1
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Solomon T, Idris O, Nwaubani D, Baral R, Sherchan SP. Comparative analysis of membrane filter diameters for detection of selected viruses in wastewater samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:173973. [PMID: 38876339 DOI: 10.1016/j.scitotenv.2024.173973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Wastewater serves as a valuable source of information as it contains biological markers that have been shed by infected individuals and from other biological organisms such as plants and animals. Wastewater has been proven to indicate the presence of emerging pathogens in a community before the manifestation of clinical symptoms. Several methods of concentration and nucleic acid extraction have been employed all around the world without a unified method. One such method involves the use of the adsorption extraction method (AE-method), which involves the use of electronegative membrane filters of different pore sizes. The membrane filters also differ by diameter, but no study has been reported on the effect of diameter on capture efficiency. This study was aimed at evaluating the comparative capture efficiency of two different membrane filter diameters of 45 and 90 mm with pore sizes of 0.45 μm for the detection of indicator and pathogenic viruses. Primary influent samples were obtained from two wastewater treatment plants in Baltimore, Maryland, between April 27 and June 29, 2023. A total of twenty samples were processed using 45- and 90-mm membrane filters. Nucleic acids were extracted from the filters using the QIAmp Viral RNA Mini Kit and assayed for four different targets: PMMoV, Norovirus (GI and GII), and CrAssphage by RT-qPCR. The result showed that 45 mm membrane filters had a higher combined mean capture efficiency in log10 gene copies per liter (gc/l) for crAssphage (7.40) than 90 mm membrane filters (7.10). Similarly, the 45-mm filter had higher mean capture efficiency for Norovirus GI (4.67) than the 90-mm filter (1.84) and likewise for Norovirus GII (2.14, 1.04). On the contrary, 90-mm membrane filters were observed to have better capture of PMMoV (6.84) compared to 45-mm membrane filters (6.69). This result therefore implies that 45-mm membrane filters could be more efficient for wastewater surveillance studies through the AE method for indicator viruses like CrAssphage and human disease-causing viruses like Norovirus.
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Affiliation(s)
- Tamunobelema Solomon
- Center of Research Excellence in Wastewater based epidemiology, Morgan State University, Baltimore, MD 21251, United States of America; BioEnvironmental Science Program, Morgan State University, Baltimore, MD 21251, United States of America
| | - Oladele Idris
- BioEnvironmental Science Program, Morgan State University, Baltimore, MD 21251, United States of America
| | - Daniel Nwaubani
- BioEnvironmental Science Program, Morgan State University, Baltimore, MD 21251, United States of America
| | - Rakshya Baral
- BioEnvironmental Science Program, Morgan State University, Baltimore, MD 21251, United States of America
| | - Samendra P Sherchan
- Center of Research Excellence in Wastewater based epidemiology, Morgan State University, Baltimore, MD 21251, United States of America; BioEnvironmental Science Program, Morgan State University, Baltimore, MD 21251, United States of America.
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2
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Harrington A, Vo V, Moshi MA, Chang CL, Baker H, Ghani N, Itorralba JY, Papp K, Gerrity D, Moser D, Oh EC. Environmental Surveillance of Flood Control Infrastructure Impacted by Unsheltered Individuals Leads to the Detection of SARS-CoV-2 and Novel Mutations in the Spike Gene. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2024; 11:410-417. [PMID: 38752195 PMCID: PMC11095249 DOI: 10.1021/acs.estlett.3c00938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 05/18/2024]
Abstract
In the United States, the growing number of people experiencing homelessness has become a socioeconomic crisis with public health ramifications, recently exacerbated by the COVID-19 pandemic. We hypothesized that the environmental surveillance of flood control infrastructure may be an effective approach to understand the prevalence of infectious disease. From December 2021 through July 2022, we tested for SARS-CoV-2 RNA from two flood control channels known to be impacted by unsheltered individuals residing in upstream tunnels. Using qPCR, we detected SARS-CoV-2 RNA in these environmental water samples when significant COVID-19 outbreaks were occurring in the surrounding community. We also performed whole genome sequencing to identify SARS-CoV-2 lineages. Variant compositions were consistent with those of geographically and temporally matched municipal wastewater samples and clinical specimens. However, we also detected 10 of 22 mutations specific to the Alpha variant in the environmental water samples collected during January 2022-one year after the Alpha infection peak. We also identified mutations in the spike gene that have never been identified in published reports. Our findings demonstrate that environmental surveillance of flood control infrastructure may be an effective tool to understand public health conditions among unsheltered individuals-a vulnerable population that is underrepresented in clinical surveillance data.
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Affiliation(s)
- Anthony Harrington
- Laboratory
of Neurogenetics and Precision Medicine, College of Sciences, Neuroscience Interdisciplinary
Ph.D. program, Department of Brain Health, Department of Internal Medicine, Kirk Kerkorian
School of Medicine at UNLV, University of
Nevada Las Vegas, Las Vegas, Nevada 89154, United States
| | - Van Vo
- Laboratory
of Neurogenetics and Precision Medicine, College of Sciences, Neuroscience Interdisciplinary
Ph.D. program, Department of Brain Health, Department of Internal Medicine, Kirk Kerkorian
School of Medicine at UNLV, University of
Nevada Las Vegas, Las Vegas, Nevada 89154, United States
| | - Michael A. Moshi
- Laboratory
of Neurogenetics and Precision Medicine, College of Sciences, Neuroscience Interdisciplinary
Ph.D. program, Department of Brain Health, Department of Internal Medicine, Kirk Kerkorian
School of Medicine at UNLV, University of
Nevada Las Vegas, Las Vegas, Nevada 89154, United States
| | - Ching-Lan Chang
- Laboratory
of Neurogenetics and Precision Medicine, College of Sciences, Neuroscience Interdisciplinary
Ph.D. program, Department of Brain Health, Department of Internal Medicine, Kirk Kerkorian
School of Medicine at UNLV, University of
Nevada Las Vegas, Las Vegas, Nevada 89154, United States
| | - Hayley Baker
- Laboratory
of Neurogenetics and Precision Medicine, College of Sciences, Neuroscience Interdisciplinary
Ph.D. program, Department of Brain Health, Department of Internal Medicine, Kirk Kerkorian
School of Medicine at UNLV, University of
Nevada Las Vegas, Las Vegas, Nevada 89154, United States
| | - Nabih Ghani
- Laboratory
of Neurogenetics and Precision Medicine, College of Sciences, Neuroscience Interdisciplinary
Ph.D. program, Department of Brain Health, Department of Internal Medicine, Kirk Kerkorian
School of Medicine at UNLV, University of
Nevada Las Vegas, Las Vegas, Nevada 89154, United States
| | - Jose Yani Itorralba
- Laboratory
of Neurogenetics and Precision Medicine, College of Sciences, Neuroscience Interdisciplinary
Ph.D. program, Department of Brain Health, Department of Internal Medicine, Kirk Kerkorian
School of Medicine at UNLV, University of
Nevada Las Vegas, Las Vegas, Nevada 89154, United States
| | - Katerina Papp
- Southern
Nevada Water Authority, P.O. Box 99954, Las Vegas Nevada 89193, United States
| | - Daniel Gerrity
- Southern
Nevada Water Authority, P.O. Box 99954, Las Vegas Nevada 89193, United States
| | - Duane Moser
- Division
of Hydrologic Sciences, Desert Research
Institute, Las Vegas, Nevada 89119, United States
| | - Edwin C. Oh
- Laboratory
of Neurogenetics and Precision Medicine, College of Sciences, Neuroscience Interdisciplinary
Ph.D. program, Department of Brain Health, Department of Internal Medicine, Kirk Kerkorian
School of Medicine at UNLV, University of
Nevada Las Vegas, Las Vegas, Nevada 89154, United States
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3
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Kumblathan T, Liu Y, Crisol M, Pang X, Hrudey SE, Le XC, Li XF. Advances in wastewater analysis revealing the co-circulating viral trends of noroviruses and Omicron subvariants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170887. [PMID: 38350564 DOI: 10.1016/j.scitotenv.2024.170887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/19/2024] [Accepted: 02/08/2024] [Indexed: 02/15/2024]
Abstract
Co-presence of enveloped and non-enveloped viruses is common both in community circulation and in wastewater. Community surveillance of infections requires robust methods enabling simultaneous quantification of multiple viruses in wastewater. Using enveloped SARS-CoV-2 Omicron subvariants and non-enveloped norovirus (NoV) as examples, this study reports a robust method that integrates electronegative membrane (EM) concentration, viral inactivation, and RNA preservation (VIP) with efficient capture and enrichment of the viral RNA on magnetic (Mag) beads, and direct detection of RNA on the beads. This method provided improved viral recoveries of 80 ± 4 % for SARS-CoV-2 and 72 ± 5 % for Murine NoV. Duplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays with newly designed degenerate primer-probe sets offered high PCR efficiencies (90-91 %) for NoV (GI and GII) targets and were able to detect as few as 15 copies of the viral RNA per PCR reaction. This technique, combined with duplex detection of NoV and multiplex detection of Omicron, successfully quantified NoV (GI and GII) and Omicron variants in the same sets of 94 influent wastewater samples collected from two large wastewater systems between July 2022 and June 2023. The wastewater viral RNA results showed temporal changes of both NoV and Omicron variants in the same wastewater systems and revealed an inverse relationship of their emergence. This study demonstrated the importance of a robust analytical platform for simultaneous surveillance of enveloped and non-enveloped viruses in wastewater. The ability to sensitively determine multiple viral pathogens in wastewater will advance applications of wastewater surveillance as a complementary public health tool.
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Affiliation(s)
- Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Mary Crisol
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Xiaoli Pang
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2B7, Canada; Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta T6G 2J2, Canada
| | - Steve E Hrudey
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada.
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4
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Perry WB, Chrispim MC, Barbosa MRF, de Souza Lauretto M, Razzolini MTP, Nardocci AC, Jones O, Jones DL, Weightman A, Sato MIZ, Montagner C, Durance I. Cross-continental comparative experiences of wastewater surveillance and a vision for the 21st century. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170842. [PMID: 38340868 DOI: 10.1016/j.scitotenv.2024.170842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
The COVID-19 pandemic has brought the epidemiological value of monitoring wastewater into sharp focus. The challenges of implementing and optimising wastewater monitoring vary significantly from one region to another, often due to the array of different wastewater systems around the globe, as well as the availability of resources to undertake the required analyses (e.g. laboratory infrastructure and expertise). Here we reflect on the local and shared challenges of implementing a SARS-CoV-2 monitoring programme in two geographically and socio-economically distinct regions, São Paulo state (Brazil) and Wales (UK), focusing on design, laboratory methods and data analysis, and identifying potential guiding principles for wastewater surveillance fit for the 21st century. Our results highlight the historical nature of region-specific challenges to the implementation of wastewater surveillance, including previous experience of using wastewater surveillance, stakeholders involved, and nature of wastewater infrastructure. Building on those challenges, we then highlight what an ideal programme would look like if restrictions such as resource were not a constraint. Finally, we demonstrate the value of bringing multidisciplinary skills and international networks together for effective wastewater surveillance.
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Affiliation(s)
| | - Mariana Cardoso Chrispim
- Environmental and Biosciences Department, School of Business, Innovation and Sustainability, Halmstad University, Kristian IV:s väg 3, 30118 Halmstad, Sweden
| | - Mikaela Renata Funada Barbosa
- Environmental Analysis Department, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil; NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Marcelo de Souza Lauretto
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Arts, Sciences and Humanities, University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo CEP 03828-000, Brazil
| | - Maria Tereza Pepe Razzolini
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Public Health, University of Sao Paulo, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Adelaide Cassia Nardocci
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Public Health, University of Sao Paulo, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Owen Jones
- School of Mathematics, Cardiff University, Cardiff CF24 4AG, UK
| | - Davey L Jones
- Environment Centre Wales, Bangor University, Bangor LL57 2UW, UK; Food Futures Institute, Murdoch University, Murdoch WA 6105, Australia
| | | | - Maria Inês Zanoli Sato
- Environmental Analysis Department, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil; NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Cassiana Montagner
- Environmental Chemistry Laboratory, Institute of Chemistry, University of Campinas, Campinas, São Paulo 13083970, Brazil
| | - Isabelle Durance
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.
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5
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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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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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7
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Devianto LA, Sano D. Systematic review and meta-analysis of human health-related protein markers for realizing real-time wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165304. [PMID: 37419365 DOI: 10.1016/j.scitotenv.2023.165304] [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: 03/29/2023] [Revised: 06/07/2023] [Accepted: 07/02/2023] [Indexed: 07/09/2023]
Abstract
For effective implementation of the wastewater-based epidemiology (WBE) approach, real-time quantification of markers in wastewater is critical for data acquisition before data interpretation, dissemination, and decision-making. This can be achieved by using biosensor technology, but whether the quantification/detection limits of different types of biosensors comply with the concentration of WBE markers in wastewater is unclear. In the present study, we identified promising protein markers with relatively high concentrations in wastewater samples and analyzed biosensor technologies that are potentially available for real-time WBE. The concentrations of potential protein markers in stool and urine samples were obtained through systematic review and meta-analysis. We examined 231 peer-review papers to collect information regarding potential protein markers that can enable us to achieve real-time monitoring using biosensor technology. Fourteen markers in stool samples were identified at the ng/g level, presumably equivalent to ng/L of wastewater after dilution. Moreover, relatively high average concentrations of fecal inflammatory proteins were observed, e.g., fecal calprotectin, clusterin, and lactoferrin. Fecal calprotectin exhibited the highest average log concentration among the markers identified in stool samples with its mean value being 5.24 [95 % CI: 5.05, 5.42] ng/g. We identified 50 protein markers in urine samples at the ng/mL level. Uromodulin (4.48 [95 % CI: 4.20, 4.76] ng/mL) and plasmin (4.18 [95 % CI: 3.15, 5.21] ng/mL) had the top two highest log concentrations in urine samples. Furthermore, the quantification limit of some electrochemical- and optical-based biosensors was found to be around the femtogram/mL level, which is sufficiently low to detect protein markers in wastewater even after dilution in sewer pipes.
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Affiliation(s)
- Luhur Akbar Devianto
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8579, Japan; Department of Environmental Engineering, Faculty of Agriculture Technology, Brawijaya University, Malang 65145, Indonesia.
| | - Daisuke Sano
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8579, Japan; Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan; Wastewater Information Research Center, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan.
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8
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Kumblathan T, Liu Y, Pang X, Hrudey SE, Le XC, Li XF. Quantification and Differentiation of SARS-CoV-2 Variants in Wastewater for Surveillance. ENVIRONMENT & HEALTH (WASHINGTON, D.C.) 2023; 1:203-213. [PMID: 37736345 PMCID: PMC10510104 DOI: 10.1021/envhealth.3c00089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 09/23/2023]
Abstract
Wastewater surveillance plays an important role in the monitoring of infections of SARS-CoV-2 at the community level. We report here the determination of SARS-CoV-2 and differentiation of its variants of concern in 294 wastewater samples collected from two major Canadian cities from May 2021 to March 2023. The overall method of analysis involved extraction of the virus and viral components using electronegative membranes, in situ stabilization and concentration of the viral RNA onto magnetic beads, and direct analysis of the viral RNA on the magnetic beads. Multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays, targeting specific and naturally selected mutations in SARS-CoV-2, enabled detection and differentiation of the Alpha, Beta, Gamma, Delta, and Omicron variants. An Omicron triplex RT-qPCR assay targeting three mutations, HV 69-70 deletion, K417N, and L452R, was able to detect and differentiate the Omicron BA.1/BA.3, BA.2/XBB, and BA.4/5. This assay had efficiencies of 90-104% for all three mutation targets and a limit of detection of 28 RNA copies per reaction. Analyses of 294 wastewater samples collected over a two-year span showed the concentrations and trends of Alpha, Beta, Gamma, Delta, and Omicron variants as they emerge in two major Canadian cities participating in the wastewater surveillance program. The trends of specific variants were consistent with clinical reports for the same period. At the beginning of each wave, the corresponding variants were detectable in wastewater. For example, RNA concentrations of the BA.2 variant were as high as 104 copies per 100 mL of wastewater collected in January 2022, when approximately only 50-60 clinical cases of BA.2 infection were reported in Canada. These results show that the strategy and highly sensitive assays for the variants of concern in wastewater are potentially useful for the detection of newly emerging SARS-CoV-2 variants and other viruses for future community biomonitoring.
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Affiliation(s)
- Teresa Kumblathan
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Yanming Liu
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Xiaoli Pang
- Division
of Diagnostic and Applied Microbiology, Department of Laboratory Medicine
and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2B7
- Public
Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada T6G 2J2
| | - Steve E. Hrudey
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - X. Chris Le
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
- Division
of Diagnostic and Applied Microbiology, Department of Laboratory Medicine
and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2B7
- Public
Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada T6G 2J2
| | - Xing-Fang Li
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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9
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Kumblathan T, Liu Y, Qiu Y, Pang L, Hrudey SE, Le XC, Li XF. An efficient method to enhance recovery and detection of SARS-CoV-2 RNA in wastewater. J Environ Sci (China) 2023; 130:139-148. [PMID: 37032030 PMCID: PMC9554329 DOI: 10.1016/j.jes.2022.10.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 05/25/2023]
Abstract
Wastewater surveillance (WS) of SARS-CoV-2 currently requires multiple steps and suffers low recoveries and poor sensitivity. Here, we report an improved analytical method with high sensitivity and recovery to quantify SARS-CoV-2 RNA in wastewater. To improve the recovery, we concentrated SARS-CoV-2 viral particles and RNA from both the solid and aqueous phases of wastewater using an electronegative membrane (EM). The captured viral particles and RNA on the EM were incubated in our newly developed viral inactivation and RNA preservation (VIP) buffer. Subsequently, the RNA was concentrated on magnetic beads and inhibitors removed by washing. Without eluting, the RNA on the magnetic beads was directly detected using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Analysis of SARS-CoV-2 pseudovirus (SARS-CoV-2 RNA in a noninfectious viral coat) spiked to wastewater samples showed an improved recovery of 80%. Analysis of 120 wastewater samples collected twice weekly between May 2021 and February 2022 from two wastewater treatment plants showed 100% positive detection, which agreed with the results independently obtained by a provincial public health laboratory. The concentrations of SARS-CoV-2 RNA in these wastewater samples ranged from 2.4×102 to 2.9×106 copies per 100 mL of wastewater. Our method's capability of detecting trace and diverse concentrations of SARS-CoV-2 in complex wastewater samples is attributed to the enhanced recovery of SARS-CoV-2 RNA and efficient removal of PCR inhibitors. The improved method for the recovery and detection of viral RNA in wastewater is important for wastewater surveillance, complementing clinical diagnostic tests for public health protection.
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Affiliation(s)
- Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yuanyuan Qiu
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 2G3, Canada
| | - Lilly Pang
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 2G3, Canada; Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, T6G 2G3, Canada
| | - Steve E Hrudey
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
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10
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Liu Y, Kumblathan T, Tao J, Xu J, Feng W, Xiao H, Hu J, Huang CV, Wu Y, Zhang H, Li XF, Le XC. Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle. Trends Analyt Chem 2023; 165:117107. [PMID: 37317683 PMCID: PMC10204347 DOI: 10.1016/j.trac.2023.117107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Molecular detection of SARS-CoV-2 in gargle and saliva complements the standard analysis of nasopharyngeal swabs (NPS) specimens. Although gargle and saliva specimens can be readily obtained non-invasively, appropriate collection and processing of gargle and saliva specimens are critical to the accuracy and sensitivity of the overall analytical method. This review highlights challenges and recent advances in the treatment of gargle and saliva samples for subsequent analysis using reverse transcription polymerase chain reaction (RT-PCR) and isothermal amplification techniques. Important considerations include appropriate collection of gargle and saliva samples, on-site inactivation of viruses in the sample, preservation of viral RNA, extraction and concentration of viral RNA, removal of substances that inhibit nucleic acid amplification reactions, and the compatibility of sample treatment protocols with the subsequent nucleic acid amplification and detection techniques. The principles and approaches discussed in this review are applicable to molecular detection of other microbial pathogens.
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Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jingyang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Huyan Xiao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Camille V Huang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yiping Wu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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11
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Atoui A, Cordevant C, Chesnot T, Gassilloud B. SARS-CoV-2 in the environment: Contamination routes, detection methods, persistence and removal in wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163453. [PMID: 37059142 PMCID: PMC10091716 DOI: 10.1016/j.scitotenv.2023.163453] [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: 12/30/2022] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/01/2023]
Abstract
The present study reviewed the occurrence of SARS-CoV-2 RNA and the evaluation of virus infectivity in feces and environmental matrices. The detection of SARS-CoV-2 RNA in feces and wastewater samples, reported in several studies, has generated interest and concern regarding the possible fecal-oral route of SARS-CoV-2 transmission. To date, the presence of viable SARS-CoV-2 in feces of COVID-19 infected people is not clearly confirmed although its isolation from feces of six different patients. Further, there is no documented evidence on the infectivity of SARS-CoV-2 in wastewater, sludge and environmental water samples, although the viral genome has been detected in these matrices. Decay data revealed that SARS-CoV-2 RNA persisted longer than infectious particle in all aquatic environment, indicating that genome quantification of SARS-CoV-2 does not imply the presence of infective viral particles. In addition, this review also outlined the fate of SARS-CoV-2 RNA during the different steps in the wastewater treatment plant and focusing on the virus elimination along the sludge treatment line. Studies showed complete removal of SARS-CoV-2 during the tertiary treatment. Moreover, thermophilic sludge treatments present high efficiency in SARS-CoV-2 inactivation. Further studies are required to provide more evidence with respect to the inactivation behavior of infectious SARS-CoV-2 in different environmental matrices and to examine factors affecting SARS-CoV-2 persistence.
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Affiliation(s)
- Ali Atoui
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France.
| | - Christophe Cordevant
- ANSES, Strategy and Programs Department, Research and Reference Division, Maisons-Alfort F-94 700, France
| | - Thierry Chesnot
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France
| | - Benoît Gassilloud
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France
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12
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Fuzzen M, Harper NBJ, Dhiyebi HA, Srikanthan N, Hayat S, Bragg LM, Peterson SW, Yang I, Sun JX, Edwards EA, Giesy JP, Mangat CS, Graber TE, Delatolla R, Servos MR. An improved method for determining frequency of multiple variants of SARS-CoV-2 in wastewater using qPCR assays. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163292. [PMID: 37030387 PMCID: PMC10079313 DOI: 10.1016/j.scitotenv.2023.163292] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 06/01/2023]
Abstract
Wastewater-based surveillance has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Variants of Concern (VOCs) have been detected in wastewater by use of reverse transcription polymerase chain reaction (RT-PCR) or whole genome sequencing (WGS). Rapid, reliable RT-PCR assays continue to be needed to determine the relative frequencies of VOCs and sub-lineages in wastewater-based surveillance programs. The presence of multiple mutations in a single region of the N-gene allowed for the design of a single amplicon, multiple probe assay, that can distinguish among several VOCs in wastewater RNA extracts. This approach which multiplexes probes designed to target mutations associated with specific VOC's along with an intra-amplicon universal probe (non-mutated region) was validated in singleplex and multiplex. The prevalence of each mutation (i.e. VOC) is estimated by comparing the abundance of the targeted mutation with a non-mutated and highly conserved region within the same amplicon. This is advantageous for the accurate and rapid estimation of variant frequencies in wastewater. The N200 assay was applied to monitor frequencies of VOCs in wastewater extracts from several communities in Ontario, Canada in near real time from November 28, 2021 to January 4, 2022. This includes the period of the rapid replacement of the Delta variant with the introduction of the Omicron variant in these Ontario communities in early December 2021. The frequency estimates using this assay were highly reflective of clinical WGS estimates for the same communities. This style of qPCR assay, which simultaneously measures signal from a non-mutated comparator probe and multiple mutation-specific probes contained within a single qPCR amplicon, can be applied to future assay development for rapid and accurate estimations of variant frequencies.
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Affiliation(s)
- Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
| | | | - Hadi A Dhiyebi
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Nivetha Srikanthan
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Samina Hayat
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Leslie M Bragg
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Shelley W Peterson
- One-Health Division, Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3M4, Canada
| | - Ivy Yang
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - J X Sun
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Elizabeth A Edwards
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - John P Giesy
- Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
| | - Chand S Mangat
- One-Health Division, Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3M4, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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13
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Kang Y, Wang J, Zhang W, Xu Y, Xu B, Qu G, Yu Y, Yan B, Su G. RNA extraction-free workflow integrated with a single-tube CRISPR-Cas-based colorimetric assay for rapid SARS-CoV-2 detection in different environmental matrices. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131487. [PMID: 37148798 PMCID: PMC10125216 DOI: 10.1016/j.jhazmat.2023.131487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/31/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
On-site environmental surveillance of viruses is increasingly important for infection prevention and pandemic control. Herein, we report a facile single-tube colorimetric assay for detecting severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from environmental compartments. Using glycerol as the phase separation additive, reverse transcription recombinase polymerase amplification (RT-RPA), CRISPR-Cas system activation, G-quadruplex (G4) cleavage, and G4-based colorimetric reaction were performed in a single tube. To further simplify the test, viral RNA genomes used for the one-tube assay were obtained via acid/base treatment without further purification. The whole assay from sampling to visual readout was completed within 30 min at a constant temperature without the need for sophisticated instruments. Coupling the RT-RPA to CRISPR-Cas improved the reliability by avoiding false positive results. Non-labeled cost-effective G4-based colorimetric systems are highly sensitive to CRISPR-Cas cleavage events, and the proposed assay reached the limit of detection of 0.84 copies/µL. Moreover, environmental samples from contaminated surfaces and wastewater were analyzed using this facile colorimetric assay. Given its simplicity, sensitivity, specificity, and cost-effectiveness, our proposed colorimetric assay is highly promising for applications in on-site environmental surveillance of viruses.
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Affiliation(s)
- Yuliang Kang
- School of Pharmacy, Nantong University, Nantong 226001, China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Jiali Wang
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Wensi Zhang
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Yuhang Xu
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Bohui Xu
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yanyan Yu
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Bing Yan
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou 510006, China.
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong 226001, China.
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14
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Le C. Sensitivity of wastewater surveillance: What is the minimum COVID-19 cases required in population for SARS-CoV-2 RNA to be detected in wastewater? J Environ Sci (China) 2023; 125:851-853. [PMID: 36375967 PMCID: PMC9392869 DOI: 10.1016/j.jes.2022.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Connie Le
- Li Ka Shing Institute of Virology, Department of Radiation Oncology, and Cross Cancer Institute, University of Alberta, Edmonton, Alberta T6G 2G3, Canada.
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15
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Gao Z, Li P, Lin H, Lin W, Ren Y. Biomarker selection strategies based on compound stability in wastewater-based epidemiology. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:5516-5529. [PMID: 36418835 PMCID: PMC9684832 DOI: 10.1007/s11356-022-24268-y] [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: 07/07/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
The specific compositions of human excreta in sewage can be used as biomarkers to indicate the disease prevalence, health status, and lifestyle of the population living in the investigated catchment. It is important for guiding and evaluating public health policies as well as promoting human health development. Among several parameters of wastewater-based epidemiology (WBE), the decay of biomarkers during transportation in sewer and storage plays a crucial role in the back-calculation of population consumption. In this paper, we summarized the stability data of common biomarkers in storage at different temperatures and in-sewer transportation. Among them, cardiovascular drugs and antidiabetic drugs are very stable which can be used as biomarkers; most of the illicit drugs are stable except for cocaine, heroin, and tetrahydrocannabinol which could be substituted by their metabolites as biomarkers. There are some losses for part of antibiotics and antidepressants even in frozen storage. Rapid detection of contagious viruses is a new challenge for infectious disease control. With the deeper and broader study of biomarkers, it is expected that the reliable application of the WBE will be a useful addition to epidemiological studies.
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Affiliation(s)
- Zhihan Gao
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Ping Li
- Datansha Branch of Guangzhou Sewage Treatment Co., Ltd, Guangzhou, 510163, China
| | - Han Lin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Wenting Lin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Yuan Ren
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China.
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China.
- The Key Laboratory of Environmental Protection and Eco-Remediation of Guangdong Regular Higher Education Institution, Guangzhou, 510006, China.
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16
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Zhang X, Zhang L, Wang Y, Zhang M, Zhou J, Liu X, Wang Y, Qu C, Han W, Hou M, Deng F, Luo Y, Mao Y, Gu W, Dong Z, Pan Y, Zhang D, Tang S, Zhang L. Detection of the SARS-CoV-2 Delta Variant in the Transboundary Rivers of Yunnan, China. ACS ES&T WATER 2022; 2:2367-2377. [PMID: 37552741 PMCID: PMC9631342 DOI: 10.1021/acsestwater.2c00224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 05/30/2023]
Abstract
Ruili and Longchuan, two border counties in southwestern China, are facing epidemic control challenges due to the high rate of COVID-19 infections originating from neighboring Myanmar. Here, we aimed to establish the applicability of wastewater and environmental water surveillance of SARS-CoV-2 and conduct whole-genome sequencing (WGS) to trace the possible infection origin. In August 2021, total 72 wastewater and river water samples were collected from 32 sampling sites. SARS-CoV-2 ORF1ab and N genes were measured by RT-qPCR. We found that 19 samples (26.39%) were positive, and the viral loads of ORF1ab and N genes were 6.62 × 102-2.55×105 and 1.86 × 103-2.32 × 105 copies/L, respectively. WGS further indicated the sequences in two transboundary river samples, and one hospital wastewater sample belonged to the delta variant, suggesting that the infection source might be areas with high COVID-19 delta variant incidence in Southeast Asia (e.g., Myanmar). We reported for the first time the detection and quantification of SARS-CoV-2 RNA in the transboundary rivers of Myanmar-China. Our findings demonstrate that wastewater and environmental water may provide independent and nonintrusive surveillance points to monitor the global spread of emerging COVID-19 variants of concern, particularly in high-risk regions or border areas with considerable epidemic challenges and poor wastewater treatment facilities.
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Affiliation(s)
- Xiao Zhang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Liang Zhang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Yuanyuan Wang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Meiling Zhang
- Acute Infectious Disease Prevention and Control
Institute, Yunnan Center for Disease Control and Prevention,
Kunming, Yunnan650022, China
| | - Jienan Zhou
- Acute Infectious Disease Prevention and Control
Institute, Yunnan Center for Disease Control and Prevention,
Kunming, Yunnan650022, China
| | - Xin Liu
- Ruili Center for Disease Control and
Prevention, Ruili, Yunnan678599, China
| | - Yan Wang
- Ruili Center for Disease Control and
Prevention, Ruili, Yunnan678599, China
| | - Changsheng Qu
- Longchuan Center for Disease Control and
Prevention, Longchuan, Yunnan678799, China
| | - Wenxiang Han
- Longchuan Center for Disease Control and
Prevention, Longchuan, Yunnan678799, China
| | - Min Hou
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Fuchang Deng
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Yueyun Luo
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Yixin Mao
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Wen Gu
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Zhaomin Dong
- School of Space and Environment, Beihang
University, Beijing100191, China
| | - Yang Pan
- Institute for Infectious Disease and Endemic Disease Control,
Beijing Center for Disease Prevention and Control,
Beijing100013, China
| | - Daitao Zhang
- Institute for Infectious Disease and Endemic Disease Control,
Beijing Center for Disease Prevention and Control,
Beijing100013, China
| | - Song Tang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
| | - Lan Zhang
- China CDC Key Laboratory of Environment and Population
Health, National Institute of Environmental Health, Chinese Center for
Disease Control and Prevention, Beijing100021,
China
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17
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Kumar M. Spectrum of environmental surveillance of SARS-CoV-2 fragments: Questions, quests, and conquest. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2022; 30:100401. [PMID: 36339883 PMCID: PMC9617644 DOI: 10.1016/j.coesh.2022.100401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This works examines the entire spectrum of 'Environmental Surveillance (EnvSurv)' of SARS-CoV-2 fragments i.e. the questions, quests, and conquests of the technology since early year 2020. The prime focus of the present work to document the journey with achieved objectives and remaining ambitions associated with the technology. Despite the EnvSurv may be regarded as the techniques, which rather achieved more than expected, will it win the struggle for its existence or lose its way once the pandemic and fear associated with it completely fades. Pertaining to this discussions, major researched topics were investigated, followed by enlisting of ten bullets of the past experiences along with corresponding challenges, and finally key targets for the techniques are enlisted. The article targets to be a simple guide of the journey of EnvSur in terms of its effectiveness for treatment, infectivity, monitoring & estimation (TIME) till date.
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Affiliation(s)
- Manish Kumar
- Sustainability Cluster, School of Engineering, Enery Agcres, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India
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18
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Comparison of RT-dPCR and RT-qPCR and the effects of freeze-thaw cycle and glycine release buffer for wastewater SARS-CoV-2 analysis. Sci Rep 2022; 12:20641. [PMID: 36450877 PMCID: PMC9709738 DOI: 10.1038/s41598-022-25187-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
Public health efforts to control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic rely on accurate information on the spread of the disease in the community. Acute and surveillance testing has been primarily used to characterize the extent of the disease. However, obtaining a representative sample of the human population is challenging because of limited testing capacity and incomplete testing compliance. Wastewater-based epidemiology is an agnostic alternative to surveillance testing that provides an average sample from the population served by the treatment facility. We compare the performance of reverse transcription quantitative PCR (RT-qPCR) and reverse transcription digital droplet PCR (RT-dPCR) for analysis of SARS-CoV-2 RNA in a regional wastewater treatment facility in northern Indiana, USA from the earliest stages of the pandemic. 1-L grab samples of wastewater were clarified and concentrated. Nucleic acids were extracted from aliquots and analyzed in parallel using the two methods. Synthetic viral nucleic acids were used for method development and generation of add-in standard-curves. Both methods were highly sensitive in detecting SARS-CoV-2 in wastewater, with detection limits as low as 1 copy per 500 mL wastewater. RT-qPCR and RT-dPCR provided essentially identical coefficients of variation (s/[Formula: see text] = 0.15) for triplicate measurements made on wastewater samples taken on 16 days. We also observed a sevenfold decrease in viral load from a grab sample that was frozen at - 80 °C for 92 days compared to results obtained without freezing. Freezing samples before analysis should be discouraged. Finally, we found that treatment with a glycine release buffer resulted in a fourfold inhibition in RT-qPCR signal; treatment with a glycine release buffer also should be discouraged. Despite their prevalence and convenience in wastewater analysis, glycine release and freezing samples severely and additively (~ tenfold) degraded recovery and detection of SARS-CoV-2.
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19
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Cohen A, Maile-Moskowitz A, Grubb C, Gonzalez RA, Ceci A, Darling A, Hungerford L, Fricker R, Finkielstein CV, Pruden A, Vikesland PJ. Subsewershed SARS-CoV-2 Wastewater Surveillance and COVID-19 Epidemiology Using Building-Specific Occupancy and Case Data. ACS ES&T WATER 2022; 2:2047-2059. [PMID: 37552724 PMCID: PMC9128018 DOI: 10.1021/acsestwater.2c00059] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 08/10/2023]
Abstract
To evaluate the use of wastewater-based surveillance and epidemiology to monitor and predict SARS-CoV-2 virus trends, over the 2020-2021 academic year we collected wastewater samples twice weekly from 17 manholes across Virginia Tech's main campus. We used data from external door swipe card readers and student isolation/quarantine status to estimate building-specific occupancy and COVID-19 case counts at a daily resolution. After analyzing 673 wastewater samples using reverse transcription quantitative polymerase chain reaction (RT-qPCR), we reanalyzed 329 samples from isolation and nonisolation dormitories and the campus sewage outflow using reverse transcription digital droplet polymerase chain reaction (RT-ddPCR). Population-adjusted viral copy means from isolation dormitory wastewater were 48% and 66% higher than unadjusted viral copy means for N and E genes (1846/100 mL to 2733/100 mL/100 people and 2312/100 mL to 3828/100 mL/100 people, respectively; n = 46). Prespecified analyses with random-effects Poisson regression and dormitory/cluster-robust standard errors showed that the detection of N and E genes were associated with increases of 85% and 99% in the likelihood of COVID-19 cases 8 days later (incident-rate ratio (IRR) = 1.845, p = 0.013 and IRR = 1.994, p = 0.007, respectively; n = 215), and one-log increases in swipe card normalized viral copies (copies/100 mL/100 people) for N and E were associated with increases of 21% and 27% in the likelihood of observing COVID-19 cases 8 days following sample collection (IRR = 1.206, p < 0.001, n = 211 for N; IRR = 1.265, p < 0.001, n = 211 for E). One-log increases in swipe normalized copies were also associated with 40% and 43% increases in the likelihood of observing COVID-19 cases 5 days after sample collection (IRR = 1.403, p = 0.002, n = 212 for N; IRR = 1.426, p < 0.001, n = 212 for E). Our findings highlight the use of building-specific occupancy data and add to the evidence for the potential of wastewater-based epidemiology to predict COVID-19 trends at subsewershed scales.
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Affiliation(s)
- Alasdair Cohen
- Department of Population Health Sciences,
Virginia Tech, Blacksburg, Virginia 24061, United
States
- Department of Civil and Environmental Engineering,
Virginia Tech, Blacksburg, Virginia 24061, United
States
| | - Ayella Maile-Moskowitz
- Department of Civil and Environmental Engineering,
Virginia Tech, Blacksburg, Virginia 24061, United
States
| | - Christopher Grubb
- Department of Statistics, Virginia
Tech, Blacksburg, Virginia 24061, United States
| | - Raul A. Gonzalez
- Hampton Roads Sanitation
District, Virginia Beach, Virginia 23455, United
States
| | - Alessandro Ceci
- Molecular Diagnostics Laboratory, Fralin Biomedical
Research Institute, Virginia Tech, Roanoke, Virginia 24016,
United States
| | - Amanda Darling
- Department of Population Health Sciences,
Virginia Tech, Blacksburg, Virginia 24061, United
States
- Department of Civil and Environmental Engineering,
Virginia Tech, Blacksburg, Virginia 24061, United
States
| | - Laura Hungerford
- Department of Population Health Sciences,
Virginia Tech, Blacksburg, Virginia 24061, United
States
| | - Ronald
D. Fricker
- Department of Statistics, Virginia
Tech, Blacksburg, Virginia 24061, United States
| | - Carla V. Finkielstein
- Molecular Diagnostics Laboratory, Fralin Biomedical
Research Institute, Virginia Tech, Roanoke, Virginia 24016,
United States
- Integrated Cellular Responses Laboratory, Fralin
Biomedical Research Institute at VTC, Roanoke, Virginia 24016,
United States
- Department of Biological Sciences,
Virginia Tech, Blacksburg, Virginia 24061, United
States
| | - Amy Pruden
- Department of Civil and Environmental Engineering,
Virginia Tech, Blacksburg, Virginia 24061, United
States
| | - Peter J. Vikesland
- Department of Civil and Environmental Engineering,
Virginia Tech, Blacksburg, Virginia 24061, United
States
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20
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Islam A, Hossen F, Rahman A, Sultana KF, Hasan MN, Haque A, Sosa-Hernández JE, Oyervides-Muñoz MA, Parra-Saldívar R, Ahmed T, Islam T, Dhama K, Sangkham S, Bahadur NM, Reza HM, Jakariya, Al Marzan A, Bhattacharya P, Sonne C, Ahmed F. An opinion on Wastewater-Based Epidemiological Monitoring (WBEM) with Clinical Diagnostic Test (CDT) for detecting high-prevalence areas of community COVID-19 Infections. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2022; 31:100396. [PMID: 36320818 PMCID: PMC9612100 DOI: 10.1016/j.coesh.2022.100396] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 02/17/2024]
Abstract
Wastewater-Based Epidemiological Monitoring (WBEM) is an efficient surveillance tool during the COVID-19 pandemic as it meets all requirements of a complete monitoring system including early warning, tracking the current trend, prevalence of the disease, detection of genetic diversity as well asthe up-surging SARS-CoV-2 new variants with mutations from the wastewater samples. Subsequently, Clinical Diagnostic Test is widely acknowledged as the global gold standard method for disease monitoring, despite several drawbacks such as high diagnosis cost, reporting bias, and the difficulty of tracking asymptomatic patients (silent spreaders of the COVID-19 infection who manifest nosymptoms of the disease). In this current reviewand opinion-based study, we first propose a combined approach) for detecting COVID-19 infection in communities using wastewater and clinical sample testing, which may be feasible and effective as an emerging public health tool for the long-term nationwide surveillance system. The viral concentrations in wastewater samples can be used as indicatorsto monitor ongoing SARS-CoV-2 trends, predict asymptomatic carriers, and detect COVID-19 hotspot areas, while clinical sampleshelp in detecting mostlysymptomaticindividuals for isolating positive cases in communities and validate WBEM protocol for mass vaccination including booster doses for COVID-19.
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Affiliation(s)
- Aminul Islam
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali-3814, Bangladesh
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, Bangladesh
| | - Foysal Hossen
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali-3814, Bangladesh
| | - Arifur Rahman
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali-3814, Bangladesh
| | - Khandokar Fahmida Sultana
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali-3814, Bangladesh
| | - Mohammad Nayeem Hasan
- Department of Statistics, Shahjalal University of Science & Technology, Sylhet, Bangladesh
- Joint Rohingya Response Program, Food for the Hungry, Cox's Bazar, Bangladesh
| | - Atiqul Haque
- Key Lab of Animal Epidemiology and Zoonoses of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Department of Microbiology, Faculty of Veterinary and Animal Science, Hajee Mohammad Danesh Science and Technology University, Dinajpur-5200, Bangladesh
| | | | | | | | - Tanvir Ahmed
- Department of Civil Engineering, Bangladesh University of Engineering and Technology, Dhaka-1000, Bangladesh
| | | | - Kuldeep Dhama
- Indian Veterinary Research Institute, Izzatnagar-243 122, Bareilly, Uttar Pradesh, India
| | - Sarawut Sangkham
- Department of Environmental Health, School of Public Health, University of Phayao, Muang District, 56000, Phayao, Thailand
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and TechnologyUniversity, Noakhali-3814, Bangladesh
| | - Hasan Mahmud Reza
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Jakariya
- Department of Environmental Science and Management, North South University, Bashundhara, Dhaka-1229, Bangladesh
| | - Abdullah Al Marzan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Prosun Bhattacharya
- COVID-19 Research@KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE 114 28 Stockholm, Sweden
| | - Christian Sonne
- Department of Bioscience, Arctic Research Centre (ARC), Faculty of Science and Technology, Aarhus University, Frederiksborgvej 399, PO Box 358, 4000 Roskilde, Denmark
| | - Firoz Ahmed
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali-3814, Bangladesh
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21
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Aga DS, Halwatura LM. Wastewater Surveillance of Pharmaceuticals and Genes: Challenges and Opportunities. LCGC NORTH AMERICA 2022. [DOI: 10.56530/lcgc.na.vk9190q2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Wastewater-based epidemiology (WBE) using viral nucleic acids to predict community viral outbreaks has many challenges, including interferences from the wastewater matrix. Liquid chromatography with tandem mass spectrometry (LC–MS/MS) monitoring of pharmaceutically active compounds, such as antivirals and over-the-counter drugs commonly used to relieve the symptoms of infection, could complement information provided by molecular techniques. For instance, residues of drugs associated with managing Covid-19 symptoms, including azithromycin, chloroquine, hydroxychloroquine, and lopinavir, have been detected in influent wastewater. A significant correlation can be observed between the total of Covid-19–related drugs detected and the 5-day rolling averages of reported cases. Spikes in acetaminophen concentrations can also be observed a couple of weeks before a spike in SARS-CoV-2 RNA copies in wastewater, suggesting that over-the-counter analgesic concentrations in raw sewage may be used to complement viral RNA data as an early-warning system for effective management of viral outbreaks at the community level. Sample preparation and analysis of pharmaceuticals in wastewater present unique challenges and are discussed in this article.
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22
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Kumblathan T, Piroddi N, Hrudey SE, Li XF. Wastewater Based Surveillance of SARS-CoV-2: Challenges and Perspective from a Canadian Inter-laboratory Study. J Environ Sci (China) 2022; 116:229-232. [PMID: 35219421 PMCID: PMC8789553 DOI: 10.1016/j.jes.2022.01.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Nicholas Piroddi
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Steve E Hrudey
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada.
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23
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Ramírez-Chavarría RG, Castillo-Villanueva E, Alvarez-Serna BE, Carrillo-Reyes J, Ramírez-Zamora RM, Buitrón G, Alvarez-Icaza L. Loop-mediated isothermal amplification-based electrochemical sensor for detecting SARS-CoV-2 in wastewater samples. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2022; 10:107488. [PMID: 35251932 PMCID: PMC8883760 DOI: 10.1016/j.jece.2022.107488] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/07/2022] [Accepted: 02/26/2022] [Indexed: 05/10/2023]
Abstract
The current pandemic COVID-19 caused by the coronavirus SARS-CoV-2, has generated different economic, social and public health problems. Moreover, wastewater-based epidemiology could be a predictor of the virus rate of spread to alert on new outbreaks. To assist in epidemiological surveillance, this work introduces a simple, low-cost and affordable electrochemical sensor to specifically detect N and ORF1ab genes of the SARS-CoV-2 genome. The proposed sensor works based on screen-printed electrodes acting as a disposable test strip, where the reverse transcription loop-mediated isothermal amplification (RT-LAMP) reaction takes place. Electrochemical detection relies upon methylene blue as a redox intercalator probe, to provide a diffusion-controlled current encoding the presence and concentration of RT-LAMP products, namely amplicons or double-stranded DNA. We test the performance of the sensor by testing real wastewater samples using end-point and time course measurements. Results show the ability of the electrochemical test strip to specifically detect and quantify RT-LAMP amplicons below to ~ 2.5 × 10-6 ng/μL exhibiting high reproducibility. In this sense, our RT-LAMP electrochemical sensor is an attractive, efficient and powerful tool for rapid and reliable wastewater-based epidemiology studies.
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Affiliation(s)
| | - Elizabeth Castillo-Villanueva
- Instituto de Ingeniería, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Bryan E Alvarez-Serna
- Instituto de Ingeniería, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Julián Carrillo-Reyes
- Laboratorio de Investigación en Procesos Avanzados de Tratamiento de Aguas, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro 76230, México
| | | | - Germán Buitrón
- Laboratorio de Investigación en Procesos Avanzados de Tratamiento de Aguas, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro 76230, México
| | - Luis Alvarez-Icaza
- Instituto de Ingeniería, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
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24
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Hrudey SE, Conant B. The devil is in the details: emerging insights on the relevance of wastewater surveillance for SARS-CoV-2 to public health. JOURNAL OF WATER AND HEALTH 2022; 20:246-270. [PMID: 35100171 DOI: 10.2166/wh.2021.186] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The severe health consequences and global spread of the COVID-19 pandemic have necessitated the rapid development of surveillance programs to inform public health responses. Efforts to support surveillance capacity have included an unprecedented global research response into the use of genetic signals of SARS-CoV-2 in wastewater following the initial demonstration of the virus' detectability in wastewater in early 2020. The confirmation of fecal shedding of SARS-CoV-2 from asymptomatic, infected and recovering individuals further supports the potential for wastewater analysis to augment public health conventional surveillance techniques based on clinical testing of symptomatic individuals. We have reviewed possible capabilities projected for wastewater surveillance to support pandemic management, including independent, objective and cost-effective data generation that complements and addresses attendant limitations of clinical surveillance, early detection (i.e., prior to clinical reporting) of infection, estimation of disease prevalence, tracking of trends as possible indicators of success or failure of public health measures (mask mandates, lockdowns, vaccination, etc.), informing and engaging the public about pandemic trends, an application within sewer networks to identify infection hotspots, monitoring for presence or changes in infections from institutions (e.g., long-term care facilities, prisons, educational institutions and vulnerable industrial plants) and tracking of appearance/progression of viral variants of concern.
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Affiliation(s)
- Steve E Hrudey
- Analytical & Environmental Toxicology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2G3, Canada E-mail:
| | - Bernadette Conant
- Canadian Water Network, University of Waterloo, 200 University Avenue W, Waterloo ON N2L 3G1, Canada
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25
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Street R, Mathee A, Mangwana N, Dias S, Sharma JR, Ramharack P, Louw J, Reddy T, Brocker L, Surujlal-Naicker S, Berkowitz N, Malema MS, Nkambule S, Webster C, Mahlangeni N, Gelderblom H, Mdhluli M, Gray G, Muller C, Johnson R. Spatial and Temporal Trends of SARS-CoV-2 RNA from Wastewater Treatment Plants over 6 Weeks in Cape Town, South Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:12085. [PMID: 34831841 PMCID: PMC8618134 DOI: 10.3390/ijerph182212085] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 11/22/2022]
Abstract
Recent scientific trends have revealed that the collection and analysis of data on the occurrence and fate of SARS-CoV-2 in wastewater may serve as an early warning system for COVID-19. In South Africa, the first COVID-19 epicenter emerged in the Western Cape Province. The City of Cape Town, located in the Western Cape Province, has approximately 4 million inhabitants. This study reports on the monitoring of SARS-CoV-2 RNA in the wastewater of the City of Cape Town's wastewater treatment plants (WWTPs) during the peak of the epidemic. During this period, the highest overall median viral RNA signal was observed in week 1 (9200 RNA copies/mL) and declined to 127 copies/mL in week 6. The overall decrease in the amount of detected viral SARS-CoV-2 RNA over the 6-week study period was associated with a declining number of newly identified COVID-19 cases in the city. The SARS-CoV-2 early warning system has now been established to detect future waves of COVID-19.
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Affiliation(s)
- Renée Street
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (A.M.); (M.S.M.); (S.N.); (C.W.); (N.M.)
| | - Angela Mathee
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (A.M.); (M.S.M.); (S.N.); (C.W.); (N.M.)
- Environmental Health Department, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2092, South Africa
| | - Noluxabiso Mangwana
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (N.M.); (S.D.); (J.R.S.); (P.R.); (J.L.); (C.M.); (R.J.)
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - Stephanie Dias
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (N.M.); (S.D.); (J.R.S.); (P.R.); (J.L.); (C.M.); (R.J.)
| | - Jyoti Rajan Sharma
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (N.M.); (S.D.); (J.R.S.); (P.R.); (J.L.); (C.M.); (R.J.)
| | - Pritika Ramharack
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (N.M.); (S.D.); (J.R.S.); (P.R.); (J.L.); (C.M.); (R.J.)
| | - Johan Louw
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (N.M.); (S.D.); (J.R.S.); (P.R.); (J.L.); (C.M.); (R.J.)
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Tarylee Reddy
- Biostatistics Unit, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa;
| | - Ludwig Brocker
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - Swastika Surujlal-Naicker
- Scientific Services, Water and Sanitation Department, City of Cape Town Metropolitan Municipality, Cape Town 8000, South Africa;
| | - Natacha Berkowitz
- Community Services and Health, City Health, City of Cape Town, Hertzog Boulevard, Cape Town 8001, South Africa;
| | - Mokaba Shirley Malema
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (A.M.); (M.S.M.); (S.N.); (C.W.); (N.M.)
| | - Sizwe Nkambule
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (A.M.); (M.S.M.); (S.N.); (C.W.); (N.M.)
| | - Candice Webster
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (A.M.); (M.S.M.); (S.N.); (C.W.); (N.M.)
| | - Nomfundo Mahlangeni
- Environment & Health Research Unit, South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (A.M.); (M.S.M.); (S.N.); (C.W.); (N.M.)
| | - Huub Gelderblom
- COVID-19 Prevention Network (COVPN), Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
| | - Mongezi Mdhluli
- Office of the President, South African Medical Research Council, Tygerberg 7050, South Africa;
| | - Glenda Gray
- Chief Research Operations Office, South African Medical Research Council, Tygerberg 7050, South Africa;
| | - Christo Muller
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (N.M.); (S.D.); (J.R.S.); (P.R.); (J.L.); (C.M.); (R.J.)
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
- Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg 7505, South Africa; (N.M.); (S.D.); (J.R.S.); (P.R.); (J.L.); (C.M.); (R.J.)
- Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch 7600, South Africa
- Discipline of Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
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