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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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2
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do Nascimento MCA, Smith WJM, Gebrewold M, Liu Y, Simpson SL, Bivins A, Rahal P, Ahmed W. Development and evaluation of a colorimetric LAMP based-assay targeting the Bacteroides HF183 marker for tracking sewage pollution in environmental waters. WATER RESEARCH 2024; 264:122202. [PMID: 39146849 DOI: 10.1016/j.watres.2024.122202] [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: 05/29/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 08/17/2024]
Abstract
Surface waters are vulnerable to contamination by human and animal feces, posing risks to human health due to potential exposure to enteric pathogens. This research developed a colorimetric loop-mediated isothermal amplification (cLAMP) assay to detect sewage associated Bacteroides dorei HF183/BacR287 (HF183) marker in wastewater and environmental water samples. The host sensitivity and host specificity of the assay were evaluated, and their performance was compared to the Bacteroides HF183 qPCR assay using control materials (gBlocks), environmental water samples seeded with untreated sewage, and ambient environmental water samples. In serial dilutions of control materials, qPCR produced quantifiable data across all dilutions, while cLAMP detected the marker down to 0.001 pg/µL of control materials, which was two orders of magnitude less sensitive than qPCR. All untreated sewage samples (n = 12) tested positive for HF183 by both the qPCR and cLAMP assays, demonstrating a host sensitivity value of 1.00 (maximum value of 1.00). The host specificity by analysing 70 non-human fecal nucleic acid samples revealed cLAMP's specificity value of 0.81 compared to qPCR's 0.64. When testing sewage-seeded environmental water samples, both methods detected HF183 for the lowest amount of sewage, indicating similar detection sensitivity. The application of cLAMP for tracking sewage pollution in environmental waters showed promising results, with moderate agreement between cLAMP and qPCR (κ = 0.510). However, cLAMP occasionally missed detections compared to qPCR, particularly in low-concentration samples. Overall, the cLAMP HF183 assay demonstrated promising potential as a rapid and sensitive method for detecting sewage pollution, offering a viable alternative to qPCR in certain environmental monitoring scenarios.
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Affiliation(s)
- Mariah C A do Nascimento
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia; Department of Biology, São Paulo State University - UNESP, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | | | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia; State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Stuart L Simpson
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Paula Rahal
- Department of Biology, São Paulo State University - UNESP, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
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3
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Boza JM, Amirali A, Williams SL, Currall BB, Grills GS, Mason CE, Solo-Gabriele HM, Erickson DC. Evaluation of a field deployable, high-throughput RT-LAMP device as an early warning system for COVID-19 through SARS-CoV-2 measurements in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173744. [PMID: 38844223 PMCID: PMC11249788 DOI: 10.1016/j.scitotenv.2024.173744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/02/2024] [Accepted: 06/01/2024] [Indexed: 06/16/2024]
Abstract
Quantification of SARS-CoV-2 RNA copies in wastewater can be used to estimate COVID-19 prevalence in communities. While such results are important for mitigating disease spread, SARS-CoV-2 measurements require sophisticated equipment and trained personnel, for which a centralized laboratory is necessary. This significantly impacts the time to result, defeating its purpose as an early warning detection tool. The objective of this study was to evaluate a field portable device (called MINI) for detecting SARS-CoV-2 viral loads in wastewater using real-time reverse transcriptase loop-mediated isothermal amplification (real-time RT-LAMP). The device was tested using wastewater samples collected from buildings (with 430 to 1430 inhabitants) that had known COVID-19-positive cases. Results show comparable performance of RT-LAMP against reverse transcriptase polymerase chain reaction (RT-qPCR) when detecting SARS-CoV-2 copies in wastewater. Both RT-LAMP and RT-qPCR detected SARS-CoV-2 in wastewater from buildings with at least three positive individuals within a 6-day time frame prior to diagnosis. The large 96-well throughput provided by MINI provided scalability to multi-building detection. The portability of the MINI device enabled decentralized on-site detection, significantly reducing the time to result. The overall findings support the use of RT-LAMP within the MINI configuration as an early detection system for COVID-19 infection using wastewater collected at the building scale.
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Affiliation(s)
- J M Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - A Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - S L Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - B B Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - G S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - C E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - H M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - D C Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA; Division of Nutritional Science, Cornell University, Ithaca, NY 14850, USA.
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Martínez de Alba ÁE, Morán-Diez ME, García-Prieto JC, García-Bernalt Diego J, Fernández-Soto P, Serrano León E, Monsalvo V, Casao M, Rubio MB, Hermosa R, Muro A, García-Roig M, Monte E. SARS-CoV-2 RNA Detection in Wastewater and Its Effective Correlation with Clinical Data during the Outbreak of COVID-19 in Salamanca. Int J Mol Sci 2024; 25:8071. [PMID: 39125640 PMCID: PMC11311535 DOI: 10.3390/ijms25158071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/16/2024] [Accepted: 07/20/2024] [Indexed: 08/12/2024] Open
Abstract
Wastewater treatment plants (WWTPs) are the final stage of the anthropogenic water cycle where a wide range of chemical and biological markers of human activity can be found. In COVID-19 disease contexts, wastewater surveillance has been used to infer community trends based on viral abundance and SARS-CoV-2 RNA variant composition, which has served to anticipate and establish appropriate protocols to prevent potential viral outbreaks. Numerous studies worldwide have provided reliable and robust tools to detect and quantify SARS-CoV-2 RNA in wastewater, although due to the high dilution and degradation rate of the viral RNA in such samples, the detection limit of the pathogen has been a bottleneck for the proposed protocols so far. The current work provides a comprehensive and systematic study of the different parameters that may affect the detection of SARS-CoV-2 RNA in wastewater and hinder its quantification. The results obtained using synthetic viral RNA as a template allow us to consider that 10 genome copies per µL is the minimum RNA concentration that provides reliable and consistent values for the quantification of SARS-CoV-2 RNA. RT-qPCR analysis of wastewater samples collected at the WWTP in Salamanca (western Spain) and at six pumping stations in the city showed that below this threshold, positive results must be confirmed by sequencing to identify the specific viral sequence. This allowed us to find correlations between the SARS-CoV-2 RNA levels found in wastewater and the COVID-19 clinical data reported by health authorities. The close match between environmental and clinical data from the Salamanca case study has been confirmed by similar experimental approaches in four other cities in the same region. The present methodological approach reinforces the usefulness of wastewater-based epidemiology (WBE) studies in the face of future pandemic outbreaks.
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Affiliation(s)
- Ángel Emilio Martínez de Alba
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Salamanca, Spain; (M.E.M.-D.); (M.B.R.); (R.H.); (E.M.)
| | - María Eugenia Morán-Diez
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Salamanca, Spain; (M.E.M.-D.); (M.B.R.); (R.H.); (E.M.)
| | - Juan Carlos García-Prieto
- Centre for Research and Technological Development of Water (CIDTA), University of Salamanca, 37080 Salamanca, Spain; (J.C.G.-P.); (M.G.-R.)
| | - Juan García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (P.F.-S.); (A.M.)
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (P.F.-S.); (A.M.)
| | | | | | - Marta Casao
- FCC Aqualia, 28050 Madrid, Spain; (E.S.L.); (V.M.); (M.C.)
| | - María Belén Rubio
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Salamanca, Spain; (M.E.M.-D.); (M.B.R.); (R.H.); (E.M.)
| | - Rosa Hermosa
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Salamanca, Spain; (M.E.M.-D.); (M.B.R.); (R.H.); (E.M.)
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (P.F.-S.); (A.M.)
| | - Manuel García-Roig
- Centre for Research and Technological Development of Water (CIDTA), University of Salamanca, 37080 Salamanca, Spain; (J.C.G.-P.); (M.G.-R.)
| | - Enrique Monte
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Salamanca, Spain; (M.E.M.-D.); (M.B.R.); (R.H.); (E.M.)
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5
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Hossain T, Lungu C, de Schrijver S, Kuali M, Crespo R, Reddy N, Ngubane A, Kan TW, Reddy K, Rao S, Palstra RJ, Madlala P, Ndung'u T, Mahmoudi T. Specific quantification of inducible HIV-1 reservoir by RT-LAMP. COMMUNICATIONS MEDICINE 2024; 4:123. [PMID: 38918506 PMCID: PMC11199587 DOI: 10.1038/s43856-024-00553-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Strategies toward HIV-1 cure aim to clear, inactivate, reduce, or immunologically control the virus from a pool of latently infected cells such that combination antiretroviral therapy (cART) can be safely interrupted. In order to assess the impact of any putative curative interventions on the size and inducibility of the latent HIV-1 reservoir, robust and scalable assays are needed to precisely quantify the frequency of infected cells containing inducible HIV-1. METHODS We developed Specific Quantification of Inducible HIV-1 by RT-LAMP (SQuHIVLa), leveraging the high sensitivity and specificity of RT-LAMP, performed in a single reaction, to detect and quantify cells expressing tat/rev HIV-1 multiply spliced RNA (msRNA) upon activation. The LAMP primer/probe used in SQuHIVLa was designed to exclusively detect HIV-1 tat/rev msRNA and adapted for different HIV-1 subtypes. RESULTS Using SQuHIVLa, we successfully quantify the inducible viral reservoir in CD4+ T cells from people living with HIV-1 subtypes B and C on cART. The assay demonstrates high sensitivity, specificity, and reproducibility. CONCLUSIONS SQuHIVLa offers a high throughput, scalable, and specific HIV-1 reservoir quantification tool that is amenable to resource-limited settings. This assay poses remarkable potential in facilitating the evaluation of potential interventional strategies toward achieving HIV-1 cure.
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Affiliation(s)
- Tanvir Hossain
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Cynthia Lungu
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sten de Schrijver
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mamokoena Kuali
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nicole Reddy
- Africa Health Research Institute, Durban, South Africa
| | - Ayanda Ngubane
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Tsung Wai Kan
- Department of Urology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kavidha Reddy
- Africa Health Research Institute, Durban, South Africa
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert-Jan Palstra
- Department of Urology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Paradise Madlala
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
- Division of Infection and Immunity, University College London, London, UK
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Department of Urology, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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6
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Putra HG, Surja SS, Widowati TA, Ali S, Kaisar MMM. SARS-CoV-2 RT-LAMP in saliva: enhancing the results via a combination of cooling and specimen dilution procedure. Virusdisease 2024; 35:293-301. [PMID: 39071878 PMCID: PMC11269541 DOI: 10.1007/s13337-024-00870-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 05/11/2024] [Indexed: 07/30/2024] Open
Abstract
Colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a potential and relatively simple rapid diagnostics method for COVID-19 detection. This study aims to evaluate and optimize the RT-LAMP performance on saliva specimens based on a commercially available kit.Modifications on an established protocol (Protocol A) were used, including Proteinase K supplementation (Protocol B); pre-treatment using nuclease-free water and proteinase K (Protocol C); Saliva cooling (Protocol D); saliva dilution after pre-treatment (Protocol E); lastly a combination of saliva cooling and dilution (Protocol F). Protocol performances were evaluated by comparing success rates (SR), diagnostic accuracy (DA), sensitivity, specificity, and predictive values. Additionally, a correlation between the Ct value by RT-qPCR and RT-LAMP performance was analyzed.. A total of 106 specimens were used in this study. Protocols B and C showed 100% unreadable results, therefore were paused. Protocol F showed the highest SR (87.65%) compared to other protocols, with a slight compromise to DA (81.69%), sensitivity (57.14%), specificity (97.67%), PPV (94.12%), and NPV (77.78%). In the sub-analysis of the low Ct value group (Ct < 30), Protocol F demonstrated a higher success rate (86.57%) compared to protocol A (64.18%); increased 3.08% sensitivity and 2.42% NPV; comparable DA; minor reduction in specificity (A = 100%; F = 97.67%) and PPV (A = 100%; F = 92.31%). A combination of saliva cooling-dilution substantially increased the tested kit's success rate, despite a slight decrease in specificity and PPV. Findings confirmed the saliva cooling-dilution procedure was beneficial to the test's SR, sensitivity, and NPV in the low Ct value group. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00870-1.
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Affiliation(s)
- Henry Gotama Putra
- Undergraduate Study Program, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, 14440 Indonesia
| | - Sem Samuel Surja
- Department of Parasitology, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, 14440 Indonesia
| | - Tria Asri Widowati
- Department of Parasitology, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, 14440 Indonesia
| | - Soegianto Ali
- Department of Medical Biology, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, 14440 Indonesia
- Present Address: Master in Biomedicine Study Program, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, 14440 Indonesia
| | - Maria Mardalena Martini Kaisar
- Department of Parasitology, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, 14440 Indonesia
- Present Address: Master in Biomedicine Study Program, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, 14440 Indonesia
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Rashid SA, Rajendiran S, Nazakat R, Mohammad Sham N, Khairul Hasni NA, Anasir MI, Kamel KA, Muhamad Robat R. A scoping review of global SARS-CoV-2 wastewater-based epidemiology in light of COVID-19 pandemic. Heliyon 2024; 10:e30600. [PMID: 38765075 PMCID: PMC11098849 DOI: 10.1016/j.heliyon.2024.e30600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Recently, wastewater-based epidemiology (WBE) research has experienced a strong impetus during the Coronavirus disease 2019 (COVID-19) pandemic. However, a few technical issues related to surveillance strategies, such as standardized procedures ranging from sampling to testing protocols, need to be resolved in preparation for future infectious disease outbreaks. This review highlights the study characteristics, potential use of WBE and overview of methods, as well as methods utilized to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including its variant in wastewater. A literature search was performed electronically in PubMed and Scopus according to PRISMA guidelines for relevant peer-reviewed articles published between January 2020 and March 2022. The search identified 588 articles, out of which 221 fulfilled the necessary criteria and are discussed in this review. Most global WBE studies were conducted in North America (n = 75, 34 %), followed by Europe (n = 68, 30.8 %), and Asia (n = 43, 19.5 %). The review also showed that most of the application of WBE observed were to correlate SARS-CoV-2 ribonucleic acid (RNA) trends in sewage with epidemiological data (n = 90, 40.7 %). The techniques that were often used globally for sample collection, concentration, preferred matrix recovery control and various sample types were also discussed. Overall, this review provided a framework for researchers specializing in WBE to apply strategic approaches to their research questions in achieving better functional insights. In addition, areas that needed more in-depth analysis, data collection, and ideas for new initiatives were identified.
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Affiliation(s)
- Siti Aishah Rashid
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Sakshaleni Rajendiran
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Raheel Nazakat
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Noraishah Mohammad Sham
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Nurul Amalina Khairul Hasni
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Mohd Ishtiaq Anasir
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Khayri Azizi Kamel
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Rosnawati Muhamad Robat
- Occupational & Environmental Health Unit, Public Health Division, Selangor State Health Department, Ministry of Health Malaysia, Malaysia
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8
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Chen C, Kaur G, Adiga A, Espinoza B, Venkatramanan S, Warren A, Lewis B, Crow J, Singh R, Lorentz A, Toney D, Marathe M. Wastewater-based Epidemiology for COVID-19 Surveillance: A Survey. ARXIV 2024:arXiv:2403.15291v1. [PMID: 38562450 PMCID: PMC10984000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The pandemic of COVID-19 has imposed tremendous pressure on public health systems and social economic ecosystems over the past years. To alleviate its social impact, it is important to proactively track the prevalence of COVID-19 within communities. The traditional way to estimate the disease prevalence is to estimate from reported clinical test data or surveys. However, the coverage of clinical tests is often limited and the tests can be labor-intensive, requires reliable and timely results, and consistent diagnostic and reporting criteria. Recent studies revealed that patients who are diagnosed with COVID-19 often undergo fecal shedding of SARS-CoV-2 virus into wastewater, which makes wastewater-based epidemiology (WBE) for COVID-19 surveillance a promising approach to complement traditional clinical testing. In this paper, we survey the existing literature regarding WBE for COVID-19 surveillance and summarize the current advances in the area. Specifically, we have covered the key aspects of wastewater sampling, sample testing, and presented a comprehensive and organized summary of wastewater data analytical methods. Finally, we provide the open challenges on current wastewater-based COVID-19 surveillance studies, aiming to encourage new ideas to advance the development of effective wastewater-based surveillance systems for general infectious diseases.
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Affiliation(s)
- Chen Chen
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Gursharn Kaur
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Aniruddha Adiga
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Baltazar Espinoza
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Srinivasan Venkatramanan
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Andrew Warren
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Bryan Lewis
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Justin Crow
- Virginia Department of Health, Richmond, 23219, United States
| | - Rekha Singh
- Virginia Department of Health, Richmond, 23219, United States
| | - Alexandra Lorentz
- Division of Consolidated Laboratory Services, Department of General Services, Richmond, 23219, United States
| | - Denise Toney
- Division of Consolidated Laboratory Services, Department of General Services, Richmond, 23219, United States
| | - Madhav Marathe
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
- Department of Computer Science, University of Virginia, Charlottesville, 22904, United States
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9
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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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10
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Dehghan Banadaki M, Torabi S, Rockward A, Strike WD, Noble A, Keck JW, Berry SM. Simple SARS-CoV-2 concentration methods for wastewater surveillance in low resource settings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168782. [PMID: 38000737 PMCID: PMC10842712 DOI: 10.1016/j.scitotenv.2023.168782] [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: 09/27/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Wastewater-based epidemiology (WBE) measures pathogens in wastewater to monitor infectious disease prevalence in communities. Due to the high dilution of pathogens in sewage, a concentration method is often required to achieve reliable biomarker signals. However, most of the current concentration methods rely on expensive equipment and labor-intensive processes, which limits the application of WBE in low-resource settings. Here, we compared the performance of four inexpensive and simple concentration methods to detect SARS-CoV-2 in wastewater samples: Solid Fraction, Porcine Gastric Mucin-conjugated Magnetic Beads, Calcium Flocculation-Citrate Dissolution (CFCD), and Nanotrap® Magnetic Beads (NMBs). The NMBs and CFCD methods yielded the highest concentration performance for SARS-CoV-2 (∼16-fold concentration and ∼ 41 % recovery) and require <45 min processing time. CFCD has a relatively low consumable cost (<$2 per four sample replicates). All methods can be performed with basic laboratory equipment and minimal electricity usage which enables further application of WBE in remote areas and low resource settings.
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Affiliation(s)
| | - Soroosh Torabi
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
| | - Alexus Rockward
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States
| | - William D Strike
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States
| | - Ann Noble
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
| | - James W Keck
- WWAMI School of Medicine, University of Alaska Anchorage, United States
| | - Scott M Berry
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States; Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States.
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11
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Akter J, Smith WJM, Gebrewold M, Kim I, Simpson SL, Bivins A, Ahmed W. Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167964. [PMID: 37865239 DOI: 10.1016/j.scitotenv.2023.167964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARS-CoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 × 102 GC/reaction, with greater analytical sensitivity at 2 × 101 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 × 103 GC/reaction. For SARS-CoV-2 seeded wastewater samples, the US CDC N1 assay exhibited greater analytical sensitivity than the US CDC N2, E_Sarbeco, and RT-LAMP assays. Out of 30 wastewater samples, RT-qPCR detected endogenous SARS-CoV-2 RNA in 29 samples, while RT-LAMP identified 27 positive samples, with 20 displaying consistent amplifications in all three RT-LAMP technical replicates. Agreement analysis revealed a strong concordance between RT-LAMP and the US CDC N1 and E_Sarbeco RT-qPCR assays (κ = 0.474) but lower agreement with the US CDC N2 RT-qPCR assay (κ = 0.359). Quantification of SARS-CoV-2 RNA in positive samples revealed a strong correlation between the US CDC N1 and E_Sarbeco assays, while the US CDC N1 and US CDC N2 assays exhibited weak correlation. Logistic regression analysis indicated that RT-LAMP results correlated with RNA quantified by the US CDC N1 and E_Sarbeco assays, with 95 % limits of detection of 3.99 and 3.47 log10 GC/15 mL, respectively. In conclusion, despite lower sensitivity compared to RT-qPCR assays, RT-LAMP may offer advantages for wastewater surveillance, such as rapid results (estimated as twice as fast), and simplicity, making it a valuable tool in the shifting landscape of COVID-19 wastewater surveillance. Furthermore, LAMP positive wastewater samples might be prioritized for SARS-CoV-2 sequencing due to reduced analytical sensitivity. These findings support the use of RT-LAMP as a specific and efficient method for screening wastewater samples for SARS-CoV-2, particularly in resource-limited settings.
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Affiliation(s)
- Jesmin Akter
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), 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
| | - Metasebia Gebrewold
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Ilho Kim
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea
| | | | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
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12
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Asadi M, Hamilton D, Shomachuk C, Oloye FF, De Lange C, Pu X, Osunla CA, Cantin J, El-Baroudy S, Mejia EM, Gregorchuk B, Becker MG, Mangat C, Brinkmann M, Jones PD, Giesy JP, McPhedran KN. Assessment of rapid wastewater surveillance for determination of communicable disease spread in municipalities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166541. [PMID: 37625717 DOI: 10.1016/j.scitotenv.2023.166541] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/02/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Wastewater surveillance (WS) helps to improve the understanding of the spread of communicable diseases in communities. WS can assist public health decision-makers in the design and implementation of timely mitigation measures. There is an increased need to use reliable, cost-effective, simple, and rapid WS systems, given traditional analytical (or 'gold-standard') programs are instrument/time-intensive, and dependent on highly skilled personnel. This study investigated the application of the portable GeneXpert platform for WS of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus (IAV), influenza B virus (IBV), and respiratory syncytial virus (RSV). The GeneXpert system with the Xpert Xpress-SARS-CoV-2/Flu/RSV test kit uses reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to analyze wastewater samples. From September 2022 through January 2023, wastewater samples were collected from the influents of municipal wastewater treatment plants (MWTPs) of Saskatoon, Prince Albert, and North Battleford in the province of Saskatchewan, Canada. Both raw and concentrated wastewater samples were subjected to the GeneXpert analysis. Results showed that the Saskatoon wastewater viral loads were significantly correlated to Saskatchewan's influenza and COVID-19 clinical cases, with a lead time of 10 days for IAV and a lag time of 4 days for SARS-CoV-2. Additionally, the GeneXpert analysis of the three cities' wastewater samples showed that the raw WS could capture the dynamics of SARS-CoV-2 and IAV due to their correlation with concentrated WS. Interestingly, IBV loads were not detected in any wastewater samples, while the Saskatoon and Prince Albert wastewater samples collected following the 2023 holiday season (end of December and beginning of January) were positive for RSV. This study indicates that the GeneXpert has excellent potential for use in the development of an early warning system for transmissible disease in municipalities and limited-resource communities while simultaneously providing stakeholders with an efficient WS methodology.
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Affiliation(s)
- Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel Hamilton
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Corwyn Shomachuk
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Chantel De Lange
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Xia Pu
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Charles A Osunla
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Seba El-Baroudy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edgard M Mejia
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Branden Gregorchuk
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael G Becker
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chand Mangat
- Wastewater Surveillance Unit, On-Health Division, National Microbiology Laboratory - Winnipeg, Public Health Agency of Canada, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Integrative Biology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
| | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada.
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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] [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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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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15
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Sen P, Zhang Z, Li P, Adhikari BR, Guo T, Gu J, MacIntosh AR, van der Kuur C, Li Y, Soleymani L. Integrating Water Purification with Electrochemical Aptamer Sensing for Detecting SARS-CoV-2 in Wastewater. ACS Sens 2023; 8:1558-1567. [PMID: 36926840 PMCID: PMC10042147 DOI: 10.1021/acssensors.2c02655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/02/2023] [Indexed: 03/18/2023]
Abstract
Wastewater analysis of pathogens, particularly SARS-CoV-2, is instrumental in tracking and monitoring infectious diseases in a population. This method can be used to generate early warnings regarding the onset of an infectious disease and predict the associated infection trends. Currently, wastewater analysis of SARS-CoV-2 is almost exclusively performed using polymerase chain reaction for the amplification-based detection of viral RNA at centralized laboratories. Despite the development of several biosensing technologies offering point-of-care solutions for analyzing SARS-CoV-2 in clinical samples, these remain elusive for wastewater analysis due to the low levels of the virus and the interference caused by the wastewater matrix. Herein, we integrate an aptamer-based electrochemical chip with a filtration, purification, and extraction (FPE) system for developing an alternate in-field solution for wastewater analysis. The sensing chip employs a dimeric aptamer, which is universally applicable to the wild-type, alpha, delta, and omicron variants of SARS-CoV-2. We demonstrate that the aptamer is stable in the wastewater matrix (diluted to 50%) and its binding affinity is not significantly impacted. The sensing chip demonstrates a limit of detection of 1000 copies/L (1 copy/mL), enabled by the amplification provided by the FPE system. This allows the integrated system to detect trace amounts of the virus in native wastewater and categorize the amount of contamination into trace (<10 copies/mL), medium (10-1000 copies/mL), or high (>1000 copies/mL) levels, providing a viable wastewater analysis solution for in-field use.
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Affiliation(s)
- Payel Sen
- Department of Engineering Physics,
McMaster University, Hamilton L8S 4K1,
Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton L8S 4K1,
Canada
| | - Phoebe Li
- Department of Physics, McMaster
University, Hamilton L8S 4K1, Canada
| | - Bal Ram Adhikari
- Department of Engineering Physics,
McMaster University, Hamilton L8S 4K1,
Canada
| | - Tianyi Guo
- Forsee Instruments, Ltd.,
Hamilton L8P0A1, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton L8S 4K1,
Canada
| | | | | | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences,
McMaster University, Hamilton L8S 4K1,
Canada
- School of Biomedical Engineering, McMaster
University, Hamilton L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease
Research, McMaster University, Hamilton L8S 4K1,
Canada
| | - Leyla Soleymani
- Department of Engineering Physics,
McMaster University, Hamilton L8S 4K1,
Canada
- School of Biomedical Engineering, McMaster
University, Hamilton L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease
Research, McMaster University, Hamilton L8S 4K1,
Canada
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16
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Advances in virus detection methods for wastewater-based epidemiological applications. CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2022; 6:100238. [PMID: 37520925 PMCID: PMC9339091 DOI: 10.1016/j.cscee.2022.100238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 06/08/2023]
Abstract
Wastewater-based epidemiology (WBE) is a powerful tool that has the potential to reveal the extent of an ongoing disease outbreak or to predict an emerging one. Recent studies have shown that SARS-CoV-2 concentration in wastewater may be correlated with the number of COVID-19 cases in the corresponding population. Most of the recent studies and applications of wastewater-based surveillance of SARS-CoV-2 applied the “gold standard” real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR) detection method. However, this method also has its limitations. The paper aimed to present recent improvements and applications of the PCR-based methods for SARS-CoV-2 monitoring in wastewater. Furthermore, it aimed to review alternative methods utilized and/or proposed for the detection of the virus in wastewater matrices. From the review, it was found that several studies have investigated the use of reverse-transcription digital polymerase reaction (RT-dPCR), which was generally shown to have a lower limit of detection (LOD) over the RT-qPCR. Aside from this, non-PCR-based and non-RNA based methods have also been explored for the detection of SARS-CoV-2 in wastewater, with detailed attention given to the detection of SARS-CoV-2 proteins. The potential methods for protein detection include mass spectrometry, the use of immunosensors, and nanotechnological applications. In addition, the review of recent studies also revealed two types of emerging methods related to the detection of SARS-CoV-2 in wastewater: i) capsid-integrity assays to infer about the infectivity of SARS-CoV-2 present in wastewater, and ii) alternative methods for detection of SARS-CoV-2 variants of concern (VOCs) in wastewater. The recent studies on proposed methods of SARS-CoV-2 detection in wastewater have considered improving this approach in one or more of the following aspects: rapidity, simplicity, cost, sensitivity, and specificity. However, further studies are needed in order to realize the full application of these methods for WBE in the field.
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17
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Hoar C, McClary-Gutierrez J, Wolfe MK, Bivins A, Bibby K, Silverman AI, McLellan SL. Looking Forward: The Role of Academic Researchers in Building Sustainable Wastewater Surveillance Programs. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:125002. [PMID: 36580023 PMCID: PMC9799055 DOI: 10.1289/ehp11519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND In just over 2 years, tracking the COVID-19 pandemic through wastewater surveillance advanced from early reports of successful SARS-CoV-2 RNA detection in untreated wastewater to implementation of programs in at least 60 countries. Early wastewater monitoring efforts primarily originated in research laboratories and are now transitioning into more formal surveillance programs run in commercial and public health laboratories. A major challenge in this progression has been to simultaneously optimize methods and build scientific consensus while implementing surveillance programs, particularly during the rapidly changing landscape of the pandemic. Translating wastewater surveillance results for effective use by public health agencies also remains a key objective for the field. OBJECTIVES We examined the evolution of wastewater surveillance to identify model collaborations and effective partnerships that have created rapid and sustained success. We propose needed areas of research and key roles academic researchers can play in the framework of wastewater surveillance to aid in the transition from early monitoring efforts to more formalized programs within the public health system. DISCUSSION Although wastewater surveillance has rapidly developed as a useful public health tool for tracking COVID-19, there remain technical challenges and open scientific questions that academic researchers are equipped to address. This includes validating methodology and backfilling important knowledge gaps, such as fate and transport of surveillance targets and epidemiological links to wastewater concentrations. Our experience in initiating and implementing wastewater surveillance programs in the United States has allowed us to reflect on key barriers and draw useful lessons on how to promote synergy between different areas of expertise. As wastewater surveillance programs are formalized, the working relationships developed between academic researchers, commercial and public health laboratories, and data users should promote knowledge co-development. We believe active involvement of academic researchers will contribute to building robust surveillance programs that will ultimately provide new insights into population health. https://doi.org/10.1289/EHP11519.
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Affiliation(s)
- Catherine Hoar
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, New York, USA
| | - Jill McClary-Gutierrez
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marlene K. Wolfe
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Indiana, USA
| | - Andrea I. Silverman
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, New York, USA
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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18
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Donia A, Furqan Shahid M, Hassan SU, Shahid R, Ahmad A, Javed A, Nawaz M, Yaqub T, Bokhari H. Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-Care Platform. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:364-373. [PMID: 35508752 PMCID: PMC9067896 DOI: 10.1007/s12560-022-09522-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/04/2022] [Indexed: 05/21/2023]
Abstract
Development of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of seven wastewater samples from COVID-19 hotspots. RT‑LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best target gene for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37-39), and negative for ORF1ab, suggesting that N gene could be the best target gene for SARS-CoV-2 detection. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips. This study brings the novelty involving the use of wastewater samples for detection of SARS-CoV-2 without previous virus concentration and with/without RNA extraction.
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Affiliation(s)
- Ahmed Donia
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Furqan Shahid
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sammer-ul Hassan
- Department of Mechanical Engineering, University of Hong Kong, Pok Fu Lam, Hong Kong, Hong Kong
| | - Ramla Shahid
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Aneela Javed
- Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Nawaz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Tahir Yaqub
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habib Bokhari
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
- Kohsar University Murree, Murree, Pakistan
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19
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Proboste T, James A, Charette-Castonguay A, Chakma S, Cortes-Ramirez J, Donner E, Sly P, Magalhães RJS. Research and Innovation Opportunities to Improve Epidemiological Knowledge and Control of Environmentally Driven Zoonoses. Ann Glob Health 2022; 88:93. [PMID: 36348706 PMCID: PMC9585982 DOI: 10.5334/aogh.3770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022] Open
Abstract
While zoonotic diseases are defined by transmission processes between animals and humans, for many of these diseases the presence of a contaminated environmental source is the cause of transmission. Most zoonoses depend on complex environmentally driven interactions between humans and animals, which occur along an occupational and recreational environmental continuum, including farming and animal marketing systems, environmental management systems, and community leisure environments. Environmentally driven zoonoses (EDZs) are particularly challenging to diagnose and control as their reservoirs are in the natural environment and thus often escape conventional surveillance systems that rely on host monitoring. Changes in the environment as a result of climate change [1], human population density [2], and intensification of agriculture [3] have been linked to increasing transmission events for this group of infections. As such, there is a recognised need to be able to detect the presence of EDZs in the environment as a means to better anticipate transmission events and improve source attribution investigations. Finally, the recognition that a One Health approach is needed to combat these infections is signalling to governments the need to develop policy that optimises trade-offs across human, animal, and environmental health sectors. In this review, we discuss and critically appraise the main challenges relating to the epidemiology, diagnosis, and control of environmental zoonotic disease. Using a set of exemplar diseases, including avian influenza and antimicrobial resistant pathogens, we explore the epidemiological contexts (risk factors) within which these infections not only impact human health but also contribute to animal health and environmental impacts. We then critically appraise the surveillance challenges of monitoring these infections in the environment and examine the policy trade-offs for a more integrated approach to mitigating their impacts.
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Affiliation(s)
- Tatiana Proboste
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, University of Queensland, Gatton, Australia
- Queensland Alliance for One Health Sciences, School of Veterinary Science, University of Queensland, Gatton, Australia
| | - Ameh James
- Queensland Alliance for One Health Sciences, School of Veterinary Science, University of Queensland, Gatton, Australia
| | - Adam Charette-Castonguay
- Queensland Alliance for One Health Sciences, School of Veterinary Science, University of Queensland, Gatton, Australia
| | - Shovon Chakma
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, University of Queensland, Gatton, Australia
| | - Javier Cortes-Ramirez
- Children’s Health and Environment Program, Child Health Research Centre, The University of Queensland, Brisbane, 4101 QLD, Australia
- Centre for Data Science, Queensland University of Technology, Kelvin Grove, 4059 QLD, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Peter Sly
- Children’s Health and Research Centre, Children’s Health and Environment Program, The University of Queensland, South Brisbane, Australia
| | - Ricardo J. Soares Magalhães
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, University of Queensland, Gatton, Australia
- Queensland Alliance for One Health Sciences, School of Veterinary Science, University of Queensland, Gatton, Australia
- Children’s Health and Research Centre, Children’s Health and Environment Program, The University of Queensland, South Brisbane, Australia
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20
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Jakariya M, Ahmed F, Islam MA, Al Marzan A, Hasan MN, Hossain M, Ahmed T, Hossain A, Reza HM, Hossen F, Nahla T, Rahman MM, Bahadur NM, Islam MT, Didar-Ul-Alam M, Mow N, Jahan H, Barceló D, Bibby K, Bhattacharya P. Wastewater-based epidemiological surveillance to monitor the prevalence of SARS-CoV-2 in developing countries with onsite sanitation facilities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 311:119679. [PMID: 35753547 PMCID: PMC9225114 DOI: 10.1016/j.envpol.2022.119679] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 05/23/2023]
Abstract
Wastewater-based epidemiology (WBE) has emerged as a valuable approach for forecasting disease outbreaks in developed countries with a centralized sewage infrastructure. On the other hand, due to the absence of well-defined and systematic sewage networks, WBE is challenging to implement in developing countries like Bangladesh where most people live in rural areas. Identification of appropriate locations for rural Hotspot Based Sampling (HBS) and urban Drain Based Sampling (DBS) are critical to enable WBE based monitoring system. We investigated the best sampling locations from both urban and rural areas in Bangladesh after evaluating the sanitation infrastructure for forecasting COVID-19 prevalence. A total of 168 wastewater samples were collected from 14 districts of Bangladesh during each of the two peak pandemic seasons. RT-qPCR commercial kits were used to target ORF1ab and N genes. The presence of SARS-CoV-2 genetic materials was found in 98% (165/168) and 95% (160/168) wastewater samples in the first and second round sampling, respectively. Although wastewater effluents from both the marketplace and isolation center drains were found with the highest amount of genetic materials according to the mixed model, quantifiable SARS-CoV-2 RNAs were also identified in the other four sampling sites. Hence, wastewater samples of the marketplace in rural areas and isolation centers in urban areas can be considered the appropriate sampling sites to detect contagion hotspots. This is the first complete study to detect SARS-CoV-2 genetic components in wastewater samples collected from rural and urban areas for monitoring the COVID-19 pandemic. The results based on the study revealed a correlation between viral copy numbers in wastewater samples and SARS-CoV-2 positive cases reported by the Directorate General of Health Services (DGHS) as part of the national surveillance program for COVID-19 prevention. The findings of this study will help in setting strategies and guidelines for the selection of appropriate sampling sites, which will facilitate in development of comprehensive wastewater-based epidemiological systems for surveillance of rural and urban areas of low-income countries with inadequate sewage infrastructure.
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Affiliation(s)
- Md Jakariya
- Department of Environmental Science and Management, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Firoz Ahmed
- COVID-19 Diagnostic Laboratory, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Aminul Islam
- COVID-19 Diagnostic Laboratory, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh; Advanced Molecular Laboratory, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, Bangladesh
| | - Abdullah Al Marzan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Mohammad Nayeem Hasan
- Department of Statistics, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Maqsud Hossain
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Tanvir Ahmed
- Department of Civil Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Ahmed Hossain
- Department of Public Health, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Hasan Mahmud Reza
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Foysal Hossen
- COVID-19 Diagnostic Laboratory, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Turasa Nahla
- Department of Environmental Science and Management, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Mohammad Moshiur Rahman
- Department of Environmental Science and Management, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Tahmidul Islam
- WaterAid Bangladesh, Dhaka, 1213, Bangladesh; COVID-19 Research@KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-10044, Stockholm, Sweden
| | - Md Didar-Ul-Alam
- Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Nowrin Mow
- WaterAid Bangladesh, Dhaka, 1213, Bangladesh
| | - Hasin Jahan
- WaterAid Bangladesh, Dhaka, 1213, Bangladesh
| | - Damiá Barceló
- Water, Environmental and Food Chemistry Unit (ENFOCHEM), Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Spanish National Research Council (CSIC), C. Jordi Giron 18-26, 08034, Barcelona, Spain
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Prosun Bhattacharya
- COVID-19 Research@KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-10044, Stockholm, Sweden.
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21
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Bivins A, Kaya D, Ahmed W, Brown J, Butler C, Greaves J, Leal R, Maas K, Rao G, Sherchan S, Sills D, Sinclair R, Wheeler RT, Mansfeldt C. Passive sampling to scale wastewater surveillance of infectious disease: Lessons learned from COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155347. [PMID: 35460780 PMCID: PMC9020839 DOI: 10.1016/j.scitotenv.2022.155347] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/05/2022] [Accepted: 04/13/2022] [Indexed: 05/09/2023]
Abstract
Much of what is known and theorized concerning passive sampling techniques has been developed considering chemical analytes. Yet, historically, biological analytes, such as Salmonella typhi, have been collected from wastewater via passive sampling with Moore swabs. In response to the COVID-19 pandemic, passive sampling is re-emerging as a promising technique to monitor SARS-CoV-2 RNA in wastewater. Method comparisons and disease surveillance using composite, grab, and passive sampling for SARS-CoV-2 RNA detection have found passive sampling with a variety of materials routinely produced qualitative results superior to grab samples and useful for sub-sewershed surveillance of COVID-19. Among individual studies, SARS-CoV-2 RNA concentrations derived from passive samplers demonstrated heterogeneous correlation with concentrations from paired composite samples ranging from weak (R2 = 0.27, 0.31) to moderate (R2 = 0.59) to strong (R2 = 0.76). Among passive sampler materials, electronegative membranes have shown great promise with linear uptake of SARS-CoV-2 RNA observed for exposure durations of 24 to 48 h and in several cases RNA positivity on par with composite samples. Continuing development of passive sampling methods for the surveillance of infectious diseases via diverse forms of fecal waste should focus on optimizing sampler materials for the efficient uptake and recovery of biological analytes, kit-free extraction, and resource-efficient testing methods capable of rapidly producing qualitative or quantitative data. With such refinements passive sampling could prove to be a fundamental tool for scaling wastewater surveillance of infectious disease, especially among the 1.8 billion persons living in low-resource settings served by non-traditional wastewater collection infrastructure.
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Affiliation(s)
- Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803, USA.
| | - Devrim Kaya
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA
| | - Caitlyn Butler
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, 130 Natural Resources Rd., Amherst, MA 01003, USA
| | - Justin Greaves
- School of Environmental Sustainability, Loyola University Chicago, 6364 N. Sheridan Rd, Chicago, IL 60660, USA
| | - Raeann Leal
- Loma Linda University, School of Public Health, 24951 North Circle Drive, Loma Linda, CA 92354, USA
| | - Kendra Maas
- Microbial Analyses, Resources, and Services Facility, University of Connecticut, Storrs, CT 06269, USA
| | - Gouthami Rao
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA
| | - Samendra Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA; Center for Climate and Health, Morgan State University, Baltimore, MD 21251, USA
| | - Deborah Sills
- Bucknell University, Department of Civil and Environmental Engineering, Lewisburg, PA 17837, USA
| | - Ryan Sinclair
- Loma Linda University, School of Public Health, 24951 North Circle Drive, Loma Linda, CA 92354, USA
| | - Robert T Wheeler
- Department of Molecular & Biomedical Sciences, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, USA
| | - Cresten Mansfeldt
- University of Colorado Boulder, Department of Civil, Environmental, and Architectural Engineering, 1111 Engineering Drive, Boulder, CO 80309, USA; University of Colorado Boulder, Environmental Engineering Program, 4001 Discovery Dr, Boulder, CO 80303, USA
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22
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Mthethwa NP, Amoah ID, Reddy P, Bux F, Kumari S. Fluorescence and colorimetric LAMP-based real-time detection of human pathogenic Cryptosporidium spp. from environmental samples. Acta Trop 2022; 235:106606. [DOI: 10.1016/j.actatropica.2022.106606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/01/2022]
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23
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Thongpradit S, Prasongtanakij S, Srisala S, Chanprasertyothin S, Pasomsub E, Ongphiphadhanakul B. The Detection of SARS-CoV2 Antigen in Wastewater Using an Automated Chemiluminescence Enzyme Immunoassay. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:7783. [PMID: 35805441 PMCID: PMC9265940 DOI: 10.3390/ijerph19137783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 02/01/2023]
Abstract
The SARS-CoV-2 virus, which is driving the current COVID-19 epidemic, has been detected in wastewater and is being utilized as a surveillance tool to establish an early warning system to aid in the management and prevention of future pandemics. qPCR is the method usually used to detect SARS-CoV-2 in wastewater. There has been no study using an immunoassay that is less laboratory-intensive than qPCR with a shorter turnaround time. Therefore, we aimed to evaluate the performance of an automated chemiluminescence enzyme immunoassay (CLEIA) for SARS-CoV-2 antigen in wastewater. The CLEIA assay achieved 100% sensitivity and 66.7% specificity in a field-captured wastewater sample compared to the gold standard RT-qPCR. Our early findings suggest that the SARS-CoV-2 antigen can be identified in wastewater samples using an automated CLEIA, reducing the turnaround time and improving the performance of SARS-CoV-2 wastewater monitoring during the pandemic.
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Affiliation(s)
- Supranee Thongpradit
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.T.); (S.S.); (S.C.); (B.O.)
| | - Somsak Prasongtanakij
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.T.); (S.S.); (S.C.); (B.O.)
| | - Supanart Srisala
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.T.); (S.S.); (S.C.); (B.O.)
| | - Suwannee Chanprasertyothin
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.T.); (S.S.); (S.C.); (B.O.)
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Boonsong Ongphiphadhanakul
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.T.); (S.S.); (S.C.); (B.O.)
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
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24
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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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25
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Paruch L. Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:5128. [PMID: 35564522 PMCID: PMC9105083 DOI: 10.3390/ijerph19095128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022]
Abstract
Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.
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Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research-NIBIO Oluf Thesens vei 43, 1433 Aas, Norway
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26
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Daigle J, Racher K, Hazenberg J, Yeoman A, Hannah H, Duong D, Mohammed U, Spreitzer D, Gregorchuk BSJ, Head BM, Meyers AFA, Sandstrom PA, Nichani A, Brooks JI, Mulvey MR, Mangat CS, Becker MG. A Sensitive and Rapid Wastewater Test for SARS-COV-2 and Its Use for the Early Detection of a Cluster of Cases in a Remote Community. Appl Environ Microbiol 2022; 88:e0174021. [PMID: 34985977 PMCID: PMC8904056 DOI: 10.1128/aem.01740-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/27/2021] [Indexed: 12/22/2022] Open
Abstract
Throughout the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has been used to monitor trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prevalence in the community. A major challenge in establishing wastewater surveillance programs, especially in remote areas, is the need for a well-equipped laboratory for sample analysis. Currently, no options exist for rapid, sensitive, mobile, and easy-to-use wastewater tests for SARS-CoV-2. The performance of the GeneXpert system, which offers cartridge-based, rapid molecular clinical testing for SARS-CoV-2 in a portable platform, was evaluated using wastewater as the input. The GeneXpert demonstrated a SARS-CoV-2 limit of detection in wastewater below 32 copies/mL with a sample processing time of less than an hour. Using wastewater samples collected from multiple sites across Canada during February and March 2021, a high overall agreement (97.8%) was observed between the GeneXpert assay and laboratory-developed tests regarding the presence or absence of SARS-CoV-2. Additionally, with the use of centrifugal filters, the detection threshold of the GeneXpert system was improved to <10 copies/mL in wastewater. Finally, to support on-site wastewater surveillance, GeneXpert testing was implemented in Yellowknife, a remote community in Northern Canada, where its use successfully alerted public health authorities to undetected transmission of COVID-19. The identification of SARS-CoV-2 in wastewater triggered clinical testing of recent travelers and identification of new COVID-19 cases/clusters. Taken together, these results suggest that GeneXpert is a viable option for surveillance of SARS-CoV-2 in wastewater in locations that do not have access to established testing laboratories. IMPORTANCE Wastewater-based surveillance is a powerful tool that provides an unbiased measure of COVID-19 prevalence in a community. This work describes a sensitive wastewater rapid test for SARS-CoV-2 based on a widely distributed technology, the GeneXpert. The advantages of an easy-to-use wastewater test for SARS-CoV-2 are clear: it supports surveillance in remote communities, improves access to testing, and provides faster results allowing for an immediate public health response. The application of wastewater rapid testing in a remote community facilitated the detection of a COVID-19 cluster and triggered public health action, clearly demonstrating the utility of this technology. Wastewater surveillance will become increasingly important in the postvaccination pandemic landscape as individuals with asymptomatic/mild infections continue transmitting SARS-CoV-2 but are unlikely to be tested.
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Affiliation(s)
- Jade Daigle
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kathleen Racher
- Taiga Environmental Laboratory, Department of Environmental and Natural Resources, Government of the Northwest Territories, Yellowknife, Northwest Territories, Canada
| | - Justin Hazenberg
- Department of Municipal and Community Affairs, Government of the Northwest Territories, Yellowknife, Northwest Territories, Canada
| | - Allan Yeoman
- Taiga Environmental Laboratory, Department of Environmental and Natural Resources, Government of the Northwest Territories, Yellowknife, Northwest Territories, Canada
| | - Heather Hannah
- Department of Health and Social Services, Government of the Northwest Territories, Yellowknife, Northwest Territories, Canada
| | - Diep Duong
- Taiga Environmental Laboratory, Department of Environmental and Natural Resources, Government of the Northwest Territories, Yellowknife, Northwest Territories, Canada
| | - Umar Mohammed
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Dave Spreitzer
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Branden S. J. Gregorchuk
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Breanne M. Head
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Adrienne F. A. Meyers
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Paul A. Sandstrom
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anil Nichani
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - James I. Brooks
- Antimicrobial Resistance Division, Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, Ontario, Canada
- Division of Infectious Diseases, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael R. Mulvey
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Antimicrobial Resistance and Nosocomial Infections, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chand S. Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael G. Becker
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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27
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Safford HR, Shapiro K, Bischel HN. Opinion: Wastewater analysis can be a powerful public health tool-if it's done sensibly. Proc Natl Acad Sci U S A 2022; 119:e2119600119. [PMID: 35115406 PMCID: PMC8833183 DOI: 10.1073/pnas.2119600119] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Hannah R Safford
- Department of Civil and Environmental Engineering, University of California, Davis, CA 95616
| | - Karen Shapiro
- Department of Veterinary Medicine, University of California, Davis, CA 95616
| | - Heather N Bischel
- Department of Civil and Environmental Engineering, University of California, Davis, CA 95616;
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28
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Amoah ID, Abunama T, Awolusi OO, Pillay L, Pillay K, Kumari S, Bux F. Effect of selected wastewater characteristics on estimation of SARS-CoV-2 viral load in wastewater. ENVIRONMENTAL RESEARCH 2022; 203:111877. [PMID: 34390718 PMCID: PMC8356757 DOI: 10.1016/j.envres.2021.111877] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/04/2021] [Accepted: 08/08/2021] [Indexed: 05/18/2023]
Abstract
Wastewater-based epidemiology has been used as a tool for surveillance of COVID-19 infections. This approach is dependent on the detection and quantification of SARS-CoV-2 RNA in untreated/raw wastewater. However, the quantification of the viral RNA could be influenced by the physico-chemical properties of the wastewater. This study presents the first use of Adaptive Neuro-Fuzzy Inference System (ANFIS) to determine the potential impact of physico-chemical characteristics of wastewater on the detection and concentration of SARS-CoV-2 RNA in wastewater. Raw wastewater samples from four wastewater treatment plants were investigated over four months. The physico-chemical characteristics of the raw wastewater was recorded, and the SARS-CoV-2 RNA concentration determined via amplification with droplet digital polymerase chain reaction. The wastewater characteristics considered were chemical oxygen demand, flow rate, ammonia, pH, permanganate value, and total solids. The mean SARS-CoV-2 RNA concentrations ranged from 648.1(±514.6) copies/mL to 1441.0(±1977.8) copies/mL. Among the parameters assessed using the ANFIS model, ammonia and pH showed significant association with the concentration of SARS-CoV-2 RNA measured. Increasing ammonia concentration was associated with increasing viral RNA concentration and pH between 7.1 and 7.4 were associated with the highest SARS-CoV-2 concentration. Other parameters, such as total solids, were also observed to influence the viral RNA concentration, however, this observation was not consistent across all the wastewater treatment plants. The results from this study indicate the importance of incorporating wastewater characteristic assessment into wastewater-based epidemiology for a robust and accurate COVID-19 surveillance.
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Affiliation(s)
- Isaac Dennis Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Taher Abunama
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Oluyemi Olatunji Awolusi
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Leanne Pillay
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Kriveshin Pillay
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
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