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Singh R, Ryu J, Hyoung Lee W, Kang JH, Park S, Kim K. Wastewater-borne viruses and bacteria, surveillance and biosensors at the interface of academia and field deployment. Crit Rev Biotechnol 2024:1-21. [PMID: 38973015 DOI: 10.1080/07388551.2024.2354709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 04/28/2024] [Indexed: 07/09/2024]
Abstract
Wastewater is a complex, but an ideal, matrix for disease monitoring and surveillance as it represents the entire load of enteric pathogens from a local catchment area. It captures both clinical and community disease burdens. Global interest in wastewater surveillance has been growing rapidly for infectious diseases monitoring and for providing an early warning of potential outbreaks. Although molecular detection methods show high sensitivity and specificity in pathogen monitoring from wastewater, they are strongly limited by challenges, including expensive laboratory settings and prolonged sample processing and analysis. Alternatively, biosensors exhibit a wide range of practical utility in real-time monitoring of biological and chemical markers. However, field deployment of biosensors is primarily challenged by prolonged sample processing and pathogen concentration steps due to complex wastewater matrices. This review summarizes the role of wastewater surveillance and provides an overview of infectious viral and bacterial pathogens with cutting-edge technologies for their detection. It emphasizes the practical utility of biosensors in pathogen monitoring and the major bottlenecks for wastewater surveillance of pathogens, and overcoming approaches to field deployment of biosensors for real-time pathogen detection. Furthermore, the promising potential of novel machine learning algorithms to resolve uncertainties in wastewater data is discussed.
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Affiliation(s)
- Rajendra Singh
- Department of Biological and Environmental Science, Dongguk University, Goyang, Gyeonggi-do, South Korea
| | - Jaewon Ryu
- Department of Biological and Environmental Science, Dongguk University, Goyang, Gyeonggi-do, South Korea
| | - Woo Hyoung Lee
- Department of Civil, Environmental, and Construction Engineering, University of Central FL, Orlando, FL, USA
| | - Joo-Hyon Kang
- Department of Civil and Environmental Engineering, Dongguk University-Seoul, Seoul, South Korea
| | - Sanghwa Park
- Bacteria Research Team, Freshwater Bacteria Research Department, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju-si, South Korea
| | - Keugtae Kim
- Department of Biological and Environmental Science, Dongguk University, Goyang, Gyeonggi-do, South Korea
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2
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Morecchiato F, Coppi M, Niccolai C, Antonelli A, Di Gloria L, Calà P, Mancuso F, Ramazzotti M, Lotti T, Lubello C, Rossolini GM. Evaluation of different molecular systems for detection and quantification of SARS-CoV-2 RNA from wastewater samples. J Virol Methods 2024; 328:114956. [PMID: 38796134 DOI: 10.1016/j.jviromet.2024.114956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
Wastewater-based epidemiology has proved to be a suitable approach for tracking the spread of epidemic agents including SARS-CoV-2 RNA. Different protocols have been developed for quantitative detection of SARS-CoV-2 RNA from wastewater samples, but little is known on their performance. In this study we compared three protocols based on Reverse Transcription Real Time-PCR (RT-PCR) and one based on Droplet Digital PCR (ddPCR) for SARS-CoV-2 RNA detection from 35 wastewater samples. Overall, SARS-CoV-2 RNA was detected by at least one method in 85.7 % of samples, while 51.4 %, 22.8 % and 8.6 % resulted positive with two, three or all four methods, respectively. Protocols based on commercial RT-PCR assays and on Droplet Digital PCR showed an overall higher sensitivity vs. an in-house assay. The use of more than one system, targeting different genes, could be helpful to increase detection sensitivity.
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Affiliation(s)
- Fabio Morecchiato
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Claudia Niccolai
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Leandro Di Gloria
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50, Firenze (FI) 50134, Italy
| | - Piergiuseppe Calà
- Tuscany Region, Department of Prevention Local Health Authority Tuscany Center, Via S. Salvi, 12, Firenze (FI) 50135, Italy
| | - Fabrizio Mancuso
- Ingegnerie Toscane - Area R&D, Via Bellatalla, 1, Pisa (PI) 56121, Italy
| | - Matteo Ramazzotti
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50, Firenze (FI) 50134, Italy
| | - Tommaso Lotti
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3, Firenze (FI) 50139, Italy
| | - Claudio Lubello
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3, Firenze (FI) 50139, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy.
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3
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Cha G, Zhu KJ, Fischer JM, Flores CI, Brown J, Pinto A, Hatt JK, Konstantinidis KT, Graham KE. Metagenomic evaluation of the performance of passive Moore swabs for sewage monitoring relative to composite sampling over time resolved deployments. WATER RESEARCH 2024; 253:121269. [PMID: 38359595 DOI: 10.1016/j.watres.2024.121269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/07/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
Moore swabs have re-emerged as a versatile tool in the field of wastewater-based epidemiology during the COVID-19 pandemic and offer unique advantages for monitoring pathogens in sewer systems, especially at the neighborhood-level. However, whether Moore swabs provide comparable results to more commonly used composite samples remains to be rigorously tested including the optimal duration of Moore swab deployment. This study provides new insights into these issues by comparing the results from Moore swab samples to those of paired composite samples collected from the same sewer lines continuously over six to seventy-two hours post-deployment, during low COVID-19 prevalence periods. Our results show that Moore swabs accumulated approximately 10-fold higher PMMoV concentrations (on a basis of mL of Moore swab squeezed filtrate to mL of composite sewage) and showed comparable trends in terms of bacterial species abundance when compared to composite samples. Moore swabs also generally captured higher SARS-CoV-2 N1/N2 RNA concentrations than composite samples. Moore swabs showed comparable trends in terms of abundance dynamics of the sewage microbiome to composite samples and variable signs of saturation over time that were site and/or microbial population-specific. Based on our dual ddRT-PCR and shotgun metagenomic approach, we find that Moore swabs at our sites were optimally deployed for 6 h at a time at two sites.
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Affiliation(s)
- Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kevin J Zhu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7431, USA
| | - Jamie M Fischer
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Camryn I Flores
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7431, USA
| | - Ameet Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Katherine E Graham
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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4
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Ryon MG, Langan LM, Brennan C, O'Brien ME, Bain FL, Miller AE, Snow CC, Salinas V, Norman RS, Bojes HK, Brooks BW. Influences of 23 different equations used to calculate gene copies of SARS-CoV-2 during wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170345. [PMID: 38272099 DOI: 10.1016/j.scitotenv.2024.170345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
Following the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the use of wastewater-based surveillance (WBS) has increased dramatically along with associated infrastructure globally. However, due to the global nature of its application, and various workflow adaptations (e.g., sample collection, water concentration, RNA extraction kits), numerous methods for back-calculation of gene copies per volume (gc/L) of sewage have also emerged. Many studies have considered the comparability of processing methods (e.g., water concentration, RNA extraction); however, for equations used to calculate gene copies in a wastewater sample and subsequent influences on monitoring viral trends in a community and its association with epidemiological data, less is known. Due to limited information on how many formulas exist for the calculation of SARS-CoV-2 gene copies in wastewater, we initially attempted to quantify how many equations existed in the referred literature. We identified 23 unique equations, which were subsequently applied to an existing wastewater dataset. We observed a range of gene copies based on use of different equations, along with variability of AUC curve values, and results from correlation and regression analyses. Though a number of individual laboratories appear to have independently converged on a similar formula for back-calculation of viral load in wastewater, and share similar relationships with epidemiological data, differential influences of various equations were observed for variation in PCR volumes, RNA extraction volumes, or PCR assay parameters. Such observations highlight challenges when performing comparisons among WBS studies when numerous methodologies and back-calculation methods exist. To facilitate reproducibility among studies, the different gc/L equations were packaged as an R Shiny app, which provides end users the ability to investigate variability within their datasets and support comparisons among studies.
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Affiliation(s)
- Mia G Ryon
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Laura M Langan
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA.
| | - Christopher Brennan
- Department of Entomology, Texas A&M University, TAMU 2475, College Station, TX 77843-2475, USA
| | - Megan E O'Brien
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Fallon L Bain
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Aubree E Miller
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Christine C Snow
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Victoria Salinas
- Environmental Epidemiology and Disease Registries, Texas Department of State Health Services, Austin, TX 78756, USA
| | - R Sean Norman
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, 921 Assembly St., Columbia, SC 28208, USA
| | - Heidi K Bojes
- Environmental Epidemiology and Disease Registries, Texas Department of State Health Services, Austin, TX 78756, USA
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA; Department of Public Health, Baylor University, One Bear Place #97343, Waco, TX 76798, USA.
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5
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Adamopoulos PG, Diamantopoulos MA, Boti MA, Zafeiriadou A, Galani A, Kostakis M, Markou A, Sideris DC, Avgeris M, Thomaidis NS, Scorilas A. Spike-Seq: An amplicon-based high-throughput sequencing approach for the sensitive detection and characterization of SARS-CoV-2 genetic variations in environmental samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169747. [PMID: 38159750 DOI: 10.1016/j.scitotenv.2023.169747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 12/05/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Ever since the outbreak of COVID-19 disease in Wuhan, China, different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been identified. Wastewater-based epidemiology (WBE), an approach that has been successfully applied in numerous case studies worldwide, offers a cost-effective and rapid way for monitoring trends of SARS-Cov-2 in the community level without selection bias. Despite being a gold-standard procedure, WBE is a challenging approach due to the sample instability and the moderate efficiency of SARS-CoV-2 concentration in wastewater. In the present study, we introduce Spike-Seq, a custom amplicon-based approach for the S gene sequencing of SARS-CoV-2 in wastewater samples, which enables not only the accurate identification of the existing Spike-related genetic markers, but also the estimation of their frequency in the investigated samples. The implementation of Spike-Seq involves the combination of nested PCR-based assays that efficiently amplify the entire nucleotide sequence of the S gene and next-generation sequencing, which enables the variant detection and the estimation of their frequency. In the framework of the current work, Spike-Seq was performed to investigate the mutational profile of SARS-CoV-2 in samples from the Wastewater Treatment Plant (WWTP) of Athens, Greece, which originated from multiple timepoints, ranging from March 2021 until July 2022. Our findings demonstrate that Spike-Seq efficiently detected major genetic markers of B.1.1.7 (Alpha), B.1.617.2 (Delta) as well as B.1.1.529 (Omicron) variants in wastewater samples and provided their frequency levels, showing similar variant distributions with the published clinical data from the National Public Health organization. The presented approach can prove to be a useful tool for the detection of SARS-CoV-2 in challenging wastewater samples and the identification of the existing genetic variants of S gene.
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Affiliation(s)
- Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Michaela A Boti
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasia Zafeiriadou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Greece
| | - Aikaterini Galani
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Greece
| | - Marios Kostakis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Greece
| | - Athina Markou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece; Laboratory of Clinical Biochemistry and Molecular Diagnostics, Second Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
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6
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Sharma V, Takamura H, Biyani M, Honda R. Real-Time On-Site Monitoring of Viruses in Wastewater Using Nanotrap ® Particles and RICCA Technologies. BIOSENSORS 2024; 14:115. [PMID: 38534222 DOI: 10.3390/bios14030115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/10/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
Wastewater-based epidemiology (WBE) is an effective and efficient tool for the early detection of infectious disease outbreaks in a community. However, currently available methods are laborious, costly, and time-consuming due to the low concentration of viruses and the presence of matrix chemicals in wastewater that may interfere with molecular analyses. In the present study, we designed a highly sensitive "Quick Poop (wastewater with fecal waste) Sensor" (termed, QPsor) using a joint approach of Nanotrap microbiome particles and RICCA (RNA Isothermal Co-Assisted and Coupled Amplification). Using QPsor, the WBE study showed a strong correlation with standard PEG concentrations and the qPCR technique. Using a closed format for a paper-based lateral flow assay, we were able to demonstrate the potential of our assay as a real-time, point-of-care test by detecting the heat-inactivated SARS-CoV-2 virus in wastewater at concentrations of 100 copies/mL and within one hour. As a proof-of-concept demonstration, we analyzed the presence of viral RNA of the SARS-CoV-2 virus and PMMoV in raw wastewater samples from wastewater treatment plants on-site and within 60 min. The results show that the QPsor method can be an effective tool for disease outbreak detection by combining an AI-enabled case detection model with real-time on-site viral RNA extraction and amplification, especially in the absence of intensive clinical laboratory facilities. The lab-free, lab-quality test capabilities of QPsor for viral prevalence and transmission in the community can contribute to the efficient management of pandemic situations.
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Affiliation(s)
- Vishnu Sharma
- BioSeeds Corporation, Ishikawa Create Labo-202, Asahidai 2-13, Nomi 923-1211, Ishikawa, Japan
| | - Hitomi Takamura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1164, Ishikawa, Japan
| | - Manish Biyani
- BioSeeds Corporation, Ishikawa Create Labo-202, Asahidai 2-13, Nomi 923-1211, Ishikawa, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1164, Ishikawa, Japan
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Armenta-Castro A, Núñez-Soto MT, Rodriguez-Aguillón KO, Aguayo-Acosta A, Oyervides-Muñoz MA, Snyder SA, Barceló D, Saththasivam J, Lawler J, Sosa-Hernández JE, Parra-Saldívar R. Urine biomarkers for Alzheimer's disease: A new opportunity for wastewater-based epidemiology? ENVIRONMENT INTERNATIONAL 2024; 184:108462. [PMID: 38335627 DOI: 10.1016/j.envint.2024.108462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/16/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
While Alzheimer's disease (AD) diagnosis, management, and care have become priorities for healthcare providers and researcher's worldwide due to rapid population aging, epidemiologic surveillance efforts are currently limited by costly, invasive diagnostic procedures, particularly in low to middle income countries (LMIC). In recent years, wastewater-based epidemiology (WBE) has emerged as a promising tool for public health assessment through detection and quantification of specific biomarkers in wastewater, but applications for non-infectious diseases such as AD remain limited. This early review seeks to summarize AD-related biomarkers and urine and other peripheral biofluids and discuss their potential integration to WBE platforms to guide the first prospective efforts in the field. Promising results have been reported in clinical settings, indicating the potential of amyloid β, tau, neural thread protein, long non-coding RNAs, oxidative stress markers and other dysregulated metabolites for AD diagnosis, but questions regarding their concentration and stability in wastewater and the correlation between clinical levels and sewage circulation must be addressed in future studies before comprehensive WBE systems can be developed.
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Affiliation(s)
| | - Mónica T Núñez-Soto
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Kassandra O Rodriguez-Aguillón
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Alberto Aguayo-Acosta
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Mariel Araceli Oyervides-Muñoz
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Shane A Snyder
- Nanyang Environment & Water Research Institute (NEWRI), Nanyang Technological University, Singapore
| | - Damià Barceló
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Jordi Girona, 18-26, 08034 Barcelona, Spain; Sustainability Cluster, School of Engineering at the UPES, Dehradun, Uttarakhand, India
| | - Jayaprakash Saththasivam
- Water Center, Qatar Environment & Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Qatar
| | - Jenny Lawler
- Water Center, Qatar Environment & Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Qatar
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico.
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico; Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
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Gogoi G, Singh SD, Kalyan E, Koch D, Gogoi P, Kshattry S, Mahanta HJ, Imran M, Pandey R, Bharali P. An interpretative review of the wastewater-based surveillance of the SARS-CoV-2: where do we stand on its presence and concern? Front Microbiol 2024; 15:1338100. [PMID: 38318336 PMCID: PMC10839012 DOI: 10.3389/fmicb.2024.1338100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has been used for monitoring infectious diseases like polio, hepatitis, etc. since the 1940s. It is also being used for tracking the SARS-CoV-2 at the population level. This article aims to compile and assess the information for the qualitative and quantitative detection of the SARS-CoV-2 in wastewater. Based on the globally published studies, we highlight the importance of monitoring SARS-CoV-2 presence/detection in the wastewater and concurrently emphasize the development of early surveillance techniques. SARS-CoV-2 RNA sheds in the human feces, saliva, sputum and mucus that ultimately reaches to the wastewater and brings viral RNA into it. For the detection of the virus in the wastewater, different detection techniques have been optimized and are in use. These are based on serological, biosensor, targeted PCR, and next generation sequencing for whole genome sequencing or targeted amplicon sequencing. The presence of the SARS-CoV-2 RNA in wastewater could be used as a potential tool for early detection and devising the strategies for eradication of the virus before it is spread in the community. Additionally, with the right and timely understanding of viral behavior in the environment, an accurate and instructive model that leverages WBE-derived data may be created. This might help with the creation of technological tools and doable plans of action to lessen the negative effects of current viral epidemics or future potential outbreaks on public health and the economy. Further work toward whether presence of viral load correlates with its ability to induce infection, still needs evidence. The current increasing incidences of JN.1 variant is a case in point for continued early detection and surveillance, including wastewater.
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Affiliation(s)
- Gayatri Gogoi
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sarangthem Dinamani Singh
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Emon Kalyan
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Devpratim Koch
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pronami Gogoi
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Suman Kshattry
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Hridoy Jyoti Mahanta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Md Imran
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Rajesh Pandey
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Pankaj Bharali
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Thapar I, Langan LM, Davis H, Norman RS, Bojes HK, Brooks BW. Influence of storage conditions and multiple freeze-thaw cycles on N1 SARS-CoV-2, PMMoV, and BCoV signal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165098. [PMID: 37392884 PMCID: PMC10307669 DOI: 10.1016/j.scitotenv.2023.165098] [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: 03/28/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
Wastewater-based epidemiology/wastewater-based surveillance (WBE/WBS) continues to serve as an effective means of monitoring various diseases, including COVID-19 and the emergence of SARS-CoV-2 variants, at the population level. As the use of WBE expands, storage conditions of wastewater samples will play a critical role in ensuring the accuracy and reproducibility of results. In this study, the impacts of water concentration buffer (WCB), storage temperature, and freeze-thaw cycles on the detection of SARS-CoV-2 and other WBE-related gene targets were examined. Freeze-thawing of concentrated samples did not significantly affect (p > 0.05) crossing/cycle threshold (Ct) value for any of the gene targets studied (SARS-CoV-2 N1, PMMoV, and BCoV). However, use of WCB during concentration resulted in a significant (p < 0.05) decrease in Ct for all targets, and storage at -80 °C (in contrast to -20 °C) appeared preferable for wastewater storage signal stability based on decreased Ct values, although this was only significantly different (p < 0.05) for the BCoV target. Interestingly, when Ct values were converted to gene copies per influent sample, no significant differences (p > 0.05) were observed in any of the targets examined. Stability of RNA targets in concentrated wastewater against freeze-thaw degradation supports archiving of concentrated samples for use in retrospective examination of COVID-19 trends and tracing SARS-CoV-2 variants and potentially other viruses, and provides a starting point for establishing a consistent procedure for specimen collection and storage for the WBE/WBS community.
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Affiliation(s)
- Isha Thapar
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA
| | - Laura M Langan
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA.
| | - Haley Davis
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US-1, Fort Pierce, FL 34946, USA
| | - R Sean Norman
- Department of Environmental Health Sciences, Arnold School of Public Health, South Carolina, 921 Assembly St., Columbia, SC 29208, USA
| | - Heidi K Bojes
- Environmental Epidemiology and Disease Registries Section, Texas Department of State Health Services, Austin, TX 78756, USA
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA; Institute of Biomedical Studies, Baylor University, One Bear Place #97224, Waco, TX 76798, USA
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10
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Carrascal M, Sánchez-Jiménez E, Fang J, Pérez-López C, Ginebreda A, Barceló D, Abian J. Sewage Protein Information Mining: Discovery of Large Biomolecules as Biomarkers of Population and Industrial Activities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37463250 PMCID: PMC10399289 DOI: 10.1021/acs.est.3c00535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Wastewater-based epidemiology has been revealed as a powerful approach for surveying the health and lifestyle of a population. In this context, proteins have been proposed as potential biomarkers that complement the information provided by currently available methods. However, little is known about the range of molecular species and dynamics of proteins in wastewater and the information hidden in these protein profiles is still to be uncovered. In this study, we investigated the protein composition of wastewater from 10 municipalities in Catalonia with diverse populations and industrial activities at three different times of the year. The soluble fraction of this material was analyzed using liquid chromatography high-resolution tandem mass spectrometry using a shotgun proteomics approach. The complete proteomic profile, distribution among different organisms, and semiquantitative analysis of the main constituents are described. Excreta (urine and feces) from humans, and blood and other residues from livestock were identified as the two main protein sources. Our findings provide new insights into the characterization of wastewater proteomics that allow for the proposal of specific bioindicators for wastewater-based environmental monitoring. This includes human and animal population monitoring, most notably for rodent pest control (immunoglobulins (Igs) and amylases) and livestock processing industry monitoring (albumins).
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Affiliation(s)
- Montserrat Carrascal
- Biological and Environmental Proteomics Group, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
| | - Ester Sánchez-Jiménez
- Biological and Environmental Proteomics Group, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Jie Fang
- Biological and Environmental Proteomics Group, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Carlos Pérez-López
- Biological and Environmental Proteomics Group, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Antoni Ginebreda
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Damià Barceló
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Studies (IDAEA-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Joaquin Abian
- Biological and Environmental Proteomics Group, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), Rosellón 161, E-08036 Barcelona, Spain
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11
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Tavazzi S, Cacciatori C, Comero S, Fatta-Kassinos D, Karaolia P, Iakovides IC, Loutsiou P, Gutierrez-Aguirre I, Lengar Z, Bajde I, Tenson T, Kisand V, Laas P, Panksep K, Tammert H, Mariani G, Skejo H, Gawlik BM. Short-term stability of wastewater samples for storage and shipment in the context of the EU Sewage Sentinel System for SARS-CoV-2. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:109623. [PMID: 36890876 PMCID: PMC9979635 DOI: 10.1016/j.jece.2023.109623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
In the context of an EU-wide surveillance system for SARS-CoV-2 in wastewater, recommended by the European Commission, this study aims to provide scientific support to the adequacy of transport and storage conditions of samples both in terms of duration and samples temperature. Three laboratories in Slovenia, Cyprus and Estonia investigated the short-term, one-week, isochronous stability of wastewater samples by RT-qPCR based detection of SARS-CoV-2 genes. The results were tested for statistical significance to determine uncertainty of quantification and shelf-life, at testing temperatures of + 20 °C and - 20 °C, relative to reference at + 4 °C. Samples were collected from three urban wastewater treatment plant influents and analysed respectively for SARS-CoV-2 genes N1, N2 (Laboratory 1), N2, E (Laboratory 2) and N3 (Laboratory 3), with various analytical methods. For a period of 7/8 days at + 20 °C, decreasing trends of measured concentrations were observed for all genes resulting in instability according to the statistical analysis, while at - 20 °C the trend of variation was stable only for N1, N2 (Laboratory 1) and N3 (Laboratory 3). Trends for gene E concentrations at - 20 °C (Laboratory 2) could not be tested statistically for stability because of lack of data. Over a period of just 3 days at + 20 °C, the variation was statistically non-significant indicating stability for genes N1, E and N3 for laboratories 1, 2 and 3, respectively. Nonetheless, the outcome of the study presents evidence to support the choice of the selected temperature at which samples shall be preserved during storage before analysis or transport to the laboratory. The conditions (+4 °C, ∼ few days) chosen for EU wastewater surveillance are in accordance with these results, highlighting the importance of stability testing of environmental samples to determine the short-term analytical uncertainty.
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Affiliation(s)
- S Tavazzi
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - C Cacciatori
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - S Comero
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - D Fatta-Kassinos
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - P Karaolia
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - I C Iakovides
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - P Loutsiou
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | | | - Z Lengar
- National Institute of Biology, Vecna Pot 111, SI-1000 Ljubljana, Slovenia
| | - I Bajde
- National Institute of Biology, Vecna Pot 111, SI-1000 Ljubljana, Slovenia
| | - T Tenson
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - V Kisand
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - P Laas
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - K Panksep
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - H Tammert
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - G Mariani
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - H Skejo
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - B M Gawlik
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
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12
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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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13
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Psichoudaki M, Mina T, Savvidou M, Mina C, Michael C, Fatta-Kassinos D. Wastewater-based monitoring of illicit drugs in Cyprus by UPLC-MS/MS: The impact of the COVID-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158747. [PMID: 36108831 PMCID: PMC9467927 DOI: 10.1016/j.scitotenv.2022.158747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 05/14/2023]
Abstract
The outbreak and spread of COVID-19 impacted through various ways the lives of millions of humans globally. In this work, wastewater-based epidemiology (WBE) was applied to investigate the effect of the actions taken by the Republic of Cyprus to confine COVID-19 on the use of illicit stimulant drugs. Daily influent samples were collected from the six main wastewater treatment plants (WWTPs) of the country i) before lockdown (3-9 April 2019), ii) during lockdown (21-27 April 2020), iii) during the post-lockdown period (14-20 July 2020), and, iv) during each season of the following year (20-26 April 2021, 19-25 July 2021, 11-17 October 2021, 25 December 2021-2 January 2022), and analyzed for amphetamine, methamphetamine, MDMA and cocaine. In most areas, amphetamine and methamphetamine use was not affected during the confinement period, but as availability of the substances decreased with time, a drop in their use was observed when most restriction measures were eased (up to 9- and 22-fold decrease, respectively). The limitations on social interactions and events during the quarantine period seem to have led to the reduction of MDMA and cocaine and driven a sharp decrease of their use in most areas studied (up to 11 and 6 times lower, respectively). However, the re-opening of activities led to a pronounced consumption increase, reaching maximum daily values of 800 and 2691 mg/1000 inhabitants/day, respectively. In 2021, drug use was re-established to lower levels. The examination of weekly patterns during this year revealed higher weekend use of methamphetamine, MDMA and cocaine. Our results suggest that both the implementation and the easing of COVID-19 related measures affected the availability and the use of drugs. This study also provides the first insight on the consumption of illicit drugs in the Republic of Cyprus during pre-, post- and pandemic times and demonstrates the importance of WBE.
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Affiliation(s)
- M Psichoudaki
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - T Mina
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus; Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678, Nicosia, Cyprus
| | - M Savvidou
- Cyprus National Addictions Authority, 2027 Nicosia, Cyprus
| | - C Mina
- Cyprus National Addictions Authority, 2027 Nicosia, Cyprus
| | - C Michael
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - D Fatta-Kassinos
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus; Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678, Nicosia, Cyprus.
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14
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Qin N, Liu Z, Zhao L, Bao M, Mei X, Li D. Promising instrument-free detections of various analytes using smartphones with Spotxel ® Reader. ANAL SCI 2022; 39:139-148. [PMID: 36460855 PMCID: PMC9718457 DOI: 10.1007/s44211-022-00216-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022]
Abstract
In consideration of the problems related to food safety, environmental pollution, and the spread of infected diseases nowadays, we urgently need testing methods that can be easily performed by common people. Smartphone-based detections are promising for general applications. However, some of these analytical strategies require a combination of accessories and instruments, such as portable electrochemical workstations, mini multi-mode microplate readers, and complex temperature control devices, etc., which are small but still expensive. Herein, we comprehensively introduce a free app (Spotxel® Reader) that can provide accurate data analysis for microplate or parallel-format test sensors without an instrument. By simulating the optical signal of the test samples through a smartphone, the sensing results can be obtained for free. We discuss the detection strategies involved in the reported smartphone-based analyses using Spotxel® Reader. Prospects for the development of this free app for future detection applications are presented. This review aims to popularize free analysis software, so that ordinary people may realize convenient tests.
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Affiliation(s)
- Ningyi Qin
- Department of Pharmacy, Jinzhou Medical University, Jinzhou, 121000 China
| | - Zirui Liu
- Liaoning Provincial Key Laboratory of Medical Testing, Jinzhou Medical University, Jinzhou, 121001 China
| | - Lanbin Zhao
- The Third Affiliated Hospital, Jinzhou Medical University, Jinzhou, People’s Republic of China
| | - Mengfan Bao
- Department of Pharmacy, Jinzhou Medical University, Jinzhou, 121000 China
| | - Xifan Mei
- Liaoning Provincial Key Laboratory of Medical Testing, Jinzhou Medical University, Jinzhou, 121001 China ,The Third Affiliated Hospital, Jinzhou Medical University, Jinzhou, People’s Republic of China
| | - Dan Li
- Department of Pharmacy, Jinzhou Medical University, Jinzhou, 121000 China
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15
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Evaluation of viral concentration and extraction methods for SARS-CoV-2 recovery from wastewater using droplet digital and quantitative RT-PCR. CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2022; 6:100224. [PMID: 37520924 PMCID: PMC9222221 DOI: 10.1016/j.cscee.2022.100224] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 05/19/2023]
Abstract
The ongoing pandemic caused by the emergence of SARS-CoV-2 has resulted in millions of deaths worldwide despite the various measures announced by the authorities. Wastewater-based epidemiology has the ability to provide a day-to-day estimation of the number of infected people in a fast and cost-effective manner. However, owing to the complex nature of wastewater, wastewater monitoring for viral genome copies is affected by the extensive viral fragmentation that takes place all the way to the sewage and the analytical lab. The aim of this study was to evaluate different methodologies for the concentration and extraction of viruses in wastewaters and to select and improve an option that maximizes the recovery of SARS-CoV-2. We compare 5 different concentration methods and 4 commercially available kits for the RNA extraction. To evaluate the performance and the recovery of these, SARS-CoV-2 isolated from patients was used as a spike control. Additionally, the presence of SARS-CoV-2 in all wastewater samples was determined using reverse transcription quantitative PCR (RT-qPCR) and reverse transcription droplet digital PCR (RT-ddPCR), targeting three genetic markers (N1, N2 and N3). Using spiked samples, recoveries were estimated 2.1–37.6% using different extraction kits and 0.1–2.1% using different concentration kits. It was found that a direct capture-based method, evaluated against a variety of concentration methods, is the best in terms of recovery, time and cost. Interestingly, we noticed a good agreement between the results provided by RT-qPCR and RT-ddPCR in terms of recovery. This evaluation can serve as a guide for laboratories establishing a protocol to perform wastewater monitoring of SARS-CoV-2. Overall, data presented here reinforces the validity of WBE for SARS-CoV-2 surveillance, uncovers potential caveats in the selection of concentration and extraction protocols and points towards optimal solutions to maximize its potential.
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16
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Karami C, Dargahi A, Vosoughi M, Normohammadi A, Jeddi F, Asghariazar V, Mokhtari A, Sedigh A, Zandian H, Alighadri M. SARS-CoV-2 in municipal wastewater treatment plant, collection network, and hospital wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:85577-85585. [PMID: 34264498 PMCID: PMC8280616 DOI: 10.1007/s11356-021-15374-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/06/2021] [Indexed: 05/08/2023]
Abstract
The current outbreak of coronavirus disease (COVID-19) has led to creating a public health emergency conditions since 2019. COVID-19, which is caused by SARS-CoV-2, is spread via human-to-human transmission by direct contact or droplets. Through conducting this study, we were looking for detecting SARS-CoV-2 in wastewater produced in Iran country (Ardabil, Nir, Khalkhal, and Kowsar) (wastewater collection network, wastewater treatment plant, and hospital wastewater). In this research, samples (n=76) were collected from influent and effluent of municipal and hospital wastewater treatment plants, and some samples were also collected from Ardabil municipal wastewater manholes. The sampling duration included the white (lower risk of COVID-19) and red (high risk of COVID-19) conditions. Samples were stored at -20 °C for further diagnostic tests. The specific primer and probe real-time reverse transcriptase-polymerase chain reaction (real-time PCR) targeting ORF1ab and N genes (nucleoprotein gene) were applied to detect viral genomes of the SARS-CoV-2 virus in the wastewater samples. Out of 76 samples, a total of 15 samples (19.73%) collected from wastewater in Ardabil province (Ardabil, Nir, Khalkhal, and Kowsar), were positive in terms of SARS-CoV-2. Wastewater epidemiology can facilitate detection of the incidence of pathogens through metropolises, measurement of population prevalence without direct testing, and provision of information to the public health system about the efficiency of intervening efforts. Graphical abstract.
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Affiliation(s)
- Chiman Karami
- Department of Microbiology, Parasitology and Immunology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Abdollah Dargahi
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
| | - Mehdi Vosoughi
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
- Department of Environmental Health Engineering, School of Public Health, Ardabil University of Medical Sciences, Ardabil, Iran.
| | - Ali Normohammadi
- Department of Environmental Health Engineering, School of Public Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Farhad Jeddi
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Vahid Asghariazar
- Immunology Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Ahamad Mokhtari
- Department of Environmental Health Engineering, School of Public Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Anoshirvan Sedigh
- Department of Environmental Health Engineering, School of Public Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hamed Zandian
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Morteza Alighadri
- Department of Environmental Health Engineering, School of Public Health, Ardabil University of Medical Sciences, Ardabil, Iran
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17
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Maksimovic Carvalho Ferreira O, Lengar Ž, Kogej Z, Bačnik K, Bajde I, Milavec M, Županič A, Mehle N, Kutnjak D, Ravnikar M, Gutierrez-Aguirre I. Evaluation of Methods and Processes for Robust Monitoring of SARS-CoV-2 in Wastewater. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:384-400. [PMID: 35999429 PMCID: PMC9398038 DOI: 10.1007/s12560-022-09533-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/01/2022] [Indexed: 05/15/2023]
Abstract
The SARS-CoV-2 pandemic has accelerated the development of virus concentration and molecular-based virus detection methods, monitoring systems and overall approach to epidemiology. Early into the pandemic, wastewater-based epidemiology started to be employed as a tool for tracking the virus transmission dynamics in a given area. The complexity of wastewater coupled with a lack of standardized methods led us to evaluate each step of the analysis individually and see which approach gave the most robust results for SARS-CoV-2 monitoring in wastewater. In this article, we present a step-by-step, retrospective view on the method development and implementation for the case of a pilot monitoring performed in Slovenia. We specifically address points regarding the thermal stability of the samples during storage, screening for the appropriate sample concentration and RNA extraction procedures and real-time PCR assay selection. Here, we show that the temperature and duration of the storage of the wastewater sample can have a varying impact on the detection depending on the structural form in which the SARS-CoV-2 target is present. We found that concentration and RNA extraction using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using semi-automated kit from Promega give the most optimal results out of the seven methods tested. Lastly, we confirm the use of N1 and N2 assays developed by the CDC (USA) as the best performing assays among four tested in combination with Fast Virus 1-mastermix. Data show a realistic overall process for method implementation as well as provide valuable information in regards to how different approaches in the analysis compare to one another under the specific conditions present in Slovenia during a pilot monitoring running from the beginning of the pandemic.
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Affiliation(s)
- Olivera Maksimovic Carvalho Ferreira
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
- International Postgraduate School Jožef Stefan, Jamova cesta 39, 1000, Ljubljana, Slovenia.
| | - Živa Lengar
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Zala Kogej
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
- International Postgraduate School Jožef Stefan, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Katarina Bačnik
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Irena Bajde
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Mojca Milavec
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Anže Županič
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Dvorec Lanthieri, Glavni trg 8, 5271, Vipava, Slovenia
| | - Denis Kutnjak
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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18
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West NW, Vasquez AA, Bahmani A, Khan MF, Hartrick J, Turner CL, Shuster W, Ram JL. Sensitive detection of SARS-CoV-2 molecular markers in urban community sewersheds using automated viral RNA purification and digital droplet PCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157547. [PMID: 35872187 PMCID: PMC9303066 DOI: 10.1016/j.scitotenv.2022.157547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
Wastewater based epidemiology (WBE) has emerged as a strategy to identify, locate, and manage outbreaks of COVID-19, and thereby possibly prevent surges in cases, which overwhelm local to global health care networks. The WBE process is based on assaying municipal wastewater for molecular markers of the SARS-CoV-2 virus. Standard processes for purifying viral RNA from municipal wastewater are often time-consuming and require the handling of large quantities of wastewater, negatively affecting throughput, timely reporting, and safety. We demonstrate here an automated, faster system to purify viral RNA from smaller volumes of wastewater but with increased sensitivity for detection of SARS-CoV-2 markers. We document the effectiveness of this new approach by way of comparison to the PEG/NaCl/Qiagen method prescribed by the State of Michigan for SARS-CoV-2 wastewater monitoring and show its application to several Detroit sewersheds. Specifically, compared to the PEG/NaCl/Qiagen method, viral RNA purification using the PerkinElmer Chemagic™ 360 lowered handling time, decreased the amount of wastewater required by ten-fold, increased the amount of RNA isolated per μl of final elution product by approximately five-fold, and effectively removed ddPCR inhibitors from most sewershed samples. For detection of markers on the borderline of viral detectability, we found that use of the Chemagic™ 360 enabled the measurement of viral markers in a significant number of samples for which the result with the PEG/NaCl/Qiagen method was below the level of detectability. The improvement in detectability of the viral markers might be particularly important for early warning to public health authorities at the beginning of an outbreak. Applied to sewersheds in Detroit, the technique enabled more sensitive detection of SARS-CoV-2 markers with good correlation between wastewater signals and COVID-19 cases in the sewersheds. We also discuss advantages and disadvantages of several automated RNA purification systems, made by Promega, PerkinElmer, and ThermoFisher.
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Affiliation(s)
- Nicholas W West
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Adrian A Vasquez
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Azadeh Bahmani
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Mohammed F Khan
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | | | | | - William Shuster
- Department of Civil and Environmental Engineering, Wayne State University, Detroit, MI 48202, USA
| | - Jeffrey L Ram
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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19
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Mendoza Grijalva L, Brown B, Cauble A, Tarpeh WA. Diurnal Variability of SARS-CoV-2 RNA Concentrations in Hourly Grab Samples of Wastewater Influent during Low COVID-19 Incidence. ACS ES&T WATER 2022; 2:2125-2133. [PMID: 37552729 PMCID: PMC9063989 DOI: 10.1021/acsestwater.2c00061] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/31/2022] [Accepted: 04/06/2022] [Indexed: 06/17/2023]
Abstract
Wastewater-based epidemiology (WBE) has been widely deployed during the COVID-19 pandemic, but with limited evaluation of the utility of discrete sampling for large sewersheds and low COVID-19 incidence. In this study, SARS-CoV-2 RNA was measured in 72 consecutive hourly influent grab samples collected at a wastewater treatment plant serving nearly 500 000 residents when incidence was low (approximately 20 cases per 100 000). We characterized diurnal variability and relationships between SARS-CoV-2 RNA detection and physicochemical covariates [flow rate, total ammonia nitrogen (TAN), and total solids (TS)]. The highest detection rate observed was 82% during the first peak flow, which occurred in the early afternoon (14:00). Higher detection rates were also observed when sampling above median TAN concentrations (71%; p < 0.01; median = 40.26 mg of NH4/L). SARS-CoV-2 RNA concentrations were weakly correlated with flow rate (Kendall's τ = 0.16; p < 0.01), TAN (τ = 0.19; p < 0.05), and TS (τ = 0.18; p < 0.01), suggesting generally low RNA sewer discharges as expected at low incidence. Our results elucidated sensible adjustments to maximize detection rates, including using multiple gene targets, collecting duplicate samples, and sampling during higher flow and TAN discharges. Optimizing the lower-incidence bounds of WBE can help assess its suitability for verifying COVID-19 reemergence or eradication.
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Affiliation(s)
- Lorelay Mendoza Grijalva
- Department of Civil and Environmental Engineering,
Stanford University, Stanford, California 94305,
United States
| | - Blake Brown
- Central Contra Costa Sanitary
District, Martinez, California 94553, United
States
| | - Amanda Cauble
- Central Contra Costa Sanitary
District, Martinez, California 94553, United
States
| | - William A. Tarpeh
- Department of Civil and Environmental Engineering,
Stanford University, Stanford, California 94305,
United States
- Department of Chemical Engineering,
Stanford University, Stanford, California 94305,
United States
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20
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Langan LM, O’Brien M, Rundell ZC, Back JA, Ryan BJ, Chambliss CK, Norman RS, Brooks BW. Comparative Analysis of RNA-Extraction Approaches and Associated Influences on RT-qPCR of the SARS-CoV-2 RNA in a University Residence Hall and Quarantine Location. ACS ES&T WATER 2022; 2:1929-1943. [PMID: 37552714 PMCID: PMC9063990 DOI: 10.1021/acsestwater.1c00476] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 05/09/2023]
Abstract
Wastewater-based epidemiology (WBE) provides an early warning and trend analysis approach for determining the presence of COVID-19 in a community and complements clinical testing in assessing the population level, even as viral loads fluctuate. Here, we evaluate combinations of two wastewater concentration methods (i.e., ultrafiltration and composite supernatant-solid), four pre-RNA extraction modifications, and three nucleic acid extraction kits using two different wastewater sampling locations. These consisted of a quarantine facility containing clinically confirmed COVID-19-positive inhabitants and a university residence hall. Of the combinations examined, composite supernatant-solid with pre-RNA extraction consisting of water concentration and RNA/DNA shield performed the best in terms of speed and sensitivity. Further, of the three nucleic acid extraction kits examined, the most variability was associated with the Qiagen kit. Focusing on the quarantine facility, viral concentrations measured in wastewater were generally significantly related to positive clinical cases, with the relationship dependent on method, modification, kit, target, and normalization, although results were variable-dependent on individual time points (Kendall's Tau-b (τ) = 0.17 to 0.6) or cumulatively (Kendall's Tau-b (τ) = -0.048 to 1). These observations can support laboratories establishing protocols to perform wastewater surveillance and monitoring efforts for COVID-19.
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Affiliation(s)
- Laura M. Langan
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Megan O’Brien
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Zach C. Rundell
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Jeffrey A. Back
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Benjamin J. Ryan
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
| | - C. Kevin Chambliss
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Chemistry and Biochemistry,
Baylor University, One Bear Place #97348, Waco, Texas 76798,
United States
| | - R. Sean Norman
- Environmental Health Sciences, Arnold
School of Public Health, South Carolina, 921 Assembly Street, Columbia,
South Carolina 29208, United States
| | - Bryan W. Brooks
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Institute of Biomedical Studies, Baylor
University, One Bear Place #97224, Waco, Texas 76798, United
States
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21
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Ganesh PS, Kim SY. A comparison of conventional and advanced electroanalytical methods to detect SARS-CoV-2 virus: A concise review. CHEMOSPHERE 2022; 307:135645. [PMID: 35817176 PMCID: PMC9270057 DOI: 10.1016/j.chemosphere.2022.135645] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Respiratory viruses are a serious threat to human wellbeing that can cause pandemic disease. As a result, it is critical to identify virus in a timely, sensitive, and precise manner. The present novel coronavirus-2019 (COVID-19) disease outbreak has increased these concerns. The research of developing various methods for COVID-19 virus identification is one of the most rapidly growing research areas. This review article compares and addresses recent improvements in conventional and advanced electroanalytical approaches for detecting COVID-19 virus. The popular conventional methods such as polymerase chain reaction (PCR), loop mediated isothermal amplification (LAMP), serology test, and computed tomography (CT) scan with artificial intelligence require specialized equipment, hours of processing, and specially trained staff. Many researchers, on the other hand, focused on the invention and expansion of electrochemical and/or bio sensors to detect SARS-CoV-2, demonstrating that they could show a significant role in COVID-19 disease control. We attempted to meticulously summarize recent advancements, compare conventional and electroanalytical approaches, and ultimately discuss future prospective in the field. We hope that this review will be helpful to researchers who are interested in this interdisciplinary field and desire to develop more innovative virus detection methods.
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Affiliation(s)
- Pattan-Siddappa Ganesh
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education (KoreaTech), Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Sang-Youn Kim
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education (KoreaTech), Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
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22
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Wartell BA, Proano C, Bakalian L, Kaya D, Croft K, McCreary M, Lichtenstein N, Miske V, Arcellana P, Boyer J, Benschoten IV, Anderson M, Crabb A, Gilson S, Gourley A, Wheeler T, Trest B, Bowman G, Kjellerup BV. Implementing wastewater surveillance for SARS-CoV-2 on a university campus: Lessons learned. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2022; 94:e10807. [PMID: 36372781 PMCID: PMC9827968 DOI: 10.1002/wer.10807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Wastewater surveillance, also known as wastewater-based epidemiology (WBE), has been successfully used to detect SARS-CoV-2 and other viruses in sewage in many locations in the United States and globally. This includes implementation of the surveillance on college and university campuses. A two-phase study was conducted during the 2020-2021 academic year to test the feasibility of a WBE system on campus and to supplement the clinical COVID-19 testing performed for the student, staff, and faculty body. The primary objective during the Fall 2020 semester was to monitor a large portion of the on-campus population and to obtain an understanding of the spreading of the SARS-CoV-2 virus. The Spring 2021 objective was focused on selected residence halls and groups of residents on campus, as this was more efficient and relevant for an effective follow-up response. Logistical problems and planning oversights initially occurred but were corrected with improved communication and experience. Many lessons were learned, including effective mapping, site planning, communication, personnel organization, and equipment management, and obtained along the way, thereby paving an opportune guide for future planning efforts. PRACTITIONER POINTS: WBE was successful in the detection of many SARS-CoV-2 variants incl. Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron. Careful planning and contingencies were essential for a successful implementation of a SARS-CoV-2 monitoring program. A surveillance program may be important for detection and monitoring of other public health relevant targets in wastewater incl. bacteria, viruses, fungi and viruses. Diverse lessons were learned incl. effective mapping, site planning, communication, personnel organization, and equipment management, thereby providing a guide for future planning efforts.
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Affiliation(s)
- Brian A. Wartell
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Camila Proano
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Lena Bakalian
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Devrim Kaya
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Kristen Croft
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Michael McCreary
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Naomi Lichtenstein
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Victoria Miske
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Patricia Arcellana
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Jessica Boyer
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Isabelle Van Benschoten
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Marya Anderson
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Andrea Crabb
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Susan Gilson
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Anthony Gourley
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Tim Wheeler
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Brian Trest
- Facilities ManagementUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Glynnis Bowman
- Facilities ManagementUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Birthe V. Kjellerup
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
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23
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Dargahi A, Vosoughi M, Normohammadi A, Sedigh A, Gholizadeh H, Sadeghi H, Karami C, Jeddi F. Investigating SARS-CoV-2 RNA in five municipal wastewater treatment plants, hospital wastewater and wastewater collection networks during the COVID-19 pandemic in Ardabil Province, Iran. APPLIED WATER SCIENCE 2022; 12:256. [PMID: 36277855 PMCID: PMC9579531 DOI: 10.1007/s13201-022-01773-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Since 2019, the outbreak of coronavirus with acute respiratory symptoms has caused an epidemic worldwide. Transmission of the disease through respiratory droplets was announced as the main mode of transmission in 2020. But in this study, we discussed the method of indirect transmission of the virus through sewage. In this study, effluents related to urban and hospital wastewater treatment plants in 5 regions of Ardabil Province (northwest of Iran) were investigated. In this research, 120 samples were kept in pre-test conditions (temperature -20 degrees Celsius). To identify the viral genome, special primer and chain reaction probe targeting ORF1ab and N (nucleoprotein gene) genes were used. Out of a total of 120 samples, a total of 3 samples were positive. Wastewater epidemiology (WBE) can be considered as a cost-effective method in the diagnosis and prediction of pathogenic agents. And be considered an effective method for decision-making in order to protect the health of citizens.
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Affiliation(s)
- Abdollah Dargahi
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mehdi Vosoughi
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Ali Normohammadi
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Environmental Health Engineering, School of Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Anoshirvan Sedigh
- Department of Environmental Health Engineering, School of Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Helia Gholizadeh
- Department of Environmental Health Engineering, School of Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hadi Sadeghi
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Environmental Health Engineering, School of Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Chiman Karami
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Farhad Jeddi
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
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24
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Yi H, Liu J, Yao J, Wang R, Shi W, Lu C. Photoluminescence Mechanism of Carbon Dots: Triggering Multiple Color Emissions through Controlling the Degree of Protonation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196517. [PMID: 36235054 PMCID: PMC9571308 DOI: 10.3390/molecules27196517] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022]
Abstract
Carbon dots (CDs) have excellent optical properties, low toxicity and easy preparation, which have led to them being widely used in biomedicine, sensing and optical devices. However, although great progress has been made in the preparation of CDs, the detailed exploration of their photoluminescence (PL) mechanism is still under debate due to their complex structures and surface functionalities. Here, we proposed a single change in the pH of the synthesis condition, which had no effect on the CDs intrinsic core states and avoided the mutual influence of multiple PL origins. The m-phenylenediamine (m–PD) served as a carbon source, whose protonation degree determined the surface state of the resulting CDs and the accompanying fluorescence characteristics. The as-obtained CDs materials can be applied in the chemical sensor and anti-counterfeiting fields in a targeted manner. Therefore, our work not only contributes to the explanation of the CDs PL mechanism, but also obtains a series of CDs materials with controllable PL properties.
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25
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Rousis NI, Li Z, Bade R, McLachlan MS, Mueller JF, O'Brien JW, Samanipour S, Tscharke BJ, Thomaidis NS, Thomas KV. Socioeconomic status and public health in Australia: A wastewater-based study. ENVIRONMENT INTERNATIONAL 2022; 167:107436. [PMID: 35914338 DOI: 10.1016/j.envint.2022.107436] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/22/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Analysis of untreated municipal wastewater is recognized as an innovative approach to assess population exposure to or consumption of various substances. Currently, there are no published wastewater-based studies investigating the relationships between catchment social, demographic, and economic characteristics with chemicals using advanced non-targeted techniques. In this study, fifteen wastewater samples covering 27% of the Australian population were collected during a population Census. The samples were analysed with a workflow employing liquid chromatography high-resolution mass spectrometry and chemometric tools for non-target analysis. Socioeconomic characteristics of catchment areas were generated using Geospatial Information Systems software. Potential correlations were explored between pseudo-mass loads of the identified compounds and socioeconomic and demographic descriptors of the wastewater catchments derived from Census data. Markers of public health (e.g., cardiac arrhythmia, cardiovascular disease, anxiety disorder and type 2 diabetes) were identified in the wastewater samples by the proposed workflow. They were positively correlated with descriptors of disadvantage in education, occupation, marital status and income, and negatively correlated with descriptors of advantage in education and occupation. In addition, markers of polypropylene glycol (PPG) and polyethylene glycol (PEG) related compounds were positively correlated with housing and occupation disadvantage. High positive correlations were found between separated and divorced people and specific drugs used to treat cardiac arrhythmia, cardiovascular disease, and depression. Our robust non-targeted methodology in combination with Census data can identify relationships between biomarkers of public health, human behaviour and lifestyle and socio-demographics of whole populations. Furthermore, it can identify specific areas and socioeconomic groups that may need more assistance than others for public health issues. This approach complements important public health information and enables large-scale national coverage with a relatively small number of samples.
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Affiliation(s)
- Nikolaos I Rousis
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, QLD 4102, Australia; Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece.
| | - Zhe Li
- Department of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Richard Bade
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, QLD 4102, Australia
| | - Michael S McLachlan
- Department of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jochen F Mueller
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, QLD 4102, Australia
| | - Jake W O'Brien
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, QLD 4102, Australia
| | - Saer Samanipour
- Faculty of Science, Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park, 904 GD Amsterdam, the Netherlands
| | - Benjamin J Tscharke
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, QLD 4102, Australia
| | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Kevin V Thomas
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 20 Cornwall Street, Woolloongabba, QLD 4102, Australia
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26
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Analytical Chemistry: Tasks, Resolutions and Future Standpoints of the Quantitative Analyses of Environmental Complex Sample Matrices. ANALYTICA 2022. [DOI: 10.3390/analytica3030022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Currently, the challenges that analytical chemistry has to face are ever greater and more complex both from the point of view of the selectivity of analytical methods and their sensitivity. This is especially true in quantitative analysis, where various methods must include the development and validation of new materials, strategies, and procedures to meet the growing need for rapid, sensitive, selective, and green methods. In this context, given the International Guidelines, which over time, are updated and which set up increasingly stringent “limits”, constant innovation is required both in the pre-treatment procedures and in the instrumental configurations to obtain reliable, accurate, and reproducible information. In addition, the environmental field certainly represents the greatest challenge, as analytes are often present at trace and ultra-trace levels. These samples containing analytes at ultra-low concentration levels, therefore, require very labor-intensive sample preparation procedures and involve the high consumption of organic solvents that may not be considered “green”. In the literature, in recent years, there has been a strong development of increasingly high-performing sample preparation techniques, often “solvent-free”, as well as the development of hyphenated instrumental configurations that allow for reaching previously unimaginable levels of sensitivity. This review aims to provide an update of the most recent developments currently in use in sample pre-treatment and instrument configurations in the environmental field, also evaluating the role and future developments of analytical chemistry in light of upcoming challenges and new goals yet to be achieved.
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27
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Lou EG, Sapoval N, McCall C, Bauhs L, Carlson-Stadler R, Kalvapalle P, Lai Y, Palmer K, Penn R, Rich W, Wolken M, Brown P, Ensor KB, Hopkins L, Treangen TJ, Stadler LB. Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 35395314 DOI: 10.2139/ssrn.4022373] [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] [Indexed: 05/09/2023]
Abstract
Over the course of the COVID-19 pandemic, variants of SARS-CoV-2 have emerged that are more contagious and more likely to cause breakthrough infections. Targeted amplicon sequencing approach is a gold standard for identification and analysis of variants. However, when applied to environmental samples such as wastewater, it remains unclear how sensitive this method is for detecting variant-associated mutations in environmental samples. Here we directly compare a targeted amplicon sequencing approach (using ARTIC v3; hereafter referred to as sequencing) with RT-ddPCR quantification for the detection of five mutations that are characteristic of variants of concern (VoCs) in wastewater samples. In total, 547 wastewater samples were analyzed using both methods in parallel. When we observed positive mutation detections by RT-ddPCR, 42.6% of the detection events were missed by sequencing, due to negative detection or the limited read coverage at the mutation position. Further, when sequencing reported negative or depth-limited mutation detections, 26.7% of those events were instead positive detections by RT-ddPCR, highlighting the relatively poor sensitivity of sequencing. No or weak associations were observed between quantitative measurements of target mutations determined by RT-ddPCR and sequencing. These findings caution the use of quantitative measurements of SARS-CoV-2 variants in wastewater samples determined solely based on sequencing.
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Affiliation(s)
- Esther G Lou
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Camille McCall
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Lauren Bauhs
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Russell Carlson-Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Prashant Kalvapalle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Yanlai Lai
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Kyle Palmer
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Ryker Penn
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Whitney Rich
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Madeline Wolken
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Pamela Brown
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Katherine B Ensor
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX 77005, United States of America
| | - Loren Hopkins
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America; Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX 77005, United States of America
| | - Todd J Treangen
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America.
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Lou EG, Sapoval N, McCall C, Bauhs L, Carlson-Stadler R, Kalvapalle P, Lai Y, Palmer K, Penn R, Rich W, Wolken M, Brown P, Ensor KB, Hopkins L, Treangen TJ, Stadler LB. Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155059. [PMID: 35395314 PMCID: PMC8983075 DOI: 10.1016/j.scitotenv.2022.155059] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
Over the course of the COVID-19 pandemic, variants of SARS-CoV-2 have emerged that are more contagious and more likely to cause breakthrough infections. Targeted amplicon sequencing approach is a gold standard for identification and analysis of variants. However, when applied to environmental samples such as wastewater, it remains unclear how sensitive this method is for detecting variant-associated mutations in environmental samples. Here we directly compare a targeted amplicon sequencing approach (using ARTIC v3; hereafter referred to as sequencing) with RT-ddPCR quantification for the detection of five mutations that are characteristic of variants of concern (VoCs) in wastewater samples. In total, 547 wastewater samples were analyzed using both methods in parallel. When we observed positive mutation detections by RT-ddPCR, 42.6% of the detection events were missed by sequencing, due to negative detection or the limited read coverage at the mutation position. Further, when sequencing reported negative or depth-limited mutation detections, 26.7% of those events were instead positive detections by RT-ddPCR, highlighting the relatively poor sensitivity of sequencing. No or weak associations were observed between quantitative measurements of target mutations determined by RT-ddPCR and sequencing. These findings caution the use of quantitative measurements of SARS-CoV-2 variants in wastewater samples determined solely based on sequencing.
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Affiliation(s)
- Esther G Lou
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Camille McCall
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Lauren Bauhs
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Russell Carlson-Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Prashant Kalvapalle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Yanlai Lai
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Kyle Palmer
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Ryker Penn
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Whitney Rich
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Madeline Wolken
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America
| | - Pamela Brown
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America
| | - Katherine B Ensor
- Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX 77005, United States of America
| | - Loren Hopkins
- Houston Health Department, 8000 N. Stadium Dr., Houston, TX 77054, United States of America; Department of Statistics, Rice University, 6100 Main Street MS 138, Houston, TX 77005, United States of America
| | - Todd J Treangen
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, United States of America
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, MS 519, Houston, TX 77005, United States of America.
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Hyllestad S, Myrmel M, Lomba JAB, Jordhøy F, Schipper SK, Amato E. Effectiveness of environmental surveillance of SARS-CoV-2 as an early warning system during the first year of the COVID-19 pandemic: a systematic review. JOURNAL OF WATER AND HEALTH 2022; 20:1223-1242. [PMID: 36044191 DOI: 10.2166/wh.2022.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Since infected persons shed SARS-CoV-2 in faeces before symptoms appear, environmental surveillance (ES) may serve as an early warning system (EWS) for COVID-19 and new variants of concern. The ES of SARS-CoV-2 has been widely reviewed; however, its effectiveness as an EWS for SARS-CoV-2 in terms of timeliness, sensitivity and specificity has not been systematically assessed. We conducted a systematic review to identify and synthesise evidence on the ES of SARS-CoV-2 as an EWS to evaluate the added value for public health. Of 1,014 studies identified, we considered 29 for a qualitative synthesis of the timeliness of ES as an EWS for COVID-19, while six studies were assessed for the ability to detect new variants and two for both aims. The synthesis indicates ES may serve as an EWS of 1-2 weeks. ES could complement clinical surveillance for SARS-CoV-2; however, its cost-benefit value for public health decisions needs to be assessed based on the stage of the pandemic and resources available. Studies focusing methodological knowledge gaps as well as how to use and interpret ES signals for public health actions are needed, as is the sharing of knowledge within countries/areas with long experience of such surveillance.
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Affiliation(s)
- Susanne Hyllestad
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jose Antonio Baz Lomba
- Department of Environmental Chemistry and Technology, Norwegian Institute for Water Research (NIVA), Oslo, Norway
| | - Fredrik Jordhøy
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Svanhild Kjørsvik Schipper
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Ettore Amato
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
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30
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A Review on SARS-CoV-2 Genome in the Aquatic Environment of Africa: Prevalence, Persistence and the Future Prospects. WATER 2022. [DOI: 10.3390/w14132020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The COVID-19 pandemic (Coronavirus disease 2019) remains problematic in all its manifestations on the global stage where countless events of human-to-human exposure have led to fatal cases; thus, the aftermath being an unprecedented public health concern, with inaccessible health care and the instability of economies and financial institutions. These pose massive obstacles that can insatiably devour existing human resources causing negative impacts, especially in developing countries. Tracking the origin, dissemination and mutating strains of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) on population-wide scales is a somewhat overwhelming task, with the urgent need to map the dissemination and magnitude of SARS-CoV-2 in near real-time. This review paper focuses on the poor sanitation of some waterbodies and wastewater management policies in low-income African countries, highlighting how these contribute to the COVID-19 pandemic on the continent. Since the outbreak of the novel coronavirus pandemic, there has been an upsurge in scientific literature and studies concerning SARS-CoV-2 with different opinions and findings. The current paper highlights the challenges and also summarizes the environmental aspects related to the monitoring and fate of the SARS-CoV-2 genomes in the aquatic milieu of Sub-Saharan Africa.
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31
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Yanaç K, Adegoke A, Wang L, Uyaguari M, Yuan Q. Detection of SARS-CoV-2 RNA throughout wastewater treatment plants and a modeling approach to understand COVID-19 infection dynamics in Winnipeg, Canada. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153906. [PMID: 35218826 PMCID: PMC8864809 DOI: 10.1016/j.scitotenv.2022.153906] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 05/07/2023]
Abstract
Although numerous studies have detected SARS-CoV-2 RNA in wastewater and attempted to find correlations between the concentration of SARS-CoV-2 RNA and the number of cases, no consensus has been reached on sample collection and processing, and data analysis. Moreover, the fate of SARS-CoV-2 in wastewater treatment plants is another issue, specifically regarding the discharge of the virus into environmental settings and the water cycle. The current study monitored SARS-CoV-2 RNA in influent and effluent wastewater samples with three different concentration methods and sludge samples over six months (July to December 2020) to compare different virus concentration methods, assess the fate of SARS-CoV-2 RNA in wastewater treatment plants, and describe the potential relationship between SARS-CoV-2 RNA concentrations in influent and infection dynamics. Skimmed milk flocculation (SMF) resulted in 15.27 ± 3.32% recovery of an internal positive control, Armored RNA, and a high positivity rate of SARS-CoV-2 RNA in stored wastewater samples compared to ultrafiltration methods employing a prefiltration step to eliminate solids in fresh wastewater samples. Our results suggested that SARS-CoV-2 RNA may predominate in solids, and therefore, concentration methods focusing on both supernatant and solid fractions may result in better recovery. SARS-CoV-2 RNA was detected in influent and primary sludge samples but not in secondary and final effluent samples, indicating a significant reduction during primary and secondary treatments. SARS-CoV-2 RNA was first detected in influent on September 30th, 2020. A decay-rate formula was applied to estimate initial concentrations of late-processed samples with SMF. A model based on shedding rate and new cases was applied to estimate SARS-CoV-2 RNA concentrations and the number of active shedders. Inferred sensitivity of observed and modeled concentrations to the fluctuations in new cases and test-positivity rates indicated a potential contribution of newly infected individuals to SARS-CoV-2 RNA loads in wastewater.
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Affiliation(s)
- Kadir Yanaç
- Department of Civil Engineering, University of Manitoba, Winnipeg, Canada
| | - Adeola Adegoke
- Department of Statistics, University of Manitoba, Winnipeg, Canada
| | - Liqun Wang
- Department of Statistics, University of Manitoba, Winnipeg, Canada
| | - Miguel Uyaguari
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Qiuyan Yuan
- Department of Civil Engineering, University of Manitoba, Winnipeg, Canada.
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Kapoor V, Al-Duroobi H, Phan DC, Palekar RS, Blount B, Rambhia KJ. Wastewater surveillance for SARS-CoV-2 to support return to campus: Methodological considerations and data interpretation. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2022; 27:100362. [PMID: 35402756 PMCID: PMC8975751 DOI: 10.1016/j.coesh.2022.100362] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The COVID-19 pandemic has been challenging for various institutions such as school systems due to widespread closures. As schools re-open their campuses to in-person education, there is a need for frequent screening and monitoring of the virus to ensure the safety of students and staff and to limit risk to the surrounding community. Wastewater surveillance (WWS) of SARS-CoV-2 is a rapid and economical approach to determine the extent of COVID-19 in the community. The focus of this review is on the emergence of WWS as a tool for safe return to school campuses, taking into account methodological considerations such as site selection, sample collection and processing, SARS-CoV-2 quantification, and data interpretation. Recently published studies on the implementation of COVID-19 WWS on school and college campuses were reviewed. While there are several logistical and technical challenges, WWS can be used to inform decision-making at the school campus and/or building level.
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Affiliation(s)
- Vikram Kapoor
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Haya Al-Duroobi
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Duc C Phan
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, San Antonio, TX 78249, USA
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Longer amplicons provide better sensitivity for electrochemical sensing of viral nucleic acid in water samples using PCB electrodes. Sci Rep 2022; 12:8814. [PMID: 35614180 PMCID: PMC9130999 DOI: 10.1038/s41598-022-12818-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/04/2022] [Indexed: 12/13/2022] Open
Abstract
The importance of monitoring environmental samples has gained a lot of prominence since the onset of COVID-19 pandemic, and several surveillance efforts are underway using gold standard, albeit expensive qPCR-based techniques. Electrochemical DNA biosensors could offer a potential cost-effective solution suitable for monitoring of environmental water samples in lower middle income countries. In this work, we demonstrate electrochemical detection of amplicons as long as \documentclass[12pt]{minimal}
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\begin{document}$${503}\,\hbox {bp}$$\end{document}503bp obtained from Phi6 bacteriophage (a popular surrogate for SARS-CoV-2) isolated from spiked lake water samples, using ENIG finish PCB electrodes with no surface modification. The electrochemical sensor response is thoroughly characterised for two DNA fragments of different lengths (\documentclass[12pt]{minimal}
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\begin{document}$${117}\,\hbox {bp}$$\end{document}117bp and \documentclass[12pt]{minimal}
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\begin{document}$${503}\,\hbox {bp}$$\end{document}503bp), and the impact of salt in PCR master mix on methylene blue (MB)-DNA interactions is studied. Our findings establish that length of the DNA fragment significantly determines electrochemical sensitivity, and the ability to detect long amplicons without gel purification of PCR products demonstrated in this work bodes well for realisation of fully-automated solutions for in situ measurement of viral load in water samples.
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Radu E, Masseron A, Amman F, Schedl A, Agerer B, Endler L, Penz T, Bock C, Bergthaler A, Vierheilig J, Hufnagl P, Korschineck I, Krampe J, Kreuzinger N. Emergence of SARS-CoV-2 Alpha lineage and its correlation with quantitative wastewater-based epidemiology data. WATER RESEARCH 2022; 215:118257. [PMID: 35303559 PMCID: PMC8898540 DOI: 10.1016/j.watres.2022.118257] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 02/22/2022] [Accepted: 03/05/2022] [Indexed: 05/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) gave rise to an international public health emergency in 3 months after its emergence in Wuhan, China. Typically for an RNA virus, random mutations occur constantly leading to new lineages, incidental with a higher transmissibility. The highly infective alpha lineage, firstly discovered in the UK, led to elevated mortality and morbidity rates as a consequence of Covid-19, worldwide. Wastewater surveillance proved to be a powerful tool for early detection and subsequent monitoring of the dynamics of SARS-CoV-2 and its variants in a defined catchment. Using a combination of sequencing and RT-qPCR approaches, we investigated the total SARS-CoV-2 concentration and the emergence of the alpha lineage in wastewater samples in Vienna, Austria linking it to clinical data. Based on a non-linear regression model and occurrence of signature mutations, we conclude that the alpha variant was present in Vienna sewage samples already in December 2020, even one month before the first clinical case was officially confirmed and reported by the health authorities. This provides evidence that a well-designed wastewater monitoring approach can provide a fast snapshot and may detect the circulating lineages in wastewater weeks before they are detectable in the clinical samples. Furthermore, declining 14 days prevalence data with simultaneously increasing SARS-CoV-2 total concentration in wastewater indicate a different shedding behavior for the alpha variant. Overall, our results support wastewater surveillance to be a suitable approach to spot early circulating SARS-CoV-2 lineages based on whole genome sequencing and signature mutations analysis.
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Affiliation(s)
- Elena Radu
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz, 13/2261, 1040, Vienna, Austria; Institute of Virology Stefan S. Nicolau, Romanian Academy of Science, 285 Mihai Bravu Avenue, 030304, Bucharest, Romania
| | - Amandine Masseron
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz, 13/2261, 1040, Vienna, Austria
| | - Fabian Amman
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Anna Schedl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090, Vienna, Austria
| | - Julia Vierheilig
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz, 13/2261, 1040, Vienna, Austria
| | - Peter Hufnagl
- Austrian Agency for Health and Food Safety AGES, Department for Medical Microbiology and Hygiene, Währingerstraße 25A, 1090, Vienna, Austria
| | - Irina Korschineck
- Ingenetix GmbH, Arsenalstraße 11/Hüttenbrennergasse 5, 1030, Vienna, Austria
| | - Jörg Krampe
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz, 13/2261, 1040, Vienna, Austria
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, TU Wien, Karlsplatz, 13/2261, 1040, Vienna, Austria.
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Bertels X, Demeyer P, Van den Bogaert S, Boogaerts T, van Nuijs ALN, Delputte P, Lahousse L. Factors influencing SARS-CoV-2 RNA concentrations in wastewater up to the sampling stage: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153290. [PMID: 35066048 PMCID: PMC8772136 DOI: 10.1016/j.scitotenv.2022.153290] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/27/2021] [Accepted: 01/16/2022] [Indexed: 04/15/2023]
Abstract
Wastewater-based surveillance (WBS) for SARS-CoV-2 RNA is a promising complementary approach to monitor community viral circulation. A myriad of factors, however, can influence RNA concentrations in wastewater, impeding its epidemiological value. This article aims to provide an overview and discussion of factors up to the sampling stage that impact SARS-CoV-2 RNA concentration estimates in wastewater. To this end, a systematic review was performed in three databases (MEDLINE, Web of Science and Embase) and two preprint servers (MedRxiv and BioRxiv). Two authors independently screened and selected articles published between January 1, 2019 and May 4, 2021. A total of 22 eligible articles were included in this systematic review. The following factors up to sampling were identified to have an influence on SARS-CoV-2 RNA concentrations in wastewater and its interpretation: (i) shedding-related factors, including faecal shedding parameters (i.e. shedding pattern, recovery, rate, and load distribution), (ii) population size, (iii) in-sewer factors, including solid particles, organic load, travel time, flow rate, wastewater pH and temperature, and (iv) sampling strategy. In conclusion, factors influencing SARS-CoV-2 RNA concentration estimates in wastewater were identified and research gaps were discussed. The identification of these factors supports the need for further research on WBS for COVID-19.
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Affiliation(s)
- Xander Bertels
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Phaedra Demeyer
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Siel Van den Bogaert
- Laboratory for Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.
| | - Tim Boogaerts
- Toxicological Centre, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.
| | - Alexander L N van Nuijs
- Toxicological Centre, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.
| | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.
| | - Lies Lahousse
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
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36
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Paruch L. Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:5128. [PMID: 35564522 PMCID: PMC9105083 DOI: 10.3390/ijerph19095128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022]
Abstract
Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.
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Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research-NIBIO Oluf Thesens vei 43, 1433 Aas, Norway
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37
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High-throughput optical assays for sensing serine hydrolases in living systems and their applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Boogaerts T, Van den Bogaert S, Van Poelvoorde LAE, El Masri D, De Roeck N, Roosens NHC, Lesenfants M, Lahousse L, Van Hoorde K, van Nuijs ALN, Delputte P. Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. Viruses 2022; 14:610. [PMID: 35337017 PMCID: PMC8953730 DOI: 10.3390/v14030610] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Since the beginning of the COVID-19 pandemic, the wastewater-based epidemiology (WBE) of SARS-CoV-2 has been used as a complementary indicator to follow up on the trends in the COVID-19 spread in Belgium and in many other countries. To further develop the use of WBE, a multiplex digital polymerase chain reaction (dPCR) assay was optimized, validated and applied for the measurement of emerging SARS-CoV-2 variants of concern (VOC) in influent wastewater (IWW) samples. Key mutations were targeted in the different VOC strains, including SΔ69/70 deletion, N501Y, SΔ241 and SΔ157. The presented bioanalytical method was able to distinguish between SARS-CoV-2 RNA originating from the wild-type and B.1.1.7, B.1.351 and B.1.617.2 variants. The dPCR assay proved to be sensitive enough to detect low concentrations of SARS-CoV-2 RNA in IWW since the limit of detection of the different targets ranged between 0.3 and 2.9 copies/µL. This developed WBE approach was applied to IWW samples originating from different Belgian locations and was able to monitor spatio-temporal changes in the presence of targeted VOC strains in the investigated communities. The present dPCR assay developments were realized to bring added-value to the current national WBE of COVID-19 by also having the spatio-temporal proportions of the VoC in presence in the wastewaters.
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Affiliation(s)
- Tim Boogaerts
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium;
| | - Siel Van den Bogaert
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
| | - Laura A. E. Van Poelvoorde
- Scientific Directorate of Biological Health Risks, Service Transerversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (L.A.E.V.P.); (N.H.C.R.)
| | - Diala El Masri
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
| | - Naomi De Roeck
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
| | - Nancy H. C. Roosens
- Scientific Directorate of Biological Health Risks, Service Transerversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (L.A.E.V.P.); (N.H.C.R.)
| | - Marie Lesenfants
- Scientific Directorate of Epidemiology and Public Health, Service Epidemiology of Infectious Diseases, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium;
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium;
| | - Koenraad Van Hoorde
- Scientific Directorate of Infectious Diseases in Humans, Service Foodborne Pathogens, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium;
| | | | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
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Evaluation of Pre-Analytical and Analytical Methods for Detecting SARS-CoV-2 in Municipal Wastewater Samples in Northern Italy. WATER 2022. [DOI: 10.3390/w14050833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
(1) Background: The surveillance of SARS-CoV-2 RNA in urban wastewaters allows one to monitor the presence of the virus in a population, including asymptomatic and symptomatic individuals, capturing the real circulation of this pathogen. The aim of this study was to evaluate the performance of different pre-analytical and analytical methods for identifying the presence of SARS-CoV-2 in untreated municipal wastewaters samples by conducting an inter-laboratory proficiency test. (2) Methods: three methods of concentration, namely, (A) Dextran and PEG-6000 two-phase separation, (B) PEG-8000 precipitation without a chloroform purification step and (C) PEG-8000 precipitation with a chloroform purification step were combined with three different protocols of RNA extraction by using commercial kits and were tested by using two primers/probe sets in three different master mixes. (3) Results: PEG-8000 precipitation without chloroform treatment showed the best performance in the SARS-CoV-2 recovery; no major differences were observed among the protocol of RNA extraction and the one-step real-time RT-PCR master mix kits. The highest analytic sensitivity was observed by using primers/probe sets targeting the N1/N3 fragments of SARS-CoV-2. (4) Conclusions: PEG-8000 precipitation in combination with real-time RT-PCR targeting the N gene (two fragments) was the best performing workflow for the detection of SARS-CoV-2 RNA in municipal wastewaters.
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Tharak A, Kopperi H, Hemalatha M, Kiran U, C. G. G, Moharir S, Mishra RK, Mohan SV. Longitudinal and Long-Term Wastewater Surveillance for COVID-19: Infection Dynamics and Zoning of Urban Community. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19052697. [PMID: 35270390 PMCID: PMC8910010 DOI: 10.3390/ijerph19052697] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023]
Abstract
Wastewater-based epidemiology (WBE) is emerging as a potential approach to study the infection dynamics of SARS-CoV-2 at a community level. Periodic sewage surveillance can act as an indicative tool to predict the early surge of pandemic within the community and understand the dynamics of infection and, thereby, facilitates for proper healthcare management. In this study, we performed a long-term epidemiological surveillance to assess the SARS-CoV-2 spread in domestic sewage over one year (July 2020 to August 2021) by adopting longitudinal sampling to represent a selected community (~2.5 lakhs population). Results indicated temporal dynamics in the viral load. A consistent amount of viral load was observed during the months from July 2020 to November 2020, suggesting a higher spread of the viral infection among the community, followed by a decrease in the subsequent two months (December 2020 and January 2021). A marginal increase was observed during February 2021, hinting at the onset of the second wave (from March 2021) that reached it speak in April 2021. Dynamics of the community infection rates were calculated based on the viral gene copies to assess the severity of COVID-19 spread. With the ability to predict the infection spread, longitudinal WBE studies also offer the prospect of zoning specific areas based on the infection rates. Zoning of the selected community based on the infection rates assists health management to plan and manage the infection in an effective way. WBE promotes clinical inspection with simultaneous disease detection and management, in addition to an advance warning signal to anticipate outbreaks, with respect to the slated community/zones, to tackle, prepare for and manage the pandemic.
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Affiliation(s)
- Athmakuri Tharak
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; (A.T.); (H.K.); (M.H.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
| | - Harishankar Kopperi
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; (A.T.); (H.K.); (M.H.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
| | - Manupati Hemalatha
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; (A.T.); (H.K.); (M.H.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
| | - Uday Kiran
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, India; (G.C.G.); (S.M.)
| | - Gokulan C. G.
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, India; (G.C.G.); (S.M.)
| | - Shivranjani Moharir
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, India; (G.C.G.); (S.M.)
| | - Rakesh K. Mishra
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, India; (G.C.G.); (S.M.)
- Correspondence: (R.K.M.); (S.V.M.)
| | - S. Venkata Mohan
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; (A.T.); (H.K.); (M.H.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
- Correspondence: (R.K.M.); (S.V.M.)
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Wade MJ, Lo Jacomo A, Armenise E, Brown MR, Bunce JT, Cameron GJ, Fang Z, Farkas K, Gilpin DF, Graham DW, Grimsley JMS, Hart A, Hoffmann T, Jackson KJ, Jones DL, Lilley CJ, McGrath JW, McKinley JM, McSparron C, Nejad BF, Morvan M, Quintela-Baluja M, Roberts AMI, Singer AC, Souque C, Speight VL, Sweetapple C, Walker D, Watts G, Weightman A, Kasprzyk-Hordern B. Understanding and managing uncertainty and variability for wastewater monitoring beyond the pandemic: Lessons learned from the United Kingdom national COVID-19 surveillance programmes. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127456. [PMID: 34655869 PMCID: PMC8498793 DOI: 10.1016/j.jhazmat.2021.127456] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic has put unprecedented pressure on public health resources around the world. From adversity, opportunities have arisen to measure the state and dynamics of human disease at a scale not seen before. In the United Kingdom, the evidence that wastewater could be used to monitor the SARS-CoV-2 virus prompted the development of National wastewater surveillance programmes. The scale and pace of this work has proven to be unique in monitoring of virus dynamics at a national level, demonstrating the importance of wastewater-based epidemiology (WBE) for public health protection. Beyond COVID-19, it can provide additional value for monitoring and informing on a range of biological and chemical markers of human health. A discussion of measurement uncertainty associated with surveillance of wastewater, focusing on lessons-learned from the UK programmes monitoring COVID-19 is presented, showing that sources of uncertainty impacting measurement quality and interpretation of data for public health decision-making, are varied and complex. While some factors remain poorly understood, we present approaches taken by the UK programmes to manage and mitigate the more tractable sources of uncertainty. This work provides a platform to integrate uncertainty management into WBE activities as part of global One Health initiatives beyond the pandemic.
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Affiliation(s)
- Matthew J Wade
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK.
| | - Anna Lo Jacomo
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Bristol University, Department of Engineering Mathematics, Bristol BS8 1TW, UK
| | - Elena Armenise
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Mathew R Brown
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Joshua T Bunce
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK; Department for Environment, Food and Rural Affairs, Seacole Building, 2 Marsham Street, London SW1P 4DF, UK
| | - Graeme J Cameron
- Scottish Environment Protection Agency, Strathallan House, Stirling FK9 4TZ, UK
| | - Zhou Fang
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Kata Farkas
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor LL57 2UW, UK
| | - Deidre F Gilpin
- Queen's University Belfast, School of Pharmacy, Lisburn Road, Belfast BT9 7BL, UK
| | - David W Graham
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Jasmine M S Grimsley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK
| | - Alwyn Hart
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Till Hoffmann
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Imperial College London, Department of Mathematics, London SW7 2AZ, UK
| | - Katherine J Jackson
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David L Jones
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor LL57 2UW, UK; The University of Western Australia, UWA School of Agriculture and Environment, Perth, WA 6009, Australia
| | - Chris J Lilley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK
| | - John W McGrath
- Queen's University Belfast, School of Biological Sciences, Chlorine Gardens, Belfast BT9 5DL, UK
| | - Jennifer M McKinley
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Cormac McSparron
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Behnam F Nejad
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Mario Morvan
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, UK
| | - Marcos Quintela-Baluja
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Adrian M I Roberts
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Andrew C Singer
- UK Centre for Ecology and Hydrology, Benson Lane, Wallingford OX10 8BB, UK
| | - Célia Souque
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University of Oxford, Department of Zoology, Mansfield Road, Oxford OX1 3SZ, UK
| | - Vanessa L Speight
- University of Sheffield, Department of Civil and Structural Engineering, Mappin Street, Sheffield S1 3JD, UK
| | - Chris Sweetapple
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University of Exeter, Centre for Water Systems, College of Engineering, Mathematics and Physical Sciences, Exeter EX4 4QF, UK
| | - David Walker
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth DT4 8UB, UK
| | - Glenn Watts
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Andrew Weightman
- Cardiff University, Cardiff School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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Castiglioni S, Schiarea S, Pellegrinelli L, Primache V, Galli C, Bubba L, Mancinelli F, Marinelli M, Cereda D, Ammoni E, Pariani E, Zuccato E, Binda S. SARS-CoV-2 RNA in urban wastewater samples to monitor the COVID-19 pandemic in Lombardy, Italy (March-June 2020). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150816. [PMID: 34627901 PMCID: PMC8497959 DOI: 10.1016/j.scitotenv.2021.150816] [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: 08/05/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 04/15/2023]
Abstract
Wastewater-based viral surveillance was proposed as a promising approach to monitor the circulation of SARS-CoV-2 in the general population. The aim of this study was to develop an analytical method to detect SARS-CoV-2 RNA in urban wastewater, and apply it to follow the trends of epidemic in the framework of a surveillance network in the Lombardy region (Northern Italy). This area was the first hotspot of COVID-19 in Europe and was severely affected. Composite 24 h samples were collected weekly in eight cities from end-March to mid-June 2020 (first peak of the pandemic). The method developed and optimized, involved virus concentration using PEG centrifugation, and one-step real-time RT-PCR for analysis. SARS-CoV-2 RNA was identified in 65 (61%) out of 107 samples, and the viral concentrations (up to 2.1 E + 05 copies/L) were highest in March-April. By mid-June, wastewater samples tested negative in all the cities corresponding to the very low number of cases recorded in the same period. Viral loads were calculated considering the wastewater daily flow rate and the population served by each wastewater treatment plant, and were used for inter- city comparison. The highest viral loads were found in Brembate, Ranica and Lodi corresponding to the hotspots of the first peak of pandemic. The pattern of decrease of SARS-CoV-2 in wastewater was closely comparable to the decline of active COVID-19 cases in the population, reflecting the effect of lock-down. This study tested wastewater surveillance of SARS-CoV-2 to follow the pandemic trends in one of most affected areas worldwide, demonstrating that it can integrate ongoing virological surveillance of COVID-19, providing information from both symptomatic and asymptomatic individuals, and monitoring the effect of health interventions.
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Affiliation(s)
- Sara Castiglioni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy.
| | - Silvia Schiarea
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Valeria Primache
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Laura Bubba
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Federica Mancinelli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy
| | | | | | | | - Elena Pariani
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Ettore Zuccato
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy
| | - Sandro Binda
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
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43
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Zhu Y, Wu X, Gu A, Dobelle L, Cid C, Li J, Hoffmann MR. Membrane-Based In-Gel Loop-Mediated Isothermal Amplification (mgLAMP) System for SARS-CoV-2 Quantification in Environmental Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:862-873. [PMID: 34967203 PMCID: PMC8751019 DOI: 10.1021/acs.est.1c04623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 05/06/2023]
Abstract
Since the COVID-19 pandemic is expected to become endemic, quantification of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in ambient waters is critical for environmental surveillance and for early detection of outbreaks. Herein, we report the development of a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system that is designed for the rapid point-of-use quantification of SARS-CoV-2 particles in environmental waters. The mgLAMP system integrates the viral concentration, in-assay viral lysis, and on-membrane hydrogel-based RT-LAMP quantification using enhanced fluorescence detection with a target-specific probe. With a sample-to-result time of less than 1 h, mgLAMP successfully detected SARS-CoV-2 below 0.96 copies/mL in Milli-Q water. In surface water, the lowest detected SARS-CoV-2 concentration was 93 copies/mL for mgLAMP, while the reverse transcription quantitative polymerase chain reaction (RT-qPCR) with optimal pretreatment was inhibited at 930 copies/mL. A 3D-printed portable device is designed to integrate heated incubation and fluorescence illumination for the simultaneous analysis of nine mgLAMP assays. Smartphone-based imaging and machine learning-based image processing are used for the interpretation of results. In this report, we demonstrate that mgLAMP is a promising method for large-scale environmental surveillance of SARS-CoV-2 without the need for specialized equipment, highly trained personnel, and labor-intensive procedures.
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Affiliation(s)
- Yanzhe Zhu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Xunyi Wu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Alan Gu
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Leopold Dobelle
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Clément
A. Cid
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Jing Li
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
| | - Michael R. Hoffmann
- Linde Laboratories, California
Institute of Technology, Pasadena, California 91125, United States
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44
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Calderón-Franco D, Orschler L, Lackner S, Agrawal S, Weissbrodt DG. Monitoring SARS-CoV-2 in sewage: Toward sentinels with analytical accuracy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150244. [PMID: 34798752 PMCID: PMC8428994 DOI: 10.1016/j.scitotenv.2021.150244] [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: 07/10/2021] [Revised: 08/21/2021] [Accepted: 09/05/2021] [Indexed: 05/07/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemia has been one of the most difficult challenges humankind has recently faced. Wastewater-based epidemiology has emerged as a tool for surveillance and mitigation of potential viral outbreaks, circumventing biases introduced by clinical patient testing. Due to the situation urgency, protocols followed for isolating viral RNA from sewage were not adapted for such sample matrices. In parallel to their implementation for fast collection of data to sustain surveillance and mitigation decisions, molecular protocols need to be harmonized to deliver accurate, reproducible, and comparable analytical outputs. Here we studied analytical variabilities linked to viral RNA isolation methods from sewage. Three different influent wastewater volumes were used to assess the effects of filtered volumes (50, 100 or 500 mL) for capturing viral particles. Three different concentration strategies were tested: electronegative membranes, polyethersulfone membranes, and anion-exchange diethylaminoethyl cellulose columns. To compare the number of viral particles, different RNA isolation methods (column-based vs. magnetic beads) were compared. The effect of extra RNA purification steps and different RT-qPCR strategies (one step vs. two-step) were also evaluated. Results showed that the combination of 500 mL filtration volume through electronegative membranes and without multiple RNA purification steps (using column-based RNA purification) using two-step RT-qPCR avoided false negatives when basal viral load in sewage are present and yielded more consistent results during the surveillance done during the second-wave in Delft (The Hague area, The Netherlands). By paving the way for standardization of methods for the sampling, concentration and molecular detection of SARS-CoV-2 viruses from sewage, these findings can help water and health surveillance authorities to use and trust results coming from wastewater based epidemiology studies in order to anticipate SARS-CoV-2 outbreaks.
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Affiliation(s)
- David Calderón-Franco
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Laura Orschler
- Technische Universität Darmstadt, Institute IWAR, 8 Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - Susanne Lackner
- Technische Universität Darmstadt, Institute IWAR, 8 Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - Shelesh Agrawal
- Technische Universität Darmstadt, Institute IWAR, 8 Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
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Alygizakis N, Galani A, Rousis NI, Aalizadeh R, Dimopoulos MA, Thomaidis NS. Change in the chemical content of untreated wastewater of Athens, Greece under COVID-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149230. [PMID: 34364275 PMCID: PMC8321698 DOI: 10.1016/j.scitotenv.2021.149230] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 04/14/2023]
Abstract
COVID-19 pandemic spread rapidly worldwide with unanticipated effects on mental health, lifestyle, stability of economies and societies. Although many research groups have already reported SARS-CoV-2 surveillance in untreated wastewater, only few studies evaluated the implications of the pandemic on the use of chemicals by influent wastewater analysis. Wide-scope target and suspect screening were used to monitor the effects of the pandemic on the Greek population through wastewater-based epidemiology. Composite 24 h influent wastewater samples were collected from the wastewater treatment plant of Athens during the first lockdown and analyzed by liquid chromatography mass spectrometry. A wide range of compounds was investigated (11,286), including antipsychotic drugs, illicit drugs, tobacco compounds, food additives, pesticides, biocides, surfactants and industrial chemicals. Mass loads of chemical markers were estimated and compared with the data obtained under non-COVID-19 conditions (campaign 2019). The findings revealed increases in surfactants (+196%), biocides (+152%), cationic quaternary ammonium surfactants (used as surfactants and biocides) (+331%), whereas the most important decreases were estimated for tobacco (-33%) and industrial chemicals (-52%). The introduction of social-restriction measures by the government affected all aspects of life.
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Affiliation(s)
- Nikiforos Alygizakis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece.
| | - Aikaterini Galani
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Nikolaos I Rousis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Reza Aalizadeh
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Meletios-Athanasios Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, 15528 Athens, Greece
| | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece.
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Mainardi PH, Bidoia ED. Challenges and emerging perspectives of an international SARS-CoV-2 epidemiological surveillance in wastewater. AN ACAD BRAS CIENC 2021; 93:e20210163. [PMID: 34878048 DOI: 10.1590/0001-3765202120210163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/23/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 is a new type of coronavirus capable to infect humans and cause the severe acute respiratory syndrome COVID-19, a disease that has been causing huge impacts across the Earth. COVID-19 patients, including mild, pre-symptomatic and asymptomatic cases, were often seen to contain infectious fragments of SARS-CoV-2 in feces and urine samples. Therefore, studies to detect the new coronavirus in wastewater, which collect and concentrate human excreta, have been extremely useful as a viral tracking tool in communities. This type of monitoring, in addition to serve as a non-invasive early warning of COVID-19 outbreaks, would provide better predictions about the SARS-CoV-2 spread and strongly contribute to maintenance the global health. Although current methods to detect viruses in wastewater, based on molecular RT-PCR and RT-qPCR techniques, were considered as reliable and provided accurate qualitative and quantitative results, they have been facing considerable challenges concerning the SARS-CoV-2 surveillance. In this review, the methods used to detect the SARS-CoV-2 in wastewater and the challenges to implement an international viral monitoring network were described. The article also addressed the emerging perspectives associated with the SARS-CoV-2 epidemiological surveillance in this environment and the importance of a worldwide collaboration to generate and disseminate the detection results.
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Affiliation(s)
- Pedro H Mainardi
- Universidade Estadual Paulista Júlio de Mesquita Filho /UNESP, Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Av. 24A, 1515, Bela Vista, 13506900 Rio Claro, SP, Brazil
| | - Ederio D Bidoia
- Universidade Estadual Paulista Júlio de Mesquita Filho /UNESP, Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Av. 24A, 1515, Bela Vista, 13506900 Rio Claro, SP, Brazil
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47
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Wang Q, Liu L. On the Critical Role of Human Feces and Public Toilets in the Transmission of COVID-19: Evidence from China. SUSTAINABLE CITIES AND SOCIETY 2021; 75:103350. [PMID: 34540563 PMCID: PMC8433098 DOI: 10.1016/j.scs.2021.103350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 05/05/2023]
Abstract
The surprising spread speed of the COVID-19 pandemic creates an urgent need for investigating the transmission chain or transmission pattern of COVID-19 beyond the traditional respiratory channels. This study therefore examines whether human feces and public toilets play a critical role in the transmission of COVID-19. First, it develops a theoretical model that simulates the transmission chain of COVID-19 through public restrooms. Second, it uses stabilized epidemic data from China to empirically examine this theory, conducting an empirical estimation using a two-stage least squares (2SLS) model with appropriate instrumental variables (IVs). This study confirms that the wastewater directly promotes the transmission of COVID-19 within a city. However, the role of garbage in this transmission chain is more indirect in the sense that garbage has a complex relationship with public toilets, and it promotes the transmission of COVID-19 within a city through interaction with public toilets and, hence, human feces. These findings have very strong policy implications in the sense that if we can somehow use the ratio of public toilets as a policy instrument, then we can find a way to minimize the total number of infections in a region. As shown in this study, pushing the ratio of public toilets (against open defecation) to the local population in a city to its optimal level would help to reduce the total infection in a region.
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Affiliation(s)
- Qiuyun Wang
- School of Economics, Southwestern University of Finance and Economics, P.R China
| | - Lu Liu
- School of Economics, Southwestern University of Finance and Economics, P.R China
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Picó Y, Barceló D. Mass Spectrometry in Wastewater-Based Epidemiology for the Determination of Small and Large Molecules as Biomarkers of Exposure: Toward a Global View of Environment and Human Health under the COVID-19 Outbreak. ACS OMEGA 2021; 6:30865-30872. [PMID: 34841130 PMCID: PMC8613814 DOI: 10.1021/acsomega.1c04362] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/22/2021] [Indexed: 05/08/2023]
Abstract
Wastewater-based epidemiology (WBE) estimates collective consumption or exposure to chemicals or pathogens by monitoring the substances excreted in the population's wastewater. Advances in mass spectrometry (MS) and the application of some clinical diagnostic tools and proteomics to wastewater fingerprinting have been linked to the discovery of new biomarkers and indicators of population health and are broadening the scope of WBE that nowadays cover not only small molecule biomarkers but also genetic biomarkers, large molecules, viruses, infection diseases, resistance, etc. This mini-review highlights recent WBE advances using MS and how this progress can create a fingerprint of a city's health hazards, habits, and lifestyle, which is gaining in public health emphasis.
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Affiliation(s)
- Yolanda Picó
- Environmental
and Food Safety Research Group-University of Valencia (SAMA-UV), Desertification
Research Centre (CIDE), Joint Center CSIC-University
of Valencia-Generalitat Valenciana, Moncada Naquera Road km 4.3, 46113 Moncada, Valencia, Spain
| | - Damià Barceló
- Water
and Soil Quality Research Group, Department of Environmental Chemistry, IDAEA-CSIC, C/Jordi Girona 18−26, 08034 Barcelona, Spain
- Catalan
Institute for Water Research, ICRA − CERCA, Technological Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
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Rafiee M, Isazadeh S, Mohseni-Bandpei A, Mohebbi SR, Jahangiri-Rad M, Eslami A, Dabiri H, Roostaei K, Tanhaei M, Amereh F. Moore swab performs equal to composite and outperforms grab sampling for SARS-CoV-2 monitoring in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148205. [PMID: 34102442 PMCID: PMC8170911 DOI: 10.1016/j.scitotenv.2021.148205] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) approaches to detect SARS-CoV-2 in municipal wastewater can provide unique information on the incidence or prevalence of COVID-19 in community. However, there are several technical challenges coupled with sewage sampling for SARS-CoV-2, including intermittent shedding of viruses, sampling time, volume, and frequency. Sampling schemes thus may need to be tailored to reach out highly sensitive, accurate, and reliable results. Herein, we compared the accuracy and threshold cycle (Ct) profiles of SARS-CoV-2 in Moore swabs, composite (16-h), and grab samples taken from sewage manholes (n = 17) at the Middle Eastern city of Tehran, Iran, on two occasions (November 2020 and May 2021). Samples were concentrated by polyethylene glycol precipitation and the corresponding Ct values for CDC 'N' and 'ORF1ab' assays were derived by means of real time RT-qPCR. Overall, the Moore swabs performed equal to samples composited over 16 h for qualitative monitoring, and 34/34 (100%) were positive for SARS-CoV-2. The 'N' assay showed the highest detection frequency as compared to 'ORF1ab'. The mean Moore swab Ct profiles were more consistent with 16 h composite sampling as compared with corresponding grab samples, providing hints as to the best sampling protocol to adopt when planning a sewage monitoring campaign particularly under WBE. Furthermore, our analyses on local differences showed somewhat higher virus copy numbers in the southern areas. The experimental design of this study revealed that the Moore swab and composite samples are more sensitive than grab samples, suggesting that the collection of grab samples may be inappropriate for characterizing total number of viral RNA copies in sewage samples. Given the transiently presence of human host-restricted infections such as SARS-CoV-2 and the simplicity and affordability of Moore swab, the method is well suited for disease surveillance in resource poor regions struggling with limited capacity for clinical testing.
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Affiliation(s)
- Mohammad Rafiee
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Siavash Isazadeh
- Environmental Research and Development, American Water Works, Delran, NJ, USA
| | - Anoushiravan Mohseni-Bandpei
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Jahangiri-Rad
- Water Purification Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Akbar Eslami
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Dabiri
- Department of Medical Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Kasra Roostaei
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Tanhaei
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Amereh
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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50
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Boogaerts T, Jacobs L, De Roeck N, Van den Bogaert S, Aertgeerts B, Lahousse L, van Nuijs ALN, Delputte P. An alternative approach for bioanalytical assay optimization for wastewater-based epidemiology of SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:148043. [PMID: 34323818 PMCID: PMC8152210 DOI: 10.1016/j.scitotenv.2021.148043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 05/02/2023]
Abstract
Wastewater-based epidemiology of SARS-CoV-2 could play a role in monitoring the spread of the virus in the population and controlling possible outbreaks. However, sensitive sample preparation and detection methods are necessary to detect trace levels of SARS-CoV-2 RNA in influent wastewater (IWW). Unlike predecessors, method optimization of a SARS-CoV-2 RNA concentration and detection procedure was performed with IWW samples with high viral SARS-CoV-2 RNA loads. This is of importance since the SARS-CoV-2 genome in IWW might have already been subject to in-sewer degradation into smaller genome fragments or might be present in a different form (e.g. cell debris, …). Centricon Plus-70 (100 kDa) centrifugal filter devices resulted in the lowest and most reproducible Ct-values for SARS-CoV-2 RNA. Lowering the molecular weight cut-off did not improve our limit of detection and quantification (approximately 100 copies/μL for all genes). Quantitative polymerase chain reaction (qPCR) was employed for the amplification of the N1, N2, N3 and E-gene fragments. This is one of the first studies to apply digital polymerase chain reaction (dPCR) for the detection of SARS-CoV-2 RNA in IWW. dPCR showed high variability at low concentration levels (100 copies/μL), indicating that variability in bioanalytical methods for wastewater-based epidemiology of SARS-CoV-2 might be substantial. dPCR results in IWW were in line with the results found with qPCR. On average, the N2-gene fragment showed high in-sample stability in IWW for 10 days of storage at 4 °C. Between-sample variability was substantial due to the low native concentrations in IWW. Additionally, the E-gene fragment proved to be less stable compared to the N2-gene fragment and showed higher variability. Freezing the IWW samples resulted in a 10-fold decay of loads of the N2- and E-gene fragment in IWW.
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Affiliation(s)
- Tim Boogaerts
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
| | - Lotte Jacobs
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Naomi De Roeck
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Siel Van den Bogaert
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Bert Aertgeerts
- Academic Centre for General Practice, KU Leuven, Kapucijnenvoer 7, 3000 Leuven, Belgium
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | | | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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