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Chen X, Balliew J, Bauer CX, Deegan J, Gitter A, Hanson BM, Maresso AW, Tisza MJ, Troisi CL, Rios J, Mena KD, Boerwinkle E, Wu F. RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.12.24310301. [PMID: 39040200 PMCID: PMC11261926 DOI: 10.1101/2024.07.12.24310301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study utilized receptor-binding domain (RBD) amplicon sequencing of wastewater samples to monitor the SARS-CoV-2 community dynamics and evolution in El Paso, TX. Over 17 months, we identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Our findings demonstrated early detection of variants and identification of unreported outbreaks, while showing strong consistency with clinical genome sequencing data at the local, state, and national levels. Alpha diversity analyses revealed significant periodical variations, with the highest diversity observed in winter and the outbreak lag phases, likely due to lower competition among variants before the outbreak growth phase. The data underscores the importance of low transmission periods for rapid mutation and variant evolution. This study highlights the effectiveness of integrating RBD amplicon sequencing with wastewater surveillance in tracking viral evolution, understanding variant emergence, and enhancing public health preparedness.
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Affiliation(s)
- Xingwen Chen
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - John Balliew
- El Paso Water Utility, El Paso, TX, United States
| | - Cici X Bauer
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Jennifer Deegan
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Anna Gitter
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Blake M Hanson
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Anthony W Maresso
- TAILOR Labs, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Michael J Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Catherine L Troisi
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Janelle Rios
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Kristina D Mena
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Fuqing Wu
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
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Subroyen S, Pillay L, Bux F, Kumari S. Evaluating storage conditions and enhancement strategies on viral biomarker recovery for WBE applications. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 90:213-224. [PMID: 39007315 DOI: 10.2166/wst.2024.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/31/2024] [Indexed: 07/16/2024]
Abstract
Wastewater-based epidemiology (WBE) is a valuable disease surveillance tool. However, little is known on how factors such as transportation, storage, and wastewater characteristics influence the accuracy of the quantification methods. Hence, this study investigated the impact of storage temperatures and physicochemical characteristics of wastewater on SARS-CoV-2 and influenza A stability using droplet digital PCR. Additionally, strategies to enhance viral recovery were explored. Municipal influent wastewater stored between ±25 and -80 °C was assessed for a period of 84 days to determine viral degradation. Degradation up to 94.1% of influenza A and SARS-CoV-2 was observed in all samples with the highest at ±25 °C. Viral degradation was correlated to the changes in wastewater physicochemical characteristics. The low degradation observed of SARS-CoV-2 in the spiked pellets were indicative of viral adhesion to wastewater solids, which correlated with changes in pH. Ultrasonication frequencies ranging from 4 to 16 kHz, increased SARS-CoV-2 concentrations in the supernatant between 3.30 and 35.65%, indicating viral RNA attachment to wastewater solids. These results highlight the importance of additional pretreatment methods for maximizing RNA recovery from wastewater samples. Based on these findings, it was deduced that wastewater preservation studies are essential, and pretreatment should be included in the WBE methodology.
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Affiliation(s)
- Sueyanka Subroyen
- 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
| | - Faizal Bux
- 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 E-mail:
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Oh C, Xun G, Lane ST, Petrov VA, Zhao H, Nguyen TH. Portable, single nucleotide polymorphism-specific duplex assay for virus surveillance in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168701. [PMID: 37992833 DOI: 10.1016/j.scitotenv.2023.168701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
The Argonaute protein from the archaeon Pyrococcus furiosus (PfAgo) is a DNA-guided nuclease that targets DNA with any sequence. We designed a virus detection assay in which the PfAgo enzyme cleaves the reporter probe, thus generating fluorescent signals when amplicons from a reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay contain target sequences. We confirmed that the RT-LAMP-PfAgo assay for the SARS-CoV-2 Delta variant produced significantly higher fluorescent signals (p < 0.001) when a single nucleotide polymorphism (SNP), exclusive to the Delta variant, was present, compared to the samples without the SNP. Additionally, the duplex assay for Pepper mild mottle virus (PMMOV) and SARS-CoV-2 detection produced specific fluorescent signals (FAM or ROX) only when the corresponding sequences were present. Furthermore, the RT-LAMP-PfAgo assay does not require dilution to reduce the impact of environmental inhibitors. The limit of detection of the PMMOV assay, determined with 30 wastewater samples, was 28 gc/μL, with a 95 % confidence interval of [11,103]. Finally, using a point-of-use device, the RT-LAMP-PfAgo assay successfully detected PMMOV in wastewater samples. Based on our findings, we conclude that the RT-LAMP-PfAgo assay can be used as a portable, SNP-specific duplex assay, which will significantly improve virus surveillance in wastewater.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA.
| | - Guanhua Xun
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Stephan Thomas Lane
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
| | - Vassily Andrew Petrov
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
| | - Huimin Zhao
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States; Departments of Chemical and Biomolecular Engineering, Chemistry, and Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States; Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
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Zhu J, Lu H, Lin Q, Zhang T, Chen G, Zhou Y, Sui G. Fucoidan-based antibody-free magnetic nanoparticle for on-site detection of waterborne SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168619. [PMID: 37977397 DOI: 10.1016/j.scitotenv.2023.168619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
The portable and sensitive point-of-care-test (POCT) method is in urgent need to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for ensuring public health and safety. However, detection of trace number of pathogens in real water sample from the environment still faces challenges, because complex environment disruptors can rapidly degrade targets. Herein, magnetic beads coated with fucoidan and polydopamine (Fuc-PDA-MBs) were introduced as the capture carrier for pretreatment of samples. Fucoidan, a sulfated polysaccharide, can recognize the SARS-CoV-2 spike (S1) protein receptor-binding domain (S1 RBD) and was chosen for replacement of antibody in enrichment. Environmental water seeded with SARS-CoV-2 spike pseudovirus was applied to test performance of Fuc-PDA-MBs method. Under optimal conditions, the use of Fuc-PDA-MBs showed average 76 % capture efficiency at SARS-CoV-2 spike pseudovirus concentration ranging from 107.62 to 104.34 gene copies (gc)/L. Compared with Electronegative filtration (ENF), Fuc-PDA-MBs showed better virion sorption effectiveness. Fuc-PDA-MBs also validated by raw contaminated urban wastewater and showed high recovery results for SARS-CoV-2 variants. To rapidly detect virus in POCT, nucleic acid extraction-free Loop-Mediated Isothermal Amplification (LAMP) was used for simplifying experimental process. The Fuc-PDA-MBs-LAMP assay showed the quantitation limit of sample (LOQ) was 105.49 gc/L. The whole procedure could be completed within 90 min, including 30 min for virus pre-enrichment, 10 min nucleic acid release and 45 min LAMP analysis. Compared with regular antibody-based immunodetection, this integrated system provides broad-spectrum, economic way to detect SARS-CoV-2 mutants in complex environments and also adaptable for high throughput test, which might be used for on-site early warning of SARS-CoV-2 outbreaks in developing area.
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Affiliation(s)
- Jinhui Zhu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Huijun Lu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Qiuyuan Lin
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Tong Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Guang Chen
- Shanghai Chengtou Wastewater Treatment Co., LtD., Shanghai 201203, China
| | - Yang Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China; Shanghai Institute of Infectious Disease and Biosecurity, Shanghai 200032, China.
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5
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Gogoi G, Singh SD, Kalyan E, Koch D, Gogoi P, Kshattry S, Mahanta HJ, Imran M, Pandey R, Bharali P. An interpretative review of the wastewater-based surveillance of the SARS-CoV-2: where do we stand on its presence and concern? Front Microbiol 2024; 15:1338100. [PMID: 38318336 PMCID: PMC10839012 DOI: 10.3389/fmicb.2024.1338100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has been used for monitoring infectious diseases like polio, hepatitis, etc. since the 1940s. It is also being used for tracking the SARS-CoV-2 at the population level. This article aims to compile and assess the information for the qualitative and quantitative detection of the SARS-CoV-2 in wastewater. Based on the globally published studies, we highlight the importance of monitoring SARS-CoV-2 presence/detection in the wastewater and concurrently emphasize the development of early surveillance techniques. SARS-CoV-2 RNA sheds in the human feces, saliva, sputum and mucus that ultimately reaches to the wastewater and brings viral RNA into it. For the detection of the virus in the wastewater, different detection techniques have been optimized and are in use. These are based on serological, biosensor, targeted PCR, and next generation sequencing for whole genome sequencing or targeted amplicon sequencing. The presence of the SARS-CoV-2 RNA in wastewater could be used as a potential tool for early detection and devising the strategies for eradication of the virus before it is spread in the community. Additionally, with the right and timely understanding of viral behavior in the environment, an accurate and instructive model that leverages WBE-derived data may be created. This might help with the creation of technological tools and doable plans of action to lessen the negative effects of current viral epidemics or future potential outbreaks on public health and the economy. Further work toward whether presence of viral load correlates with its ability to induce infection, still needs evidence. The current increasing incidences of JN.1 variant is a case in point for continued early detection and surveillance, including wastewater.
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Affiliation(s)
- Gayatri Gogoi
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sarangthem Dinamani Singh
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Emon Kalyan
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Devpratim Koch
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pronami Gogoi
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Suman Kshattry
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Hridoy Jyoti Mahanta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Md Imran
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Rajesh Pandey
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Pankaj Bharali
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Awan J, Faherty LJ, Willis HH. Navigating Uncertainty in Public Health Decisionmaking: The Role of a Value of Information Framework in Threat Agnostic Biosurveillance. Health Secur 2024; 22:39-44. [PMID: 38079227 DOI: 10.1089/hs.2023.0070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024] Open
Affiliation(s)
- Jalal Awan
- Jalal Awan, MS, MPhil, PhD, is an Energy and Climate Policy Analyst, The Utility Reform Network, Oakland, CA, and an Assistant Policy Researcher, RAND Corporation, Santa Monica, CA
| | - Laura J Faherty
- Laura J. Faherty, MD, MPH, MSHP, is a Physician Policy Researcher, RAND Corporation, and an Attending Physician, Maine Medical Center, Portland, ME
| | - Henry H Willis
- Henry H. Willis, PhD, is a Senior Policy Researcher, RAND Corporation, Pittsburgh, PA
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Han JJ, Song HA, Pierson SL, Shen-Gunther J, Xia Q. Emerging Infectious Diseases Are Virulent Viruses-Are We Prepared? An Overview. Microorganisms 2023; 11:2618. [PMID: 38004630 PMCID: PMC10673331 DOI: 10.3390/microorganisms11112618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/10/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The recent pandemic caused by SARS-CoV-2 affected the global population, resulting in a significant loss of lives and global economic deterioration. COVID-19 highlighted the importance of public awareness and science-based decision making, and exposed global vulnerabilities in preparedness and response systems. Emerging and re-emerging viral outbreaks are becoming more frequent due to increased international travel and global warming. These viral outbreaks impose serious public health threats and have transformed national strategies for pandemic preparedness with global economic consequences. At the molecular level, viral mutations and variations are constantly thwarting vaccine efficacy, as well as diagnostic, therapeutic, and prevention strategies. Here, we discuss viral infectious diseases that were epidemic and pandemic, currently available treatments, and surveillance measures, along with their limitations.
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Affiliation(s)
- Jasmine J. Han
- Division of Gynecologic Oncology, Department of Gynecologic Surgery and Obstetrics, Department of Clinical Investigation, Brooke Army Medical Center, San Antonio, TX 78234, USA
| | - Hannah A. Song
- Department of Bioengineering, University of California, Los Angeles, CA 90024, USA;
| | - Sarah L. Pierson
- Department of Clinical Investigation, Brooke Army Medical Center, San Antonio, TX 78234, USA;
| | - Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, San Antonio, TX 78234, USA;
| | - Qingqing Xia
- Department of Clinical Investigation, Brooke Army Medical Center, San Antonio, TX 78234, USA;
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Mare R, Mare C, Hadarean A, Hotupan A, Rus T. COVID-19 and Water Variables: Review and Scientometric Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:957. [PMID: 36673718 PMCID: PMC9859563 DOI: 10.3390/ijerph20020957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
COVID-19 has changed the world since 2020, and the field of water specifically, boosting scientific productivity (in terms of published articles). This paper focuses on the influence of COVID-19 on scientific productivity with respect to four water variables: (i) wastewater, (ii) renewable water resources, (iii) freshwater withdrawal, and (iv) access to improved and safe drinking water. The field's literature was firstly reviewed, and then the maps were built, emphasizing the strong connections between COVID-19 and water-related variables. A total of 94 countries with publications that assess COVID-19 vs. water were considered and evaluated for how they clustered. The final step of the research shows that, on average, scientific productivity on the water topic was mostly conducted in countries with lower COVID-19 infection rates but higher development levels as represented by gross domestic product (GDP) per capita and the human development index (HDI). According to the statistical analysis, the water-related variables are highly significant, with positive coefficients. This validates that countries with higher water-related values conducted more research on the relationship with COVID-19. Wastewater and freshwater withdrawal had the highest impact on the scientific productivity with respect to COVID-19. Access to safe drinking water becomes insignificant in the presence of the development parameters.
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Affiliation(s)
- Roxana Mare
- Department of Building Services Engineering, Faculty of Building Services Engineering, Technical University of Cluj-Napoca, 128-130 21 Decembrie 1989 Blv., 400604 Cluj-Napoca, Romania
| | - Codruța Mare
- Department of Statistics-Forecasts-Mathematics, Faculty of Economics and Business Administration, Babes-Bolyai University, 58-60 Teodor Mihali Str., 400591 Cluj-Napoca, Romania
- Interdisciplinary Centre for Data Science, Babes-Bolyai University, 68 Avram Iancu Str., 4th Floor, 400083 Cluj-Napoca, Romania
| | - Adriana Hadarean
- Department of Building Services Engineering, Faculty of Building Services Engineering, Technical University of Cluj-Napoca, 128-130 21 Decembrie 1989 Blv., 400604 Cluj-Napoca, Romania
| | - Anca Hotupan
- Department of Building Services Engineering, Faculty of Building Services Engineering, Technical University of Cluj-Napoca, 128-130 21 Decembrie 1989 Blv., 400604 Cluj-Napoca, Romania
| | - Tania Rus
- Department of Building Services Engineering, Faculty of Building Services Engineering, Technical University of Cluj-Napoca, 128-130 21 Decembrie 1989 Blv., 400604 Cluj-Napoca, Romania
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Murni IK, Oktaria V, Handley A, McCarthy DT, Donato CM, Nuryastuti T, Supriyati E, Putri DAD, Sari HM, Laksono IS, Thobari JA, Bines JE. The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia. PLoS One 2022; 17:e0274793. [PMID: 36240187 PMCID: PMC9565423 DOI: 10.1371/journal.pone.0274793] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Wastewater-based epidemiology (WBE) surveillance as an early warning system (EWS) for monitoring community transmission of SARS-CoV-2 in low- and middle-income country (LMIC) settings, where diagnostic testing capacity is limited, needs further exploration. We explored the feasibility to conduct a WBE surveillance in Indonesia, one of the global epicenters of the COVID-19 pandemic in the middle of 2021, with the fourth largest population in the world where sewer and non-sewered sewage systems are implemented. The feasibility and resource capacity to collect samples on a weekly or fortnightly basis with grab and/or passive sampling methods, as well as to conduct qualitative and quantitative identification of SARS-CoV-2 ribonucleic acid (RNA) using real-time RT-PCR (RT-qPCR) testing of environmental samples were explored. MATERIALS AND METHODS We initiated a routine surveillance of wastewater and environmental sampling at three predetermined districts in Special Region of Yogyakarta Province. Water samples were collected from central and community wastewater treatment plants (WWTPs), including manholes flowing to the central WWTP, and additional soil samples were collected for the near source tracking (NST) locations (i.e., public spaces where people congregate). RESULTS We began collecting samples in the Delta wave of the COVID-19 pandemic in Indonesia in July 2021. From a 10-week period, 54% (296/544) of wastewater and environmental samples were positive for SARS-CoV-2 RNA. The sample positivity rate decreased in proportion with the reported incidence of COVID-19 clinical cases in the community. The highest positivity rate of 77% in week 1, was obtained for samples collected in July 2021 and decreased to 25% in week 10 by the end of September 2021. CONCLUSION A WBE surveillance system for SARS-CoV-2 in Indonesia is feasible to monitor the community burden of infections. Future studies testing the potential of WBE and EWS for signaling early outbreaks of SARS-CoV-2 transmissions in this setting are required.
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Affiliation(s)
- Indah K. Murni
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Medicine, Child Health Department, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- * E-mail: (IKM); (VO)
| | - Vicka Oktaria
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Medicine, Department of Biostatistics, Epidemiology and Population Health, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- * E-mail: (IKM); (VO)
| | - Amanda Handley
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Medicines Development for Global Health, Southbank, Victoria, Australia
| | - David T. McCarthy
- Department of Civil Engineering, Environmental and Public Health Microbiology Lab (EPHM Lab), Monash University, Clayton, Victoria, Australia
| | - Celeste M. Donato
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Titik Nuryastuti
- Faculty of Medicine, Department of Microbiology, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Faculty of Medicine, Center for Tropical Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Astuti Dharma Putri
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendri Marinda Sari
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ida Safitri Laksono
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Medicine, Child Health Department, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Jarir At Thobari
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Julie E. Bines
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Department of Gastroenterology and Clinical Nutrition, Royal Children’s Hospital Melbourne, Parkville, Victoria, Australia
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10
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Mahmoudi T, Naghdi T, Morales-Narváez E, Golmohammadi H. Toward smart diagnosis of pandemic infectious diseases using wastewater-based epidemiology. Trends Analyt Chem 2022; 153:116635. [PMID: 35440833 PMCID: PMC9010328 DOI: 10.1016/j.trac.2022.116635] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/21/2022] [Accepted: 04/07/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 outbreak revealed fundamental weaknesses of current diagnostic systems, particularly in prediction and subsequently prevention of pandemic infectious diseases (PIDs). Among PIDs detection methods, wastewater-based epidemiology (WBE) has been demonstrated to be a favorable mean for estimation of community-wide health. Besides, by going beyond purely sensing usages of WBE, it can be efficiently exploited in Healthcare 4.0/5.0 for surveillance, monitoring, control, and above all prediction and prevention, thereby, resulting in smart sensing and management of potential outbreaks/epidemics/pandemics. Herein, an overview of WBE sensors for PIDs is presented. The philosophy behind the smart diagnosis of PIDs using WBE with the help of digital technologies is then discussed, as well as their characteristics to be met. Analytical techniques that are pushing the frontiers of smart sensing and have a high potential to be used in the smart diagnosis of PIDs via WBE are surveyed. In this context, we underscore key challenges ahead and provide recommendations for implementing and moving faster toward smart diagnostics.
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Sobsey MD. Absence of virological and epidemiological evidence that SARS-CoV-2 poses COVID-19 risks from environmental fecal waste, wastewater and water exposures. JOURNAL OF WATER AND HEALTH 2022; 20:126-138. [PMID: 35100160 DOI: 10.2166/wh.2021.182] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This review considers evidence for infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presence and COVID-19 infection and illness resulting from exposure to environmental fecal wastes and waters. There is no documented evidence that (1) infectious, replication-capable SARS-CoV-2 is present in environmental fecal wastes, wastewater or water, and (2) well-documented epidemiological evidence of COVID-19 infection, illness or death has never been reported for these exposure media. COVID-19 is transmitted mainly by direct personal contact and respiratory secretions as airborne droplets and aerosols, and less so by respiratory-secreted fomites via contact (touch) exposures. While SARS-CoV-2 often infects the gastrointestinal tract of infected people, its presence as infectious, replication-capable virus in environmental fecal wastes and waters has never been documented. There is only rare and unquantified evidence of infectious, replication-capable SARS-CoV-2 in recently shed feces of COVID-19 hospital patients. The human infectivity dose-response relationship of SARS-CoV-2 is unknown, thereby making it impossible to estimate evidence-based quantitative health effects assessments by quantitative microbial risk assessment methods requiring both known exposure assessment and health effects assessment data. The World Health Organization, Water Environment Federation, US Centers for Disease Control and Prevention and others do not consider environmental fecal wastes and waters as sources of exposure to infectious SARS-CoV-2 causing COVID-19 infection and illness.
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Affiliation(s)
- Mark D Sobsey
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA E-mail:
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Wang Q, Liu L. On the Critical Role of Human Feces and Public Toilets in the Transmission of COVID-19: Evidence from China. SUSTAINABLE CITIES AND SOCIETY 2021; 75:103350. [PMID: 34540563 PMCID: PMC8433098 DOI: 10.1016/j.scs.2021.103350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 05/05/2023]
Abstract
The surprising spread speed of the COVID-19 pandemic creates an urgent need for investigating the transmission chain or transmission pattern of COVID-19 beyond the traditional respiratory channels. This study therefore examines whether human feces and public toilets play a critical role in the transmission of COVID-19. First, it develops a theoretical model that simulates the transmission chain of COVID-19 through public restrooms. Second, it uses stabilized epidemic data from China to empirically examine this theory, conducting an empirical estimation using a two-stage least squares (2SLS) model with appropriate instrumental variables (IVs). This study confirms that the wastewater directly promotes the transmission of COVID-19 within a city. However, the role of garbage in this transmission chain is more indirect in the sense that garbage has a complex relationship with public toilets, and it promotes the transmission of COVID-19 within a city through interaction with public toilets and, hence, human feces. These findings have very strong policy implications in the sense that if we can somehow use the ratio of public toilets as a policy instrument, then we can find a way to minimize the total number of infections in a region. As shown in this study, pushing the ratio of public toilets (against open defecation) to the local population in a city to its optimal level would help to reduce the total infection in a region.
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Affiliation(s)
- Qiuyun Wang
- School of Economics, Southwestern University of Finance and Economics, P.R China
| | - Lu Liu
- School of Economics, Southwestern University of Finance and Economics, P.R China
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Jmii H, Gharbi-Khelifi H, Assaoudi R, Aouni M. Detection of SARS-CoV-2 in the sewerage system in Tunisia: a promising tool to confront COVID-19 pandemic. Future Virol 2021; 16:10.2217/fvl-2021-0050. [PMID: 34659444 PMCID: PMC8516351 DOI: 10.2217/fvl-2021-0050] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 09/20/2021] [Indexed: 12/17/2022]
Abstract
Aim: The current study undertaken in Tunisia examines the use of wastewaters to monitor SARS-CoV-2 circulation. Materials & methods: Viral genetic materials collected in wastewaters during two different periods (September-October 2020 and February-April 2021) were concentrated using the adsorption-elution method. SARS-CoV-2 genes were researched by real-time PCR. Results: During the first period of the study, viral RNA was detected in 61.11% of the analyzed samples collected from Monastir city with a rate of 88.88% for raw wastewaters and 33.33% for treated wastewaters. Then, during the second period of the study, the quantitative analysis of wastewaters collected from seven governorates showed the presence of viral RNA among around 25% of them with variable RNA loads. The increased amounts of viral RNA detected in wastewaters were accompanied by an increase in the number of COVID-19 patients in Tunisia. Conclusion: Our results emphasize the importance of sewage survey in SARS-CoV-2 tracking.
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Affiliation(s)
- Habib Jmii
- Laboratory of Transmissible Diseases & Biologically Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Hakima Gharbi-Khelifi
- Laboratory of Transmissible Diseases & Biologically Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Faculty of Sciences and Techniques of Sidi Bouzid, University of Kairouan, Tunisia
| | - Raouia Assaoudi
- Laboratory of Transmissible Diseases & Biologically Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Faculty of Sciences and Techniques of Sidi Bouzid, University of Kairouan, Tunisia
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases & Biologically Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
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