featured papers detailing surveillance of COVID-19 transmission (n=187). Surveillance of other infectious diseases was also described, including other pathogens (n=12). Other public health topics included vaccines (n=9), mental health (n=11), substance use (n=4), healthy nutrition (n=1), maternal and child health (n=3), antimicrobial resistance (n=2), and misinformation (n=6). The literature was dominated by applications of digital surveillance, for example, by using big data through mobility tracking and infodemiology (n=163). Wastewater surveillance was also heavily represented (n=48). Other papers described adaptations to programs or methods that existed prior to the COVID-19 pandemic (n=9). The scoping search also found 109 papers that discuss the ethical, legal, security, and equity implications of emerging surveillance methods. The peer reviewer public health epidemiologists noted that additional changes likely exist, beyond what has been reported and available for evidence syntheses. CONCLUSIONS The COVID-19 pandemic accelerated advancements in surveillance and the adoption of new technologies, especially for digital and wastewater surveillance methods. Given the investments in these systems, further applications for public health surveillance are likely. The literature for surveillance methods was dominated by surveillance of infectious diseases, particularly COVID-19. A substantial amount of literature on the ethical, legal, security, and equity implications of these emerging surveillance methods also points to a need for cautious consideration of potential harm.
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Affiliation(s)
- Emily C Clark
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
| | - Sophie Neumann
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
| | - Stephanie Hopkins
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
| | - Alyssa Kostopoulos
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
| | - Leah Hagerman
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
| | - Maureen Dobbins
- National Collaborating Centre for Methods and Tools, Hamilton, ON, Canada
- School of Nursing, McMaster University, Hamilton, ON, Canada
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27
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Valdivia-Carrera CA, Ho-Palma AC, Munguia-Mercado A, Gonzalez-Pizarro K, Ibacache-Quiroga C, Dinamarca A, Stehlík M, Rusiñol M, Girones R, Lopez-Urbina MT, Basaldua Galarza A, Gonzales-Gustavson E. Surveillance of SARS-CoV-2, rotavirus, norovirus genogroup II, and human adenovirus in wastewater as an epidemiological tool to anticipate outbreaks of COVID-19 and acute gastroenteritis in a city without a wastewater treatment plant in the Peruvian Highlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167161. [PMID: 37730068 DOI: 10.1016/j.scitotenv.2023.167161] [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: 09/15/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has demonstrated that Wastewater Based Epidemiology is a fast and economical alternative for monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the community level in high-income countries. In the present study, wastewater from a city in the Peruvian Highlands, which lacks a wastewater treatment plant, was monitored for one year to assess the relationship between the concentration of SARS-CoV-2 and the reported cases of COVID-19 in the community. Additionally, we compared the relationship between rotavirus (RV), norovirus genogroup II (NoV GGII), and human adenovirus (HAdV) with the number of reported cases of acute gastroenteritis. Before commencing the analysis of the samples, the viral recovery efficacy of three processing methods was determined in spiked wastewater with SARS-CoV-2. This evaluation demonstrated the highest recovery rate with direct analysis (72.2 %), as compared to ultrafiltration (50.8 %) and skimmed milk flocculation (5.6 %). Wastewater monitoring revealed that 72 % (36/50) of the samples tested positive for SARS-CoV-2, with direct analysis yielding the highest detection frequency and quantification of SARS-CoV-2. Furthermore, a strong correlation was observed between the concentration of SARS-CoV-2 in wastewater and the reported cases of COVID-19, mainly when we shift the concentration of SARS-CoV-2 by two weeks, which allows us to anticipate the onset of the fourth and fifth waves of the pandemic in Peru up to two weeks in advance. All samples processed using the skimmed milk flocculation method tested positive and showed high concentrations of RV, NoV GGII, and HAdV. In fact, the highest RV concentrations were detected up to four weeks before outbreaks of acute gastroenteritis reported in children under four years of age. In conclusion, the results of this study suggest that periodic wastewater monitoring is an excellent epidemiological tool for surveillance and can anticipate outbreaks of infectious diseases, such as COVID-19, in low- and middle-income countries.
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Affiliation(s)
- Cesar A Valdivia-Carrera
- Tropical and Highlands Veterinary Research Institute, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Jr. 28 de Julio s/n, Km 34, margen izquierda, Carretera Central, El Mantaro, Jauja, Junin, Peru; Department of Animal Health and Public Health, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalacion 2800, San Borja, Lima, Peru.
| | - Ana C Ho-Palma
- Department of Human Medicine, School of Human Medicine, Universidad Nacional del Centro del Peru, Av. Mariscal Castilla 3909, Huancayo, Peru.
| | - Astrid Munguia-Mercado
- Tropical and Highlands Veterinary Research Institute, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Jr. 28 de Julio s/n, Km 34, margen izquierda, Carretera Central, El Mantaro, Jauja, Junin, Peru.
| | - Karoll Gonzalez-Pizarro
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile.
| | - Claudia Ibacache-Quiroga
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile; Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile.
| | - Alejandro Dinamarca
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile; Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso, Chile.
| | - Milan Stehlík
- Institute of Statistics, Universidad de Valparaiso, Av. Gran Bretana 1111, Valparaiso, Chile; Linz Institute of Technology & Department of Applied Statistics, Johannes Kepler University in Linz, Altenberger Straße 69, 4040 Linz, Austria.
| | - Marta Rusiñol
- Laboratory of Virus Contaminants of Water and Food, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.
| | - Maria T Lopez-Urbina
- Laboratory of Veterinary Epidemiology and Economics, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalacion 2800, San Borja, Lima, Peru.
| | - Anani Basaldua Galarza
- Department of Human Medicine, School of Human Medicine, Universidad Nacional del Centro del Peru, Av. Mariscal Castilla 3909, Huancayo, Peru; Dirección Ejecutiva de Epidemiología, Dirección Regional de Salud, Jr. Julio Cesar Tello 488, Huancayo 12004, Junin, Peru.
| | - Eloy Gonzales-Gustavson
- Tropical and Highlands Veterinary Research Institute, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Jr. 28 de Julio s/n, Km 34, margen izquierda, Carretera Central, El Mantaro, Jauja, Junin, Peru; Department of Animal Health and Public Health, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalacion 2800, San Borja, Lima, Peru.
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Chettleburgh C, Ma SX, Swinwood-Sky M, McDougall H, Kireina D, Taggar G, McBean E, Parreira V, Goodridge L, Habash M. Evaluation of four human-associated fecal biomarkers in wastewater in Southern Ontario. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166542. [PMID: 37660819 DOI: 10.1016/j.scitotenv.2023.166542] [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: 06/01/2023] [Revised: 07/26/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
Human fecal biomarkers (HFBs) have a longstanding history in the field of microbial source tracking (MST) serving as indicators of human fecal contamination in drinking and recreational water. Further, HFBs have aided in recent efforts to monitor human pathogen transmission within communities. The dilution of wastewater from various sources throughout the sewershed cannot be controlled and human fecal biomarkers (HFBs) can be used to normalize target human pathogen concentrations so that fluctuations in fecal matter in wastewater can be accounted for. In the current study, we monitored the prevalence of four HFBs - including two viruses, Pepper mild mottle virus (PMMoV), cross-assembly phage (crAssphage), as well as two human-associated Bacteroides markers, HF183 and BacHuman - in wastewater samples from ten Southern Ontario wastewater treatment plants and evaluated their temporal and spatial variation in context of environmental factors that may impact the ability of HFB to normalize pathogen concentrations in wastewater. Environmental variables including precipitation, wastewater flow rate, temperature, and concentrated mass were also analyzed for their potential correlation with HFB variation in wastewater. The four HFBs were detected at high concentrations across all 10 sampling locations. The median concentrations across all sampling sites were: PMMoV 3.6 Log gene copies (GC)/mL; crAssphage 5.0 Log GC/mL; HF183 6.8 Log GC/mL and BacHuman 6.9 Log GC/mL. All HFBs were found to be similarly stratified across all 10 sites, and the bacterial markers were consistently found at higher concentration compared to the viral HFBs at all sites. The coefficient of variation (CV) for each HFB was used to characterize the variability of each biomarker at each sewershed. BacHuman and crAssphage were found to have lower CV than PMMoV and HF183, indicating that BacHuman and crAssphage may perform better in reflecting the variations in abundance of human feces in wastewater or MST applications.
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Affiliation(s)
| | | | | | | | - Devita Kireina
- Department of Food Science, Canada; Canadian Research Institute for Food Safety, Canada
| | - Gurleen Taggar
- Department of Food Science, Canada; Canadian Research Institute for Food Safety, Canada
| | - Edward McBean
- School of Engineering, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - Valeria Parreira
- Department of Food Science, Canada; Canadian Research Institute for Food Safety, Canada
| | - Lawrence Goodridge
- Department of Food Science, Canada; Canadian Research Institute for Food Safety, Canada
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Wiesner-Friedman C, Brinkman NE, Wheaton E, Nagarkar M, Hart C, Keely SP, Varughese E, Garland J, Klaver P, Turner C, Barton J, Serre M, Jahne M. Characterizing Spatial Information Loss for Wastewater Surveillance Using crAssphage: Effect of Decay, Temperature, and Population Mobility. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:20802-20812. [PMID: 38015885 DOI: 10.1021/acs.est.3c05587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Populations contribute information about their health status to wastewater. Characterizing how that information degrades in transit to wastewater sampling locations (e.g., wastewater treatment plants and pumping stations) is critical to interpret wastewater responses. In this work, we statistically estimate the loss of information about fecal contributions to wastewater from spatially distributed populations at the census block group resolution. This was accomplished with a hydrologically and hydraulically influenced spatial statistical approach applied to crAssphage (Carjivirus communis) load measured from the influent of four wastewater treatment plants in Hamilton County, Ohio. We find that we would expect to observe a 90% loss of information about fecal contributions from a given census block group over a travel time of 10.3 h. This work demonstrates that a challenge to interpreting wastewater responses (e.g., during wastewater surveillance) is distinguishing between a distal but large cluster of contributions and a near but small contribution. This work demonstrates new modeling approaches to improve measurement interpretation depending on sewer network and wastewater characteristics (e.g., geospatial layout, temperature variability, population distribution, and mobility). This modeling can be integrated into standard wastewater surveillance methods and help to optimize sewer sampling locations to ensure that different populations (e.g., vulnerable and susceptible) are appropriately represented.
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Affiliation(s)
- Corinne Wiesner-Friedman
- Oak Ridge Institute for Science and Education, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Nichole E Brinkman
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Emily Wheaton
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Maitreyi Nagarkar
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Chloe Hart
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Scott P Keely
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Eunice Varughese
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Jay Garland
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
| | - Peter Klaver
- LimnoTech, 501 Avis Drive, Ann Arbor, Michigan 48108, United States
| | - Carrie Turner
- LimnoTech, 501 Avis Drive, Ann Arbor, Michigan 48108, United States
| | - John Barton
- Metropolitan Sewer District of Greater Cincinnati, 1081 Woodrow Street, Cincinnati, Ohio 45204, United States
| | - Marc Serre
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michael Jahne
- Office of Research and Development, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, United States
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30
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Bowes DA, Henke KB, Driver EM, Newell ME, Block I, Shaffer G, Varsani A, Scotch M, Halden RU. Enhanced detection of mpox virus in wastewater using a pre-amplification approach: A pilot study informing population-level monitoring of low-titer pathogens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166230. [PMID: 37574063 PMCID: PMC10592092 DOI: 10.1016/j.scitotenv.2023.166230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
A recent outbreak of the mpox virus (MPXV) occurred in non-endemic regions of the world beginning in May 2022. Pathogen surveillance systems faced pressure to quickly establish response protocols, offering an opportunity to employ wastewater-based epidemiology (WBE) for population-level monitoring. The pilot study reported herein aimed to: (i) develop a reliable protocol for MPXV DNA detection in wastewater which would reduce false negative reporting, (ii) test this protocol on wastewater from various regions across the United States, and (iii) conduct a state of the science review of the current literature reporting on experimental methods for MPXV detection using WBE. Twenty-four-hour composite samples of untreated municipal wastewater were collected from the states of New Jersey, Georgia, Illinois, Texas, Arizona, and Washington beginning July 3rd, 2022 through October 16th, 2022 (n = 60). Samples underwent vacuum filtration, DNA extraction from captured solids, MPXV DNA pre-amplification, and qPCR analysis. Of the 60 samples analyzed, a total of eight (13%) tested positive for MPXV in the states of Washington, Texas, New Jersey, and Illinois. The presence of clade IIb MPXV DNA in these samples was confirmed via Sanger sequencing and integration of pre-amplification prior to qPCR decreased the rate of false negative detections by 87% as compared to qPCR analysis alone. Wastewater-derived detections of MPXV were compared to clinical datasets, with 50% of detections occurring as clinical cases were increasing/peaking and 50% occurring as clinical cases waned. Results from the literature review (n = 9 studies) revealed successful strategies for the detection of MPXV DNA in wastewater, however also emphasized a need for further method optimization and standardization. Overall, this work highlights the use of pre-amplification prior to qPCR detection as a means to capture the presence of MPXV DNA in community wastewater and offers guidance for monitoring low-titer pathogens via WBE.
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Affiliation(s)
- Devin A Bowes
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Katherine B Henke
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Erin M Driver
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Melanie Engstrom Newell
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Izabella Block
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Gray Shaffer
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
| | - Arvind Varsani
- The Biodesign Institute Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School of Life Sciences, Arizona State University, 427 E. Tyler Mall, Tempe, AZ 85281, USA; Center of Evolution and Medicine, Arizona State University, 427 E. Tyler Mall, Tempe, AZ 85281, USA
| | - Matthew Scotch
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ 85004, USA
| | - Rolf U Halden
- The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; School for Sustainable Engineering and the Built Environment, Arizona State University, 660 S. College Ave., Tempe, AZ 85281, USA; OneWaterOneHealth, The Arizona State University Foundation, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA; Global Futures Laboratory, Arizona State University, 800 S. Cady Mall, Tempe, AZ 85281, USA.
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31
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Triggiano F, De Giglio O, Apollonio F, Brigida S, Fasano F, Mancini P, Bonanno Ferraro G, Veneri C, La Rosa G, Suffredini E, Lucentini L, Ungaro N, Di Vittorio G, Mongelli O, Albano N, Montagna MT. Wastewater-based Epidemiology and SARS-CoV-2: Variant Trends in the Apulia Region (Southern Italy) and Effect of Some Environmental Parameters. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:331-341. [PMID: 37735299 PMCID: PMC10654208 DOI: 10.1007/s12560-023-09565-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
During the COVID-19 pandemic, wastewater monitoring has been used to monitor the levels of SARS-CoV-2 RNA entering the sewerage system. In Italy, the Istituto Superiore di Sanità coordinated the SARI project (Sorveglianza Ambientale Reflue in Italia) to detect SARS-CoV-2 and its variants. In this study, the concentration of SARS-CoV-2 and its variants in raw wastewater against COVID-19 cases was evaluated together with the effect of temperature and precipitation on virus spread. We validated a predictive model, proposed by De Giglio et al., 2021, to establish the number of COVID-19 cases/100,000 inhabitants. A receiver operating characteristic curve model was applied to predict the number of COVID-19 cases and Poisson regression was applied to study the effect of temperature and rainfall on viral load. In Apulia, from October 2021 to December 2022, we analyzed 1041 samples, of which 985 (94.6%) tested positive for SARS-CoV-2. Median atmospheric temperature was inversely proportional to viral load in wastewater; no correlation was found with precipitation. The predictive model confirmed that at least 11 cases/100,000 inhabitants would occur in the 15 days following the detection of the virus in wastewater. Environmental surveillance of SARS-CoV-2 can be used to map the virus and its variants.
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Affiliation(s)
- Francesco Triggiano
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Osvalda De Giglio
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy.
| | - Francesca Apollonio
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Silvia Brigida
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Campus Ecotekne, Monteroni di Lecce, Lecce, 73047, Italy
| | - Fabrizio Fasano
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Giusy Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Carolina Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Luca Lucentini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Nicola Ungaro
- Agency for the Environmental Prevention and Protection (ARPA Puglia), Corso Trieste 27, Bari, 70126, Italy
| | | | - Onofrio Mongelli
- Department of Health Promotion and Animal Welfare, Apulia Region, Bari, Italy
| | - Nelhudoff Albano
- Department of Health Promotion and Animal Welfare, Apulia Region, Bari, Italy
| | - Maria Teresa Montagna
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
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Lin T, Karthikeyan S, Satterlund A, Schooley R, Knight R, De Gruttola V, Martin N, Zou J. Optimizing campus-wide COVID-19 test notifications with interpretable wastewater time-series features using machine learning models. Sci Rep 2023; 13:20670. [PMID: 38001346 PMCID: PMC10673837 DOI: 10.1038/s41598-023-47859-2] [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: 04/02/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023] Open
Abstract
During the COVID-19 pandemic, wastewater surveillance of the SARS CoV-2 virus has been demonstrated to be effective for population surveillance at the county level down to the building level. At the University of California, San Diego, daily high-resolution wastewater surveillance conducted at the building level is being used to identify potential undiagnosed infections and trigger notification of residents and responsive testing, but the optimal determinants for notifications are unknown. To fill this gap, we propose a pipeline for data processing and identifying features of a series of wastewater test results that can predict the presence of COVID-19 in residences associated with the test sites. Using time series of wastewater results and individual testing results during periods of routine asymptomatic testing among UCSD students from 11/2020 to 11/2021, we develop hierarchical classification/decision tree models to select the most informative wastewater features (patterns of results) which predict individual infections. We find that the best predictor of positive individual level tests in residence buildings is whether or not the wastewater samples were positive in at least 3 of the past 7 days. We also demonstrate that the tree models outperform a wide range of other statistical and machine models in predicting the individual COVID-19 infections while preserving interpretability. Results of this study have been used to refine campus-wide guidelines and email notification systems to alert residents of potential infections.
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Affiliation(s)
- Tuo Lin
- Department of Biostatistics, University of Florida, Gainesville, FL, 32608, USA
| | - Smruthi Karthikeyan
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alysson Satterlund
- Student Affairs, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert Schooley
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Victor De Gruttola
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Natasha Martin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jingjing Zou
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, 92093, USA.
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Schmiege D, Kraiselburd I, Haselhoff T, Thomas A, Doerr A, Gosch J, Schoth J, Teichgräber B, Moebus S, Meyer F. Analyzing community wastewater in sub-sewersheds for the small-scale detection of SARS-CoV-2 variants in a German metropolitan area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165458. [PMID: 37454854 DOI: 10.1016/j.scitotenv.2023.165458] [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: 04/06/2023] [Revised: 06/09/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
Wastewater surveillance of SARS-CoV-2 proved useful, including for identifying the local appearance of newly identified virus variants. Previous studies focused on wastewater treatment plants (WWTP) with sewersheds of several hundred thousand people or at single building level, representing only a small number of people. Both approaches may prove inadequate for small-scale intra-urban inferences for early detection of emerging or novel virus variants. Our study aims (i) to analyze SARS-CoV-2 single nucleotide variants (SNVs) in wastewater of sub-sewersheds and WWTP using whole genome sequencing in order to (ii) investigate the potential of small-scale detection of novel known SARS-CoV-2 variants of concern (VOC) within a metropolitan wastewater system. We selected three sub-sewershed sampling sites, based on estimated population- and built environment-related indicators, and the inlet of the receiving WWTP in the Ruhr region, Germany. Untreated wastewater was sampled weekly between October and December 2021, with a total of 22 samples collected. SARS-CoV-2 RNA was analyzed by RT-qPCR and whole genome sequencing. For all samples, genome sequences were obtained, while only 13 samples were positive for RT-qPCR. We identified multiple specific SARS-CoV-2 SNVs in the wastewater samples of the sub-sewersheds and the WWTP. Identified SNVs reflected the dominance of VOC Delta at the time of sampling. Interestingly, we could identify an Omicron-specific SNV in one sub-sewershed. A concurrent wastewater study sampling the same WWTP detected the VOC Omicron one week later. Our observations suggest that the small-scale approach may prove particularly useful for the detection and description of spatially confined emerging or existing virus variants circulating in populations. Future studies applying small-scale sampling strategies taking into account the specific features of the wastewater system will be useful to analyze temporal and spatial variance in more detail.
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Affiliation(s)
- Dennis Schmiege
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130 Essen, Germany.
| | - Ivana Kraiselburd
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany
| | - Timo Haselhoff
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130 Essen, Germany
| | - Alexander Thomas
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany
| | - Adrian Doerr
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany
| | - Jule Gosch
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany
| | - Jens Schoth
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, 45128 Essen, Germany
| | | | - Susanne Moebus
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130 Essen, Germany
| | - Folker Meyer
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany
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Goodwin JM, Golder PM, LeClair AR, Jun SC, Huckstep OJ, Steel JJ, Balboni AL. Designing a Wastewater-Based Epidemiology Study at the U.S. Air Force Academy: Using Severe Acute Respiratory Syndrome Coronavirus 2 to Test a Sentinel System for Early Disease Outbreak Detection. Mil Med 2023; 188:e3675-e3679. [PMID: 37405705 DOI: 10.1093/milmed/usad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/19/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023] Open
Abstract
INTRODUCTION The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) in wastewater has been proposed as a sentinel surveillance epidemiological tool for detection of infectious disease at a community level and as a complementary approach to syndromic surveillance of infectious disease outbreaks. We have designed a study to test the presence and quantity of SARS-CoV2, the virus responsible for COVID19, in the wastewater treatment facility (WWTF) of the U.S. Air Force Academy. MATERIALS AND METHODS Wastewater samples were tested in the laboratory to quantify the amount of SARS-CoV2 RNA using reverse transcription-quantitative polymerase chain reaction. Raw SARS-CoV2 viral titer in wastewater was normalized to the viral titer of a fecal marker, pepper mild mottle virus, to correct for dilutions. Temporal and spatial trends of COVID19 were analyzed. Furthermore, we compared wastewater analysis results against clinical data to assist public health decisions. RESULTS Preliminary data suggest that wastewater analysis can provide temporal and spatial trends of COVID19. The geographically discrete WWTF at the U.S. Air Force suggests that wastewater testing is a useful approach to developing a comprehensive sentinel surveillance system. CONCLUSIONS Together with ongoing syndromic surveillance data, this proof-of-concept study seeks to determine whether early detection of SARS-CoV2 in a closed system WWTF correlates to changes in community and clinically reported COVID19. The well-documented population served by the geographically discrete WWTF at the U.S. Air Force Academy may serve to better elucidate the adjunctive role of wastewater testing in a comprehensive surveillance system. These results may be of particular interest to the DoD and local commanders given the WWTFs under their immediate control and the information that these studies may provide in support of operational readiness through early detection of disease outbreaks.
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Affiliation(s)
- Jordan M Goodwin
- Department of Biology, US Air Force Academy, USAFA, CO 80840, USA
| | - Philip M Golder
- Department of Biology, US Air Force Academy, USAFA, CO 80840, USA
| | - Amy R LeClair
- Department of Biology, US Air Force Academy, USAFA, CO 80840, USA
| | - Samuel C Jun
- Department of Biology, US Air Force Academy, USAFA, CO 80840, USA
| | - Odaro J Huckstep
- Department of Biology, US Air Force Academy, USAFA, CO 80840, USA
- Life Science Research Center, US Air Force Academy, USAFA, CO 80840, USA
| | - J Jordan Steel
- Department of Biology, US Air Force Academy, USAFA, CO 80840, USA
| | - Armand L Balboni
- Department of Biology, US Air Force Academy, USAFA, CO 80840, USA
- Life Science Research Center, US Air Force Academy, USAFA, CO 80840, USA
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Shrestha S, Malla B, Angga MS, Sthapit N, Raya S, Hirai S, Rahmani AF, Thakali O, Haramoto E. Long-term SARS-CoV-2 surveillance in wastewater and estimation of COVID-19 cases: An application of wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165270. [PMID: 37400022 DOI: 10.1016/j.scitotenv.2023.165270] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
The role of wastewater-based epidemiology (WBE), a powerful tool to complement clinical surveillance, has increased as many grassroots-level facilities, such as municipalities and cities, are actively involved in wastewater monitoring, and the clinical testing of coronavirus disease 2019 (COVID-19) is downscaled widely. This study aimed to conduct long-term wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Yamanashi Prefecture, Japan, using one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay and estimate COVID-19 cases using a cubic regression model that is simple to implement. Influent wastewater samples (n = 132) from a wastewater treatment plant were collected normally once weekly between September 2020 and January 2022 and twice weekly between February and August 2022. Viruses in wastewater samples (40 mL) were concentrated by the polyethylene glycol precipitation method, followed by RNA extraction and RT-qPCR. The K-6-fold cross-validation method was used to select the appropriate data type (SARS-CoV-2 RNA concentration and COVID-19 cases) suitable for the final model run. SARS-CoV-2 RNA was successfully detected in 67 % (88 of 132) of the samples tested during the whole surveillance period, 37 % (24 of 65) and 96 % (64 of 67) of the samples collected before and during 2022, respectively, with concentrations ranging from 3.5 to 6.3 log10 copies/L. This study applied a nonnormalized SARS-CoV-2 RNA concentration and nonstandardized data for running the final 14-day (1 to 14 days) offset models to estimate weekly average COVID-19 cases. Comparing the parameters used for a model evaluation, the best model showed that COVID-19 cases lagged 3 days behind the SARS-CoV-2 RNA concentration in wastewater samples during the Omicron variant phase (year 2022). Finally, 3- and 7-day offset models successfully predicted the trend of COVID-19 cases from September 2022 until February 2023, indicating the applicability of WBE as an early warning tool.
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Affiliation(s)
- Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Made Sandhyana Angga
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Niva Sthapit
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sunayana Raya
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Soichiro Hirai
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Aulia Fajar Rahmani
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Ocean Thakali
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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36
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Chen W, Bibby K. Making waves: Establishing a modeling framework to evaluate novel targets for wastewater-based surveillance. WATER RESEARCH 2023; 245:120573. [PMID: 37688859 DOI: 10.1016/j.watres.2023.120573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/27/2023] [Accepted: 09/02/2023] [Indexed: 09/11/2023]
Abstract
Wastewater-based surveillance (WBS) monitoring of pathogens circulating within a community provides an improved understanding of the occurrence and spread of infectious diseases. However, the potential suitability of WBS for novel disease targets is unclear, including many emerging and neglected diseases. The current ad hoc approach of conducting wastewater detection experiments on novel disease targets to determine their suitability for WBS monitoring is resource intensive and may stall investment in this promising technology. In addition, detections, or non-detections, without the context of disease prevalence and shedding by infected individuals are difficult to interpret upon initial WBS target development. In this paper, we present a WBS feasibility analysis framework to identify which diseases are theoretically appropriate for WBS applications and to improve the initial interpretation of target detections. We then discuss five primary factors that influence the probability of detection in WBS monitoring - genome shedding rate, infection rate, per capita wastewater usage, process limit of detection (PLOD), and the number of PCR replicates. Clarifying the relationships between these factors and the likelihood of detection enhances quantitative insights into applying WBS, guiding researchers and stakeholders into mitigating inherent uncertainties of wastewater monitoring and subsequent improvements in WBS outcomes, thereby supporting future investment and expansion of WBS research, especially in novel disease targets.
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Affiliation(s)
- William Chen
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, United States
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, United States.
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Lee J, Acosta N, Waddell BJ, Du K, Xiang K, Van Doorn J, Low K, Bautista MA, McCalder J, Dai X, Lu X, Chekouo T, Pradhan P, Sedaghat N, Papparis C, Buchner Beaudet A, Chen J, Chan L, Vivas L, Westlund P, Bhatnagar S, Stefani S, Visser G, Cabaj J, Bertazzon S, Sarabi S, Achari G, Clark RG, Hrudey SE, Lee BE, Pang X, Webster B, Ghali WA, Buret AG, Williamson T, Southern DA, Meddings J, Frankowski K, Hubert CRJ, Parkins MD. Campus node-based wastewater surveillance enables COVID-19 case localization and confirms lower SARS-CoV-2 burden relative to the surrounding community. WATER RESEARCH 2023; 244:120469. [PMID: 37634459 DOI: 10.1016/j.watres.2023.120469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023]
Abstract
Wastewater-based surveillance (WBS) has been established as a powerful tool that can guide health policy at multiple levels of government. However, this approach has not been well assessed at more granular scales, including large work sites such as University campuses. Between August 2021 and April 2022, we explored the occurrence of SARS-CoV-2 RNA in wastewater using qPCR assays from multiple complimentary sewer catchments and residential buildings spanning the University of Calgary's campus and how this compared to levels from the municipal wastewater treatment plant servicing the campus. Real-time contact tracing data was used to evaluate an association between wastewater SARS-CoV-2 burden and clinically confirmed cases and to assess the potential of WBS as a tool for disease monitoring across worksites. Concentrations of wastewater SARS-CoV-2 N1 and N2 RNA varied significantly across six sampling sites - regardless of several normalization strategies - with certain catchments consistently demonstrating values 1-2 orders higher than the others. Relative to clinical cases identified in specific sewersheds, WBS provided one-week leading indicator. Additionally, our comprehensive monitoring strategy enabled an estimation of the total burden of SARS-CoV-2 for the campus per capita, which was significantly lower than the surrounding community (p≤0.001). Allele-specific qPCR assays confirmed that variants across campus were representative of the community at large, and at no time did emerging variants first debut on campus. This study demonstrates how WBS can be efficiently applied to locate hotspots of disease activity at a very granular scale, and predict disease burden across large, complex worksites.
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Affiliation(s)
- Jangwoo Lee
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Barbara J Waddell
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Kristine Du
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Kevin Xiang
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Jennifer Van Doorn
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Kashtin Low
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Maria A Bautista
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Janine McCalder
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Xiaotian Dai
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada
| | - Xuewen Lu
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada
| | - Thierry Chekouo
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada; Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, USA
| | - Puja Pradhan
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Navid Sedaghat
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Chloe Papparis
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Alexander Buchner Beaudet
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Jianwei Chen
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Leslie Chan
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Laura Vivas
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | | | - Srijak Bhatnagar
- Department of Biological Sciences, University of Calgary, Calgary, Canada; Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada
| | - September Stefani
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Gail Visser
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Jason Cabaj
- Department of Community Health Sciences, University of Calgary, Calgary, Canada; Department of Medicine, University of Calgary and Alberta Health Services, Calgary, Canada; Provincial Population & Public Health, Alberta Health Services, Calgary, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, Canada
| | | | - Shahrzad Sarabi
- Department of Geography, University of Calgary, Calgary, Canada
| | - Gopal Achari
- Department of Civil Engineering, University of Calgary, Calgary, Canada
| | - Rhonda G Clark
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Steve E Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Analytical and Environmental Toxicology, University of Alberta, Edmonton, Alberta, Canada
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada; Women & Children's Health Research Institute, Li Ka Shing Institute of Virology, Edmonton, Alberta, Canada
| | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Alberta Precision Laboratories, Public Health Laboratory, Alberta Health Services, Edmonton, Alberta, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - Brendan Webster
- Occupational Health Staff Wellness, University of Calgary, Calgary, Canada
| | - William Amin Ghali
- Department of Community Health Sciences, University of Calgary, Calgary, Canada; Department of Medicine, University of Calgary and Alberta Health Services, Calgary, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, Canada; Centre for Health Informatics, University of Calgary, Calgary, Canada
| | - Andre Gerald Buret
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Tyler Williamson
- Department of Community Health Sciences, University of Calgary, Calgary, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, Canada; Centre for Health Informatics, University of Calgary, Calgary, Canada
| | - Danielle A Southern
- Department of Community Health Sciences, University of Calgary, Calgary, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, Canada; Centre for Health Informatics, University of Calgary, Calgary, Canada
| | - Jon Meddings
- Department of Medicine, University of Calgary and Alberta Health Services, Calgary, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Medicine, University of Calgary and Alberta Health Services, Calgary, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, Canada.
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38
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Koirala P, Dhakal S, Malla B, Ghimire A, Siddiqui MA, Dawadi P. SARS-CoV-2 Burden in Wastewater and its Elimination Using Disinfection. Microbiol Insights 2023; 16:11786361231201598. [PMID: 37745090 PMCID: PMC10517603 DOI: 10.1177/11786361231201598] [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: 06/09/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Background Pathogenic viruses have been abundant and diverse in wastewater, reflecting the pattern of infection in humans. Human feces, urine, and perhaps other washouts that frequently circulate in sewage systems may contaminate wastewater with SARS-CoV-2. It's crucial to effectively disinfect wastewater since poorly handled wastewater could put the population at risk of infection. Aims To emphasize the presence and spread of SARS-CoV-2 in sewage (wastewater) through viral shedding from the patients to detect the virus in the population using wastewater-based epidemiology. Also, to effectively manage the transmission of SARS-CoV-2 and reduce the spread of the virus in the population using disinfectants is highlighted. Methods We evaluated articles from December 2019 to August 2022 that addressed SARS-CoV-2 shedding in wastewater and surveillance through wastewater-based epidemiology. We included the papers on wastewater disinfection for the elimination of SARS-CoV-2. Google Scholar, PubMed, and Research4Life are the three electronic databases from which all of the papers were retrieved. Results It is possible for viral shedding to get into the wastewater. The enumeration of viral RNA from it can be used to monitor virus circulation in the human community. SARS-CoV-2 can be removed from wastewater by using modern disinfection techniques such as sodium hypochlorite, liquid chlorine, chlorine dioxide, peracetic acid, and ultraviolet light. Conclusion SARS-CoV-2 burden estimates at the population level can be obtained via longitudinal examination of wastewater, and SARS-CoV-2 can be removed from the wastewater through disinfection.
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Affiliation(s)
- Prashanna Koirala
- National Animal Breeding and Genetics Research Center, Nepal Agricultural Research Council, Lalitpur, Nepal
| | - Sandesh Dhakal
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Bikram Malla
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Archana Ghimire
- Department of Development Education, School of Education, Kathmandu University, Hattiban, Lalitpur, Nepal
| | - Mohammad Ataullah Siddiqui
- Molecular Biotechnology Unit, Faculty of Science, Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | - Prabin Dawadi
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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39
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Bowes D, Darling A, Driver EM, Kaya D, Maal-Bared R, Lee LM, Goodman K, Adhikari S, Aggarwal S, Bivins A, Bohrerova Z, Cohen A, Duvallet C, Elnimeiry RA, Hutchison JM, Kapoor V, Keenum I, Ling F, Sills D, Tiwari A, Vikesland P, Ziels R, Mansfeldt C. Structured Ethical Review for Wastewater-Based Testing in Support of Public Health. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12969-12980. [PMID: 37611169 PMCID: PMC10484207 DOI: 10.1021/acs.est.3c04529] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Wastewater-based testing (WBT) for SARS-CoV-2 has rapidly expanded over the past three years due to its ability to provide a comprehensive measurement of disease prevalence independent of clinical testing. The development and simultaneous application of WBT measured biomarkers for research activities and for the pursuit of public health goals, both areas with well-established ethical frameworks. Currently, WBT practitioners do not employ a standardized ethical review process, introducing the potential for adverse outcomes for WBT professionals and community members. To address this deficiency, an interdisciplinary workshop developed a framework for a structured ethical review of WBT. The workshop employed a consensus approach to create this framework as a set of 11 questions derived from primarily public health guidance. This study retrospectively applied these questions to SARS-CoV-2 monitoring programs covering the emergent phase of the pandemic (3/2020-2/2022 (n = 53)). Of note, 43% of answers highlight a lack of reported information to assess. Therefore, a systematic framework would at a minimum structure the communication of ethical considerations for applications of WBT. Consistent application of an ethical review will also assist in developing a practice of updating approaches and techniques to reflect the concerns held by both those practicing and those being monitored by WBT supported programs.
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Affiliation(s)
- Devin
A. Bowes
- Biodesign
Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, United States
- Center on
Forced Displacement, Boston University, 111 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Amanda Darling
- Department
of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, 415 Durham Hall; Blacksburg, Virginia 24061, United States
| | - Erin M. Driver
- Biodesign
Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, United States
| | - Devrim Kaya
- School of
Chemical, Biological, and Environmental Engineering, Oregon State University, 105 26th St, Corvallis, Oregon 97331, United States
- School of
Public Health, San Diego State University, San Diego and Imperial Valley, California 92182, United States
| | - Rasha Maal-Bared
- Quality
Assurance and Environment, EPCOR Water Services Inc., EPCOR Tower, 2000−10423 101
Street NW, Edmonton, Alberta T5H 0E7, Canada
| | - Lisa M. Lee
- Department
of Population Health Sciences and Division of Scholarly Integrity
and Research Compliance, Virginia Tech, 300 Turner St. NW, Suite 4120 (0497), Blacksburg, Virginia 24061, United States
| | - Kenneth Goodman
- Institute
for Bioethics and Health Policy, Miller School of Medicine, University of Miami, Miami, Florida 33101, United States
| | - Sangeet Adhikari
- Biodesign
Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, United States
| | - Srijan Aggarwal
- Department
of Civil, Geological, and Environmental Engineering, University of Alaska Fairbanks, 1764 Tanana Loop, Fairbanks, Alaska 99775, United States
| | - Aaron Bivins
- Department
of Civil & Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, Louisiana 70803, United States
| | - Zuzana Bohrerova
- The Ohio
State University, Department of Civil, Environmental
and Geodetic Engineering, 2070 Neil Avenue, 470 Hitchcock Hall, Columbus, Ohio 43210, United States
| | - Alasdair Cohen
- Department
of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, 415 Durham Hall; Blacksburg, Virginia 24061, United States
- Department
of Population Health Sciences, Virginia
Tech, 205 Duck Pond Drive, Blacksburg, Virginia 24061, United States
| | - Claire Duvallet
- Biobot
Analytics, Inc., 501
Massachusetts Avenue; Cambridge, Massachusetts 02139, United States
| | - Rasha A. Elnimeiry
- Public
Health Outbreak Coordination, Informatics, Surveillance (PHOCIS) Office—Surveillance
Section, Division of Disease Control and Health Statistics, Washington State Department of Health, 111 Israel Rd SE, Tumwater, Washington 98501, United States
| | - Justin M. Hutchison
- Department
of Civil, Environmental, and Architectural Engineering, University of Kansas, 1530 W 15th St, Lawrence, Kansas 66045, United States
| | - Vikram Kapoor
- School
of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, Texas 78249, United States
| | - Ishi Keenum
- Complex
Microbial Systems Group, National Institute
of Standards and Technology, 100 Bureau Dr, Gaithersburg, Maryland 20899, United States
| | - Fangqiong Ling
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Deborah Sills
- Department
of Civil and Environmental Engineering, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Ananda Tiwari
- Department
of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöberginkatu 2,
P.O. Box 66, FI 00014 Helsinki, Finland
- Expert
Microbiology Unit, Finnish Institute for
Health and Welfare, FI 70600 Kuopio, Finland
| | - Peter Vikesland
- Department
of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, 415 Durham Hall; Blacksburg, Virginia 24061, United States
| | - Ryan Ziels
- Department
of Civil Engineering, The University of
British Columbia, 6250
Applied Science Ln #2002, Vancouver, BC V6T 1Z4, Canada
| | - Cresten Mansfeldt
- Department
of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, UCB 428, Boulder, Colorado 80309, United States
- Environmental
Engineering Program, University of Colorado
Boulder, UCB 607, Boulder, Colorado 80309, United States
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Yoo BK, Iwamoto R, Chung U, Sasaki T, Kitajima M. Economic Evaluation of Wastewater Surveillance Combined with Clinical COVID-19 Screening Tests, Japan. Emerg Infect Dis 2023; 29:1608-1617. [PMID: 37486197 PMCID: PMC10370838 DOI: 10.3201/eid2908.221775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
The COVID-19 pandemic has imposed substantial burdens on the global society. To find an optimal combination of wastewater surveillance and clinical testing for tracking COVID-19, we evaluated the economic efficiency of hypothetical screening options at a single facility in Japan. To conduct cost-benefit analyses, we developed standard decision models in which we assumed model parameters from literature and primary data, such as screening policies used at the Tokyo Olympic and Paralympic Village in 2021. We compared hypothetical 2-step screening options that used clinical PCR to diagnose COVID-19 after a positive result from primary screening using antigen tests (option 1) or wastewater surveillance (option 2). Our simulation results indicated that option 2 likely would be economically more justifiable than option 1, particularly at lower incidence levels. Our findings could help justify and promote the use of wastewater surveillance as a primary screening at a facility level for COVID-19 and other infectious diseases.
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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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Lekhanya T, Musvuugwa T, Mashifana T, Modley LAS. Measurement of SARS-CoV-2 RNA in wastewater: A case study of the Northern Cape, South Africa. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 88:355-366. [PMID: 37522438 PMCID: wst_2023_197 DOI: 10.2166/wst.2023.197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
The SARS-CoV-2 pandemic has resulted in the infection and death of many South Africans. This is in part due to a lack of testing facilities, equipment, and staff in many areas, particularly those with low population densities. The study focused on the infection dynamics of the virus in the Northern Cape province in all five municipalities investigating wastewater-based surveillance for the province. Reverse transcription was used to identify the virus, and SARS-CoV-2 RNA was detected in a batch of wastewater from four of the five areas sampled and was collected in the months that fall within the third wave of COVID as well as the winter season (May-July). The detection of the SARS-CoV-2 RNA correlated with infection statistics as well as the seasonality of the virus. This research showed a positive result in using wastewater epidemiology to track the spread of the virus but also highlighted the need for improved methodology when it comes to this surveillance. This includes sampling smaller areas and frequent sampling in multiple areas to show clear patterns within smaller, sparsely populated communities.
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Affiliation(s)
- Thapelo Lekhanya
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Johannesburg, South Africa E-mail:
| | - Tendai Musvuugwa
- Department of Biological and Agricultural Sciences, Sol Plaatjie University, Kimberley, South Africa
| | - Tebogo Mashifana
- Department of Chemical Engineering, University of Johannesburg, P.O. Box 17011, Doornfontein 2088, South Africa
| | - Lee-Ann Sade Modley
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Johannesburg, South Africa
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43
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Shingleton JW, Lilley CJ, Wade MJ. Evaluating the theoretical performance of aircraft wastewater monitoring as a tool for SARS-CoV-2 surveillance. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001975. [PMID: 37347725 DOI: 10.1371/journal.pgph.0001975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023]
Abstract
Air travel plays an important role in the cross-border spread of infectious diseases. During the SARS-CoV-2 pandemic many countries introduced strict border testing protocols to monitor the incursion of the virus. However, high implementation costs and significant inconvenience to passengers have led public health authorities to consider alternative methods of disease surveillance at borders. Aircraft wastewater monitoring has been proposed as one such alternative. In this paper we assess the theoretical limits of aircraft wastewater monitoring and compare its performance to post-arrival border screening approaches. Using an infectious disease model, we simulate an unmitigated SARS-CoV-2 epidemic originating in a seed country and spreading to the United Kingdom (UK) through daily flights. We use a probabilistic approach to estimate the time of first detection in the UK in aircraft wastewater and respiratory swab screening. Across a broad range of model parameters, our analysis indicates that the median time between the first incursion and detection in wastewater would be approximately 17 days (IQR: 7-28 days), resulting in a median of 25 cumulative cases (IQR: 6-84 cases) in the UK at the point of detection. Comparisons to respiratory swab screening suggest that aircraft wastewater monitoring is as effective as random screening of 20% of passengers at the border, using a test with 95% sensitivity. For testing regimes with sensitivity of 85% or less, the required coverage to outperform wastewater monitoring increases to 30%. Analysis of other model parameters suggests that wastewater monitoring is most effective when used on long-haul flights where probability of defecation is above 30%, and when the target pathogen has high faecal shedding rates and reasonable detectability in wastewater. These results demonstrate the potential use cases of aircraft wastewater monitoring and its utility in a wider system of public health surveillance.
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Affiliation(s)
- Joseph W Shingleton
- Analytics & Data Science Directorate, UK Health Security Agency, Nobel House, Smith Square, London, United Kingdom
| | - Chris J Lilley
- Analytics & Data Science Directorate, UK Health Security Agency, Nobel House, Smith Square, London, United Kingdom
| | - Matthew J Wade
- Analytics & Data Science Directorate, UK Health Security Agency, Nobel House, Smith Square, London, United Kingdom
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44
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Torabi S, Amirsoleimani A, Dehghan Banadaki M, Strike WD, Rockward A, Noble A, Liversedge M, Keck JW, Berry SM. Stabilization of SARS-CoV-2 RNA in wastewater via rapid RNA extraction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:162992. [PMID: 36948314 PMCID: PMC10028336 DOI: 10.1016/j.scitotenv.2023.162992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/21/2022] [Accepted: 03/17/2023] [Indexed: 05/13/2023]
Abstract
Wastewater-based Epidemiology (WBE) has contributed to surveillance of SARS-CoV-2 in communities across the world. Both symptomatic and asymptomatic patients with COVID-19 can shed the virus through the gastrointestinal tract, enabling the quantification of the virus in stool and ultimately in wastewater (WW). Unfortunately, instability of SARS-CoV-2 RNA in wastewater limits the utility of WBE programs, particularly in remote/rural regions where reliable cold storage and/or rapid shipping may be unavailable. This study examined whether rapid SARS-CoV-2 RNA extraction on the day of sample collection could minimize degradation. Importantly, the extraction technology used in these experiments, termed exclusion-based sample preparation (ESP), is lightweight, portable, and electricity-free, making it suitable for implementation in remote settings. We demonstrated that immediate RNA extraction followed by ambient storage significantly increased the RNA half-life compared to raw wastewater samples stored at both 4 °C or ambient temperature. Given that RNA degradation negatively impacts both the sensitivity and precision of WBE measurements, efforts must be made to mitigate degradation in order to maximize the potential impact of WBE on public health.
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Affiliation(s)
- Soroosh Torabi
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States of America
| | - Atena Amirsoleimani
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States of America
| | - Mohammad Dehghan Banadaki
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States of America
| | - William Dalton Strike
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States of America
| | - Alexus Rockward
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States of America
| | - Ann Noble
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States of America
| | - Matthew Liversedge
- Department of Family and Community Medicine, College of Medicine, University of Kentucky, United States of America
| | - James W Keck
- Department of Family and Community Medicine, College of Medicine, University of Kentucky, United States of America
| | - Scott M Berry
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States of America; Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States of America.
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45
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Bowes DA, Darling A, Driver EM, Kaya D, Maal-Bared R, Lee LM, Goodman K, Adhikari S, Aggarwal S, Bivins A, Bohrerova Z, Cohen A, Duvallet C, Elnimeiry RA, Hutchison JM, Kapoor V, Keenum I, Ling F, Sills D, Tiwari A, Vikesland P, Ziels R, Mansfeldt C. Structured Ethical Review for Wastewater-Based Testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.12.23291231. [PMID: 37398480 PMCID: PMC10312843 DOI: 10.1101/2023.06.12.23291231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Wastewater-based testing (WBT) for SARS-CoV-2 has rapidly expanded over the past three years due to its ability to provide a comprehensive measurement of disease prevalence independent of clinical testing. The development and simultaneous application of the field blurred the boundary between measuring biomarkers for research activities and for pursuit of public health goals, both areas with well-established ethical frameworks. Currently, WBT practitioners do not employ a standardized ethical review process (or associated data management safeguards), introducing the potential for adverse outcomes for WBT professionals and community members. To address this deficiency, an interdisciplinary group developed a framework for a structured ethical review of WBT. The workshop employed a consensus approach to create this framework as a set of 11-questions derived from primarily public health guidance because of the common exemption of wastewater samples to human subject research considerations. This study retrospectively applied the set of questions to peer- reviewed published reports on SARS-CoV-2 monitoring campaigns covering the emergent phase of the pandemic from March 2020 to February 2022 (n=53). Overall, 43% of the responses to the questions were unable to be assessed because of lack of reported information. It is therefore hypothesized that a systematic framework would at a minimum improve the communication of key ethical considerations for the application of WBT. Consistent application of a standardized ethical review will also assist in developing an engaged practice of critically applying and updating approaches and techniques to reflect the concerns held by both those practicing and being monitored by WBT supported campaigns. Abstract Figure Synopsis Development of a structured ethical review facilitates retrospective analysis of published studies and drafted scenarios in the context of wastewater-based testing.
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Affiliation(s)
- Devin A. Bowes
- Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287
- Center on Forced Displacement, Boston University, 111 Cummington Mall, Boston, MA, 02215
| | - Amanda Darling
- Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street; 415 Durham Hall; Blacksburg, VA 24061
| | - Erin M. Driver
- Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287
| | - Devrim Kaya
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 105 26th St, Corvallis, Oregon 97331
- School of Public Health, San Diego State University, San Diego and Imperial Valley, CA
| | - Rasha Maal-Bared
- Quality Assurance and Environment, EPCOR Water Services Inc., EPCOR Tower, 2000–10423 101 Street NW, Edmonton, Alberta, CA
| | - Lisa M. Lee
- Department of Population Health Sciences and Division of Scholarly Integrity and Research Compliance, Virginia Tech, 300 Turner St. NW, Suite 4120 (0497), Blacksburg, VA 24061
| | - Kenneth Goodman
- Institute for Bioethics and Health Policy, Miller School of Medicine, University of Miami, Miami, Florida
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287
| | - Srijan Aggarwal
- Department of Civil, Geological, and Environmental Engineering, University of Alaska Fairbanks, 1764 Tanana Loop, Fairbanks, AK 99775
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803
| | - Zuzana Bohrerova
- The Ohio State University, Department of Civil, Environmental and Geodetic Engineering, 2070 Neil Avenue, 470 Hitchcock Hall, Columbus, OH 43210
| | - Alasdair Cohen
- Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street; 415 Durham Hall; Blacksburg, VA 24061
- Department of Population Health Sciences, Virginia Tech, 205 Duck Pond Drive, Blacksburg, VA 24061
| | - Claire Duvallet
- Biobot Analytics, Inc., 501 Massachusetts Avenue; Cambridge, MA; 02139
| | - Rasha A. Elnimeiry
- Public Health Outbreak Coordination, Informatics, Surveillance (PHOCIS) Office – Surveillance Section, Division of Disease Control and Health Statistics, Washington State Department of Health, 111 Israel Rd SE, Tumwater, WA 98501
| | - Justin M. Hutchison
- Department of Civil, Environmental, and Architectural Engineering, University of Kansas, 1530 W 15th St, Lawrence, KS 66045
| | - Vikram Kapoor
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249
| | - Ishi Keenum
- Complex Microbial Systems Group, National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD 20899
| | - Fangqiong Ling
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130
| | - Deborah Sills
- Department of Civil and Environmental Engineering, Bucknell University, Lewisburg, PA, 17837
| | - Ananda Tiwari
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöberginkatu 2 P.O. Box 66 FI 00014 Helsinki, Finland
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Peter Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street; 415 Durham Hall; Blacksburg, VA 24061
| | - Ryan Ziels
- Department of Civil Engineering, the University of British Columbia, 6250 Applied Science Ln #2002, Vancouver, BC V6T 1Z4
| | - Cresten Mansfeldt
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, UCB 428, Boulder, CO 80309
- Environmental Engineering Program, University of Colorado Boulder, UCB 607, Boulder, CO 80309
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Phan T, Brozak S, Pell B, Ciupe SM, Ke R, Ribeiro RM, Gitter A, Mena KD, Perelson AS, Kuang Y, Wu F. Prolonged viral shedding from noninfectious individuals confounds wastewater-based epidemiology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.08.23291144. [PMID: 37333173 PMCID: PMC10274979 DOI: 10.1101/2023.06.08.23291144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Wastewater surveillance has been widely used to track and estimate SARS-CoV-2 incidence. While both infectious and recovered individuals shed virus into wastewater, epidemiological inferences using wastewater often only consider the viral contribution from the former group. Yet, the persistent shedding in the latter group could confound wastewater-based epidemiological inference, especially during the late stage of an outbreak when the recovered population outnumbers the infectious population. To determine the impact of recovered individuals' viral shedding on the utility of wastewater surveillance, we develop a quantitative framework that incorporates population-level viral shedding dynamics, measured viral RNA in wastewater, and an epidemic dynamic model. We find that the viral shedding from the recovered population can become higher than the infectious population after the transmission peak, which leads to a decrease in the correlation between wastewater viral RNA and case report data. Furthermore, the inclusion of recovered individuals' viral shedding into the model predicts earlier transmission dynamics and slower decreasing trends in wastewater viral RNA. The prolonged viral shedding also induces a potential delay in the detection of new variants due to the time needed to generate enough new cases for a significant viral signal in an environment dominated by virus shed by the recovered population. This effect is most prominent toward the end of an outbreak and is greatly affected by both the recovered individuals' shedding rate and shedding duration. Our results suggest that the inclusion of viral shedding from non-infectious recovered individuals into wastewater surveillance research is important for precision epidemiology.
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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
| | - Stanca M. Ciupe
- Department of Mathematics, Virginia Tech, Blacksburg, VA 24060, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Anna Gitter
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Texas Epidemic Public Health Institute, TX, 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, TX, 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, TX, USA
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47
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Kallem P, Hegab H, Alsafar H, Hasan SW, Banat F. SARS-CoV-2 detection and inactivation in water and wastewater: Review on analytical methods, limitations and future research recommendations. Emerg Microbes Infect 2023:2222850. [PMID: 37279167 DOI: 10.1080/22221751.2023.2222850] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been detected in wastewater. Wastewater-based epidemiology (WBE) is a practical and cost-effective tool for the assessment and controlling of pandemics and probably for examining SARS-CoV-2 presence. Implementation of WBE during the outbreaks is not without limitations. Temperature, suspended solids, pH, and disinfectants affect the stability of viruses in wastewater. Due to these limitations, instruments and techniques have been utilized to detect SARS-CoV-2. SARS-CoV-2 has been detected in sewage using various concentration methods and computer-aided analyzes. RT-qPCR, ddRT-PCR, multiplex PCR, RT-LAMP, and electrochemical immunosensors have been employed to detect low levels of viral contamination. Inactivation of SARS-CoV-2 is a crucial preventive measure against coronavirus disease 2019 (COVID-19). To better assess the role of wastewater as a transmission route, detection, and quantification methods need to be refined. In this paper, the latest improvements in quantification, detection, and inactivation of SARS-CoV-2 in wastewater are explained. Finally, limitations and future research recommendations are thoroughly described.
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Affiliation(s)
- Parashuram Kallem
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- Environmental Health and Safety Program, College of Health Sciences, Abu Dhabi University, Abu Dhabi P.O. Box 59911, United Arab Emirates
| | - Hanaa Hegab
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- 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
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Emirates Bio-research center, Ministry of interior, Abu Dhabi, United Arab Emirates
| | - Shadi W Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Fawzi Banat
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
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Wang T, Wang C, Myshkevych Y, Mantilla-Calderon D, Talley E, Hong PY. SARS-CoV-2 wastewater-based epidemiology in an enclosed compound: A 2.5-year survey to identify factors contributing to local community dissemination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162466. [PMID: 36868271 PMCID: PMC9977070 DOI: 10.1016/j.scitotenv.2023.162466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Long-term (>2.5 years) surveillance of SARS-CoV-2 RNA concentrations in wastewater was conducted within an enclosed university compound. This study aims to demonstrate how coupling wastewater-based epidemiology (WBE) with meta-data can identify which factors contribute toward the dissemination of SARS-CoV-2 within a local community. Throughout the pandemic, the temporal dynamics of SARS-CoV-2 RNA concentrations were tracked by quantitative polymerase chain reaction and analyzed in the context of the number of positive swab cases, the extent of human movement, and intervention measures. Our findings suggest that during the early phase of the pandemic, when strict lockdown was imposed, the viral titer load in the wastewater remained below detection limits, with <4 positive swab cases reported over a 14-day period in the compound. After the lockdown was lifted and global travel gradually resumed, SARS-CoV-2 RNA was first detected in the wastewater on 12 August 2020 and increased in frequency thereafter, despite high vaccination rates and mandatory face-covering requirements in the community. Accompanied by a combination of the Omicron surge and significant global travel by community members, SARS-CoV-2 RNA was detected in most of the weekly wastewater samples collected in late December 2021 and January 2022. With the cease of mandatory face covering, SARS-CoV-2 was detected in at least two of the four weekly wastewater samples collected from May through August 2022. Retrospective Nanopore sequencing revealed the presence of the Omicron variant in the wastewater with a multitude of amino acid mutations, from which we could infer the likely geographical origins through bioinformatic analysis. This study demonstrated that long-term tracking of the temporal dynamics and sequencing of variants in wastewater would aid in identifying which factors contribute the most to SARS-CoV-2 dissemination within the local community, facilitating an appropriate public health response to control future outbreaks as we now live with endemic SARS-CoV-2.
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Affiliation(s)
- Tiannyu Wang
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Changzhi Wang
- Bioengineering Program, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yevhen Myshkevych
- Environmental Science and Engineering Program, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - David Mantilla-Calderon
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Erik Talley
- Health, Safety and Environment, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Bioengineering Program, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Environmental Science and Engineering Program, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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49
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Chua FJD, Kim SY, Hill E, Cai JW, Lee WL, Gu X, Afri Affandi SA, Kwok WCG, Ng W, Leifels M, Armas F, Chandra F, Chen H, Alm EJ, Tay M, Wong CCJ, Ng LC, Wuertz S, Thompson JR. Co-incidence of BA.1 and BA.2 at the start of Singapore's Omicron wave revealed by Community and University Campus wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162611. [PMID: 36871716 DOI: 10.1016/j.scitotenv.2023.162611] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Wastewater surveillance (WWS) has been globally recognised to be a useful tool in quantifying SARS-CoV-2 RNA at the community and residential levels without biases associated with case-reporting. The emergence of variants of concern (VOCs) have given rise to an unprecedented number of infections even though populations are increasingly vaccinated. This is because VOCs have been reported to possess higher transmissibility and can evade host immune responses. The B.1.1.529 lineage (Omicron) has severely disrupted global plans to return to normalcy. In this study, we developed an allele-specific (AS) RT-qPCR assay which simultaneously targets the stretch of deletions and mutations in the spike protein from position 24-27 for quantitative detection of Omicron BA.2. Together with previous assays that detect mutations associated with Omicron BA.1 (deletion at position 69 and 70) and all Omicron (mutation at position 493 and 498), we report the validation and time series of these assays from September 2021 to May 2022 using influent samples from two wastewater treatment plants and across four University campus sites in Singapore. Viral RNA concentrations at the treatment plants corroborate with locally reported clinical cases, AS RT-qPCR assays revealed co-incidence of Omicron BA.1 and BA.2 on 12 January 2022, almost two months after initial BA.1 detection in South Africa and Botswana. BA.2 became the dominant variant by the end of January 2022 and completely displaced BA.1 by mid-March 2022. University campus sites were similarly positive for BA.1 and/or BA.2 in the same week as first detection at the treatment plants, where BA.2 became rapidly established as the dominant lineage within three weeks. These results corroborate clinical incidence of the Omicron lineages in Singapore and indicate minimal silent circulation prior to January 2022. The subsequent simultaneous spread of both variant lineages followed strategic relaxation of safe management measures upon meeting nationwide vaccination goals.
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Affiliation(s)
- Feng Jun Desmond Chua
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Se Yeon Kim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Eric Hill
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Jia Wei Cai
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), 138602, Singapore
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), 138602, Singapore
| | - Siti Aisyah Afri Affandi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Wee Chiew Germaine Kwok
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Weijie Ng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), 138602, Singapore
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), 138602, Singapore
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), 138602, Singapore
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), 138602, Singapore; Centre for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Martin Tay
- Environmental Health Institute, National Environmental Agency, 138667, Singapore
| | | | - Lee Ching Ng
- Environmental Health Institute, National Environmental Agency, 138667, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore
| | - Janelle R Thompson
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), 138602, Singapore; Asian School of the Environment, Nanyang Technological University, 637459, Singapore.
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Schenk H, Heidinger P, Insam H, Kreuzinger N, Markt R, Nägele F, Oberacher H, Scheffknecht C, Steinlechner M, Vogl G, Wagner AO, Rauch W. Prediction of hospitalisations based on wastewater-based SARS-CoV-2 epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162149. [PMID: 36773921 PMCID: PMC9911153 DOI: 10.1016/j.scitotenv.2023.162149] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 05/03/2023]
Abstract
Wastewater-based epidemiology is widely applied in Austria since April 2020 to monitor the SARS-CoV-2 pandemic. With a steadily increasing number of monitored wastewater facilities, 123 plants covering roughly 70 % of the 9 million population were monitored as of August 2022. In this study, the SARS-CoV-2 viral concentrations in raw sewage were analysed to infer short-term hospitalisation occupancy. The temporal lead of wastewater-based epidemiological time series over hospitalisation occupancy levels facilitates the construction of forecast models. Data pre-processing techniques are presented, including the approach of comparing multiple decentralised wastewater signals with aggregated and centralised clinical data. Time‑lead quantification was performed using cross-correlation analysis and coefficient of determination optimisation approaches. Multivariate regression models were successfully applied to infer hospitalisation bed occupancy. The results show a predictive potential of viral loads in sewage towards Covid-19 hospitalisation occupancy, with an average lead time towards ICU and non-ICU bed occupancy between 14.8-17.7 days and 8.6-11.6 days, respectively. The presented procedure provides access to the trend and tipping point behaviour of pandemic dynamics and allows the prediction of short-term demand for public health services. The results showed an increase in forecast accuracy with an increase in the number of monitored wastewater treatment plants. Trained models are sensitive to changing variant types and require recalibration of model parameters, likely caused by immunity by vaccination and/or infection. The utilised approach displays a practical and rapidly implementable application of wastewater-based epidemiology to infer hospitalisation occupancy.
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Affiliation(s)
- Hannes Schenk
- Unit of Environmental Engineering, University of Innsbruck, Technikerstraße 13, Innsbruck 6020, Austria.
| | - Petra Heidinger
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz 8010, Austria.
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria.
| | - Norbert Kreuzinger
- Institute of Water Quality and Resource Management at TU Wien, Karlsplatz 13, Vienna 1040, Austria.
| | - Rudolf Markt
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria; Department of Health Sciences and Social Work, Carinthia University of Applied Sciences, St. Veiter Straße, 47, Klagenfurt 9020, Austria.
| | - Fabiana Nägele
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria.
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Müllerstraße, 44, Innsbruck 6020, Austria.
| | - Christoph Scheffknecht
- Institut für Umwelt und Lebensmittelsicherheit des Landes Vorarlberg, Montfortstraße 4, Bregenz 6900, Austria.
| | - Martin Steinlechner
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Müllerstraße, 44, Innsbruck 6020, Austria.
| | - Gunther Vogl
- Institut f¨ur Lebensmittelsicherheit, Veterinärmedizin und Umwelt, Kirchengasse 43, Klagenfurt 9020, Austria.
| | - Andreas Otto Wagner
- Department of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck 6020, Austria.
| | - Wolfgang Rauch
- Unit of Environmental Engineering, University of Innsbruck, Technikerstraße 13, Innsbruck 6020, Austria.
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