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Malla B, Shrestha S, Sthapit N, Hirai S, Raya S, Rahmani AF, Angga MS, Siri Y, Ruti AA, Haramoto E. Beyond COVID-19: Wastewater-based epidemiology for multipathogen surveillance and normalization strategies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174419. [PMID: 38960169 DOI: 10.1016/j.scitotenv.2024.174419] [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: 04/27/2024] [Revised: 06/29/2024] [Accepted: 06/29/2024] [Indexed: 07/05/2024]
Abstract
Wastewater-based epidemiology (WBE) is a critical tool for monitoring community health. Although much attention has focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a causative agent of coronavirus disease 2019 (COVID-19), other pathogens also pose significant health risks. This study quantified the presence of SARS-CoV-2, influenza A virus (Inf-A), and noroviruses of genogroups I (NoV-GI) and II (NoV-GII) in wastewater samples collected weekly (n = 170) from July 2023 to February 2024 from five wastewater treatment plants (WWTPs) in Yamanashi Prefecture, Japan, by quantitative PCR. Inf-A RNA exhibited localized prevalence with positive ratios of 59 %-82 % in different WWTPs, suggesting regional outbreaks within specific areas. NoV-GI (94 %, 160/170) and NoV-GII (100 %, 170/170) RNA were highly prevalent, with NoV-GII (6.1 ± 0.8 log10 copies/L) consistently exceeding NoV-GI (5.4 ± 0.7 log10 copies/L) RNA concentrations. SARS-CoV-2 RNA was detected in 100 % of the samples, with mean concentrations of 5.3 ± 0.5 log10 copies/L in WWTP E and 5.8 ± 0.4 log10 copies/L each in other WWTPs. Seasonal variability was evident, with higher concentrations of all pathogenic viruses during winter. Non-normalized and normalized virus concentrations by fecal indicator bacteria (Escherichia coli and total coliforms), an indicator virus (pepper mild mottle virus (PMMoV)), and turbidity revealed significant positive associations with the reported disease cases. Inf-A and NoV-GI + GII RNA concentrations showed strong correlations with influenza and acute gastroenteritis cases, particularly when normalized to E. coli (Spearman's ρ = 0.70-0.81) and total coliforms (ρ = 0.70-0.81), respectively. For SARS-CoV-2, non-normalized concentrations showed a correlation of 0.61, decreasing to 0.31 when normalized to PMMoV, suggesting that PMMoV is unsuitable. Turbidity normalization also yielded suboptimal results. This study underscored the importance of selecting suitable normalization parameters tailored to specific pathogens for accurate disease trend monitoring using WBE, demonstrating its utility beyond COVID-19 surveillance.
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Affiliation(s)
- Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Niva Sthapit
- Interdisciplinary Center for River Basin Environment, 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
| | - Sunayana Raya
- 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
| | - Made Sandhyana Angga
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Yadpiroon Siri
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Annisa Andarini Ruti
- 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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Walker DI, Witt J, Rostant W, Burton R, Davison V, Ditchburn J, Evens N, Godwin R, Heywood J, Lowther JA, Peters N, Porter J, Posen P, Wickens T, Wade MJ. Piloting wastewater-based surveillance of norovirus in England. WATER RESEARCH 2024; 263:122152. [PMID: 39096810 DOI: 10.1016/j.watres.2024.122152] [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: 02/07/2024] [Revised: 06/07/2024] [Accepted: 07/25/2024] [Indexed: 08/05/2024]
Abstract
Wastewater-based epidemiology (WBE) gained widespread use as a tool for supporting clinical disease surveillance during the COVID-19 pandemic. There is now significant interest in the continued development of WBE for other pathogens of clinical significance. In this study, approximately 3,200 samples of wastewater from across England, previously collected for quantification of SARS-CoV-2, were re-analysed for the quantification of norovirus genogroup I (GI) and II (GII). Overall, GI and GII were detected in 93% and 98% of samples respectively, and at least one of the genogroups was detected in 99% of samples. GI was found at significantly lower concentrations than GII, but the proportion of each genogroup varied over time, with GI becoming more prevalent than GII in some areas towards the end of the study period (May 2021 - March 2022). Using relative strength indices (RSI), it was possible to study the trends of each genogroup, and total norovirus over time. Increases in norovirus levels appeared to coincide with the removal of COVID-19 related lockdown restrictions within England. Local Moran's I analyses indicated several localised outbreaks of both GI and GII across England, notably the possible GI outbreak in the north of England in early 2022. Comparisons of national average norovirus concentrations in wastewater against concomitant norovirus reported case numbers showed a significant linear relationship. This highlights the potential for wastewater-based monitoring of norovirus as a valuable approach to support surveillance of norovirus in communities.
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Affiliation(s)
- David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK.
| | - Jessica Witt
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Wayne Rostant
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Robert Burton
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Vicki Davison
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Jackie Ditchburn
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Nicholas Evens
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Reg Godwin
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Jane Heywood
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - James A Lowther
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Nancy Peters
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Jonathan Porter
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Paulette Posen
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Tyler Wickens
- Environment Agency, National Monitoring Laboratories, Staplake Mount, Starcross, Devon, UK
| | - Matthew J Wade
- Data Analytics & Surveillance Group, UK Health Security Agency, 10 South Colonnade, London, UK
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Boza JM, Amirali A, Williams SL, Currall BB, Grills GS, Mason CE, Solo-Gabriele HM, Erickson DC. Evaluation of a field deployable, high-throughput RT-LAMP device as an early warning system for COVID-19 through SARS-CoV-2 measurements in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173744. [PMID: 38844223 PMCID: PMC11249788 DOI: 10.1016/j.scitotenv.2024.173744] [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: 02/26/2024] [Revised: 05/02/2024] [Accepted: 06/01/2024] [Indexed: 06/16/2024]
Abstract
Quantification of SARS-CoV-2 RNA copies in wastewater can be used to estimate COVID-19 prevalence in communities. While such results are important for mitigating disease spread, SARS-CoV-2 measurements require sophisticated equipment and trained personnel, for which a centralized laboratory is necessary. This significantly impacts the time to result, defeating its purpose as an early warning detection tool. The objective of this study was to evaluate a field portable device (called MINI) for detecting SARS-CoV-2 viral loads in wastewater using real-time reverse transcriptase loop-mediated isothermal amplification (real-time RT-LAMP). The device was tested using wastewater samples collected from buildings (with 430 to 1430 inhabitants) that had known COVID-19-positive cases. Results show comparable performance of RT-LAMP against reverse transcriptase polymerase chain reaction (RT-qPCR) when detecting SARS-CoV-2 copies in wastewater. Both RT-LAMP and RT-qPCR detected SARS-CoV-2 in wastewater from buildings with at least three positive individuals within a 6-day time frame prior to diagnosis. The large 96-well throughput provided by MINI provided scalability to multi-building detection. The portability of the MINI device enabled decentralized on-site detection, significantly reducing the time to result. The overall findings support the use of RT-LAMP within the MINI configuration as an early detection system for COVID-19 infection using wastewater collected at the building scale.
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Affiliation(s)
- J M Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - A Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - S L Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - B B Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - G S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - C E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - H M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - D C Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA; Division of Nutritional Science, Cornell University, Ithaca, NY 14850, USA.
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Sarekoski A, Lipponen A, Hokajärvi AM, Räisänen K, Tiwari A, Paspaliari D, Lehto KM, Oikarinen S, Heikinheimo A, Pitkänen T. Simultaneous biomass concentration and subsequent quantitation of multiple infectious disease agents and antimicrobial resistance genes from community wastewater. ENVIRONMENT INTERNATIONAL 2024; 191:108973. [PMID: 39182255 DOI: 10.1016/j.envint.2024.108973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/01/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Wastewater-based surveillance (WBS) of infectious disease agents is increasingly seen as a reliable source of population health data. To date, wastewater-based surveillance efforts have largely focused on individual pathogens. However, given that wastewater contains a broad range of pathogens circulating in the population, a more comprehensive approach could enhance its usability. We focused on the simultaneous detection of SARS-CoV-2, sapovirus, Campylobacter jejuni, Campylobacter coli, Salmonella spp., pathogenic Escherichia coli, Cryptosporidium spp., Giardia spp. and antimicrobial resistance genes (ARGs) of clinical relevance. To achieve this goal, biomass concentration and nucleic acid extraction methods were optimized, and samples were analyzed by using a set of (RT)-qPCR and (HT)-qPCR methods. We determined the prevalence and the spatial and temporal trends of the targeted pathogens and collected novel information on ARGs in Finnish wastewater. In addition, the use of different wastewater concentrates, namely the ultrafiltered concentrate of the supernatant and the centrifuged pellet, and the effect of freezing and thawing wastewater prior to sample processing were investigated with the indicator microbe crAssphage. Freeze-thawing of wastewater decreased the gene copy count of crAssphage in comparison to analyzing fresh samples (p < 0.001). Campylobacters were most abundant in two of the four studied summer months (30 % detection rate) and in wastewaters from regions with intensive animal farming. Salmonella, however, was detected in 40 % of the samples without any clear seasonal trends, and the highest gene copy numbers were recorded from the largest wastewater treatment plants. Beta-lactamase resistance genes that have commonly been detected in bacteria isolated from humans in Finland, namely blaCTX-M, blaOXA48, blaNDM, and blaKPC, were also frequently detected in wastewaters (100, 98, 98, and 70 % detection rates, respectively). These results confirm the reliability of using wastewater in public health surveillance and demonstrate the possibility to simultaneously perform WBS of multiple pathogens.
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Affiliation(s)
- Anniina Sarekoski
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, Agnes Sjöbergin katu 2, Helsinki FI-00014, Finland.
| | - Anssi Lipponen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland.
| | - Anna-Maria Hokajärvi
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland.
| | - Kati Räisänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Mannerheimintie 166, Helsinki FI-00271, Finland.
| | - Ananda Tiwari
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland.
| | - Dafni Paspaliari
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Mannerheimintie 166, Helsinki FI-00271, Finland.
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland.
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland.
| | - Annamari Heikinheimo
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, Agnes Sjöbergin katu 2, Helsinki FI-00014, Finland; Finnish Food Authority, Alvar Aallon katu 5, FI-60100 Seinäjoki, Finland.
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, Agnes Sjöbergin katu 2, Helsinki FI-00014, Finland.
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5
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Martínez de Alba ÁE, Morán-Diez ME, García-Prieto JC, García-Bernalt Diego J, Fernández-Soto P, Serrano León E, Monsalvo V, Casao M, Rubio MB, Hermosa R, Muro A, García-Roig M, Monte E. SARS-CoV-2 RNA Detection in Wastewater and Its Effective Correlation with Clinical Data during the Outbreak of COVID-19 in Salamanca. Int J Mol Sci 2024; 25:8071. [PMID: 39125640 PMCID: PMC11311535 DOI: 10.3390/ijms25158071] [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: 06/17/2024] [Revised: 07/16/2024] [Accepted: 07/20/2024] [Indexed: 08/12/2024] Open
Abstract
Wastewater treatment plants (WWTPs) are the final stage of the anthropogenic water cycle where a wide range of chemical and biological markers of human activity can be found. In COVID-19 disease contexts, wastewater surveillance has been used to infer community trends based on viral abundance and SARS-CoV-2 RNA variant composition, which has served to anticipate and establish appropriate protocols to prevent potential viral outbreaks. Numerous studies worldwide have provided reliable and robust tools to detect and quantify SARS-CoV-2 RNA in wastewater, although due to the high dilution and degradation rate of the viral RNA in such samples, the detection limit of the pathogen has been a bottleneck for the proposed protocols so far. The current work provides a comprehensive and systematic study of the different parameters that may affect the detection of SARS-CoV-2 RNA in wastewater and hinder its quantification. The results obtained using synthetic viral RNA as a template allow us to consider that 10 genome copies per µL is the minimum RNA concentration that provides reliable and consistent values for the quantification of SARS-CoV-2 RNA. RT-qPCR analysis of wastewater samples collected at the WWTP in Salamanca (western Spain) and at six pumping stations in the city showed that below this threshold, positive results must be confirmed by sequencing to identify the specific viral sequence. This allowed us to find correlations between the SARS-CoV-2 RNA levels found in wastewater and the COVID-19 clinical data reported by health authorities. The close match between environmental and clinical data from the Salamanca case study has been confirmed by similar experimental approaches in four other cities in the same region. The present methodological approach reinforces the usefulness of wastewater-based epidemiology (WBE) studies in the face of future pandemic outbreaks.
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Affiliation(s)
- Ángel Emilio Martínez de Alba
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Salamanca, Spain; (M.E.M.-D.); (M.B.R.); (R.H.); (E.M.)
| | - María Eugenia Morán-Diez
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Salamanca, Spain; (M.E.M.-D.); (M.B.R.); (R.H.); (E.M.)
| | - Juan Carlos García-Prieto
- Centre for Research and Technological Development of Water (CIDTA), University of Salamanca, 37080 Salamanca, Spain; (J.C.G.-P.); (M.G.-R.)
| | - Juan García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (P.F.-S.); (A.M.)
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (P.F.-S.); (A.M.)
| | | | | | - Marta Casao
- FCC Aqualia, 28050 Madrid, Spain; (E.S.L.); (V.M.); (M.C.)
| | - María Belén Rubio
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Salamanca, Spain; (M.E.M.-D.); (M.B.R.); (R.H.); (E.M.)
| | - Rosa Hermosa
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Salamanca, Spain; (M.E.M.-D.); (M.B.R.); (R.H.); (E.M.)
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (P.F.-S.); (A.M.)
| | - Manuel García-Roig
- Centre for Research and Technological Development of Water (CIDTA), University of Salamanca, 37080 Salamanca, Spain; (J.C.G.-P.); (M.G.-R.)
| | - Enrique Monte
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Salamanca, Spain; (M.E.M.-D.); (M.B.R.); (R.H.); (E.M.)
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Schmiege D, Haselhoff T, Thomas A, Kraiselburd I, Meyer F, Moebus S. Small-scale wastewater-based epidemiology (WBE) for infectious diseases and antibiotic resistance: A scoping review. Int J Hyg Environ Health 2024; 259:114379. [PMID: 38626689 DOI: 10.1016/j.ijheh.2024.114379] [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: 01/12/2024] [Revised: 03/25/2024] [Accepted: 04/08/2024] [Indexed: 04/18/2024]
Abstract
Wastewater analysis can serve as a source of public health information. In recent years, wastewater-based epidemiology (WBE) has emerged and proven useful for the detection of infectious diseases. However, insights from the wastewater treatment plant do not allow for the small-scale differentiation within the sewer system that is needed to analyze the target population under study in more detail. Small-scale WBE offers several advantages, but there has been no systematic overview of its application. The aim of this scoping review is to provide a comprehensive overview of the current state of knowledge on small-scale WBE for infectious diseases, including methodological considerations for its application. A systematic database search was conducted, considering only peer-reviewed articles. Data analyses included quantitative summary and qualitative narrative synthesis. Of 2130 articles, we included 278, most of which were published since 2020. The studies analyzed wastewater at the building level (n = 203), especially healthcare (n = 110) and educational facilities (n = 80), and at the neighborhood scale (n = 86). The main analytical parameters were viruses (n = 178), notably SARS-CoV-2 (n = 161), and antibiotic resistance (ABR) biomarkers (n = 99), often analyzed by polymerase chain reaction (PCR), with DNA sequencing techniques being less common. In terms of sampling techniques, active sampling dominated. The frequent lack of detailed information on the specification of selection criteria and the characterization of the small-scale sampling sites was identified as a concern. In conclusion, based on the large number of studies, we identified several methodological considerations and overarching strategic aspects for small-scale WBE. An enabling environment for small-scale WBE requires inter- and transdisciplinary knowledge sharing across countries. Promoting the adoption of small-scale WBE will benefit from a common international conceptualization of the approach, including standardized and internationally accepted terminology. In particular, the development of good WBE practices for different aspects of small-scale WBE is warranted. This includes the establishment of guidelines for a comprehensive characterization of the local sewer system and its sub-sewersheds, and transparent reporting to ensure comparability of small-scale WBE results.
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Affiliation(s)
- Dennis Schmiege
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130, 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
| | - Ivana Kraiselburd
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131, Essen, Germany
| | - Folker Meyer
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131, Essen, Germany
| | - Susanne Moebus
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130, Essen, Germany
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Zafeiriadou A, Kaltsis L, Thomaidis NS, Markou A. Simultaneous detection of influenza A, B and respiratory syncytial virus in wastewater samples by one-step multiplex RT-ddPCR assay. Hum Genomics 2024; 18:48. [PMID: 38769549 PMCID: PMC11103825 DOI: 10.1186/s40246-024-00614-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND After the occurrence of the COVID-19 pandemic, detection of other disseminated respiratory viruses using highly sensitive molecular methods was declared essential for monitoring the spread of health-threatening viruses in communities. The development of multiplex molecular assays are essential for the simultaneous detection of such viruses even at low concentrations. In the present study, a highly sensitive and specific multiplex one-step droplet digital PCR (RT-ddPCR) assay was developed for the simultaneous detection and absolute quantification of influenza A (IAV), influenza B (IBV), respiratory syncytial virus (RSV), and beta-2-microglobulin transcript as an endogenous internal control (IC B2M). RESULTS The assay was first evaluated for analytical sensitivity and specificity, linearity, reproducibility, and recovery rates with excellent performance characteristics and then applied to 37 wastewater samples previously evaluated with commercially available and in-house quantitative real-time reverse transcription PCR (RT-qPCR) assays. IAV was detected in 16/37 (43%), IBV in 19/37 (51%), and RSV in 10/37 (27%) of the wastewater samples. Direct comparison of the developed assay with real-time RT-qPCR assays showed statistically significant high agreement in the detection of IAV (kappa Cohen's correlation coefficient: 0.834, p = 0.001) and RSV (kappa: 0.773, p = 0.001) viruses between the two assays, while the results for the detection of IBV (kappa: 0.355, p = 0.27) showed good agreement without statistical significance. CONCLUSIONS Overall, the developed one-step multiplex ddPCR assay is cost-effective, highly sensitive and specific, and can simultaneously detect three common respiratory viruses in the complex matrix of wastewater samples even at low concentrations. Due to its high sensitivity and resistance to PCR inhibitors, the developed assay could be further used as an early warning system for wastewater monitoring.
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Affiliation(s)
- Anastasia Zafeiriadou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771, ZografouAthens, Greece
| | - Lazaros Kaltsis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771, ZografouAthens, Greece
| | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771, ZografouAthens, Greece
| | - Athina Markou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771, ZografouAthens, Greece.
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Islam G, Gedge A, Ibrahim R, de Melo T, Lara-Jacobo L, Dlugosz T, Kirkwood AE, Simmons D, Desaulniers JP. The role of catchment population size, data normalization, and chronology of public health interventions on wastewater-based COVID-19 viral trends. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 937:173272. [PMID: 38763190 DOI: 10.1016/j.scitotenv.2024.173272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/28/2024] [Accepted: 05/13/2024] [Indexed: 05/21/2024]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic presented the most challenging global crisis in recent times. A pandemic caused by a novel pathogen such as SARS-CoV-2 necessitated the development of innovative techniques for the monitoring and surveillance of COVID-19 infections within communities. Wastewater surveillance (WWS) is recognized as a non-invasive, cost-effective, and valuable epidemiological tool to monitor the prevalence of COVID-19 infections in communities. Seven municipal wastewater sampling sites representing distinct sewershed communities were selected for the surveillance of the SARS-CoV-2 virus in Durham Region, Ontario, Canada over 8 months from March 2021 to October 2021. Viral RNA fragments of SARS-CoV-2 and the normalization target pepper mild mottle virus (PMMoV) were concentrated from wastewater influent using the PEG/NaCl superspeed centrifugation method and quantified using RT-qPCR. Strong significant correlations (Spearman's rs = 0.749 to 0.862, P < 0.001) were observed between SARS-CoV-2 gene copies/mL of wastewater and clinical cases reported in each delineated sewershed by onset date. Although raw wastewater offered higher correlation coefficients with clinical cases by onset date compared to PMMoV normalized data, only one site had a statistically significantly higher Spearman's correlation coefficient value for raw data than normalized data. Implementation of community stay-at-home orders and vaccinations over the course of the study period in 2021 were found to strongly correspond to decreasing SARS-CoV-2 wastewater trends in the wastewater treatment plants and upstream pumping stations.
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Affiliation(s)
- Golam Islam
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada.
| | - Ashley Gedge
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Reeta Ibrahim
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Tomas de Melo
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Linda Lara-Jacobo
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Thomas Dlugosz
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Andrea E Kirkwood
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Denina Simmons
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
| | - Jean-Paul Desaulniers
- Faculty of Science, Ontario Tech University, 2000 Simcoe St N, Oshawa, ON L1G 0C5, Canada
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9
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Tang MHE, Bennedbaek M, Gunalan V, Qvesel AG, Thorsen TH, Larsen NB, Rasmussen LD, Krogsgaard LW, Rasmussen M, Stegger M, Alexandersen S. Variations in the persistence of 5'-end genomic and subgenomic SARS-CoV-2 RNAs in wastewater from aircraft, airports and wastewater treatment plants. Heliyon 2024; 10:e29703. [PMID: 38694057 PMCID: PMC11061675 DOI: 10.1016/j.heliyon.2024.e29703] [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: 10/25/2023] [Revised: 04/08/2024] [Accepted: 04/14/2024] [Indexed: 05/03/2024] Open
Abstract
Wastewater sequencing has become a powerful supplement to clinical testing in monitoring SARS-CoV-2 infections in the post-COVID-19 pandemic era. While its applications in measuring the viral burden and main circulating lineages in the community have proved their efficacy, the variations in sequencing quality and coverage across the different regions of the SARS-CoV-2 genome are not well understood. Furthermore, it is unclear how different sample origins, viral extraction and concentration methods and environmental factors impact the reads sequenced from wastewater. Using high-coverage, amplicon-based, paired-end read sequencing of viral RNA extracted from wastewater collected directly from aircraft, pooled from different aircraft and airport buildings or from regular wastewater plants, we assessed the genome coverage across the sample groups with a focus on the 5'-end region covering the leader sequence and investigated whether it was possible to detect subgenomic RNA from viral material recovered from wastewater. We identified distinct patterns in the persistence of the different genomic regions across the different types of wastewaters and the existence of chimeric reads mapping to non-amplified regions. Our findings suggest that preservation of the 5'-end of the genome and the ability to detect subgenomic RNA reads, though highly susceptible to environment and sample processing conditions, may be indicative of the quality and amount of the viral RNA present in wastewater.
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Affiliation(s)
- Man-Hung Eric Tang
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Bennedbaek
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Amanda Gammelby Qvesel
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Theis Hass Thorsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Lasse Dam Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Lene Wulff Krogsgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, Western Australia, Australia
| | - Soren Alexandersen
- Division of Diagnostic Preparedness, Statens Serum Institut, Copenhagen, Denmark
- Department of Animal and Veterinary Sciences, Aarhus University, Tjele, Denmark
- Deakin University, School of Medicine, Waurn Ponds, Geelong, Australia
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10
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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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11
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Price M, Tscharke B, Chappell A, Kah M, Sila-Nowicka K, Morris H, Ward D, Trowsdale S. Testing methods to estimate population size for wastewater treatment plants using census data: Implications for wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:170974. [PMID: 38360313 DOI: 10.1016/j.scitotenv.2024.170974] [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: 11/30/2023] [Revised: 01/31/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
In wastewater-based epidemiology (WBE), wastewater loads are commonly reported as a per capita value. Census population counts are often used to obtain a population size to normalise wastewater loads. However, the methods used to calculate the population size of wastewater treatment plants (WWTPs) from census data are rarely reported in the WBE literature. This is problematic because the geographical extents of wastewater catchments and census area units rarely align perfectly with each other and exist at different spatial scales. This complicates efforts to estimate the number of people serviced by WWTPs in these census area units. This study compared four geospatial methods to combine wastewater catchment areas and census area units to calculate the census population size of wastewater treatment plants. These methods were applied nationally to WWTPs across New Zealand. Population estimates varied by up to 73 % between the methods, which could skew comparisons of per capita wastewater loads between sites. Variability in population estimates (relative standard deviation, RSD) was significantly higher in smaller catchments (rs = -0.727, P < .001), highlighting the importance of method selection in smaller sites. Census population estimates were broadly similar to those provided by wastewater operators, but significant variation was observed for some sites (ranging from 42 % lower to 78 % higher, RSD = 262 %). We present a widely applicable method to calculate population size from census, which involves disaggregating census area units by individual properties. The results reinforce the need for transparent reporting to maintain confidence in the comparison of WBE across sites and studies.
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Affiliation(s)
- Mackay Price
- School of Environment, University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
| | - Ben Tscharke
- Queensland Alliance for Environmental Health Sciences, University of Queensland, 20 Cornwall Street, Queensland 4102, Australia
| | - Andrew Chappell
- Institute of Environmental Science and Research Ltd., 27 Creyke Road, Christchurch 8041, New Zealand
| | - Melanie Kah
- School of Environment, University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Katarzyna Sila-Nowicka
- School of Environment, University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Helen Morris
- Institute of Environmental Science and Research Ltd., 27 Creyke Road, Christchurch 8041, New Zealand
| | - Daniel Ward
- Environment Canterbury, 200 Tuam Street, Christchurch 8011, New Zealand
| | - Sam Trowsdale
- School of Environment, University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
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12
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Inson JGM, Malla B, Amalin DM, Carvajal TM, Enriquez MLD, Hirai S, Raya S, Rahmani AF, Angga MS, Sthapit N, Shrestha S, Ruti AA, Takeda T, Kitajima M, Alam ZF, Haramoto E. Detection of SARS-CoV-2 and Omicron variant RNA in wastewater samples from Manila, Philippines. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170921. [PMID: 38350577 DOI: 10.1016/j.scitotenv.2024.170921] [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: 11/22/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 02/15/2024]
Abstract
Manila, a highly urbanized city, is listed as one of the top cities with the highest recorded number of coronavirus disease 2019 (COVID-19) cases in the Philippines. This study aimed to detect and quantify the RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the Omicron variant in 51 wastewater samples collected from three locations in Manila, namely Estero de Santa Clara, Estero de Pandacan, which are open drainages, and a sewage treatment plant (STP) at De La Salle University-Manila, between July 2022 and February 2023. Using one-step reverse transcription-quantitative polymerase chain reaction, SARS-CoV-2 and Omicron variant RNA were detected in 78 % (40/51; 4.9 ± 0.5 log10 copies/L) and 60 % (24/40; 4.4 ± 0.3 log10 copies/L) of wastewater samples collected from all sampling sites, respectively. SARS-CoV-2 RNA was detected frequently at Estero de Santa Clara (88 %, 15/17); its highest concentration was at the STP (6.3 log10 copies/L). The Omicron variant RNA was present in the samples collected (4.4 ± 0.3 log10 copies/L) from all sampling sites, with the highest concentration at the STP (4.9 log10 copies/L). Regardless of normalization, using concentrations of pepper mild mottle virus RNA, SARS-CoV-2 RNA concentrations exhibited the highest positive correlation with COVID-19 reported cases in Manila 5 days after the clinical report. These findings revealed that wastewater-based epidemiology may aid in identifying and monitoring of the presence of pathogens in open drainages and STPs in the Philippines. This paper provides the first documentation on SARS-CoV-2 and the Omicron variant in wastewater from Manila.
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Affiliation(s)
- Jessamine Gail M Inson
- Department of Biology, De La Salle University, Manila 1004, Philippines; Environmental Biomonitoring Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Divina M Amalin
- Department of Biology, De La Salle University, Manila 1004, Philippines; Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Thaddeus M Carvajal
- Department of Biology, De La Salle University, Manila 1004, Philippines; Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | | | - Soichiro Hirai
- Department of Engineering, 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
| | - Aulia Fajar Rahmani
- Department of Engineering, 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
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Annisa Andarini Ruti
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Tomoko Takeda
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan.
| | - Zeba F Alam
- Department of Biology, De La Salle University, Manila 1004, Philippines; Environmental Biomonitoring Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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13
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Li Y, Ash K, Alamilla I, Joyner D, Williams DE, McKay PJ, Green B, DeBlander S, North C, Kara-Murdoch F, Swift C, Hazen TC. COVID-19 trends at the University of Tennessee: predictive insights from raw sewage SARS-CoV-2 detection and evaluation and PMMoV as an indicator for human waste. Front Microbiol 2024; 15:1379194. [PMID: 38605711 PMCID: PMC11007199 DOI: 10.3389/fmicb.2024.1379194] [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: 01/30/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has become a valuable tool for monitoring the prevalence of SARS-CoV-2 on university campuses. However, concerns about effectiveness of raw sewage as a COVID-19 early warning system still exist, and it's not clear how useful normalization by simultaneous comparison of Pepper Mild Mottle Virus (PMMoV) is in addressing variations resulting from fecal discharge dilution. This study aims to contribute insights into these aspects by conducting an academic-year field trial at the student residences on the University of Tennessee, Knoxville campus, raw sewage. This was done to investigate the correlations between SARS-CoV-2 RNA load, both with and without PMMoV normalization, and various parameters, including active COVID-19 cases, self-isolations, and their combination among all student residents. Significant positive correlations between SARS-CoV-2 RNA load a week prior, during the monitoring week, and the subsequent week with active cases. Despite these correlations, normalization by PMMoV does not enhance these associations. These findings suggest the potential utility of SARS-CoV-2 RNA load as an early warning indicator and provide valuable insights into the application and limitations of WBE for COVID-19 surveillance specifically within the context of raw sewage on university campuses.
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Affiliation(s)
- Ye Li
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
| | - Kurt Ash
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Dominique Joyner
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
| | - Daniel Edward Williams
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Peter J. McKay
- Battelle Memorial Institute, Columbus, OH, United States
| | - Brianna Green
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Sydney DeBlander
- College of Natural Science, Michigan State University, East Lansing, MI, United States
| | - Carman North
- Student Health Center, University of Tennessee, Knoxville, TN, United States
| | - Fadime Kara-Murdoch
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
- Battelle Memorial Institute, Columbus, OH, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Cynthia Swift
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Terry C. Hazen
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
- Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
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14
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Amirali A, Babler KM, Sharkey ME, Beaver CC, Boone MM, Comerford S, Cooper D, Currall BB, Goodman KW, Grills GS, Kobetz E, Kumar N, Laine J, Lamar WE, Mason CE, Reding BD, Roca MA, Ryon K, Schürer SC, Shukla BS, Solle NS, Stevenson M, Tallon JJ, Vidović D, Williams SL, Yin X, Solo-Gabriele HM. Wastewater based surveillance can be used to reduce clinical testing intensity on a university campus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170452. [PMID: 38296085 PMCID: PMC10923133 DOI: 10.1016/j.scitotenv.2024.170452] [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: 11/09/2023] [Revised: 12/30/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Abstract
Clinical testing has been a vital part of the response to and suppression of the COVID-19 pandemic; however, testing imposes significant burdens on a population. College students had to contend with clinical testing while simultaneously dealing with health risks and the academic pressures brought on by quarantines, changes to virtual platforms, and other disruptions to daily life. The objective of this study was to analyze whether wastewater surveillance can be used to decrease the intensity of clinical testing while maintaining reliable measurements of diseases incidence on campus. Twelve months of human health and wastewater surveillance data for eight residential buildings on a university campus were analyzed to establish how SARS-CoV-2 levels in the wastewater can be used to minimize clinical testing burden on students. Wastewater SARS-CoV-2 levels were used to create multiple scenarios, each with differing levels of testing intensity, which were compared to the actual testing volumes implemented by the university. We found that scenarios in which testing intensity fluctuations matched rise and falls in SARS-CoV-2 wastewater levels had stronger correlations between SARS-CoV-2 levels and recorded clinical positives. In addition to stronger correlations, most scenarios resulted in overall fewer weekly clinical tests performed. We suggest the use of wastewater surveillance to guide COVID-19 testing as it can significantly increase the efficacy of COVID-19 surveillance while reducing the burden placed on college students during a pandemic. Future efforts should be made to integrate wastewater surveillance into clinical testing strategies implemented on college campuses.
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Affiliation(s)
- Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Kristina M Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Mark E Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136, FL, USA
| | - Cynthia C Beaver
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Melinda M Boone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Samuel Comerford
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136, FL, USA
| | | | - Benjamin B Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Kenneth W Goodman
- Frost Institute for Data Science & Computing, University of Miami, Coral Gables, FL 33146, USA; Institute for Bioethics and Health Policy, University of Miami Miller School of Medicine, Miami, 33136, FL, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Erin Kobetz
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136, FL, USA
| | - Naresh Kumar
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Walter E Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL 33136, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Brian D Reding
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Matthew A Roca
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA
| | - Stephan C Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL 33146, USA
| | - Bhavarth S Shukla
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136, FL, USA
| | - Natasha Schaefer Solle
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136, FL, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mario Stevenson
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - John J Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL 33146, USA
| | - Dušica Vidović
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Sion L Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xue Yin
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA.
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15
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Carducci A, Federigi I, Lauretani G, Muzio S, Pagani A, Atomsa NT, Verani M. Critical Needs for Integrated Surveillance: Wastewater-Based and Clinical Epidemiology in Evolving Scenarios with Lessons Learned from SARS-CoV-2. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:38-49. [PMID: 38168848 DOI: 10.1007/s12560-023-09573-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024]
Abstract
During the COVID-19 pandemic, wastewater-based epidemiology (WBE) and clinical surveillance have been used as tools for analyzing the circulation of SARS-CoV-2 in the community, but both approaches can be strongly influenced by some sources of variability. From the challenging perspective of integrating environmental and clinical data, we performed a correlation analysis between SARS-CoV-2 concentrations in raw sewage and incident COVID-19 cases in areas served by medium-size wastewater treatment plants (WWTPs) from 2021 to 2023. To this aim, both datasets were adjusted for several sources of variability: WBE data were adjusted for factors including the analytical protocol, sewage flow, and population size, while clinical data adjustments considered the demographic composition of the served population. Then, we addressed the impact on the correlation of differences among sewerage networks and variations in the frequency and type of swab tests due to changes in political and regulatory scenarios. Wastewater and clinical data were significantly correlated when restrictive containment measures and limited movements were in effect (ρ = 0.50) and when COVID-19 cases were confirmed exclusively through molecular testing (ρ = 0.49). Moreover, a positive (although weak) correlation arose for WWTPs located in densely populated areas (ρ = 0.37) and with shorter sewerage lengths (ρ = 0.28). This study provides methodological approaches for interpreting WBE and clinical surveillance data, which could also be useful for other infections. Data adjustments and evaluation of possible sources of bias need to be carefully considered from the perspective of integrated environmental and clinical surveillance of infections.
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Affiliation(s)
- Annalaura Carducci
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
| | - Ileana Federigi
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy.
| | - Giulia Lauretani
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
| | - Sara Muzio
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
| | - Alessandra Pagani
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
| | - Nebiyu Tariku Atomsa
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
| | - Marco Verani
- Laboratory of Hygiene and Environmental Virology, Department of Biology, University of Pisa, Via S. Zeno 35/39, 56127, Pisa, Italy
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16
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Baz Lomba JA, Pires J, Myrmel M, Arnø JK, Madslien EH, Langlete P, Amato E, Hyllestad S. Effectiveness of environmental surveillance of SARS-CoV-2 as an early-warning system: Update of a systematic review during the second year of the pandemic. JOURNAL OF WATER AND HEALTH 2024; 22:197-234. [PMID: 38295081 PMCID: wh_2023_279 DOI: 10.2166/wh.2023.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The aim of this updated systematic review was to offer an overview of the effectiveness of environmental surveillance (ES) of SARS-CoV-2 as a potential early-warning system (EWS) for COVID-19 and new variants of concerns (VOCs) during the second year of the pandemic. An updated literature search was conducted to evaluate the added value of ES of SARS-CoV-2 for public health decisions. The search for studies published between June 2021 and July 2022 resulted in 1,588 publications, identifying 331 articles for full-text screening. A total of 151 publications met our inclusion criteria for the assessment of the effectiveness of ES as an EWS and early detection of SARS-CoV-2 variants. We identified a further 30 publications among the grey literature. ES confirms its usefulness as an EWS for detecting new waves of SARS-CoV-2 infection with an average lead time of 1-2 weeks for most of the publication. ES could function as an EWS for new VOCs in areas with no registered cases or limited clinical capacity. Challenges in data harmonization and variant detection require standardized approaches and innovations for improved public health decision-making. ES confirms its potential to support public health decision-making and resource allocation in future outbreaks.
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Affiliation(s)
- Jose Antonio Baz Lomba
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway E-mail:
| | - João Pires
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway; ECDC fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jorunn Karterud Arnø
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Elisabeth Henie Madslien
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Petter Langlete
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Ettore Amato
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Susanne Hyllestad
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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17
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Rao G, Capone D, Zhu K, Knoble A, Linden Y, Clark R, Lai A, Kim J, Huang CH, Bivins A, Brown J. Simultaneous detection and quantification of multiple pathogen targets in wastewater. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.23.23291792. [PMID: 37425908 PMCID: PMC10327253 DOI: 10.1101/2023.06.23.23291792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Wastewater-based epidemiology has emerged as a critical tool for public health surveillance, building on decades of environmental surveillance work for pathogens such as poliovirus. Work to date has been limited to monitoring a single pathogen or small numbers of pathogens in targeted studies; however, few studies consider simultaneous quantitative analysis of a wide variety of pathogens, which could greatly increase the utility of wastewater surveillance. We developed a novel quantitative multi-pathogen surveillance approach (35 pathogen targets including bacteria, viruses, protozoa, and helminths) using TaqMan Array Cards (TAC) and applied the method on concentrated wastewater samples collected at four wastewater treatment plants in Atlanta, GA from February to October of 2020. From sewersheds serving approximately 2 million people, we detected a wide range of targets including many we expected to find in wastewater (e.g., enterotoxigenic E. coli and Giardia in 97% of 29 samples at stable concentrations) as well as unexpected targets including Strongyloides stercoralis (a human threadworm rarely observed in the USA). Other notable detections included SARS-CoV-2, but also several pathogen targets that are not commonly included in wastewater surveillance like Acanthamoeba spp., Balantidium coli, Entamoeba histolytica, astrovirus, norovirus, and sapovirus. Our data suggest broad utility in expanding the scope of enteric pathogen surveillance in wastewaters, with potential for application in a variety of settings where pathogen quantification in fecal waste streams can inform public health surveillance and selection of control measures to limit infections.
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Affiliation(s)
- Gouthami Rao
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Drew Capone
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, IN, USA
| | - Kevin Zhu
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Abigail Knoble
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yarrow Linden
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ryan Clark
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda Lai
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juhee Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ching-Hua Huang
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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18
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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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19
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Babler KM, Sharkey ME, Amirali A, Boone MM, Comerford S, Currall BB, Grills GS, Laine J, Mason CE, Reding B, Schürer S, Stevenson M, Vidović D, Williams SL, Solo-Gabriele HM. Expanding a Wastewater-Based Surveillance Methodology for DNA Isolation from a Workflow Optimized for SARS-CoV-2 RNA Quantification. J Biomol Tech 2023; 34:3fc1f5fe.dfa8d906. [PMID: 38268997 PMCID: PMC10805363 DOI: 10.7171/3fc1f5fe.dfa8d906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Wastewater-based surveillance (WBS) is a noninvasive, epidemiological strategy for assessing the spread of COVID-19 in communities. This strategy was based upon wastewater RNA measurements of the viral target, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The utility of WBS for assessing the spread of COVID-19 has motivated research to measure targets beyond SARS-CoV-2, including pathogens containing DNA. The objective of this study was to establish the necessary steps for isolating DNA from wastewater by modifying a long-standing RNA-specific extraction workflow optimized for SARS-CoV-2 detection. Modifications were made to the sample concentration process and included an evaluation of bead bashing prior to the extraction of either DNA or RNA. Results showed that bead bashing reduced detection of RNA from wastewater but improved recovery of DNA as assessed by quantitative polymerase chain reaction (qPCR). Bead bashing is therefore not recommended for the quantification of RNA viruses using qPCR. Whereas for Mycobacterium bacterial DNA isolation, bead bashing was necessary for improving qPCR quantification. Overall, we recommend 2 separate workflows, one for RNA viruses that does not include bead bashing and one for other microbes that use bead bashing for DNA isolation. The experimentation done here shows that current-standing WBS program methodologies optimized for SARS-CoV-2 need to be modified and reoptimized to allow for alternative pathogens to be readily detected and monitored, expanding its utility as a tool for public health assessment.
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Affiliation(s)
- Kristina M. Babler
- Department of ChemicalEnvironmental and Materials
EngineeringUniversity of MiamiCoral GablesFlorida33124USA
| | - Mark E. Sharkey
- Department of MedicineUniversity of Miami Miller School
of MedicineMiamiFlorida33136USA
| | - Ayaaz Amirali
- Department of ChemicalEnvironmental and Materials
EngineeringUniversity of MiamiCoral GablesFlorida33124USA
| | - Melinda M. Boone
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - Samuel Comerford
- Department of MedicineUniversity of Miami Miller School
of MedicineMiamiFlorida33136USA
| | - Benjamin B. Currall
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - George S. Grills
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - Jennifer Laine
- Environmental Health and SafetyUniversity of MiamiMiamiFlorida33136USA
| | - Christopher E. Mason
- Department of Physiology and BiophysicsWeill Cornell
MedicineNew YorkNew York10065USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud
Institute for Computational BiomedicineWeill Cornell MedicineNew
YorkNew York10065USA
- The WorldQuant Initiative for Quantitative PredictionWeill Cornell MedicineNew YorkNew YorkUSA 10065USA
| | - Brian Reding
- Environmental Health and SafetyUniversity of MiamiMiamiFlorida33136USA
| | - Stephan Schürer
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
- Department of Molecular and Cellular PharmacologyUniversity of Miami Miller School of MedicineMiamiFlorida33136USA
- Institute for Data Science & Computing, University of
MiamiCoral GablesFlorida33146USA
| | - Mario Stevenson
- Department of MedicineUniversity of Miami Miller School
of MedicineMiamiFlorida33136USA
| | - Dušica Vidović
- Department of Molecular and Cellular PharmacologyUniversity of Miami Miller School of MedicineMiamiFlorida33136USA
| | - Sion L. Williams
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - Helena M. Solo-Gabriele
- Department of ChemicalEnvironmental and Materials
EngineeringUniversity of MiamiCoral GablesFlorida33124USA
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20
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Acosta N, Dai X, Bautista MA, Waddell BJ, Lee J, Du K, McCalder J, Pradhan P, Papparis C, Lu X, Chekouo T, Krusina A, Southern D, Williamson T, Clark RG, Patterson RA, Westlund P, Meddings J, Ruecker N, Lammiman C, Duerr C, Achari G, Hrudey SE, Lee BE, Pang X, Frankowski K, Hubert CRJ, Parkins MD. Wastewater-based surveillance can be used to model COVID-19-associated workforce absenteeism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165172. [PMID: 37379934 PMCID: PMC10292917 DOI: 10.1016/j.scitotenv.2023.165172] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 06/21/2023] [Accepted: 06/25/2023] [Indexed: 06/30/2023]
Abstract
Wastewater-based surveillance (WBS) of infectious diseases is a powerful tool for understanding community COVID-19 disease burden and informing public health policy. The potential of WBS for understanding COVID-19's impact in non-healthcare settings has not been explored to the same degree. Here we examined how SARS-CoV-2 measured from municipal wastewater treatment plants (WWTPs) correlates with workforce absenteeism. SARS-CoV-2 RNA N1 and N2 were quantified three times per week by RT-qPCR in samples collected at three WWTPs servicing Calgary and surrounding areas, Canada (1.4 million residents) between June 2020 and March 2022. Wastewater trends were compared to workforce absenteeism using data from the largest employer in the city (>15,000 staff). Absences were classified as being COVID-19-related, COVID-19-confirmed, and unrelated to COVID-19. Poisson regression was performed to generate a prediction model for COVID-19 absenteeism based on wastewater data. SARS-CoV-2 RNA was detected in 95.5 % (85/89) of weeks assessed. During this period 6592 COVID-19-related absences (1896 confirmed) and 4524 unrelated absences COVID-19 cases were recorded. A generalized linear regression using a Poisson distribution was performed to predict COVID-19-confirmed absences out of the total number of absent employees using wastewater data as a leading indicator (P < 0.0001). The Poisson regression with wastewater as a one-week leading signal has an Akaike information criterion (AIC) of 858, compared to a null model (excluding wastewater predictor) with an AIC of 1895. The likelihood-ratio test comparing the model with wastewater signal with the null model shows statistical significance (P < 0.0001). We also assessed the variation of predictions when the regression model was applied to new data, with the predicted values and corresponding confidence intervals closely tracking actual absenteeism data. Wastewater-based surveillance has the potential to be used by employers to anticipate workforce requirements and optimize human resource allocation in response to trackable respiratory illnesses like COVID-19.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
| | - Xiaotian Dai
- Department of Mathematics and Statistics, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Maria A Bautista
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Barbara J Waddell
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
| | - Jangwoo Lee
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
| | - Kristine Du
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
| | - Janine McCalder
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada; Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Puja Pradhan
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada; Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Chloe Papparis
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada; Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Xuewen Lu
- Department of Mathematics and Statistics, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Thierry Chekouo
- Department of Mathematics and Statistics, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada; Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware St. S.E., Minneapolis, MN 55455, USA
| | - Alexander Krusina
- Department of Community Health Sciences, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada; Department of Medicine, University of Calgary and Alberta Health Services, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
| | - Danielle Southern
- Department of Community Health Sciences, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada; Department of Medicine, University of Calgary and Alberta Health Services, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
| | - Tyler Williamson
- Department of Community Health Sciences, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada; Department of Medicine, University of Calgary and Alberta Health Services, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada; O'Brien Institute for Public Health, University of Calgary, 3280 Hospital Dr NW, Calgary, Alberta T2N 4Z6, Canada
| | - Rhonda G Clark
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Raymond A Patterson
- Haskayne School of Business, University of Calgary, SH 250, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | | | - Jon Meddings
- Department of Medicine, University of Calgary and Alberta Health Services, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada
| | - Norma Ruecker
- Water Services, City of Calgary, 625 25 Ave SE, Calgary, Alberta T2G 4k8, Canada
| | - Christopher Lammiman
- Calgary Emergency Management Agency (CEMA), City of Calgary, 673 1 St NE, Calgary, Alberta T2E 6R2, Canada
| | - Coby Duerr
- Calgary Emergency Management Agency (CEMA), City of Calgary, 673 1 St NE, Calgary, Alberta T2E 6R2, Canada
| | - Gopal Achari
- Department of Civil Engineering, University of Calgary, 622 Collegiate Pl NW, T2N 4V8, Canada
| | - Steve E Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, 116 St. and 85 Ave, Edmonton, Alberta T6G 2R3, Canada; Analytical and Environmental Toxicology, University of Alberta, 116 St. and 85 Ave, Edmonton, Alberta T6G 2R3, Canada
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, 116 St. and 85 Ave, Edmonton, Alberta T6G 2R3, Canada; Women & Children's Health Research Institute, 116 St. and 85 Ave, Edmonton, Alberta T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, 116 St. and 85 Ave, Edmonton, Alberta T6G 2R3, Canada
| | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, 116 St. and 85 Ave, Edmonton, Alberta T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, 116 St. and 85 Ave, Edmonton, Alberta T6G 2R3, Canada; Alberta Precision Laboratories, Public Health Laboratory, Alberta Health Services, 116 St. and 85 Ave, Edmonton, Alberta T6G 2R3, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, 3131 210 Ave SE, Calgary, Alberta T0L 0X0, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada; Department of Medicine, University of Calgary and Alberta Health Services, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada; Snyder Institute for Chronic Diseases, University of Calgary and Alberta Health Services, 3330 Hospital Drive NW, Calgary, Alberta T2N 4N1, Canada.
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21
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Babler K, Sharkey M, Arenas S, Amirali A, Beaver C, Comerford S, Goodman K, Grills G, Holung M, Kobetz E, Laine J, Lamar W, Mason C, Pronty D, Reding B, Schürer S, Schaefer Solle N, Stevenson M, Vidović D, Solo-Gabriele H, Shukla B. Detection of the clinically persistent, pathogenic yeast spp. Candida auris from hospital and municipal wastewater in Miami-Dade County, Florida. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165459. [PMID: 37442462 PMCID: PMC10543605 DOI: 10.1016/j.scitotenv.2023.165459] [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: 04/22/2023] [Revised: 06/14/2023] [Accepted: 07/08/2023] [Indexed: 07/15/2023]
Abstract
The use of wastewater-based surveillance (WBS) for detecting pathogens within communities has been growing since the beginning of the COVID-19 pandemic with early efforts investigating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA in wastewater. Recent efforts have shed light on the utilization of WBS for alternative targets, such as fungal pathogens, like Candida auris, in efforts to expand the technology to assess non-viral targets. The objective of this study was to extend workflows developed for SARS-CoV-2 quantification to evaluate whether C. auris can be recovered from wastewater, inclusive of effluent from a wastewater treatment plant (WWTP) and from a hospital with known numbers of patients colonized with C. auris. Measurements of C. auris in wastewater focused on culture-based methods and quantitative PCR (qPCR). Results showed that C. auris can be cultured from wastewater and that levels detected by qPCR were higher in the hospital wastewater compared to the wastewater from the WWTP, suggesting either dilution or degradation of this pathogenic yeast at downstream collection points. The results from this study illustrate that WBS can extend beyond SARS-CoV-2 monitoring to evaluate additional non-viral pathogenic targets and demonstrates that C. auris isolated from wastewater is competent to replicate in vitro using fungal-specific culture media.
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Affiliation(s)
- Kristina Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Mark Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sebastian Arenas
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Cynthia Beaver
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Samuel Comerford
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Kenneth Goodman
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL, USA
| | - George Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michelle Holung
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Erin Kobetz
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Walter Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL 33136, USA
| | - Christopher Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Darryl Pronty
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Reding
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Stephan Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL, USA
| | - Natasha Schaefer Solle
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Dusica Vidović
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Helena Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Bhavarth Shukla
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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22
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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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23
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Sharkey ME, Babler KM, Shukla BS, Abelson SM, Alsuliman B, Amirali A, Comerford S, Grills GS, Kumar N, Laine J, Lee J, Lamar WE, Mason CE, Penso J, Reding BD, Schürer SC, Stevenson M, Vidović D, Solo-Gabriele HM. Monkeypox viral nucleic acids detected using both DNA and RNA extraction workflows. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 890:164289. [PMID: 37216988 PMCID: PMC10213602 DOI: 10.1016/j.scitotenv.2023.164289] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023]
Abstract
Molecular methods have been used to detect human pathogens in wastewater with sampling typically performed at wastewater treatment plants (WWTP) and upstream locations within the sewer system. A wastewater-based surveillance (WBS) program was established at the University of Miami (UM) in 2020, which included measurements of SARS-CoV-2 levels in wastewater from its hospital and within the regional WWTP. In addition to the development of a SARS-CoV-2 quantitative PCR (qPCR) assay, qPCR assays to detect other human pathogens of interest were also developed at UM. Here we report on the use of a modified set of reagents published by the CDC to detect nucleic acids of Monkeypox virus (MPXV) which emerged during May of 2022 to become a concern worldwide. Samples collected from the University hospital and from the regional WWTP were processed through DNA and RNA workflows and analyzed by qPCR to detect a segment of the MPXV CrmB gene. Results show positive detections of MPXV nucleic acids in the hospital and wastewater treatment plant wastewater which coincided with clinical cases in the community and mirrored the overall trend of nationwide MPXV cases reported to the CDC. We recommend the expansion of current WBS programs' methods to detect a broader range of pathogens of concern in wastewater and present evidence that viral RNA in human cells infected by a DNA virus can be detected in wastewater.
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Affiliation(s)
- Mark E Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kristina M Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA
| | - Bhavarth S Shukla
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Samantha M Abelson
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bader Alsuliman
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA
| | - Samuel Comerford
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Naresh Kumar
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL, USA
| | - Jisue Lee
- University of Miami Health System, Miami, FL, USA
| | - Walter E Lamar
- Facilities Safety & Compliance, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, USA
| | - Johnathon Penso
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Brian D Reding
- Environmental Health and Safety, University of Miami, Miami, FL, USA
| | - Stephan C Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL, USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Dušica Vidović
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA.
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24
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Zhan Q, Solo-Gabriele HM, Sharkey ME, Amirali A, Beaver CC, Boone MM, Comerford S, Cooper D, Cortizas EM, Cosculluela GA, Currall BB, Grills GS, Kobetz E, Kumar N, Laine J, Lamar WE, Lyu J, Mason CE, Reding BD, Roca MA, Schürer SC, Shukla BS, Solle NS, Suarez MM, Stevenson M, Tallon JJ, Thomas C, Vidović D, Williams SL, Yin X, Zarnegarnia Y, Babler KM. Correlative analysis of wastewater trends with clinical cases and hospitalizations through five dominant variant waves of COVID-19. ACS ES&T WATER 2023; 3:2849-2862. [PMID: 38487696 PMCID: PMC10936583 DOI: 10.1021/acsestwater.3c00032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Wastewater-based epidemiology (WBE) has been utilized to track community infections of Coronavirus Disease 2019 (COVID-19) by detecting RNA of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), within samples collected from wastewater. The correlations between community infections and wastewater measurements of the RNA can potentially change as SARS-CoV-2 evolves into new variations by mutating. This study analyzed SARS-CoV-2 RNA, and indicators of human waste in wastewater from two sewersheds of different scales (University of Miami (UM) campus and Miami-Dade County Central District wastewater treatment plant (CDWWTP)) during five internally defined COVID-19 variant dominant periods (Initial, Pre-Delta, Delta, Omicron and Post-Omicron wave). SARS-CoV-2 RNA quantities were compared against COVID-19 clinical cases and hospitalizations to evaluate correlations with wastewater SARS-CoV-2 RNA. Although correlations between documented clinical cases and hospitalizations were high, prevalence for a given wastewater SARS-CoV-2 level varied depending upon the variant analyzed. The correlative relationship was significantly steeper (more cases per level found in wastewater) for the Omicron-dominated period. For hospitalization, the relationships were steepest for the Initial wave, followed by the Delta wave with flatter slopes during all other waves. Overall results were interpreted in the context of SARS-CoV-2 virulence and vaccination rates among the community.
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Affiliation(s)
- Qingyu Zhan
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Helena Maria Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Mark E. Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Cynthia C. Beaver
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Melinda M. Boone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Samuel Comerford
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | | | - Elena M. Cortizas
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Gabriella A. Cosculluela
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Benjamin B. Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Erin Kobetz
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Naresh Kumar
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL 33136 USA
| | - Walter E. Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL 33136 USA
| | - Jiangnan Lyu
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021 USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Brian D. Reding
- Environmental Health and Safety, University of Miami, Miami, FL 33136 USA
| | - Matthew A. Roca
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Stephan C. Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL 33136 USA
- Institute for Data Science & Computing, University of Miami, Coral Gables, FL 33146 USA
| | - Bhavarth S. Shukla
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Natasha Schaefer Solle
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Maritza M. Suarez
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Mario Stevenson
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - John J. Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL 33146 USA
| | - Collette Thomas
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Dušica Vidović
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL 33136 USA
| | - Sion L. Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Xue Yin
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Yalda Zarnegarnia
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Kristina Marie Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
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25
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Li X, Liu H, Gao L, Sherchan SP, Zhou T, Khan SJ, van Loosdrecht MCM, Wang Q. Wastewater-based epidemiology predicts COVID-19-induced weekly new hospital admissions in over 150 USA counties. Nat Commun 2023; 14:4548. [PMID: 37507407 PMCID: PMC10382499 DOI: 10.1038/s41467-023-40305-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Although the coronavirus disease (COVID-19) emergency status is easing, the COVID-19 pandemic continues to affect healthcare systems globally. It is crucial to have a reliable and population-wide prediction tool for estimating COVID-19-induced hospital admissions. We evaluated the feasibility of using wastewater-based epidemiology (WBE) to predict COVID-19-induced weekly new hospitalizations in 159 counties across 45 states in the United States of America (USA), covering a population of nearly 100 million. Using county-level weekly wastewater surveillance data (over 20 months), WBE-based models were established through the random forest algorithm. WBE-based models accurately predicted the county-level weekly new admissions, allowing a preparation window of 1-4 weeks. In real applications, periodically updated WBE-based models showed good accuracy and transferability, with mean absolute error within 4-6 patients/100k population for upcoming weekly new hospitalization numbers. Our study demonstrated the potential of using WBE as an effective method to provide early warnings for healthcare systems.
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Affiliation(s)
- Xuan Li
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Huan Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Li Gao
- South East Water, 101 Wells Street, Frankston, VIC, 3199, Australia
| | - Samendra P Sherchan
- Department of Biology, Morgan State University, Baltimore, MD, USA
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Ting Zhou
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, the Netherlands
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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26
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Abelson S, Penso J, Alsuliman B, Babler K, Sharkey M, Stevenson M, Grills G, Mason CE, Solo-Gabriele H, Kumar N. COVID-19 Case and Mortality Surveillance using Daily SARS-CoV-2 in Wastewater Samples adjusting for Meteorological Conditions and Sample pH. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.12.23292570. [PMID: 37502918 PMCID: PMC10370245 DOI: 10.1101/2023.07.12.23292570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background Wastewater monitoring is increasingly used for community surveillance of infectious diseases, especially after the COVID-19 pandemic as the genomic footprints of pathogens shed by infected individuals can be traced in the environment. However, detection and concentration of pathogens in the environmental samples and their efficacy in predicting infectious diseases can be influenced by meteorological conditions and quality of samples. Objectives This research examines whether meteorological conditions and sample pH affect SARS-CoV-2 concentrations in wastewater samples, and whether the association of SARS-CoV-2 with COVID-19 cases and mortality improves when adjusted for meteorological conditions and sample pH value in Miami-Dade County, FL. Methods Daily wastewater samples were collected from Miami-Dade Wastewater Treatment Plant in Key Biscayne, Florida from August 2021 to August 2022. The samples were analyzed for pH and spiked with OC43. RNA was extracted from the concentrated wastewater sample and SARS-CoV-2 was quantified using qPCR. COVID-19 and mortality data were acquired from the Centers for Disease Control and Prevention (CDC) and meteorological data from the National Climatic Data Center. COVID-19 case and mortality rates were modelled with respect to time-lagged wastewater SARS-CoV-2 adjusting for meteorological conditions, and sample pH value and OC43 recovery. Results Temperature, dew point, pH values and OC43 recovery showed significant associations with wastewater SARS-CoV-2. Time-lagged wastewater SARS-CoV-2 showed significant associations with COVID-19 case and mortality incidence rates. This association improved when wastewater SARS-CoV-2 levels were adjusted for (or instrumented on) meteorological conditions, OC43 recovery, and sample pH. A 0.47% change in COVID-19 case incidence rate was associated with 1% change in wastewater SARS-CoV-2 (β ~ 0.47; 95% CI = 0.29 - 0.64; p < 0.001). A 0.12 % change in COVID-19 mortality rate was associated with 1 % change in SARS-CoV-2 in wastewater 44 days prior. A 0.07% decline in COVID-19 mortality rate was associated with a unit increase in ambient temperature 28 days prior. Discussion Time lagged wastewater SARS-CoV-2 (and its adjustment for sample pH and RNA recovery) and meteorological conditions can be used for the surveillance of COVID-19 case and mortality. These findings can be extrapolated to improve the surveillance of other infectious diseases by proactive measurements of infectious agent(s) in the wastewater samples, adjusting for meteorological conditions and sample pH value.
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Affiliation(s)
- Samantha Abelson
- Department of Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Johnathon Penso
- Department of Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Bader Alsuliman
- Department of Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Kristina Babler
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, Florida
| | - Mark Sharkey
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, US
| | - Mario Stevenson
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, US
| | - George Grills
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, US
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University
| | - Helena Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, Florida
| | - Naresh Kumar
- Department of Public Health, University of Miami Miller School of Medicine, Miami, Florida
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27
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Liu P, Guo L, Cavallo M, Cantrell C, Hilton SP, Nguyen A, Long A, Dunbar J, Barbero R, Barclay R, Sablon O, Wolfe M, Lepene B, Moe C. Comparison of Nanotrap ® Microbiome A Particles, membrane filtration, and skim milk workflows for SARS-CoV-2 concentration in wastewater. Front Microbiol 2023; 14:1215311. [PMID: 37476666 PMCID: PMC10354513 DOI: 10.3389/fmicb.2023.1215311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/12/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA monitoring in wastewater has become an important tool for Coronavirus Disease 2019 (COVID-19) surveillance. Grab (quantitative) and passive samples (qualitative) are two distinct wastewater sampling methods. Although many viral concentration methods such as the usage of membrane filtration and skim milk are reported, these methods generally require large volumes of wastewater, expensive lab equipment, and laborious processes. Methods The objectives of this study were to compare two workflows (Nanotrap® Microbiome A Particles coupled with MagMax kit and membrane filtration workflows coupled with RNeasy kit) for SARS-CoV-2 recovery in grab samples and two workflows (Nanotrap® Microbiome A Particles and skim milk workflows coupled with MagMax kit) for SARS-CoV-2 recovery in Moore swab samples. The Nanotrap particle workflow was initially evaluated with and without the addition of the enhancement reagent 1 (ER1) in 10 mL wastewater. RT-qPCR targeting the nucleocapsid protein was used for detecting SARS-CoV-2 RNA. Results Adding ER1 to wastewater prior to viral concentration significantly improved viral concentration results (P < 0.0001) in 10 mL grab and swab samples processed by automated or manual Nanotrap workflows. SARS-CoV-2 concentrations in 10 mL grab and Moore swab samples with ER1 processed by the automated workflow as a whole showed significantly higher (P < 0.001) results than 150 mL grab samples using the membrane filtration workflow and 250 mL swab samples using the skim milk workflow, respectively. Spiking known genome copies (GC) of inactivated SARS-CoV-2 into 10 mL wastewater indicated that the limit of detection of the automated Nanotrap workflow was ~11.5 GC/mL using the RT-qPCR and 115 GC/mL using the digital PCR methods. Discussion These results suggest that Nanotrap workflows could substitute the traditional membrane filtration and skim milk workflows for viral concentration without compromising the assay sensitivity. The manual workflow can be used in resource-limited areas, and the automated workflow is appropriate for large-scale COVID-19 wastewater-based surveillance.
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Affiliation(s)
- Pengbo Liu
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Lizheng Guo
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Matthew Cavallo
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Caleb Cantrell
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
- Ceres Nanosciences, Inc., Manassas, VA, United States
| | - Stephen Patrick Hilton
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Anh Nguyen
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Audrey Long
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Jillian Dunbar
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | | | | | - Orlando Sablon
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Marlene Wolfe
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Ben Lepene
- Ceres Nanosciences, Inc., Manassas, VA, United States
| | - Christine Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
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28
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Wani H, Menon S, Desai D, D’Souza N, Bhathena Z, Desai N, Rose JB, Shrivastava S. Wastewater-Based Epidemiology of SARS-CoV-2: Assessing Prevalence and Correlation with Clinical Cases. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:131-143. [PMID: 37133676 PMCID: PMC10155169 DOI: 10.1007/s12560-023-09555-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/18/2023] [Indexed: 05/04/2023]
Abstract
Wastewater-based epidemiology has been recognized as a tool to monitor the progress of COVID-19 pandemic worldwide. The study presented herein aimed at quantitating the SARS-CoV-2 RNA in the wastewaters, predicting the number of infected individuals in the catchment areas, and correlating it with the clinically reported COVID-19 cases. Wastewater samples (n = 162) from different treatment stages were collected from three wastewater treatment plants (WWTPs) from Mumbai city during the 2nd surge of COVID-19 (April 2021 to June 2021). SARS-CoV-2 causing COVID-19, was detected in 76.2% and 4.8% of raw and secondary treated (n = 63 each) wastewater samples respectively while all tertiary treated samples (n = 36) were negative. The quantity of SARS-CoV-2 RNA determined as gene copies/100 mL varied among all the three WWTPs under study. The gene copy numbers thus obtained were further used to estimate the number of infected individuals within the population served by these WWTPs using two published methods. A positive correlation (p < 0.05) was observed between the estimated number of infected individuals and clinically confirmed COVID-19 cases reported during the sampling period in two WWTPs. Predicted infected individuals calculated in this study were 100 times higher than the reported COVID-19 cases in all the WWTPs assessed. The study findings demonstrated that the present wastewater treatment technologies at the three WWTPs studied were adequate to remove the virus. However, SARS-CoV-2 genome surveillance with emphasis on monitoring its variants should be implemented as a routine practice to prepare for any future surge in infections.
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Affiliation(s)
- Hima Wani
- Bhavan’s Research Center, Bhavan’s College Campus, Andheri West, Mumbai, Maharashtra 400058 India
| | - Smita Menon
- Bhavan’s Research Center, Bhavan’s College Campus, Andheri West, Mumbai, Maharashtra 400058 India
- Department of Microbiology, Bhavan’s College, Andheri West, Mumbai, Maharashtra 400058 India
| | - Dipen Desai
- Bhavan’s Research Center, Bhavan’s College Campus, Andheri West, Mumbai, Maharashtra 400058 India
| | - Nishita D’Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824 USA
| | - Zarine Bhathena
- Department of Microbiology, Bhavan’s College, Andheri West, Mumbai, Maharashtra 400058 India
| | - Nishith Desai
- Bhavan’s Research Center, Bhavan’s College Campus, Andheri West, Mumbai, Maharashtra 400058 India
| | - Joan B. Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824 USA
| | - Sandhya Shrivastava
- Bhavan’s Research Center, Bhavan’s College Campus, Andheri West, Mumbai, Maharashtra 400058 India
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29
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Tierney BT, Foox J, Ryon KA, Butler D, Damle N, Young BG, Mozsary C, Babler KM, Yin X, Carattini Y, Andrews D, Solle NS, Kumar N, Shukla B, Vidovic D, Currall B, Williams SL, Schürer SC, Stevenson M, Amirali A, Beaver CC, Kobetz E, Boone MM, Reding B, Laine J, Comerford S, Lamar WE, Tallon JJ, Hirschberg JW, Proszynski J, Sharkey ME, Church GM, Grills GS, Solo-Gabriele HM, Mason CE. Geospatially-resolved public-health surveillance via wastewater sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.31.23290781. [PMID: 37398062 PMCID: PMC10312847 DOI: 10.1101/2023.05.31.23290781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Wastewater, which contains everything from pathogens to pollutants, is a geospatially-and temporally-linked microbial fingerprint of a given population. As a result, it can be leveraged for monitoring multiple dimensions of public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (n=1,419 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County from 2020-2022. First, we used targeted amplicon sequencing (n=966) to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with clinical caseloads from University students (N = 1,503) and Miami-Dade County hospital patients (N = 3,939 patients), as well as an 8-day earlier detection of the Delta variant in wastewater vs. in patients. Additionally, in 453 metatranscriptomic samples, we demonstrate that different wastewater sampling locations have clinically and public-health-relevant microbiota that vary as a function of the size of the human population they represent. Through assembly, alignment-based, and phylogenetic approaches, we also detect multiple clinically important viruses (e.g., norovirus ) and describe geospatial and temporal variation in microbial functional genes that indicate the presence of pollutants. Moreover, we found distinct profiles of antimicrobial resistance (AMR) genes and virulence factors across campus buildings, dorms, and hospitals, with hospital wastewater containing a significant increase in AMR abundance. Overall, this effort lays the groundwork for systematic characterization of wastewater to improve public health decision making and a broad platform to detect emerging pathogens.
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30
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Rainey AL, Liang S, Bisesi JH, Sabo-Attwood T, Maurelli AT. A multistate assessment of population normalization factors for wastewater-based epidemiology of COVID-19. PLoS One 2023; 18:e0284370. [PMID: 37043469 PMCID: PMC10096268 DOI: 10.1371/journal.pone.0284370] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/29/2023] [Indexed: 04/13/2023] Open
Abstract
Wastewater-based epidemiology (WBE) has become a valuable tool for monitoring SARS-CoV-2 infection trends throughout the COVID-19 pandemic. Population biomarkers that measure the relative human fecal contribution to normalize SARS-CoV-2 wastewater concentrations are needed for improved analysis and interpretation of community infection trends. The Centers for Disease Control and Prevention National Wastewater Surveillance System (CDC NWSS) recommends using the wastewater flow rate or human fecal indicators as population normalization factors. However, there is no consensus on which normalization factor performs best. In this study, we provided the first multistate assessment of the effects of flow rate and human fecal indicators (crAssphage, F+ Coliphage, and PMMoV) on the correlation of SARS-CoV-2 wastewater concentrations and COVID-19 cases using the CDC NWSS dataset of 182 communities across six U.S. states. Flow normalized SARS-CoV-2 wastewater concentrations produced the strongest correlation with COVID-19 cases. The correlation from the three human fecal indicators were significantly lower than flow rate. Additionally, using reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) significantly improved correlation values over samples that were analyzed with real-time reverse transcription quantitative polymerase chain reaction (rRT-qPCR). Our assessment shows that utilizing flow normalization with RT-ddPCR generate the strongest correlation between SARS-CoV-2 wastewater concentrations and COVID-19 cases.
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Affiliation(s)
- Andrew L. Rainey
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Song Liang
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Joseph H. Bisesi
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - Tara Sabo-Attwood
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - Anthony T. Maurelli
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
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31
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Babler KM, Sharkey ME, Abelson S, Amirali A, Benitez A, Cosculluela GA, Grills GS, Kumar N, Laine J, Lamar W, Lamm ED, Lyu J, Mason CE, McCabe PM, Raghavender J, Reding BD, Roca MA, Schürer SC, Stevenson M, Szeto A, Tallon JJ, Vidović D, Zarnegarnia Y, Solo-Gabriele HM. Degradation rates influence the ability of composite samples to represent 24-hourly means of SARS-CoV-2 and other microbiological target measures in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161423. [PMID: 36623667 PMCID: PMC9817413 DOI: 10.1016/j.scitotenv.2023.161423] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/25/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
The utility of using severe-acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA for assessing the prevalence of COVID-19 within communities begins with the design of the sample collection program. The objective of this study was to assess the utility of 24-hour composites as representative samples for measuring multiple microbiological targets in wastewater, and whether normalization of SARS-CoV-2 by endogenous targets can be used to decrease hour to hour variability at different watershed scales. Two sets of experiments were conducted, in tandem with the same wastewater, with samples collected at the building, cluster, and community sewershed scales. The first set of experiments focused on evaluating degradation of microbiological targets: SARS-CoV-2, Simian Immunodeficiency Virus (SIV) - a surrogate spiked into the wastewater, plus human waste indicators of Pepper Mild Mottle Virus (PMMoV), Beta-2 microglobulin (B2M), and fecal coliform bacteria (FC). The second focused on the variability of these targets from samples, collected each hour on the hour. Results show that SARS-CoV-2, PMMoV, and B2M were relatively stable, with minimal degradation over 24-h. SIV, which was spiked-in prior to analysis, degraded significantly and FC increased significantly over the course of 24 h, emphasizing the possibility for decay and growth within wastewater. Hour-to-hour variability of the source wastewater was large between each hour of sampling relative to the variability of the SARS-CoV-2 levels calculated between sewershed scales; thus, differences in SARS-CoV-2 hourly variability were not statistically significant between sewershed scales. Results further provided that the quantified representativeness of 24-h composite samples (i.e., statistical equivalency compared against hourly collected grabs) was dependent upon the molecular target measured. Overall, improvements made by normalization were minimal within this study. Degradation and multiplication for other targets should be evaluated when deciding upon whether to collect composite or grab samples in future studies.
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Affiliation(s)
- Kristina M Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Mark E Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Samantha Abelson
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Aymara Benitez
- Miami-Dade Water and Sewer Department, Miami, FL 33149, USA
| | - Gabriella A Cosculluela
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Naresh Kumar
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Walter Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL 33136, USA
| | - Erik D Lamm
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Jiangnan Lyu
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Philip M McCabe
- Department of Psychology, University of Miami, Coral Gables, FL 33146, USA; Department of Biomedical Engineering, University of Miami, Coral Gables, FL 33146, USA
| | | | - Brian D Reding
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Matthew A Roca
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Stephan C Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL, USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Angela Szeto
- Department of Psychology, University of Miami, Coral Gables, FL 33146, USA
| | - John J Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL 33146, USA
| | - Dusica Vidović
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yalda Zarnegarnia
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA.
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32
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Saingam P, Li B, Nguyen Quoc B, Jain T, Bryan A, Winkler MKH. Wastewater surveillance of SARS-CoV-2 at intra-city level demonstrated high resolution in tracking COVID-19 and calibration using chemical indicators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161467. [PMID: 36626989 PMCID: PMC9825140 DOI: 10.1016/j.scitotenv.2023.161467] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/17/2022] [Accepted: 01/04/2023] [Indexed: 05/12/2023]
Abstract
Wastewater-based epidemiology has proven to be a supportive tool to better comprehend the dynamics of the COVID-19 pandemic. As the disease moves into endemic stage, the surveillance at wastewater sub-catchments such as pump station and manholes is providing a novel mechanism to examine the reemergence and to take measures that can prevent the spread. However, there is still a lack of understanding when it comes to wastewater-based epidemiology implementation at the smaller intra-city level for better granularity in data, and dilution effect of rain precipitation at pump stations. For this study, grab samples were collected from six areas of Seattle between March-October 2021. These sampling sites comprised five manholes and one pump station with population ranging from 2580 to 39,502 per manhole/pump station. The wastewater samples were analyzed for SARS-CoV-2 RNA concentrations, and we also obtained the daily COVID-19 cases (from individual clinical testing) for each corresponding sewershed, which ranged from 1 to 12 and the daily incidence varied between 3 and 64 per 100,000 of population. Rain precipitation lowered viral RNA levels and sensitivity of viral detection but wastewater total ammonia (NH4+-N) and phosphate (PO43--P) were shown as potential chemical indicators to calibrate/level out the dilution effect. These chemicals showed the potential in improving the wastewater surveillance capacity of COVID-19.
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Affiliation(s)
- Prakit Saingam
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA.
| | - Bo Li
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Bao Nguyen Quoc
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Tanisha Jain
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Andrew Bryan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Mari K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA.
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33
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Sangsanont J, Rattanakul S, Makkaew P, Precha N, Rukthanapitak P, Sresung M, Siri Y, Kitajima M, Takeda T, Haramoto E, Puenpa J, Wanlapakorn N, Poovorawan Y, Mongkolsuk S, Sirikanchana K. Wastewater monitoring in tourist cities as potential sentinel sites for near real-time dynamics of imported SARS-CoV-2 variants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160317. [PMID: 36436629 PMCID: PMC9691270 DOI: 10.1016/j.scitotenv.2022.160317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/29/2022] [Accepted: 11/16/2022] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) complements the clinical surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants' distribution in populations. Many developed nations have established national and regional WBE systems; however, governance and budget constraints could be obstacles for low- and middle-income countries. An urgent need thus exists to identify hotspots to serve as sentinel sites for WBE. We hypothesized that representative wastewater treatment plants (WWTPs) in two international gateway cities, Bangkok and Phuket, Thailand, could be sentineled for SARS-CoV-2 and its variants to reflect the clinical distribution patterns at city level and serve as early indicators of new variants entering the country. Municipal wastewater samples (n = 132) were collected from eight representative municipal WWTPs in Bangkok and Phuket during 19 sampling events from October 2021 to March 2022, which were tested by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) using the US CDC N1 and N2 multiplex and variant (Alpha, Delta, and Omicron BA.1 and BA.2) singleplex assays. The variant detection ratios from Bangkok and Phuket followed similar trends to the national clinical testing data, and each variant's viral loads agreed with the daily new cases (3-d moving average). Omicron BA.1 was detected in Phuket wastewater prior to Bangkok, possibly due to Phuket's WWTPs serving tourist communities. We found that the Omicron BA.1 and BA.2 viral loads predominantly drove the SARS-CoV-2 resurgence. We also noted a shifting pattern in the Bangkok WBE from a 22-d early warning in early 2021 to a near real-time pattern in late 2021. The potential application of tourist hotspots for WBE to indicate the arrival of new variants and re-emerging or unprecedented infectious agents could support tourism-dependent economies by complementing the reduced clinical regulations while maintaining public health protection via wastewater surveillance.
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Affiliation(s)
- Jatuwat Sangsanont
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Water Science and Technology for Sustainable Environmental Research Group, Chulalongkorn University, Bangkok 10330, Thailand
| | - Surapong Rattanakul
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Prasert Makkaew
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Nopadol Precha
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Pratchaya Rukthanapitak
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Montakarn Sresung
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Yadpiroon Siri
- Environmental, Safety Technology and Health Program, School of Public Health, Walailak University, Thaiburi, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Hokkaido 060-8628, Japan
| | - Tomoko Takeda
- Department of Earth and Planetary Science, The University of Tokyo, 113-0033, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi 400-8511, Japan
| | - Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand.
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34
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Gagliano E, Biondi D, Roccaro P. Wastewater-based epidemiology approach: The learning lessons from COVID-19 pandemic and the development of novel guidelines for future pandemics. CHEMOSPHERE 2023; 313:137361. [PMID: 36427570 PMCID: PMC9678975 DOI: 10.1016/j.chemosphere.2022.137361] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) provides a comprehensive real-time framework of population attitude and health status. This approach is attracting the interest of medical community and health authorities to monitor the prevalence of a virus (such as the severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) among a community. Indeed, WBE is currently fine-tuning as environmental surveillance tool for coronavirus disease 2019 (COVID-19) pandemic. After a bibliometric analysis conducted to discover the research trends in WBE field, this work aimed to side-by-side compare the conventional method based on clinical testing with WBE approach. Furthermore, novel guidelines were developed to apply the WBE approach to a pandemic. The growing interest on WBE approach for COVID-19 pandemic is demonstrated by looking at the sharp increase in scientific papers published in the last years and at the ongoing studies on viral quantification methods and analytical procedures. The side-by-side comparison highlighted the ability of WBE to identify the hot-spot areas faster than the conventional approach, reducing the costs (e.g., rational use of available resources) and the gatherings at medical centers. Contrary to clinical testing, WBE has the surveillance capacity for preventing the virus resurgence, including asymptomatic contribution, and ensuring the preservation of medical staff health by avoiding the exposure to the virus infection during clinical testing. As extensively reported, the time in collecting epidemiological data is crucial for establishing the prevention and mitigation measures that are essential for curbing a pandemic. The developed guidelines can help to build a WBE system useful to control any future pandemic.
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Affiliation(s)
- Erica Gagliano
- Department of Civil Engineering and Architecture, University of Catania, Catania, Italy; Department of Civil, Chemical and Environmental Engineering, University of Genoa, Genoa, Italy
| | - Deborah Biondi
- Department of Civil Engineering and Architecture, University of Catania, Catania, Italy
| | - Paolo Roccaro
- Department of Civil Engineering and Architecture, University of Catania, Catania, Italy.
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35
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Solo-Gabriele HM, Kumar S, Abelson S, Penso J, Contreras J, Babler KM, Sharkey ME, Mantero AMA, Lamar WE, Tallon JJ, Kobetz E, Solle NS, Shukla BS, Kenney RJ, Mason CE, Schürer SC, Vidovic D, Williams SL, Grills GS, Jayaweera DT, Mirsaeidi M, Kumar N. Predicting COVID-19 cases using SARS-CoV-2 RNA in air, surface swab and wastewater samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159188. [PMID: 36202365 PMCID: PMC9529341 DOI: 10.1016/j.scitotenv.2022.159188] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 05/08/2023]
Abstract
Genomic footprints of pathogens shed by infected individuals can be traced in environmental samples, which can serve as a noninvasive method of infectious disease surveillance. The research evaluates the efficacy of environmental monitoring of SARS-CoV-2 RNA in air, surface swabs and wastewater to predict COVID-19 cases. Using a prospective experimental design, air, surface swabs, and wastewater samples were collected from a college dormitory housing roughly 500 students from March to May 2021 at the University of Miami, Coral Gables, FL. Students were randomly screened for COVID-19 during the study period. SARS-CoV-2 concentration in environmental samples was quantified using Volcano 2nd Generation-qPCR. Descriptive analyses were conducted to examine the associations between time-lagged SARS-CoV-2 in environmental samples and COVID-19 cases. SARS-CoV-2 was detected in air, surface swab and wastewater samples on 52 (63.4 %), 40 (50.0 %) and 57 (68.6 %) days, respectively. On 19 (24 %) of 78 days SARS-CoV-2 was detected in all three sample types. COVID-19 cases were reported on 11 days during the study period and SARS-CoV-2 was also detected two days before the case diagnosis on all 11 (100 %), 9 (81.8 %) and 8 (72.7 %) days in air, surface swab and wastewater samples, respectively. SARS-CoV-2 detection in environmental samples was an indicator of the presence of local COVID-19 cases and a 3-day lead indicator for a potential outbreak at the dormitory building scale. Proactive environmental surveillance of SARS-CoV-2 or other pathogens in multiple environmental media has potential to guide targeted measures to contain and/or mitigate infectious disease outbreaks within communities.
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Affiliation(s)
- Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, FL, United States of America
| | - Shelja Kumar
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America
| | - Samantha Abelson
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America
| | - Johnathon Penso
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America
| | - Julio Contreras
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America
| | - Kristina M Babler
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, FL, United States of America
| | - Mark E Sharkey
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Alejandro M A Mantero
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America
| | - Walter E Lamar
- Facilities Safety & Compliance, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - John J Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL, United States of America
| | - Erin Kobetz
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States of America; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Natasha Schaefer Solle
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States of America; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Bhavarth S Shukla
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Richard J Kenney
- Department of Housing & Residential Life, University of Miami, Coral Gables, FL, United States of America
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, United States of America
| | - Stephan C Schürer
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America; Institute for Data Science & Computing, University of Miami, Coral Gables, FL, United States of America; Department of Molecular & Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Dusica Vidovic
- Department of Molecular & Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Sion L Williams
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - George S Grills
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Dushyantha T Jayaweera
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Jacksonville, FL, United States of America
| | - Naresh Kumar
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, United States of America.
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Maal-Bared R, Qiu Y, Li Q, Gao T, Hrudey SE, Bhavanam S, Ruecker NJ, Ellehoj E, Lee BE, Pang X. Does normalization of SARS-CoV-2 concentrations by Pepper Mild Mottle Virus improve correlations and lead time between wastewater surveillance and clinical data in Alberta (Canada): comparing twelve SARS-CoV-2 normalization approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158964. [PMID: 36167131 PMCID: PMC9508694 DOI: 10.1016/j.scitotenv.2022.158964] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 05/02/2023]
Abstract
Wastewater-based surveillance (WBS) data normalization is an analyte measurement correction that addresses variations resulting from dilution of fecal discharge by non-sanitary sewage, stormwater or groundwater infiltration. No consensus exists on what WBS normalization parameters result in the strongest correlations and lead time between SARS-CoV-2 WBS data and COVID-19 cases. This study compared flow, population size and biomarker normalization impacts on the correlations and lead times for ten communities in twelve sewersheds in Alberta (Canada) between September 2020 and October 2021 (n = 1024) to determine if normalization by Pepper Mild Mottle Virus (PMMoV) provides any advantages compared to other normalization parameters (e.g., flow, reported and dynamic population sizes, BOD, TSS, NH3, TP). PMMoV concentrations (GC/mL) corresponded with plant influent flows and were highest in the urban centres. SARS-CoV-2 target genes E, N1 and N2 were all negatively associated with wastewater influent pH, while PMMoV was positively associated with temperature. Pooled data analysis showed that normalization increased ρ-values by almost 0.1 and was highest for ammonia, TKN and TP followed by PMMoV. Normalization by other parameters weakened associations. None of the differences were statistically significant. Site-specific correlations showed that normalization of SARS-CoV-2 data by PMMoV only improved correlations significantly in two of the twelve systems; neither were large sewersheds or combined sewer systems. In five systems, normalization by traditional wastewater strength parameters and dynamic population estimates improved correlations. Lead time ranged between 1 and 4 days in both pooled and site-specific comparisons. We recommend that WBS researchers and health departments: a) Investigate WWTP influent properties (e.g., pH) in the WBS planning phase and use at least two parallel approaches for normalization only if shown to provide value; b) Explore normalization by wastewater strength parameters and dynamic population size estimates further; and c) Evaluate purchasing an influent flow meter in small communities to support long-term WBS efforts and WWTP management.
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Affiliation(s)
- Rasha Maal-Bared
- Quality Assurance and Environment, EPCOR Water, Edmonton, Alberta, Canada.
| | - Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Qiaozhi Li
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Tiejun Gao
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Steve E Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sudha Bhavanam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Norma J Ruecker
- Water Quality Services, City of Calgary, Calgary, Alberta, Canada
| | - Erik Ellehoj
- Ellehoj Redmond Consulting, Edmonton, Alberta, Canada
| | - Bonita E Lee
- Department of Paediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, Alberta, Canada
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37
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Armas F, Chandra F, Lee WL, Gu X, Chen H, Xiao A, Leifels M, Wuertz S, Alm EJ, Thompson J. Contextualizing Wastewater-Based surveillance in the COVID-19 vaccination era. ENVIRONMENT INTERNATIONAL 2023; 171:107718. [PMID: 36584425 PMCID: PMC9783150 DOI: 10.1016/j.envint.2022.107718] [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: 03/31/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2 wastewater-based surveillance (WBS) offers a tool for cost-effective oversight of a population's infections. In the past two years, WBS has proven to be crucial for managing the pandemic across different geographical regions. However, the changing context of the pandemic due to high levels of COVID-19 vaccination warrants a closer examination of its implication towards SARS-CoV-2 WBS. Two main questions were raised: 1) Does vaccination cause shedding of viral signatures without infection? 2) Does vaccination affect the relationship between wastewater and clinical data? To answer, we review historical reports of shedding from viral vaccines in use prior to the COVID-19 pandemic including for polio, rotavirus, influenza and measles infection and provide a perspective on the implications of different COVID-19 vaccination strategies with regard to the potential shedding of viral signatures into the sewershed. Additionally, we reviewed studies that looked into the relationship between wastewater and clinical data and how vaccination campaigns could have affected the relationship. Finally, analyzing wastewater and clinical data from the Netherlands, we observed changes in the relationship concomitant with increasing vaccination coverage and switches in dominant variants of concern. First, that no vaccine-derived shedding is expected from the current commercial pipeline of COVID-19 vaccines that may confound interpretation of WBS data. Secondly, that breakthrough infections from vaccinated individuals contribute significantly to wastewater signals and must be interpreted in light of the changing dynamics of shedding from new variants of concern.
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Affiliation(s)
- Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore.
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38
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Oh C, Zhou A, O'Brien K, Jamal Y, Wennerdahl H, Schmidt AR, Shisler JL, Jutla A, Schmidt AR, Keefer L, Brown WM, Nguyen TH. Application of neighborhood-scale wastewater-based epidemiology in low COVID-19 incidence situations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158448. [PMID: 36063927 PMCID: PMC9436825 DOI: 10.1016/j.scitotenv.2022.158448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/08/2022] [Accepted: 08/28/2022] [Indexed: 05/17/2023]
Abstract
Wastewater-based epidemiology (WBE), an emerging approach for community-wide COVID-19 surveillance, was primarily characterized at large sewersheds such as wastewater treatment plants serving a large population. Although informed public health measures can be better implemented for a small population, WBE for neighborhood-scale sewersheds is less studied and not fully understood. This study applied WBE to seven neighborhood-scale sewersheds (average population of 1471) from January to November 2021. Community testing data showed an average of 0.004 % incidence rate in these sewersheds (97 % of monitoring periods reported two or fewer daily infections). In 92 % of sewage samples, SARS-CoV-2 N gene fragments were below the limit of quantification. We statistically determined 10-2.6 as the threshold of the SARS-CoV-2 N gene concentration normalized to pepper mild mottle virus (N/PMMOV) to alert high COVID-19 incidence rate in the studied sewershed. This threshold of N/PMMOV identified neighborhood-scale outbreaks (COVID-19 incidence rate higher than 0.2 %) with 82 % sensitivity and 51 % specificity. Importantly, neighborhood-scale WBE can discern local outbreaks that would not otherwise be identified by city-scale WBE. Our findings suggest that neighborhood-scale WBE is an effective community-wide disease surveillance tool when COVID-19 incidence is maintained at a low level.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States.
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States
| | - Kate O'Brien
- School of Integrative Biology, University of Illinois Urbana-Champaign, United States
| | - Yusuf Jamal
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, United States
| | - Hayden Wennerdahl
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, United States
| | - Arthur R Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States
| | - Joanna L Shisler
- Department of Microbiology, University of Illinois Urbana-Champaign, United States
| | - Antarpreet Jutla
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, United States
| | - Arthur R Schmidt
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States
| | - Laura Keefer
- Illinois State Water Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, United States
| | - William M Brown
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, United States
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States; Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
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39
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Mitranescu A, Uchaikina A, Kau AS, Stange C, Ho J, Tiehm A, Wurzbacher C, Drewes JE. Wastewater-Based Epidemiology for SARS-CoV-2 Biomarkers: Evaluation of Normalization Methods in Small and Large Communities in Southern Germany. ACS ES&T WATER 2022; 2:2460-2470. [PMID: 37552738 PMCID: PMC9578648 DOI: 10.1021/acsestwater.2c00306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/21/2022] [Accepted: 09/27/2022] [Indexed: 06/18/2023]
Abstract
In the context of the COVID-19 pandemic, wastewater-based epidemiology (WBE) emerged as a useful tool to account for the prevalence of SARS-CoV-2 infections on a population scale. In this study, we analyzed wastewater samples from three large (>300,000 people served) and four small (<25,000 people served) communities throughout southern Germany from August to December 2021, capturing the fourth infection wave in Germany dominated by the Delta variant (B.1.617.2). As dilution can skew the SARS-CoV-2 biomarker concentrations in wastewater, normalization to wastewater parameters can improve the relationship between SARS-CoV-2 biomarker data and clinical prevalence data. In this study, we investigated the suitability and performance of various normalization parameters. Influent flow data showed strong relationships to precipitation data; accordingly, flow-normalization reacted distinctly to precipitation events. Normalization by surrogate viruses CrAssphage and pepper mild mottle virus showed varying performance for different sampling sites. The best normalization performance was achieved with a mixed fecal indicator calculated from both surrogate viruses. Analyzing the temporal and spatial variation of normalization parameters proved to be useful to explain normalization performance. Overall, our findings indicate that the performance of surrogate viruses, flow, and hydro-chemical data is site-specific. We recommend testing the suitability of normalization parameters individually for specific sewage systems.
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Affiliation(s)
- Alexander Mitranescu
- Chair of Urban Water Systems Engineering,
Technical University of Munich, Am Coulombwall 3,
85748Garching, Germany
| | - Anna Uchaikina
- Chair of Urban Water Systems Engineering,
Technical University of Munich, Am Coulombwall 3,
85748Garching, Germany
| | - Anna-Sonia Kau
- Chair of Urban Water Systems Engineering,
Technical University of Munich, Am Coulombwall 3,
85748Garching, Germany
| | - Claudia Stange
- Department of Water Microbiology, TZW:
DVGW-Technologiezentrum Wasser, Karlsruher Straße 84, 76139Karlsruhe,
Germany
| | - Johannes Ho
- Department of Water Microbiology, TZW:
DVGW-Technologiezentrum Wasser, Karlsruher Straße 84, 76139Karlsruhe,
Germany
| | - Andreas Tiehm
- Department of Water Microbiology, TZW:
DVGW-Technologiezentrum Wasser, Karlsruher Straße 84, 76139Karlsruhe,
Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering,
Technical University of Munich, Am Coulombwall 3,
85748Garching, Germany
| | - Jörg E. Drewes
- Chair of Urban Water Systems Engineering,
Technical University of Munich, Am Coulombwall 3,
85748Garching, Germany
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40
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Babler KM, Amirali A, Sharkey ME, Williams SL, Boone MM, Cosculluela GA, Currall BB, Grills GS, Laine J, Mason CE, Reding BD, Schürer SC, Stevenson M, Vidovic D, Solo-Gabriele HM. Comparison of Electronegative Filtration to Magnetic Bead-Based Concentration and V2G-qPCR to RT-qPCR for Quantifying Viral SARS-CoV-2 RNA from Wastewater. ACS ES&T WATER 2022; 2:2004-2013. [PMID: 37601294 PMCID: PMC10438908 DOI: 10.1021/acsestwater.2c00047] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Methods of wastewater concentration (electronegative filtration (ENF) versus magnetic bead-based concentration (MBC)) were compared for the analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), beta-2 microglobulin, and human-coronavirus OC43. Using ENF as the concentration method, two quantitative Polymerase Chain Reaction (qPCR) analytical methods were also compared: Volcano 2nd Generation (V2G)-qPCR and reverse transcriptase (RT)-qPCR measuring three different targets of the virus responsible for the COVID-19 illness (N1, modified N3, and ORF1ab). Correlations between concentration methods were strong and statistically significant for SARS-CoV-2 (r=0.77, p<0.001) and B2M (r=0.77, p<0.001). Comparison of qPCR analytical methods indicate that, on average, each method provided equivalent results with average ratios of 0.96, 0.96 and 1.02 for N3 to N1, N3 to ORF1ab, and N1 to ORF1ab and were supported by significant (p<0.001) correlation coefficients (r =0.67 for V2G (N3) to RT (N1), r =0.74 for V2G (N3) to RT (ORF1ab), r = 0.81 for RT (N1) to RT (ORF1ab)). Overall results suggest that the two concentration methods and qPCR methods provide equivalent results, although variability is observed for individual measurements. Given the equivalency of results, additional advantages and disadvantages, as described in the discussion, are to be considered when choosing an appropriate method.
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Affiliation(s)
- Kristina M. Babler
- Department of Chemical, Environmental and Materials Engineering, Coral Gables, FL USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental and Materials Engineering, Coral Gables, FL USA
| | - Mark E. Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL USA
| | - Sion L. Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - Melinda M. Boone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | | | - Benjamin B. Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
| | - Jennifer Laine
- Department of Physiology and Biophysics and the WorldQuant Initiative, Weill Cornell Medicine, New York City, NY USA
| | | | - Brian D. Reding
- Department of Physiology and Biophysics and the WorldQuant Initiative, Weill Cornell Medicine, New York City, NY USA
| | - Stephan C. Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL USA
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL USA
- Institute for Data Science & Computing, University of Miami, Coral Gables, FL USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL USA
| | - Dusica Vidovic
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL USA
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41
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Relationship between SARS-CoV-2 in wastewater and clinical data from five wastewater sheds. JOURNAL OF HAZARDOUS MATERIALS ADVANCES 2022; 8:100159. [PMID: 36619827 PMCID: PMC9448702 DOI: 10.1016/j.hazadv.2022.100159] [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: 05/22/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 01/17/2023]
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global pandemic starting in 2019 with nearly 500 million confirmed cases as of April 2022. Infection with SARS-CoV-2 is accompanied by shedding of virus in stool, and its presence in wastewater samples has been documented globally. Therefore, monitoring of SARS-CoV-2 in wastewater offers a promising approach to assess the pandemic situation covering pre-symptomatic and asymptomatic cases in areas with limited clinical testing. In this study, the presence of SARS-CoV-2 RNA in wastewater from five wastewater resource recovery facilities (WRRFs), located in two adjacent counties, was investigated and compared with the number of clinical COVID-19 cases during a 2020-2021 outbreak in United States. Statistical correlation analyses of SARS-CoV-2 viral abundance in wastewater and COVID-19 daily vs weekly clinical cases was performed. While a weak correlation on a daily basis was observed, this correlation improved when weekly clinical case data were applied. The viral fecal indicator Pepper Mild Mottle Virus (PMMoV) was furthermore used to assess the effects of normalization and the impact of dilution due to infiltration in the wastewater sheds. Normalization did not improve the correlations with clinical data. However, PMMoV provided important information about infiltration and presence of industrial wastewater discharge in the wastewater sheds. This study showed the utility of WBE to assist in public health responses to COVID-19, emphasizing that routine monitoring of large WRRFs could provide sufficient information for large-scale dynamics.
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42
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Lu Z, Brunton AE, Mohebnasab M, Deloney A, Williamson KJ, Layton BA, Mansell S, Brawley-Chesworth A, Abrams P, Wilcox KA, Franklin FA, McWeeney SK, Streblow DN, Fan G, Hansel DE. Community-Based SARS-CoV-2 Testing Using Saliva or Nasopharyngeal Swabs to Compare the Performance of Weekly COVID-19 Screening to Wastewater SARS-CoV-2 Signals. ACS ES&T WATER 2022; 2:1667-1677. [PMID: 37552730 PMCID: PMC9528017 DOI: 10.1021/acsestwater.2c00177] [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: 04/20/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 08/10/2023]
Abstract
Multiple studies worldwide have confirmed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be detected in wastewater. However, there is a lack of data directly comparing the wastewater SARS-CoV-2 RNA concentration with the prevalence of coronavirus disease 2019 (COVID-19) in individuals living in sewershed areas. Here, we correlate wastewater SARS-CoV-2 signals with SARS-CoV-2 positivity rates in symptomatic and asymptomatic individuals and compare positivity rates in two underserved communities in Portland, Oregon to those reported in greater Multnomah County. 403 individuals were recruited via two COVID-19 testing sites over a period of 16 weeks. The weekly SARS-CoV-2 positivity rate in our cohort ranged from 0 to 21.7% and trended higher than symptomatic positivity rates reported by Multnomah County (1.9-8.7%). Among the 362 individuals who reported symptom status, 76 were symptomatic and 286 were asymptomatic. COVID-19 was detected in 35 participants: 24 symptomatic, 9 asymptomatic, and 2 of unknown symptomatology. Wastewater testing yielded 0.33-149.9 viral RNA genomic copies/L/person and paralleled community COVID-19 positive test rates. In conclusion, wastewater sampling accurately identified increased SARS-CoV-2 within a community. Importantly, the rate of SARS-CoV-2 positivity in underserved areas is higher than positivity rates within the County as a whole, suggesting a disproportionate burden of SARS-CoV-2 in these communities.
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Affiliation(s)
- Zhengchun Lu
- Department of Pathology & Laboratory Medicine,
Oregon Health & Science University, Portland,
Oregon97239, United States
| | - Amanda E. Brunton
- School of Public Health, Oregon Health
& Science University—Portland State University, Portland,
Oregon97239, United States
| | - Maedeh Mohebnasab
- Department of Pathology & Laboratory Medicine,
Oregon Health & Science University, Portland,
Oregon97239, United States
| | - Anthony Deloney
- Self Enhancement, Inc.,
Portland, Oregon97227, United States
| | - Kenneth J. Williamson
- Department of Research and Innovation,
Clean Water Services, Hillsboro, Oregon97123, United
States
| | - Blythe A. Layton
- Department of Research and Innovation,
Clean Water Services, Hillsboro, Oregon97123, United
States
| | - Scott Mansell
- Department of Research and Innovation,
Clean Water Services, Hillsboro, Oregon97123, United
States
| | | | - Peter Abrams
- City of Portland Bureau of Environmental
Services, Portland, Oregon97204, United States
| | - Kimberly A. Wilcox
- Department of Pathology & Laboratory Medicine,
Oregon Health & Science University, Portland,
Oregon97239, United States
| | - F. Abron Franklin
- School of Public Health, Epidemiology Division,
Oregon Health & Science University—Portland State
University, Portland, Oregon97239, United States
- Departments of Community Health and Preventive Medicine
and Graduate Education in Public Health, Morehouse School of
Medicine, Atlanta, Georgia30310, United States
| | - Shannon K. McWeeney
- Knight Cancer Institute, Oregon Health
and Science University, Portland, Oregon97239, United
States
- Division of Bioinformatics and Computational Biology,
Department of Medical Informatics and Clinical Epidemiology, Oregon Health
and Science University, Portland, Oregon97239, United
States
| | - Daniel N. Streblow
- Vaccine & Gene Therapy Institute,
Oregon Health & Science University, Beaverton,
Oregon97006United States
- Division of Pathobiology and Immunology,
Oregon National Primate Research Center, Beaverton,
Oregon97006, United States
| | - Guang Fan
- Department of Pathology & Laboratory Medicine,
Oregon Health & Science University, Portland,
Oregon97239, United States
| | - Donna E. Hansel
- Department of Pathology & Laboratory Medicine,
Oregon Health & Science University, Portland,
Oregon97239, United States
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43
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Mercier E, D'Aoust PM, Thakali O, Hegazy N, Jia JJ, Zhang Z, Eid W, Plaza-Diaz J, Kabir MP, Fang W, Cowan A, Stephenson SE, Pisharody L, MacKenzie AE, Graber TE, Wan S, Delatolla R. Municipal and neighbourhood level wastewater surveillance and subtyping of an influenza virus outbreak. Sci Rep 2022; 12:15777. [PMID: 36138059 DOI: 10.1101/2022.06.28.22276884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 05/27/2023] Open
Abstract
Recurrent influenza epidemics and pandemic potential are significant risks to global health. Public health authorities use clinical surveillance to locate and monitor influenza and influenza-like cases and outbreaks to mitigate hospitalizations and deaths. Currently, global integration of clinical surveillance is the only reliable method for reporting influenza types and subtypes to warn of emergent pandemic strains. The utility of wastewater surveillance (WWS) during the COVID-19 pandemic as a less resource intensive replacement or complement for clinical surveillance has been predicated on analyzing viral fragments in wastewater. We show here that influenza virus targets are stable in wastewater and partitions favorably to the solids fraction. By quantifying, typing, and subtyping the virus in municipal wastewater and primary sludge during a community outbreak, we forecasted a citywide flu outbreak with a 17-day lead time and provided population-level viral subtyping in near real-time to show the feasibility of influenza virus WWS at the municipal and neighbourhood levels in near real time using minimal resources and infrastructure.
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Affiliation(s)
- Elisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Ocean Thakali
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Nada Hegazy
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Zhihao Zhang
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Julio Plaza-Diaz
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Md Pervez Kabir
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Wanting Fang
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Aaron Cowan
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Sean E Stephenson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Lakshmi Pisharody
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Shen Wan
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada.
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Mercier E, D'Aoust PM, Thakali O, Hegazy N, Jia JJ, Zhang Z, Eid W, Plaza-Diaz J, Kabir MP, Fang W, Cowan A, Stephenson SE, Pisharody L, MacKenzie AE, Graber TE, Wan S, Delatolla R. Municipal and neighbourhood level wastewater surveillance and subtyping of an influenza virus outbreak. Sci Rep 2022; 12:15777. [PMID: 36138059 PMCID: PMC9493155 DOI: 10.1038/s41598-022-20076-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Recurrent influenza epidemics and pandemic potential are significant risks to global health. Public health authorities use clinical surveillance to locate and monitor influenza and influenza-like cases and outbreaks to mitigate hospitalizations and deaths. Currently, global integration of clinical surveillance is the only reliable method for reporting influenza types and subtypes to warn of emergent pandemic strains. The utility of wastewater surveillance (WWS) during the COVID-19 pandemic as a less resource intensive replacement or complement for clinical surveillance has been predicated on analyzing viral fragments in wastewater. We show here that influenza virus targets are stable in wastewater and partitions favorably to the solids fraction. By quantifying, typing, and subtyping the virus in municipal wastewater and primary sludge during a community outbreak, we forecasted a citywide flu outbreak with a 17-day lead time and provided population-level viral subtyping in near real-time to show the feasibility of influenza virus WWS at the municipal and neighbourhood levels in near real time using minimal resources and infrastructure.
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Affiliation(s)
- Elisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Ocean Thakali
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Nada Hegazy
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Zhihao Zhang
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Julio Plaza-Diaz
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Md Pervez Kabir
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Wanting Fang
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Aaron Cowan
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Sean E Stephenson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Lakshmi Pisharody
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Shen Wan
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, K1N 6N5, Canada.
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