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He P, Zhou W, Jiang M, Yu J, Wei H. Efficient concentration of viral nucleic acid in wastewater through surfactant releasing and a two-step magnetic bead extraction and purification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175742. [PMID: 39182763 DOI: 10.1016/j.scitotenv.2024.175742] [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: 05/20/2024] [Revised: 08/11/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Wastewater-based epidemiology (WBE) is a valuable complement to clinical monitoring, allowing for effective surveillance of viral infections in populations, and tracking the presence and the epidemiological dynamics of various infectious pathogens in communities. However, virus loads are usually low-abundant in wastewater, and current virus concentration methods for WBE are laborious and time-consuming with low recovery efficiency. To address these challenges, we have developed a magnetic bead-based semi-automated method involving extraction and purification to directly concentrate viral nucleic acids from sewage within 55 min. Prior to concentration, 0.5 % LDS was introduced to pretreat wastewater to inactivate viruses and release viral nucleic acids from both liquid and solid fractions to improve recovery. Under optimal conditions, the concentration method combined with reverse transcription-quantitative polymerase chain reaction (RT-qPCR) can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA added exogenously in wastewater as low as 4.9 copies/mL within 2.5 h, with an average recovery rate exceeding 80 %. Testing real sewages proved the applicability of the method to detect multiple viruses in different sewages. Additionally, variants of SARS-CoV-2 were successfully identified by multiplex amplicon sequencing in two samples. In conclusion, the new method could provide a much more efficient way for WBE of pathogenic viruses in various sewages.
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Affiliation(s)
- Ping He
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenhao Zhou
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengwei Jiang
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China
| | - Junping Yu
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hongping Wei
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Yang Y, Tan J, Wang F, Sun W, Shi H, Cheng Z, Xie Y, Zhou X. Preconcentration and detection of SARS-CoV-2 in wastewater: A comprehensive review. Biosens Bioelectron 2024; 263:116617. [PMID: 39094290 DOI: 10.1016/j.bios.2024.116617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/17/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) affected the health of human beings and the global economy. The patients with SARS-CoV-2 infection had viral RNA or live infectious viruses in feces. Thus, the possible transmission of SARS-CoV-2 through wastewater received great attentions. Moreover, SARS-CoV-2 in wastewater can serve as an early indicator of the infection within communities. We summarized the preconcentration and detection technology of SARS-CoV-2 in wastewater aiming at the complex matrices of wastewater and low virus concentration and compared their performance characteristics. We described the emerging tests that would be possible to realize the rapid detection of SARS-CoV-2 in fields and encourage academics to advance their technologies beyond conception. We concluded with a brief discussion on the outlook for integrating preconcentration and the detection of SARS-CoV-2 with emerging technologies.
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Affiliation(s)
- Yihan Yang
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jisui Tan
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Fan Wang
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Weiming Sun
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hanchang Shi
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zhao Cheng
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yangcun Xie
- Chinese Academy of Environmental Planning, Beijing, 100043, China.
| | - Xiaohong Zhou
- School of Environment, Tsinghua University, Beijing, 100084, China.
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3
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Dong T, Ding R, Zhou R, Shen C, Sheridan W, Paez D, Zhao Z, Wu P, Li F. A Portable Nucleic Acid Testing Platform with Photosensitization, a Three-Dimensionally Printed Multipiece Chip, and Digital Color Sensing. Anal Chem 2024; 96:6628-6633. [PMID: 38626114 DOI: 10.1021/acs.analchem.3c05897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Portable nucleic acid testing (NAT) holds great promise for point-of-care disease diagnosis and field-based applications but remains difficult to achieve. Herein, we describe a portable NAT that streamlines loop-mediated isothermal amplification with photosensitization-based color development in a fully sealed 3D-printed multipiece chip. Using a smartphone accessory and an APP, we also introduce a calibration-free quantification approach via digital color sensing and library matching. With these innovative approaches, our detection platform is highly accessible, allowing for rapid and sensitive NAT without requiring sophisticated instruments and well-trained personnel. The field applicability of our NAT platform was demonstrated by detecting tuberculosis infections in clinical sputum samples and food adulteration in commercial salmon meat products.
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Affiliation(s)
- Tianyu Dong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Ruolin Ding
- National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610064, P. R. China
| | - Rongxing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu 610064, P. R. China
| | - Chenlan Shen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
- Department of Laboratory Medicine, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu 610064, P. R. China
| | - Will Sheridan
- Nix Sensor Ltd., 286 Sanford Ave N Unit 501, Hamilton, Ontario L8L 6A1, Canada
| | - Dixon Paez
- Nix Sensor Ltd., 286 Sanford Ave N Unit 501, Hamilton, Ontario L8L 6A1, Canada
| | - Zhihe Zhao
- National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610064, P. R. China
| | - Peng Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
- Analytical & Testing Center, Sichuan University, Chengdu 610064, P. R. China
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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4
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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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5
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Toribio-Avedillo D, Gómez-Gómez C, Sala-Comorera L, Galofré B, Muniesa M. Adapted methods for monitoring influenza virus and respiratory syncytial virus in sludge and wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170636. [PMID: 38331285 DOI: 10.1016/j.scitotenv.2024.170636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Wastewater-based surveillance constitutes a valuable methodology for the continuous monitoring of viral circulation, with the capacity to function as an early warning system. It holds particular significance in scenarios where respiratory viruses exhibit overlapping clinical presentations, as occurs with SARS-CoV-2, influenza virus (IV), and respiratory syncytial virus (RSV), and allows seasonal virus outbreaks to be distinguished from COVID-19 peaks. Furthermore, sewage sludge, given it harbors concentrated human waste from a large population, serves as a substantial reservoir for pathogen detection. To effectively integrate wastewater-based epidemiology into infectious disease surveillance, the detection methods employed in wastewater samples must be adapted to the distinct characteristics of sludge matrices. In this study, we adapted and applied protocols for the detection of IV and RSV in sewage sludge, comparing their performance with the results obtained in wastewater. To assess the efficiency of these protocols, sludge and wastewater samples were spiked with IV and RSV RNA, either free or incorporated in lentiviral particles. Samples were concentrated using the aluminum hydroxide adsorption-precipitation method before viral RNA extraction. Absolute virus quantification was carried out by RT-qPCR, including an internal control to monitor potential inhibitory factors. Recovery efficiencies for both free IV and RSV RNA were 60 % in sludge, and 75 % and 71 % respectively in wastewater, whereas the values for IV and RSV RNA in lentiviral particles were 16 % and 10 % in sludge and 21 % and 17 % in wastewater respectively. Additionally, the protocol enabled the quantification of naturally occurring IV and RSV in wastewater and sludge samples collected from two wastewater treatment plants during the winter months, thus affirming the efficacy of the employed methodologies.
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Affiliation(s)
- Daniel Toribio-Avedillo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain
| | - Clara Gómez-Gómez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain
| | - Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain.
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6
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Parkins MD, Lee BE, Acosta N, Bautista M, Hubert CRJ, Hrudey SE, Frankowski K, Pang XL. Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond. Clin Microbiol Rev 2024; 37:e0010322. [PMID: 38095438 PMCID: PMC10938902 DOI: 10.1128/cmr.00103-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024] Open
Abstract
Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.
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Affiliation(s)
- Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O’Brien Institute of Public Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole Acosta
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maria Bautista
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Provincial Health Laboratory, Alberta Health Services, Calgary, Alberta, Canada
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7
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Abreu MADF, Lopes BC, Assemany PP, Souza ADR, Siniscalchi LAB. COVID-19 cases, vaccination, and SARS-CoV-2 in wastewater: insights from a Brazilian municipality. JOURNAL OF WATER AND HEALTH 2024; 22:268-277. [PMID: 38421621 PMCID: wh_2024_159 DOI: 10.2166/wh.2024.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Vaccines combatting COVID-19 demonstrate the ability to protect against disease and hospitalization, and reduce the likelihood of death caused by SARS-CoV-2. In addition, monitoring viral loads in sewage emerges as another crucial strategy in the epidemiological context, enabling early and collective detection of outbreaks. The study aimed to monitor the viral concentration of SARS-CoV-2 in untreated sewage in a Brazilian municipality. Also, it attempted to correlate these measurements with the number of clinical cases and deaths resulting from COVID-19 between July 2021 and July 2022. SARS-CoV-2 viral RNA was quantified by RT-qPCR. Pearson's correlation was performed to analyze the variables' relationship using the number of cases, deaths, vaccinated individuals, and viral concentration of SARS-CoV-2. The results revealed a significant negative correlation (p < 0.05) between the number of vaccinated individuals and the viral concentration of SARS-CoV-2, suggesting that after vaccination, the RNA viral load concentration was reduced in the sample population by the circulating concentration of wastewater. Consequently, wastewater monitoring, in addition to functioning as an early warning system for the circulation of SARS-CoV-2 and other pathogens, can offer a novel perspective that enhances decision-making, strengthens vaccination campaigns, and contributes to authorities establishing systematic networks for monitoring SARS-CoV-2.
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Affiliation(s)
- Mariana Aparecida de Freitas Abreu
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil; Applied Microbiology Laboratory at the Environmental Engineering Department of UFLA, Federal University of Lavras (UFLA), Lavras, Brazil E-mail:
| | - Bruna Coelho Lopes
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Paula Peixoto Assemany
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil; Applied Microbiology Laboratory at the Environmental Engineering Department of UFLA, Federal University of Lavras (UFLA), Lavras, Brazil
| | - Aline Dos Reis Souza
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil
| | - Luciene Alves Batista Siniscalchi
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil; Applied Microbiology Laboratory at the Environmental Engineering Department of UFLA, Federal University of Lavras (UFLA), Lavras, Brazil
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8
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Akter J, Smith WJ, Liu Y, Kim I, Simpson SL, Thai P, Korajkic A, Ahmed W. Comparison of adsorption-extraction (AE) workflows for improved measurements of viral and bacterial nucleic acid in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:167966. [PMID: 38476760 PMCID: PMC10927021 DOI: 10.1016/j.scitotenv.2023.167966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The lack of standardized methods and large differences in virus concentration and extraction workflows have hampered Severe Acute Respiratory Syndrome (SARS-CoV-2) wastewater surveillance and data reporting practices. Numerous studies have shown that adsorption-extraction (AE) method holds promise, yet several uncertainties remain regarding the optimal AE workflow. Several procedural components may influence the recovered concentrations of target nucleic acid, including membrane types, homogenization instruments, speed and duration, and lysis buffer. In this study, 42 different AE workflows that varied these components were compared to determine the optimal workflow by quantifying endogenous SARS-CoV-2, human adenovirus 40/41 (HAdV 40/41), and a bacterial marker gene of fecal contamination (Bacteroides HF183). Our findings suggest that the workflow chosen had a significant impact on SARS-CoV-2 concentrations, whereas it had minimal impact on HF183 and no effect on HAdV 40/41 concentrations. When comparing individual components in a workflow, such as membrane type (MF-Millipore™ 0.45 μm MCE vs. Isopore™ 0.40 μm), we found that they had no impact on SARS-CoV-2, HAdV 40/41, and HF183 concentrations. This suggests that at least some consumables and equipment are interchangeable. Buffer PM1 + TRIzol-based workflows yielded higher concentrations of SARS-CoV-2 than other workflows. HF183 concentrations were higher in workflows without chloroform. Similarly, higher homogenization speeds (5000-10,000 rpm) led to increased concentrations of SARS-CoV-2 and HF183 but had no effect on HAdV 40/41. Our findings indicate that minor enhancements to the AE workflow can improve the recovery of viruses and bacteria from the wastewater, leading to improved outcomes from wastewater surveillance efforts.
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Affiliation(s)
- Jesmin Akter
- Department of Civil and Environmental Engineering, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, Republic of Korea
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J.M. Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Ilho Kim
- Department of Civil and Environmental Engineering, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, Republic of Korea
| | | | - Phong Thai
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 4102 Brisbane, Australia
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
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9
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Liu Y, Yang Y, Wang G, Wang D, Shao PL, Tang J, He T, Zheng J, Hu R, Liu Y, Xu Z, Niu D, Lv J, Yang J, Xiao H, Wu S, He S, Tang Z, Liu Y, Tang M, Jiang X, Yuan J, Dai H, Zhang B. Multiplexed discrimination of SARS-CoV-2 variants via plasmonic-enhanced fluorescence in a portable and automated device. Nat Biomed Eng 2023; 7:1636-1648. [PMID: 37735541 DOI: 10.1038/s41551-023-01092-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Portable assays for the rapid identification of lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to aid large-scale efforts in monitoring the evolution of the virus. Here we report a multiplexed assay in a microarray format for the detection, via isothermal amplification and plasmonic-gold-enhanced near-infrared fluorescence, of variants of SARS-CoV-2. The assay, which has single-nucleotide specificity for variant discrimination, single-RNA-copy sensitivity and does not require RNA extraction, discriminated 12 lineages of SARS-CoV-2 (in three mutational hotspots of the Spike protein) and detected the virus in nasopharyngeal swabs from 1,034 individuals at 98.8% sensitivity and 100% specificity, with 97.6% concordance with genome sequencing in variant discrimination. We also report a compact, portable and fully automated device integrating the entire swab-to-result workflow and amenable to the point-of-care detection of SARS-CoV-2 variants. Portable, rapid, accurate and multiplexed assays for the detection of SARS-CoV-2 variants and lineages may facilitate variant-surveillance efforts.
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Affiliation(s)
- Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dou Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Pan-Lin Shao
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Tingzhen He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jintao Zheng
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yiyi Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ziyi Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dan Niu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jingkai Yang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Hongjun Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Shuai Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Shuang He
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Zhongrong Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yan Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | | | - Xingyu Jiang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
| | - Jing Yuan
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Infectious Disease Department, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.
| | - Hongjie Dai
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
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10
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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: 1] [Impact Index Per Article: 1.0] [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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11
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Liu Y, Kumblathan T, Joyce MA, Tyrrell DL, Tipples G, Pang X, Li XF, Le XC. Multiplex Assays Enable Simultaneous Detection and Identification of SARS-CoV-2 Variants of Concern in Clinical and Wastewater Samples. ACS MEASUREMENT SCIENCE AU 2023; 3:258-268. [PMID: 37600458 PMCID: PMC10152402 DOI: 10.1021/acsmeasuresciau.3c00005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 08/22/2023]
Abstract
The targeted screening and sequencing approaches for COVID-19 surveillance need to be adjusted to fit the evolving surveillance objectives which necessarily change over time. We present the development of variant screening assays that can be applied to new targets in a timely manner and enable multiplexing of targets for efficient implementation in the laboratory. By targeting the HV69/70 deletion for Alpha, K417N for Beta, K417T for Gamma, and HV69/70 deletion plus K417N for sub-variants BA.1, BA.3, BA.4, and BA.5 of Omicron, we achieved simultaneous detection and differentiation of Alpha, Beta, Gamma, and Omicron in a single assay. Targeting both T478K and P681R mutations enabled specific detection of the Delta variant. The multiplex assays used in combination, targeting K417N and T478K, specifically detected the Omicron sub-variant BA.2. The limits of detection for the five variants of concern were 4-16 copies of the viral RNA per reaction. Both assays achieved 100% clinical sensitivity and 100% specificity. Analyses of 377 clinical samples and 24 wastewater samples revealed the Delta variant in 100 clinical samples (nasopharyngeal and throat swab) collected in November 2021. Omicron BA.1 was detected in 79 nasopharyngeal swab samples collected in January 2022. Alpha, Beta, and Gamma variants were detected in 24 wastewater samples collected in May-June 2021 from two major cities of Alberta (Canada), and the results were consistent with the clinical cases of multiple variants reported in the community.
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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
| | - Michael A. Joyce
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - D. Lorne Tyrrell
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Graham Tipples
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Provincial
Laboratory for Public Health, Alberta Precision Laboratories, University of Alberta Hospitals, 8440-112 Street, Edmonton, Alberta T6G 2J2, Canada
| | - Xiaoli Pang
- Provincial
Laboratory for Public Health, Alberta Precision Laboratories, University of Alberta Hospitals, 8440-112 Street, Edmonton, Alberta T6G 2J2, Canada
- 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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12
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Belmonte-Lopes R, Barquilha CER, Kozak C, Barcellos DS, Leite BZ, da Costa FJOG, Martins WL, Oliveira PE, Pereira EHRA, Filho CRM, de Souza EM, Possetti GRC, Vicente VA, Etchepare RG. 20-Month monitoring of SARS-CoV-2 in wastewater of Curitiba, in Southern Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:76687-76701. [PMID: 37243767 PMCID: PMC10224667 DOI: 10.1007/s11356-023-27926-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
The COVID-19 pandemic resulted in the collapse of healthcare systems and led to the development and application of several approaches of wastewater-based epidemiology to monitor infected populations. The main objective of this study was to carry out a SARS-CoV-2 wastewater based surveillance in Curitiba, Southern Brazil Sewage samples were collected weekly for 20 months at the entrance of five treatment plants representing the entire city and quantified by qPCR using the N1 marker. The viral loads were correlated with epidemiological data. The correlation by sampling points showed that the relationship between the viral loads and the number of reported cases was best described by a cross-correlation function, indicating a lag between 7 and 14 days amidst the variables, whereas the data for the entire city presented a higher correlation (0.84) with the number of positive tests at lag 0 (sampling day). The results also suggest that the Omicron VOC resulted in higher titers than the Delta VOC. Overall, our results showed that the approach used was robust as an early warning system, even with the use of different epidemiological indicators or changes in the virus variants in circulation. Therefore, it can contribute to public decision-makers and health interventions, especially in vulnerable and low-income regions with limited clinical testing capacity. Looking toward the future, this approach will contribute to a new look at environmental sanitation and should even induce an increase in sewage coverage rates in emerging countries.
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Affiliation(s)
- Ricardo Belmonte-Lopes
- Graduate Program On Pathology, Parasitology, and Microbiology, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
- Basic Pathology Department, Biological Sciences Sector, Microbiological Collections of Paraná Network, Room 135/136. 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
- Basic Pathology Department, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
| | - Carlos E R Barquilha
- Graduate Program On Water Resources and Environmental Engineering, Hydraulics and Sanitation Department, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
- Hydraulics and Sanitation Department, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
| | - Caroline Kozak
- Environment Department, Maringa State University, SESI Block, 1800 Ângelo Moreira da Fonseca AvenueRoom 15, Parque Danielle, Umuarama, PR, 87506-370, Brazil
| | - Demian S Barcellos
- Hydraulics and Sanitation Department, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
| | - Bárbara Z Leite
- Research and Innovation Management, Paraná Sanitation Company (SANEPAR), 1376 Eng. Rebouças St, Rebouças, Curitiba, PR, 80215-900, Brazil
| | - Fernanda J O Gomes da Costa
- Research and Innovation Management, Paraná Sanitation Company (SANEPAR), 1376 Eng. Rebouças St, Rebouças, Curitiba, PR, 80215-900, Brazil
| | - William L Martins
- Basic Pathology Department, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
| | - Pâmela E Oliveira
- Hydraulics and Sanitation Department, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
| | - Edy H R A Pereira
- Hydraulics and Sanitation Department, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
| | - Cesar R Mota Filho
- Sanitary and Environmental Engineering Department, Federal University of Minas Gerais (UFMG), 6627 Antonio Carlos Avenue, Block 1, Room 4529, Belo Horizonte, MG, 31270-901, Brazil
| | - Emanuel M de Souza
- Biochemistry and Molecular Biology Department, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
| | - Gustavo R C Possetti
- Research and Innovation Management, Paraná Sanitation Company (SANEPAR), 1376 Eng. Rebouças St, Rebouças, Curitiba, PR, 80215-900, Brazil
| | - Vania A Vicente
- Basic Pathology Department, Biological Sciences Sector, Microbiological Collections of Paraná Network, Room 135/136. 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
- Basic Pathology Department, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil
| | - Ramiro G Etchepare
- Hydraulics and Sanitation Department, Federal University of Paraná, 100 Coronel Francisco Heráclito Dos Santos Avenue, Curitiba, PR, 81530-000, Brazil.
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13
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Ciannella S, González-Fernández C, Gomez-Pastora J. Recent progress on wastewater-based epidemiology for COVID-19 surveillance: A systematic review of analytical procedures and epidemiological modeling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:162953. [PMID: 36948304 PMCID: PMC10028212 DOI: 10.1016/j.scitotenv.2023.162953] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 05/13/2023]
Abstract
On March 11, 2020, the World Health Organization declared the coronavirus disease 2019 (COVID-19), whose causative agent is the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a pandemic. This virus is predominantly transmitted via respiratory droplets and shed via sputum, saliva, urine, and stool. Wastewater-based epidemiology (WBE) has been able to monitor the circulation of viral pathogens in the population. This tool demands both in-lab and computational work to be meaningful for, among other purposes, the prediction of outbreaks. In this context, we present a systematic review that organizes and discusses laboratory procedures for SARS-CoV-2 RNA quantification from a wastewater matrix, along with modeling techniques applied to the development of WBE for COVID-19 surveillance. The goal of this review is to present the current panorama of WBE operational aspects as well as to identify current challenges related to it. Our review was conducted in a reproducible manner by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic reviews. We identified a lack of standardization in wastewater analytical procedures. Regardless, the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) approach was the most reported technique employed to detect and quantify viral RNA in wastewater samples. As a more convenient sample matrix, we suggest the solid portion of wastewater to be considered in future investigations due to its higher viral load compared to the liquid fraction. Regarding the epidemiological modeling, the data-driven approach was consistently used for the prediction of variables associated with outbreaks. Future efforts should also be directed toward the development of rapid, more economical, portable, and accurate detection devices.
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Affiliation(s)
- Stefano Ciannella
- Department of Chemical Engineering, Texas Tech University, Lubbock 79409, TX, USA.
| | - Cristina González-Fernández
- Department of Chemical Engineering, Texas Tech University, Lubbock 79409, TX, USA; Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Avda. Los Castros, s/n, 39005 Santander, Spain.
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14
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Trigo-Tasende N, Vallejo JA, Rumbo-Feal S, Conde-Pérez K, Vaamonde M, López-Oriona Á, Barbeito I, Nasser-Ali M, Reif R, Rodiño-Janeiro BK, Fernández-Álvarez E, Iglesias-Corrás I, Freire B, Tarrío-Saavedra J, Tomás L, Gallego-García P, Posada D, Bou G, López-de-Ullibarri I, Cao R, Ladra S, Poza M. Wastewater early warning system for SARS-CoV-2 outbreaks and variants in a Coruña, Spain. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27877-3. [PMID: 37286834 DOI: 10.1007/s11356-023-27877-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
Wastewater-based epidemiology has been widely used as a cost-effective method for tracking the COVID-19 pandemic at the community level. Here we describe COVIDBENS, a wastewater surveillance program running from June 2020 to March 2022 in the wastewater treatment plant of Bens in A Coruña (Spain). The main goal of this work was to provide an effective early warning tool based in wastewater epidemiology to help in decision-making at both the social and public health levels. RT-qPCR procedures and Illumina sequencing were used to weekly monitor the viral load and to detect SARS-CoV-2 mutations in wastewater, respectively. In addition, own statistical models were applied to estimate the real number of infected people and the frequency of each emerging variant circulating in the community, which considerable improved the surveillance strategy. Our analysis detected 6 viral load waves in A Coruña with concentrations between 103 and 106 SARS-CoV-2 RNA copies/L. Our system was able to anticipate community outbreaks during the pandemic with 8-36 days in advance with respect to clinical reports and, to detect the emergence of new SARS-CoV-2 variants in A Coruña such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529 and BA.2) in wastewater with 42, 30, and 27 days, respectively, before the health system did. Data generated here helped local authorities and health managers to give a faster and more efficient response to the pandemic situation, and also allowed important industrial companies to adapt their production to each situation. The wastewater-based epidemiology program developed in our metropolitan area of A Coruña (Spain) during the SARS-CoV-2 pandemic served as a powerful early warning system combining statistical models with mutations and viral load monitoring in wastewater over time.
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Affiliation(s)
- Noelia Trigo-Tasende
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Juan A Vallejo
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Soraya Rumbo-Feal
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Kelly Conde-Pérez
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Manuel Vaamonde
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Ángel López-Oriona
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Inés Barbeito
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Mohammed Nasser-Ali
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Rubén Reif
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), University of Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
| | - Bruno K Rodiño-Janeiro
- BFlow, University of Santiago de Compostela (USC) and Health Research Institute of Santiago de Compostela (IDIS), Campus Vida, 15706, Santiago de Compostela, A Coruña, Spain
| | - Elisa Fernández-Álvarez
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Iago Iglesias-Corrás
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Borja Freire
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Javier Tarrío-Saavedra
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Laura Tomás
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
| | - Pilar Gallego-García
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
| | - David Posada
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310, Vigo, Spain
| | - Germán Bou
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Ignacio López-de-Ullibarri
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Ricardo Cao
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Susana Ladra
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Margarita Poza
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain.
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15
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Jiang G, Liu Y, Tang S, Kitajima M, Haramoto E, Arora S, Choi PM, Jackson G, D'Aoust PM, Delatolla R, Zhang S, Guo Y, Wu J, Chen Y, Sharma E, Prosun TA, Zhao J, Kumar M, Honda R, Ahmed W, Meiman J. Moving forward with COVID-19: Future research prospects of wastewater-based epidemiology methodologies and applications. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2023; 33:100458. [PMID: 37034453 PMCID: PMC10065412 DOI: 10.1016/j.coesh.2023.100458] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Wastewater-based epidemiology (WBE) has been demonstrated for its great potential in tracking of coronavirus disease 2019 (COVID-19) transmission among populations despite some inherent methodological limitations. These include non-optimized sampling approaches and analytical methods; stability of viruses in sewer systems; partitioning/retention in biofilms; and the singular and inaccurate back-calculation step to predict the number of infected individuals in the community. Future research is expected to (1) standardize best practices in wastewater sampling, analysis and data reporting protocols for the sensitive and reproducible detection of viruses in wastewater; (2) understand the in-sewer viral stability and partitioning under the impacts of dynamic wastewater flow, properties, chemicals, biofilms and sediments; and (3) achieve smart wastewater surveillance with artificial intelligence and big data models. Further specific research is essential in the monitoring of other viral pathogens with pandemic potential and subcatchment applications to maximize the benefits of WBE beyond COVID-19.
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Affiliation(s)
- Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Song Tang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Chaoyang District, Beijing 100021, China
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, 302017, India
| | - Phil M Choi
- Water Unit, Health Protection Branch, Queensland Public Health and Scientific Services, Queensland Health, Australia
| | - Greg Jackson
- Water Unit, Health Protection Branch, Queensland Public Health and Scientific Services, Queensland Health, Australia
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Shuxin Zhang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Ying Guo
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Jiangping Wu
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Yan Chen
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Elipsha Sharma
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Tanjila Alam Prosun
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Jiawei Zhao
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterey, Monterrey, 64849, Nuevo Leon, Mexico
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Japan
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Jon Meiman
- Wisconsin Department of Health Services, Madison, WI 53701, USA
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16
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Kim LH, Mikolaityte V, Kim S. Establishment of wastewater-based SARS-CoV-2 monitoring system over two years: Case studies in South Korea. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:110289. [PMID: 37292384 PMCID: PMC10240911 DOI: 10.1016/j.jece.2023.110289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/22/2023] [Accepted: 06/03/2023] [Indexed: 06/10/2023]
Abstract
With the global COVID-19 pandemic, wastewater surveillance has received a considerable attention as a method for the early identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater treatment plant (WWTP) and sewer systems. For the first time in Korea, this study utilized the wastewater surveillance technique to monitor the COVID-19 outbreak. Sampling efforts were carried out at the WWTPs in the capital city of Korea, Seoul, and Daegu the place where the first severe outbreak was reported. The RNA of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been extracted from the collected wastewater influent and primary sewage sludge samples. The outcomes were contrasted with the COVID-19 cases in the WWTPs served area. Additionally, whole transcriptome sequencing was used to compare the microbial community alterations before and after the COVID-19 outbreak and SARS-CoV-2 variations. The results demonstrated that the changes in SARS-CoV-2 RNA concentrations in the influent and sludge matched the trends of reported COVID-19 cases, especially sludge showed high-resolution data, which is well-matched when fewer COVID-19 cases (0-250) are reported. Interestingly, one month before the clinical report, we found that the SARS-CoV-2 Beta variant (South Africa, B.1.351) in the wastewater. In addition, the Aeromonas bacterial species was dominated (21.2%) among other bacterial species in wastewater after the COVID-19 outbreak, suggesting a potential indirect microbial indicator of the COVID-19 outbreak.
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Affiliation(s)
- Lan Hee Kim
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
| | - Viktorija Mikolaityte
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
| | - Sungpyo Kim
- Research Institute for Advanced Industrial Technology, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
- Department of Environmental Systems Engineering, Korea University, 2511 Sejong-ro, Sejong city 30019, Republic of Korea
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Lanzarini NM, Mannarino CF, Ribeiro AVC, Prado T, Vahia LS, Siqueira MM, Resende PC, Quintaes BR, Miagostovich MP. SARS-CoV-2 surveillance-based on municipal solid waste leachate in Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:67368-67377. [PMID: 37101215 PMCID: PMC10132925 DOI: 10.1007/s11356-023-27019-9] [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: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Municipal solid waste leachate-based epidemiology is an alternative viral tracking tool that applies fresh truck leachate as an early warning of public health emergencies. This study aimed to investigate the potential of SARS-CoV-2 surveillance based on solid waste fresh truck leachate. Twenty truck leachate samples were ultracentrifugated, nucleic acid extracted, and real-time RT-qPCR SARS-CoV-2 N1/N2 applied. Viral isolation, variant of concern (N1/N2) inference, and whole genome sequencing were also performed. SARS-CoV-2 was detected on 40% (8/20) of samples, with a concentration from 2.89 to 6.96 RNA Log10 100 mL-1. The attempt to isolate SARS-CoV-2 and recover the whole genome was not successful; however, positive samples were characterized as possible pre-variant of concern (pre-VOC), VOC Alpha (B.1.1.7) and variant of interest Zeta (P.2). This approach revealed an alternative tool to infer SARS-CoV-2 in the environment and may help the management of local surveillance, health, and social policies.
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Affiliation(s)
- Natália Maria Lanzarini
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil.
| | - Camille Ferreira Mannarino
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - André Vinicius Costa Ribeiro
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Leonardo Saboia Vahia
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | | | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
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Yang K, Guo J, Møhlenberg M, Zhou H. SARS-CoV-2 surveillance in medical and industrial wastewater-a global perspective: a narrative review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:63323-63334. [PMID: 36988799 PMCID: PMC10049894 DOI: 10.1007/s11356-023-26571-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/16/2023] [Indexed: 05/11/2023]
Abstract
The novel coronavirus SARS-CoV-2 has spread at an unprecedented rate since late 2019, leading to the global COVID-19 pandemic. During the pandemic, being able to detect SARS-CoV-2 in human populations with high coverage quickly is a huge challenge. As SARS-CoV-2 is excreted in human excreta and thus exposed to the aqueous environment through sewers, the goal is to develop an ideal, non-invasive, cost-effective epidemiological method for detecting SARS-CoV-2. Wastewater surveillance has gained widespread interest and is increasingly being investigated as an effective early warning tool for monitoring the spread and evolution of the virus. This review emphasizes important findings on SARS-CoV-2 wastewater-based epidemiology (WBE) in different continents and techniques used to detect SARS-CoV-2 in wastewater during the period 2020-2022. The results show that WBE is a valuable population-level method for monitoring SARS-CoV-2 and is a valuable early warning alert. It can assist policymakers in formulating relevant policies to avoid the negative impacts of early or delayed action. Such strategy can also help avoid unnecessary wastage of medical resources, rationalize vaccine distribution, assist early detection, and contain large-scale outbreaks.
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Affiliation(s)
- Kaiwen Yang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Liutai Road 1166, Wenjiang, Chengdu, 610000, China
| | - Jinlin Guo
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Liutai Road 1166, Wenjiang, Chengdu, 610000, China
| | - Michelle Møhlenberg
- Department of Biomedicine, Høegh-Guldbergs Gade 10, Building 1115, DK-8000, Aarhus C, Denmark
| | - Hao Zhou
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Liutai Road 1166, Wenjiang, Chengdu, 610000, China.
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