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Ofori B, Agoha RK, Bokoe EK, Armah ENA, Misita Morang'a C, Sarpong KAN. Leveraging wastewater-based epidemiology to monitor the spread of neglected tropical diseases in African communities. Infect Dis (Lond) 2024:1-15. [PMID: 38922811 DOI: 10.1080/23744235.2024.2369177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Neglected tropical diseases continue to cause a significant burden worldwide, with Africa accounting for more than one-third of the global burden. Over the past decade, progress has been made in eliminating, controlling, and eradicating these diseases in Africa. By December 2022, 47 out of 54 African countries had eliminated at least one neglected tropical disease, and more countries were close to achieving this milestone. Between 2020 and 2021, there was an 80 million reduction in people requiring intervention. However, continued efforts are needed to manage neglected tropical diseases and address their social and economic burden, as they deepen marginalisation and stigmatisation. Wastewater-based epidemiology involves analyzing wastewater to detect and quantify biomarkers of disease-causing pathogens. This approach can complement current disease surveillance systems in Africa and provide an additional layer of information for monitoring disease spread and detecting outbreaks. This is particularly important in Africa due to limited traditional surveillance methods. Wastewater-based epidemiology also provides a tsunami-like warning system for neglected tropical disease outbreaks and can facilitate timely intervention and optimised resource allocation, providing an unbiased reflection of the community's health compared to traditional surveillance systems. In this review, we highlight the potential of wastewater-based epidemiology as an innovative approach for monitoring neglected tropical disease transmission within African communities and improving existing surveillance systems. Our analysis shows that wastewater-based epidemiology can enhance surveillance of neglected tropical diseases in Africa, improving early detection and management of Buruli ulcers, hookworm infections, ascariasis, schistosomiasis, dengue, chikungunya, echinococcosis, rabies, and cysticercosis for better disease control.
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Affiliation(s)
- Benedict Ofori
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Righteous Kwaku Agoha
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Edem Kwame Bokoe
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Collins Misita Morang'a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Kwabena Amofa Nketia Sarpong
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
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2
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Gwenzi W, Adelodun B, Kumar P, Ajibade FO, Silva LFO, Choi KS, Selvarajan R, Abia ALK, Gholipour S, Mohammadi F, Nikaeen M. Human viral pathogens in the wastewater-source water-drinking water continuum: Evidence, health risks, and lessons for future outbreaks in low-income settings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170214. [PMID: 38278242 DOI: 10.1016/j.scitotenv.2024.170214] [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: 09/01/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
Human viral pathogens, including SARS-CoV-2 continue to attract public and research attention due to their disruption of society, global health, and the economy. Several earlier reviews have investigated the occurrence and fate of SARS-CoV-2 in wastewater, and the potential to use such data in wastewater-based epidemiology. However, comprehensive reviews tracking SARS-CoV-2 and other viral pathogens in the wastewater-water-drinking water continuum and the associated risk assessment are still lacking. Therefore, to address this gap, the present paper makes the following contributions: (1) critically examines the early empirical results to highlight the occurrence and stability of SARS-CoV-2 in the wastewater-source water-drinking water continuum, (2) discusses the anthropogenic and hydro(geo)logical processes controlling the circulation of SARS-CoV-2 in the wastewater-source water-drinking water continuum, (3) discusses the risky behaviour, drivers and high-risk settings in the wastewater-source water-drinking water continuum, (4) uses the available empirical data on SARS-CoV-2 occurrence in the wastewater-source water-drinking water continuum to discuss human health risks from multiple exposure pathways, gendered aspects of SARS-CoV-2 transmission via shared on-site sanitation systems, and (5) develops and risk mitigation strategy based on the available empirical evidence and quantitative human risk assessment data. Finally, it presents a comprehensive research agenda on SARS-CoV-2/COVID-19 to guide the mitigation of future similar outbreaks in low-income settings.
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Affiliation(s)
- Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, 380 New Adylin, Westgate, Harare, Zimbabwe; Currently Alexander von Humboldt Fellow and Guest/Visiting Professor at: Grassland Science and Renewable Plant Resources, Faculty of Organic Agricultural Sciences, Universität Kassel, Steinstraße 19, D-37213 Witzenhausen, Germany; Leibniz-Institut für Agrartechnik und Bioökonomie e.V. (ATB), Max-Eyth-Allee 100, D-14469, Potsdam, Germany.
| | - Bashir Adelodun
- Department of Agricultural Civil Engineering, Kyungpook National University, Daegu 41566, Republic of Korea; Department of Agricultural and Biosystems Engineering, University of Ilorin, PMB 1515, Ilorin 240003, Nigeria; Institute of Agricultural Science & Technology, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Pankaj Kumar
- Agro-Ecology and Pollution Research Laboratory, Department of Zoology and Environmental Science, Gurukula Kangri (Deemed to Be University), Haridwar 249404, India; Research and Development Division, Society for AgroEnvironmental Sustainability, Dehradun 248007, India.
| | - Fidelis Odedishemi Ajibade
- Department of Civil and Environmental Engineering, Federal University of Technology, PMB 704, Akure, 340001, Nigeria.
| | - Luis F O Silva
- Department of Civil and Environmental Engineering, Universidad de la Costa, Calle 58 #55-66, 080002 Barranquilla, Atlàntico, Colombia.
| | - Kyung Sook Choi
- Department of Agricultural Civil Engineering, Kyungpook National University, Daegu 41566, Republic of Korea; Institute of Agricultural Science & Technology, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida branch, Johannesburg, South Africa
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Environmental Research Foundation, Westville 3630, Kwazulu-Natal, South Africa
| | - Sahar Gholipour
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farzaneh Mohammadi
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahnaz Nikaeen
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran; Environment Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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3
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Al-Hazmi HE, Mohammadi A, Hejna A, Majtacz J, Esmaeili A, Habibzadeh S, Saeb MR, Badawi M, Lima EC, Mąkinia J. Wastewater reuse in agriculture: Prospects and challenges. ENVIRONMENTAL RESEARCH 2023; 236:116711. [PMID: 37487927 DOI: 10.1016/j.envres.2023.116711] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/11/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
Sustainable water recycling and wastewater reuse are urgent nowadays considering water scarcity and increased water consumption through human activities. In 2015, United Nations Sustainable Development Goal 6 (UN SDG6) highlighted the necessity of recycling wastewater to guarantee water availability for individuals. Currently, wastewater irrigation (WWI) of crops and agricultural land appears essential. The present work overviews the quality of treated wastewater in terms of soil microbial activities, and discusses challenges and benefits of WWI in line with wastewater reuse in agriculture and aquaculture irrigation. Combined conventional-advanced wastewater treatment processes are specifically deliberated, considering the harmful impacts on human health arising from WWI originating from reuse of contaminated water (salts, organic pollutants, toxic metals, and microbial pathogens i.e., viruses and bacteria). The comprehensive literature survey revealed that, in addition to the increased levels of pathogen and microbial threats to human wellbeing, poorly-treated wastewater results in plant and soil contamination with toxic organic/inorganic chemicals, and microbial pathogens. The impact of long-term emerging pollutants like plastic nanoparticles should also be established in further studies, with the development of standardized analytical techniques for such hazardous chemicals. Likewise, the reliable, long-term and extensive judgment on heavy metals threat to human beings's health should be explored in future investigations.
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Affiliation(s)
- Hussein E Al-Hazmi
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Ali Mohammadi
- Department of Engineering and Chemical Sciences, Karlstad University, 65188, Karlstad, Sweden.
| | - Aleksander Hejna
- Institute of Materials Technology, Poznan University of Technology, Poznań, Poland
| | - Joanna Majtacz
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Amin Esmaeili
- Department of Chemical Engineering, School of Engineering Technology and Industrial Trades, University of Doha for Science and Technology (UDST), 24449, Arab League St, Doha, Qatar
| | - Sajjad Habibzadeh
- Surface Reaction and Advanced Energy Materials Laboratory, Chemical Engineering Department, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233, Gdańsk, Poland.
| | - Michael Badawi
- Laboratoire de Physique et Chimie Théoriques UMR CNRS 7019, Université de Lorraine, Nancy, France
| | - Eder C Lima
- Institute of Chemistry, Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Jacek Mąkinia
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233, Gdańsk, Poland
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Opere MW. Analysing the interplay of environmental virology, public health, and sanitation: a comprehensive review from a Kenyan perspective. Front Cell Infect Microbiol 2023; 13:1256822. [PMID: 37942480 PMCID: PMC10629379 DOI: 10.3389/fcimb.2023.1256822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023] Open
Abstract
This comprehensive review examines the interplay between environmental virology, public health, and sanitation in the unique context of Kenya. The review sheds light on the specific viral threats faced by the country, including waterborne viruses, zoonotic infections, and emerging viral diseases, and their implications for public health. It explores the prevailing public health challenges in Kenya associated with environmental viromics, such as infectious viral diseases, and the rising burden of other infectious particles. The role of sanitation in mitigating viral infections is highlighted, emphasising the importance of clean water supply, proper waste management, and hygienic practises. The review also presents strategies for strengthening environmental virology research in Kenya, including enhancing laboratory capacities and leveraging technological advancements. Furthermore, the policy implications and recommendations derived from the review emphasise the need for multi-sectoral collaboration, evidence-based decision-making, and long-term investments in infrastructure and behaviour change interventions. Implementing these strategies can enhance the understanding of environmental virology, improve public health outcomes, and ensure sustainable sanitation practises in Kenya, ultimately contributing to the well-being of the population and sustainable development.
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Affiliation(s)
- Michael Wasonga Opere
- School of Pure and Applied Sciences, Kenyatta University, Nairobi, Kenya
- School of Biosciences, The University of Nottingham, Nottingham, United Kingdom
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5
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Reeves A, Shaikh WA, Chakraborty S, Chaudhuri P, Biswas JK, Maity JP. Potential transmission of SARS-CoV-2 through microplastics in sewage: A wastewater-based epidemiological review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122171. [PMID: 37437759 DOI: 10.1016/j.envpol.2023.122171] [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: 04/27/2023] [Revised: 06/24/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
In light of the current COVID-19 pandemic caused by the virus SARS-CoV-2, there is an urgent need to identify and investigate the various pathways of transmission. In addition to contact and aerosol transmission of the virus, this review investigated the possibility of its transmission via microplastics found in sewage. Wastewater-based epidemiological studies on the virus have confirmed its presence and persistence in both influent sewage as well as treated ones. The hypothesis behind the study is that the huge amount of microplastics, especially Polyvinyl Chloride and Polyethylene particles released into the open waters from sewage can become a good substrate and vector for microbes, especially Polyvinyl Chloride and Polyethylene particles, imparting stability to microbes and aiding the "plastisphere" formation. A bibliometric analysis highlights the negligence of research toward plastispheres and their presence in sewage. The ubiquity of microplastics and their release along with the virus into the open waters increases the risk of viral plastispheres. These plastispheres may be ingested by aquatic organisms facilitating reverse zoonosis and the commercial organisms already reported with accumulating microplastics through the food chain poses a risk to human populations as well. Reliance of high population density areas on open waters served by untreated sewage in economically less developed countries might bring back viral transmission.
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Affiliation(s)
- Arijit Reeves
- Department of Environmental Science, University of Calcutta, Kolkata, West Bengal, 700019, India
| | - Wasim Akram Shaikh
- Department of Basic Sciences, School of Science and Technology, The Neotia University, Sarisha, South 24 Parganas, West Bengal, 743368, India
| | - Sukalyan Chakraborty
- Department of Civil and Environmental Engineering, Birla Institute of Technology, Mesra, Jharkhand, 835215, India.
| | - Punarbasu Chaudhuri
- Department of Environmental Science, University of Calcutta, Kolkata, West Bengal, 700019, India
| | - Jayanta Kumar Biswas
- Enviromicrobiology, Ecotoxicology and Ecotechnology Research Laboratory (3E-MicroToxTech Lab), Department of Ecological Studies, University of Kalyani, Kalyani, Nadia, 741235, West Bengal, India; International Centre for Ecological Engineering, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Jyoti Prakash Maity
- Environmental Science Laboratory, Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha, 751024, India.
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6
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Potapov S, Gorshkova A, Krasnopeev A, Podlesnaya G, Tikhonova I, Suslova M, Kwon D, Patrushev M, Drucker V, Belykh O. RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters. Int J Mol Sci 2023; 24:12049. [PMID: 37569424 PMCID: PMC10418309 DOI: 10.3390/ijms241512049] [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] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
In this study, we analyzed the transcriptomes of RNA and DNA viruses from the oligotrophic water of Lake Baikal and the effluent from wastewater treatment plants (WWTPs) discharged into the lake from the towns of Severobaikalsk and Slyudyanka located on the lake shores. Given the uniqueness and importance of Lake Baikal, the issues of biodiversity conservation and the monitoring of potential virological hazards to hydrobionts and humans are important. Wastewater treatment plants discharge treated effluent directly into the lake. In this context, the identification and monitoring of allochthonous microorganisms entering the lake play an important role. Using high-throughput sequencing methods, we found that dsDNA-containing viruses of the class Caudoviricetes were the most abundant in all samples, while Leviviricetes (ssRNA(+) viruses) dominated the treated water samples. RNA viruses of the families Nodaviridae, Tombusviridae, Dicitroviridae, Picobirnaviridae, Botourmiaviridae, Marnaviridae, Solemoviridae, and Endornavirida were found in the pelagic zone of three lake basins. Complete or nearly complete genomes of RNA viruses belonging to such families as Dicistroviridae, Marnaviridae, Blumeviridae, Virgaviridae, Solspiviridae, Nodaviridae, and Fiersviridae and the unassigned genus Chimpavirus, as well as unclassified picorna-like viruses, were identified. In general, the data of sanitary/microbiological and genetic analyses showed that WWTPs inadequately purify the discharged water, but, at the same time, we did not observe viruses pathogenic to humans in the pelagic zone of the lake.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Anna Gorshkova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Andrey Krasnopeev
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Galina Podlesnaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Irina Tikhonova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Maria Suslova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Dmitry Kwon
- National Research Center Kurchatov Institute, Academician Kurchatov Square 1, 123098 Moscow, Russia
| | - Maxim Patrushev
- National Research Center Kurchatov Institute, Academician Kurchatov Square 1, 123098 Moscow, Russia
| | - Valentin Drucker
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Olga Belykh
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
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Wu H, Juel MAI, Eytcheson S, Aw TG, Munir M, Molina M. Temporal and spatial relationships of CrAssphage and enteric viral and bacterial pathogens in wastewater in North Carolina. WATER RESEARCH 2023; 239:120008. [PMID: 37192571 PMCID: PMC10896230 DOI: 10.1016/j.watres.2023.120008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/20/2023] [Accepted: 04/27/2023] [Indexed: 05/18/2023]
Abstract
Enteric disease remains one of the most common concerns for public health, particularly when it results from human exposure to surface and recreational waters contaminated with wastewater. Characterizing the temporal and spatial variation of enteric pathogens prevalent in wastewater is critical to develop approaches to mitigate their distribution in the environment. In this study, we aim to characterize pathogen variability and test the applicability of the human-associated wastewater indicator crAssphage as an indicator of enteric viral and bacterial pathogens. We conducted weekly samplings for 14 months from four wastewater treatment plants in North Carolina, USA. Untreated wastewater samples were processed using hollow fiber ultrafiltration, followed by secondary concentration methods. Adenovirus, norovirus, enterovirus, Salmonella, Shiga toxin 2 (stx2), Campylobacter, and crAssphage were measured by quantitative polymerase chain reaction (qPCR) and reverse transcriptase (rt)-qPCR. Our results revealed significant correlations between crAssphage and human adenovirus, enterovirus, norovirus, Salmonella, and Campylobacter (p<0.01). Pathogens and crAssphage concentrations in untreated wastewater showed distinct seasonal patterns, with peak concentrations of crAssphage and viral pathogens in fall and winter, while bacterial pathogens showed peaked concentrations in either winter (Campylobacter), fall (Salmonella), or summer (stx2). This study enhances the understanding of crAssphage as an alternative molecular indicator for both bacterial and viral pathogens. The findings of this study can also inform microbial modeling efforts for the prediction of the impact of wastewater pathogens on surface waters due to increased flooding events and wastewater overflows associated with climate change.
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Affiliation(s)
- Huiyun Wu
- U.S. Environmental Protection Agency, Office of Research and Development, RTP, NC, 27709, USA; Oak Ridge Institute for Science and Education, PO Box 117, Oak Ridge, Tennessee 37831 USA; Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, USA
| | - Md Ariful Islam Juel
- Department of Civil and Environmental Engineering, University of North Carolina Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Stephanie Eytcheson
- Oak Ridge Institute for Science and Education, PO Box 117, Oak Ridge, Tennessee 37831 USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, USA
| | - Mariya Munir
- Department of Civil and Environmental Engineering, University of North Carolina Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Marirosa Molina
- U.S. Environmental Protection Agency, Office of Research and Development, RTP, NC, 27709, USA.
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8
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Gao Y, Sun Z, Guo Y, Qiang Z, Ben W. Virus inactivation by sequential ultraviolet-chlorine disinfection: Synergistic effect and mechanism. CHEMOSPHERE 2023; 314:137632. [PMID: 36565762 PMCID: PMC9770000 DOI: 10.1016/j.chemosphere.2022.137632] [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: 09/30/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
The COVID-19 outbreak has raised concerns about the efficacy of the disinfection process followed in water treatment plants in preventing the spread of viruses. Ultraviolet (UV) and chlorine multi-barrier disinfection processes are commonly used in water treatment plants; however, their effects on virus inactivation are still unclear. In this study, the effects of different disinfection processes (i.e., UV, free chlorine, and their combination) on waterborne viruses were analyzed using bacteriophage surrogates (i.e., MS2 and PR772) as alternative indicators. The results showed that the inactivation rates of PR772 by either UV or free chlorine disinfection were higher than those of MS2. PR772 was approximately 1.5 times more sensitive to UV disinfection and 8.4 times more sensitive to chlorine disinfection than MS2. Sequential UV-chlorine disinfection had a synergistic effect on virus inactivation, which was enhanced by an increase in the UV dose. As compared with single free chlorine disinfection, UV irradiation at 40 mJ cm-2 enhanced MS2 and PR772 inactivation significantly with a 2.7-fold (MS2) and a 1.7-fold (PR772) increase in the inactivation rate constants on subsequent chlorination in phosphate buffered saline. The synergistic effect was also observed in real wastewater samples, in which the MS2 inactivation rate increased 1.4-fold on subsequent chlorination following UV irradiation at 40 mJ cm-2. The mechanism of the synergistic effect of sequential UV-chlorine disinfection was determined via sodium dodecyl sulfate-polyacrylamide gel electrophoresis, using MS2 as an indicator. The results showed that the synergistic effect was due to damage to MS2 surface proteins caused by previous UV disinfection, which enhanced the sensitivity of MS2 to chlorination. This study provides a feasible approach for the efficient inactivation of viruses in water supply and drainage.
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Affiliation(s)
- Ying Gao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhe Sun
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Ying Guo
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiwei Ben
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China.
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Takuissu GR, Kenmoe S, Ebogo-Belobo JT, Kengne-Ndé C, Mbaga DS, Bowo-Ngandji A, Ndzie Ondigui JL, Kenfack-Momo R, Tchatchouang S, Kenfack-Zanguim J, Lontuo Fogang R, Zeuko’o Menkem E, Kame-Ngasse GI, Magoudjou-Pekam JN, Veneri C, Mancini P, Bonanno Ferraro G, Iaconelli M, Orlandi L, Del Giudice C, Suffredini E, La Rosa G. Occurrence of Hepatitis A Virus in Water Matrices: A Systematic Review and Meta-Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1054. [PMID: 36673812 PMCID: PMC9859052 DOI: 10.3390/ijerph20021054] [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: 11/12/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Hepatitis A is a common form of viral hepatitis. It is usually transmitted through the ingestion of contaminated food and water. This systematic review was carried out to summarise the overall prevalence of Hepatitis A virus (HAV) in different water matrices: untreated and treated wastewater, surface water, groundwater, drinking water, and others (e.g., irrigation water and floodwater). The literature search was performed in four databases: PubMed, Web of Science, Global Index Medicus, and Excerpta Medica Database. Heterogeneity (I2) was assessed using the χ2 test on the Cochran Q statistic and H parameters. A total of 200 prevalence data from 144 articles were included in this meta-analysis. The overall prevalence of HAV in water matrices was 16.7% (95% CI: 13.4−20.3). The prevalence for individual matrix was as follows: 31.4% (95% CI: 23.0−40.4) untreated wastewater, 18.0% (95% CI: 9.5−28.2) treated wastewater, 15.0% (95% CI: 10.1−20.5) surface water, 2.3% (95% CI: 0.1−6.0) in groundwater, 0.3% (95% CI: 0.0−1.7) in drinking water, and 8.5% (95% CI: 3.1−15.6) in other matrices. The prevalence was higher in low-income economies (29.0%). Africa and Eastern Mediterranean were the regions with higher HAV prevalence values. This study showed a high heterogeneity (I2 > 75%) with a significant publication bias (p value Egger test < 0.001). The results of this review suggest that water matrices could be an important route of HAV transmission even in industrialized countries, despite the lower prevalence compared to less industrialized countries, and the availability of advanced water management systems. More effective water/wastewater treatment strategies are needed in developing countries to limit the environmental circulation of HAV.
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Affiliation(s)
- Guy Roussel Takuissu
- Centre for Food, Food Security and Nutrition Research, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - Sebastien Kenmoe
- Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | - Jean Thierry Ebogo-Belobo
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - Cyprien Kengne-Ndé
- Epidemiological Surveillance, Evaluation and Research Unit, National AIDS Control Committee, Yaounde, Cameroon
| | | | - Arnol Bowo-Ngandji
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | | | - Raoul Kenfack-Momo
- Department of Biochemistry, The University of Yaounde I, Yaounde, Cameroon
| | | | | | | | | | - Ginette Irma Kame-Ngasse
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | | | - Carolina Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Giusy Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Marcello Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Lidia Orlandi
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Claudia Del Giudice
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy
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10
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Kilaru P, Hill D, Anderson K, Collins MB, Green H, Kmush BL, Larsen DA. Wastewater Surveillance for Infectious Disease: A Systematic Review. Am J Epidemiol 2022; 192:305-322. [PMID: 36227259 PMCID: PMC9620728 DOI: 10.1093/aje/kwac175] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/25/2022] [Accepted: 10/05/2022] [Indexed: 02/07/2023] Open
Abstract
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to be a valuable source of information regarding SARS-CoV-2 transmission and coronavirus disease 2019 (COVID-19) cases. Although the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens that have been surveilled through wastewater. Herein we identify the infectious diseases that have been previously studied via wastewater surveillance prior to the COVID-19 pandemic. Infectious diseases and pathogens were identified in 100 studies of wastewater surveillance across 38 countries, as were themes of how wastewater surveillance and other measures of disease transmission were linked. Twenty-five separate pathogen families were identified in the included studies, with the majority of studies examining pathogens from the family Picornaviridae, including polio and nonpolio enteroviruses. Most studies of wastewater surveillance did not link what was found in the wastewater to other measures of disease transmission. Among those studies that did, the value reported varied by study. Wastewater surveillance should be considered as a potential public health tool for many infectious diseases. Wastewater surveillance studies can be improved by incorporating other measures of disease transmission at the population-level including disease incidence and hospitalizations.
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Affiliation(s)
- Pruthvi Kilaru
- Department of Public Health, Syracuse University, Syracuse, New York, United States,Des Moines University College of Osteopathic Medicine, Des Moines, Iowa, United States
| | - Dustin Hill
- Department of Public Health, Syracuse University, Syracuse, New York, United States,Graduate Program in Environmental Science, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States
| | - Kathryn Anderson
- Department of Medicine, State University of New York Upstate Medical University, Syracuse, New York, United States
| | - Mary B Collins
- Department of Environmental Studies, State University of New York College of Environmental Science, Syracuse, New York, United States
| | - Hyatt Green
- Department of Environmental Biology, State University of New York College of Environmental Science, Syracuse, New York, United States
| | - Brittany L Kmush
- Department of Public Health, Syracuse University, Syracuse, New York, United States
| | - David A Larsen
- Correspondence to Dr. Dave Larsen, Department of Public Health, Syracuse University, 430C White Hall, Syracuse, NY 13244 ()
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11
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Al-Hazmi HE, Shokrani H, Shokrani A, Jabbour K, Abida O, Mousavi Khadem SS, Habibzadeh S, Sonawane SH, Saeb MR, Bonilla-Petriciolet A, Badawi M. Recent advances in aqueous virus removal technologies. CHEMOSPHERE 2022; 305:135441. [PMID: 35764113 PMCID: PMC9233172 DOI: 10.1016/j.chemosphere.2022.135441] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 05/09/2023]
Abstract
The COVID-19 outbreak has triggered a massive research, but still urgent detection and treatment of this virus seems a public concern. The spread of viruses in aqueous environments underlined efficient virus treatment processes as a hot challenge. This review critically and comprehensively enables identifying and classifying advanced biochemical, membrane-based and disinfection processes for effective treatment of virus-contaminated water and wastewater. Understanding the functions of individual and combined/multi-stage processes in terms of manufacturing and economical parameters makes this contribution a different story from available review papers. Moreover, this review discusses challenges of combining biochemical, membrane and disinfection processes for synergistic treatment of viruses in order to reduce the dissemination of waterborne diseases. Certainly, the combination technologies are proactive in minimizing and restraining the outbreaks of the virus. It emphasizes the importance of health authorities to confront the outbreaks of unknown viruses in the future.
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Affiliation(s)
- Hussein E Al-Hazmi
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Hanieh Shokrani
- Department of Chemical Engineering, Sharif University of Technology, Azadi Ave., Tehran, Iran
| | - Amirhossein Shokrani
- Department of Mechanical Engineering, Sharif University of Technology, Azadi Ave., Tehran, Iran
| | - Karam Jabbour
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Otman Abida
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | | | - Sajjad Habibzadeh
- Surface Reaction and Advanced Energy Materials Laboratory, Chemical Engineering Department, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran.
| | - Shirish H Sonawane
- Department of Chemical Engineering, National Institute of Technology Warangal, Warangal, 506004, Telangana, India
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, G. Narutowicza 11/12 80-233, Gdańsk, Poland
| | | | - Michael Badawi
- Université de Lorraine, Laboratoire de Physique et Chimie Théoriques LPCT UMR CNRS, 7019, Nancy, France.
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12
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Gu X, Yang Y, Mao F, Lee WL, Armas F, You F, Needham DM, Ng C, Chen H, Chandra F, Gin KY. A comparative study of flow cytometry-sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant. IMETA 2022; 1:e39. [PMID: 38868719 PMCID: PMC10989988 DOI: 10.1002/imt2.39] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/30/2022] [Accepted: 06/19/2022] [Indexed: 06/14/2024]
Abstract
Traditional or "bulk" viral enrichment and amplification methods used in viral metagenomics introduce unavoidable bias in viral diversity. This bias is due to shortcomings in existing viral enrichment methods and overshadowing by the more abundant viral populations. To reduce the complexity and improve the resolution of viral diversity, we developed a strategy coupling fluorescence-activated cell sorting (FACS) with random amplification and compared this to bulk metagenomics. This strategy was validated on both influent and effluent samples from a municipal wastewater treatment plant using the Modified Ludzack-Ettinger (MLE) process as the treatment method. We found that DNA and RNA communities generated using bulk samples were mostly different from those derived following FACS for both treatments before and after MLE. Before MLE treatment, FACS identified five viral families and 512 viral annotated contigs. Up to 43% of mapped reads were not detected in bulk samples. Nucleo-cytoplasmic large DNA viral families were enriched to a greater extent in the FACS-coupled subpopulations compared with bulk samples. FACS-coupled viromes captured a single-contig viral genome associated with Anabaena phage, which was not observed in bulk samples or in FACS-sorted samples after MLE. These short metagenomic reads, which were assembled into a high-quality draft genome of 46 kbp, were found to be highly dominant in one of the pre-MLE FACS annotated virome fractions (57.4%). Using bulk metagenomics, we identified that between Primary Settling Tank and Secondary Settling Tank viromes, Virgaviridae, Astroviridae, Parvoviridae, Picobirnaviridae, Nodaviridae, and Iridoviridae were susceptible to MLE treatment. In all, bulk and FACS-coupled metagenomics are complementary approaches that enable a more thorough understanding of the community structure of DNA and RNA viruses in complex environmental samples, of which the latter is critical for increasing the sensitivity of detection of viral signatures that would otherwise be lost through bulk viral metagenomics.
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Affiliation(s)
- Xiaoqiong Gu
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Yi Yang
- NUS Environmental Research InstituteNational University of SingaporeSingaporeSingapore
| | - Feijian Mao
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Fang You
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - David M. Needham
- Monterey Bay Aquarium Research InstituteMoss LandingCaliforniaUSA
- GEOMAR Helmholtz Centre for Ocean ResearchOcean EcoSystems Biology UnitKielGermany
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Charmaine Ng
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Hongjie Chen
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Franciscus Chandra
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
| | - Karina Yew‐Hoong Gin
- Department of Civil and Environmental EngineeringNational University of SingaporeSingaporeSingapore
- NUS Environmental Research InstituteNational University of SingaporeSingaporeSingapore
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13
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Multifaceted Assessment of Wastewater-Based Epidemiology for SARS-CoV-2 in Selected Urban Communities in Davao City, Philippines: A Pilot Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19148789. [PMID: 35886640 PMCID: PMC9324557 DOI: 10.3390/ijerph19148789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023]
Abstract
Over 60 countries have integrated wastewater-based epidemiology (WBE) in their COVID-19 surveillance programs, focusing on wastewater treatment plants (WWTP). In this paper, we piloted the assessment of SARS-CoV-2 WBE as a complementary public health surveillance method in susceptible communities in a highly urbanized city without WWTP in the Philippines by exploring the extraction and detection methods, evaluating the contribution of physico-chemical–anthropogenic factors, and attempting whole-genome sequencing (WGS). Weekly wastewater samples were collected from sewer pipes or creeks in six communities with moderate-to-high risk of COVID-19 transmission, as categorized by the City Government of Davao from November to December 2020. Physico-chemical properties of the wastewater and anthropogenic conditions of the sites were noted. Samples were concentrated using a PEG-NaCl precipitation method and analyzed by RT-PCR to detect the SARS-CoV-2 N, RdRP, and E genes. A subset of nine samples were subjected to WGS using the Minion sequencing platform. SARS-CoV-2 RNA was detected in twenty-two samples (91.7%) regardless of the presence of new cases. Cycle threshold values correlated with RNA concentration and attack rate. The lack of a sewershed map in the sampled areas highlights the need to integrate this in the WBE planning. A combined analysis of wastewater physico-chemical parameters such as flow rate, surface water temperature, salinity, dissolved oxygen, and total dissolved solids provided insights on the ideal sampling location, time, and method for WBE, and their impact on RNA recovery. The contribution of fecal matter in the wastewater may also be assessed through the coliform count and in the context of anthropogenic conditions in the area. Finally, our attempt on WGS detected single-nucleotide polymorphisms (SNPs) in wastewater which included clinically reported and newly identified mutations in the Philippines. This exploratory report provides a contextualized framework for applying WBE surveillance in low-sanitation areas.
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14
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Wang S, Wasswa J, Feldman AC, Kabenge I, Kiggundu N, Zeng T. Suspect screening to support source identification and risk assessment of organic micropollutants in the aquatic environment of a Sub-Saharan African urban center. WATER RESEARCH 2022; 220:118706. [PMID: 35691193 DOI: 10.1016/j.watres.2022.118706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/21/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Organic micropollutants (OMPs) are contaminants of global concern and have garnered increasing attention in Africa, particularly in urban and urbanizing areas of Sub-Saharan Africa (SSA). In this work, we coupled suspect screening enabled by liquid chromatography-high-resolution mass spectrometry (LC-HRMS) with multivariate analysis to characterize OMPs in wastewater, surface water, and groundwater samples collected from Kampala, the capital and largest city of Uganda. Suspect screening prioritized and confirmed 157 OMPs in Kampala samples for target quantification. Many OMPs detected in Kampala samples occurred within concentration ranges similar to those documented in previous studies reporting OMP occurrence in SSA, but some have never or rarely been quantified in environmental water samples from SSA. Hierarchical cluster analysis established the source-related co-occurrence profiles of OMPs. Partial least squares regression and multiple linear regression analyses further pinpointed the concentration of nitrate and the content of a fluorescent organic matter component with excitation/emission maxima around 280/330 nm as predictors for the sample-specific cumulative concentrations of OMPs, suggesting the likely contribution of diffuse runoff and wastewater discharges to OMP occurrence in the aquatic environment of Kampala. Parallel calculations of exposure-activity ratios and multi-substance potentially affected fractions provided insights into the potential for biological effects associated with OMPs and highlighted the importance of expanded analytical coverage for screening-level risk assessments. Overall, our study demonstrates a versatile database-driven screening and data analysis methodology for the multipronged characterization of OMP contamination in a representative SSA urban center.
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Affiliation(s)
- Shiru Wang
- Department of Civil and Environmental Engineering, 151 Link Hall, Syracuse University, Syracuse, NY 13244, United States
| | - Joseph Wasswa
- Department of Civil and Environmental Engineering, 151 Link Hall, Syracuse University, Syracuse, NY 13244, United States
| | - Anna C Feldman
- Department of Civil and Environmental Engineering, 151 Link Hall, Syracuse University, Syracuse, NY 13244, United States
| | - Isa Kabenge
- Department of Agricultural and Bio-Systems Engineering, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Nicholas Kiggundu
- Department of Agricultural and Bio-Systems Engineering, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Teng Zeng
- Department of Civil and Environmental Engineering, 151 Link Hall, Syracuse University, Syracuse, NY 13244, United States.
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15
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Dzinamarira T, Pierre G, Iradukunda PG, Tungwarara N, Mukwenha S, Mpabuka E, Mataruka K, Chitungo I, Musuka G, Murewanhema G. Epidemiological surveillance of enteric viral diseases using wastewater in Africa - A rapid review. J Infect Public Health 2022; 15:703-707. [PMID: 35661916 DOI: 10.1016/j.jiph.2022.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/27/2022] [Accepted: 05/19/2022] [Indexed: 12/24/2022] Open
Abstract
Viral enteric pathogens remain an important cause of diarrhoeal outbreaks among children in sub-Saharan Africa (SSA). Consequently, diarrhoeal illness remains a significant cause of morbidity and mortality in the under-fives in SSA. These outbreaks associated with viral pathogens tend to be seasonal and early warning systems for impending outbreaks could be very crucial for triggering preventive public health response and building public health resilience to deal with increased demand for medical services. Wastewater surveillance for pathogens is an important epidemiological component that could inform early warning systems. The objective of this rapid review was to evaluate the use of wastewater for epidemiology surveillance of enteric viral pathogens. Nine studies met the inclusion criteria. Eight viral pathogens were reviewed and analysed from 6 countries that performed wastewater analysis. Six studies explored the epidemiologic significance of viral pathogens in wastewater. The findings of this review revealed that monitoring of wastewater can provide an additional tool to determine the epidemiology of viral pathogens circulating in the community thereby providing early warning of potential outbreaks using wastewater-based epidemiology methods. Five of the included studies revealed the occurrence of viral pathogens in raw sewage and treated wastewater as an indication of inefficient elimination of viruses leading to potential release into water sources which presents a public health risk, increasing the risk of inducing gastroenteritis in the population. Six studies revealed the need for public health authorities to realise the potential benefit of environmental surveillance (ES) as an additional tool to determine the epidemiology of viral pathogens circulating in each community. Despite the significant public health challenge associated with enteric viral pathogens in sub-Saharan Africa, there remains remarkable underinvestment in potentially epidemiologically beneficial research, including wastewater-based epidemiology for these infections.
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Affiliation(s)
- Tafadzwa Dzinamarira
- School of Health Systems & Public Health, University of Pretoria, Pretoria 0002, South Africa; ICAP at Columbia University, Kigali, Rwanda.
| | - Gashema Pierre
- College of Medicine and Veterinary Medicine, University of Edinburgh, UK
| | | | - Nigel Tungwarara
- Department of Health Studies, University of South Africa, South Africa
| | | | | | - Kidson Mataruka
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Itai Chitungo
- College of Medicine and Health Sciences, Faculty of Medicine, University of Zimbabwe, Harare, Zimbabwe
| | | | - Grant Murewanhema
- College of Medicine and Health Sciences, Faculty of Medicine, University of Zimbabwe, Harare, Zimbabwe
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16
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Jiang SC, Bischel HN, Goel R, Rosso D, Sherchan S, Whiteson KL, Yan T, Solo-Gabriele HM. Integrating Virus Monitoring Strategies for Safe Non-potable Water Reuse. WATER 2022; 14:1187. [PMID: 37622131 PMCID: PMC10448804 DOI: 10.3390/w14081187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Wastewater reclamation and reuse have the potential to supplement water supplies, offering resiliency in times of drought and helping meet increased water demands associated with population growth. Non-potable water reuse represents the largest potential reuse market. Yet economic constraints for new water reuse infrastructure and safety concerns due to microbial water quality, and especially viral pathogen exposure, limit widespread implementation of water reuse. Cost-effective, real-time methods to measure or indicate viral quality of recycled water would do much to instill greater confidence in the practice. This manuscript discusses advancements in monitoring and modeling of viral health risks in the context of water reuse. First, we describe the current wastewater reclamation processes and treatment technologies with an emphasis on virus removal. Second, we review technologies for the measurement of viruses, both culture- and molecular-based, along with their advantages and disadvantages. We introduce promising viral surrogates and specific pathogenic viruses that can serve as indicators of viral risk for water reuse. We suggest metagenomic analyses for viral screening and flow cytometry for quantification of virus-like particles as new approaches to complement more traditional methods. Third, we describe modeling to assess health risks through quantitative microbial risk assessments (QMRAs), the most common strategy to couple data on virus concentrations with human exposure scenarios. We then explore the potential of artificial neural networks (ANNs) to incorporate suites of data from wastewater treatment processes, water quality parameters, and viral surrogates. We recommend ANNs as a means to utilize existing water quality data, alongside new complementary measures of viral quality, to achieve cost-effective strategies to assess risks associated with infectious human viruses in recycled water. Given the review, we conclude that technologies are ready for identifying and implementing viral surrogates for health risk reduction in the next decade. Incorporating modeling with monitoring data would likely result in more robust assessment of water reuse risk.
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Affiliation(s)
- Sunny C Jiang
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697, USA
- Water-Energy Nexus Center, 844G Engineering Tower, University of California, Irvine, CA 92697-2175
| | - Heather N Bischel
- Department of Civil & Environmental Engineering, University of California, Davis CA 95616
| | - Ramesh Goel
- Department of Civil & Environmental Engineering, University of Utah, Salt Lake City, Utah 84112
| | - Diego Rosso
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697, USA
- Water-Energy Nexus Center, 844G Engineering Tower, University of California, Irvine, CA 92697-2175
| | - Samendra Sherchan
- Department of Environmental Health sciences, Tulane university, New Orleans, LA 70112
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Tao Yan
- Department of Civil and Environmental Engineering, and Water Resources Research Center, University of Hawaii at Manoa, HI 96822, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, FL, 33146, USA
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Chen C, Guo L, Yang Y, Oguma K, Hou LA. Comparative effectiveness of membrane technologies and disinfection methods for virus elimination in water: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149678. [PMID: 34416607 PMCID: PMC8364419 DOI: 10.1016/j.scitotenv.2021.149678] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/20/2021] [Accepted: 08/11/2021] [Indexed: 05/22/2023]
Abstract
The pandemic of the 2019 novel coronavirus disease (COVID-19) has brought viruses into the public horizon. Since viruses can pose a threat to human health in a low concentration range, seeking efficient virus removal methods has been the research hotspots in the past few years. Herein, a total of 1060 research papers were collected from the Web of Science database to identify technological trends as well as the research status. Based on the analysis results, this review elaborates on the state-of-the-art of membrane filtration and disinfection technologies for the treatment of virus-containing wastewater and drinking water. The results evince that membrane and disinfection methods achieve a broad range of virus removal efficiency (0.5-7 log reduction values (LRVs) and 0.09-8 LRVs, respectively) that is attributable to the various interactions between membranes or disinfectants and viruses having different susceptibility in viral capsid protein and nucleic acid. Moreover, this review discusses the related challenges and potential of membrane and disinfection technologies for customized virus removal in order to prevent the dissemination of the waterborne diseases.
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Affiliation(s)
- Chao Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No.19, Xinjiekouwai Street, Haidian District, Beijing 100875, China.
| | - Lihui Guo
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No.19, Xinjiekouwai Street, Haidian District, Beijing 100875, China.
| | - Yu Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No.19, Xinjiekouwai Street, Haidian District, Beijing 100875, China.
| | - Kumiko Oguma
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Li-An Hou
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No.19, Xinjiekouwai Street, Haidian District, Beijing 100875, China; Xi'an High-Tech Institute, Xi'an 710025, China.
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18
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Okaali DA, Kroeze C, Medema G, Burek P, Murphy H, Tumwebaze IK, Rose JB, Verbyla ME, Sewagudde S, Hofstra N. Modelling rotavirus concentrations in rivers: Assessing Uganda's present and future microbial water quality. WATER RESEARCH 2021; 204:117615. [PMID: 34492362 DOI: 10.1016/j.watres.2021.117615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Faecal pathogens can be introduced into surface water through open defecation, illegal disposal and inadequate treatment of faecal sludge and wastewater. Despite sanitation improvements, poor countries are progressing slowly towards the United Nation's Sustainable Development Goal 6 by 2030. Sanitation-associated pathogenic contamination of surface waters impacted by future population growth, urbanization and climate change receive limited attention. Therefore, a model simulating human rotavirus river inputs and concentrations was developed combining population density, sanitation coverage, rotavirus incidence, wastewater treatment and environmental survival data, and applied to Uganda. Complementary surface runoff and river discharge data were used to produce spatially explicit rotavirus outputs for the year 2015 and for two scenarios in 2050. Urban open defecation contributed 87%, sewers 9% and illegal faecal sludge disposal 3% to the annual 15.6 log10 rotavirus river inputs in 2015. Monthly concentrations fell between -3.7 (Q5) and 2.6 (Q95) log10 particles per litre, with 1.0 and 2.0 median and mean log10 particles per litre, respectively. Spatially explicit outputs on 0.0833 × 0.0833° grids revealed hotspots as densely populated urban areas. Future population growth, urbanization and poor sanitation were stronger drivers of rotavirus concentrations in rivers than climate change. The model and scenario analysis can be applied to other locations.
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Affiliation(s)
- Daniel A Okaali
- Water Systems and Global Change Group, Wageningen University & Research, Wageningen, The Netherlands.
| | - Carolien Kroeze
- Water Systems and Global Change Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Gertjan Medema
- KWR Watercycle Research Institute, Nieuwegein, The Netherlands
| | - Peter Burek
- International Institute for Applied Systems Analysis, Laxenburg, Austria
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Innocent K Tumwebaze
- School of Architecture, Building & Civil Engineering, Loughborough University, Loughborough, United Kingdom
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Matthew E Verbyla
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, CA, USA
| | - Sowed Sewagudde
- Directorate of Water Resources Management, Ministry of Water and Environment, Kampala, Uganda
| | - Nynke Hofstra
- Water Systems and Global Change Group, Wageningen University & Research, Wageningen, The Netherlands
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19
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Antiviral amphiphilic membranes based on the organometallic compound for protein removal from wastewater with fouling-resistant. JOURNAL OF POLYMER RESEARCH 2021. [DOI: 10.1007/s10965-021-02505-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021; 194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
Abstract
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, 1306 Evansdale Drive, Morgantown, WV 26505, United States.
| | - Benjamin C Davis
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Erin Milligan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Matthew Forrest Blair
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ishi Keenum
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ayella Maile-Moskowitz
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Jin Pan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Mariah Gnegy
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Krista Liguori
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Aaron J Prussin
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Linsey C Marr
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States.
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21
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Zume JT, Mariwah S, Boateng ENK. Evaluating the impacts of on-site sanitation facilities and saltwater intrusion on shallow groundwater quality in peri-urban communities of Cape Coast, Ghana. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:264. [PMID: 33847837 DOI: 10.1007/s10661-021-09059-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Populations in peri-urban communities of Sub-Saharan Africa frequently depend on shallow aquifers and on-site sanitation facilities concurrently. Routinely, domestic wells end up too close to toilet facilities, risking groundwater contamination. For coastal communities, saltwater intrusion adds to the risk of groundwater contamination. This study assessed both risks in five peri-urban communities of Cape Coast, Ghana. Groundwater samples collected from 40 domestic wells were analyzed for physicochemical and microbial constituents. Multivariate statistics including hierarchical cluster analysis (HCA) and principal component analysis (PCA) were used to classify and link contaminants to potential sources. Results indicate high enteric bacteria contamination in 98% of the samples, as well as high enrichment in physicochemical constituents, tied largely to impacts of on-site sanitation facilities. We found that wells located within 25 m of septic tanks/toilet facilities contained higher contaminant loads than those without such facilities within 25 m of their locations. Similarly, for wells located close to point sources, the closer the water table is below the land surface (within 2 m), the higher the contaminant loads. Lastly, using molar ratios of Cl-/HCO3- and Na+/Cl- with R-mode HCA, the study isolated a few wells, located within 2 km of the coastline, that are experiencing effects of saltwater intrusion. Overall, this study provides useful information for aiding groundwater quality mitigation policy, and the baseline data for aiding future investigations in the study area. It also has broader policy implications for other peri-urban settings throughout Ghana and the entire Sub-Saharan Africa.
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Affiliation(s)
- Joseph T Zume
- Department of Geography and Earth Science, Shippensburg University of Pennsylvania, 1871 Old Main Dr, Shippensburg, PA, 17257, USA.
| | - Simon Mariwah
- Department of Geography and Regional Planning, University of Cape Coast, Cape Coast, Ghana
| | - Ebenezer N K Boateng
- Department of Geography and Regional Planning, University of Cape Coast, Cape Coast, Ghana
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22
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Cervantes-Avilés P, Moreno-Andrade I, Carrillo-Reyes J. Approaches applied to detect SARS-CoV-2 in wastewater and perspectives post-COVID-19. JOURNAL OF WATER PROCESS ENGINEERING 2021; 40:101947. [PMID: 35592728 PMCID: PMC7846222 DOI: 10.1016/j.jwpe.2021.101947] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/16/2020] [Accepted: 01/26/2021] [Indexed: 05/03/2023]
Abstract
Currently, SARS-CoV-2 has been detected in the influent of wastewater treatment plants (WWTP), pumping stations, manholes, sewer networks and sludge of WWTP and facilities of countries as France, Spain, Italy, Netherlands, United States, Australia, Ecuador, Brazil and Japan. Although this virus has been detected in the wastewater streams, there is no robust method for its detection and quantification in wastewater. This review compiled and analyzed the virus concentration approaches applied to detect the SARS-CoV-2, besides to provide insights about the methodology for viral concentration, limit of detection, occurrence, persistence, and perspectives post-COVID-19 related with the implications of the virus presence in wastewater. The SARS-COV-2 detection in wastewater has been related to virus concentration methods, which present different recovery rates of the virus. The most used viral concentration methods have been the polyethylene glycol (PEG) for precipitation of viral material and the ultrafiltration at molecular weight level. After viral concentration, the detection and quantification of SARS-COV-2 in wastewater are mainly via quantitative reverse transcription polymerase chain reaction (RT-qPCR), which is the clinical assay adapted for environmental purposes. Although in some experiments the positive control during RT-qPCR is running a surrogated virus (e.g., Mengovirus or Dengue virus), RT-qPCR or reverse transcription droplet digital PCR (RT-ddPCR) targeting the gene encoding nucleocapsid (N1, N2 and N3) of SARS-COV-2 are highly recommended to calculate the limit of detection in wastewater samples. Current results suggest that a rigorous methodology to elucidate the positive cases in a region from genomic copies in wastewater is needed.
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Affiliation(s)
- Pabel Cervantes-Avilés
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Vía Atlixcáyotl 5718, Reserva Territorial Atlixcáyotl, Puebla, Pue, CP 72453, Mexico
| | - Iván Moreno-Andrade
- Laboratory for Research on Advanced Processes for Water Treatment, Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Queretaro, CP 76230, Mexico
| | - Julián Carrillo-Reyes
- Laboratory for Research on Advanced Processes for Water Treatment, Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Queretaro, CP 76230, Mexico
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23
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Romanis CS, Pearson LA, Neilan BA. Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies. J Microbiol Methods 2020; 180:106123. [PMID: 33316292 DOI: 10.1016/j.mimet.2020.106123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022]
Abstract
Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled water due to their production of extracellular polymeric substances, which hinder microfiltration, and toxins, which pose a health risk to end-users. A variety of methods are employed by water utilities for the identification and monitoring of cyanobacteria and their toxins in WWTFs, including microscopy, flow cytometry, ELISA, chemoanalytical methods, and more recently, molecular methods. Here we review the literature on the occurrence and significance of cyanobacterial blooms in WWTFs and discuss the pros and cons of the various strategies for monitoring these potentially hazardous events. Particular focus is directed towards next-generation metagenomic sequencing technologies for the development of site-specific cyanobacterial bloom management strategies. Long-term multi-omic observations will enable the identification of indicator species and the development of site-specific bloom dynamics models for the mitigation and management of cyanobacterial blooms in WWTFs. While emerging metagenomic tools could potentially provide deep insight into the diversity and flux of problematic cyanobacterial species in these systems, they should be considered a complement to, rather than a replacement of, quantitative chemoanalytical approaches.
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Affiliation(s)
- Caitlin S Romanis
- School of Environmental and Life Sciences, University of Newcastle, Newcastle 2308, Australia
| | - Leanne A Pearson
- School of Environmental and Life Sciences, University of Newcastle, Newcastle 2308, Australia
| | - Brett A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Newcastle 2308, Australia.
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24
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Polo D, Quintela-Baluja M, Corbishley A, Jones DL, Singer AC, Graham DW, Romalde JL. Making waves: Wastewater-based epidemiology for COVID-19 - approaches and challenges for surveillance and prediction. WATER RESEARCH 2020; 186:116404. [PMID: 32942178 PMCID: PMC7480445 DOI: 10.1016/j.watres.2020.116404] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/13/2020] [Accepted: 09/06/2020] [Indexed: 05/17/2023]
Abstract
The presence of SARS-CoV-2 in the feces of infected patients and wastewater has drawn attention, not only to the possibility of fecal-oral transmission but also to the use of wastewater as an epidemiological tool. The COVID-19 pandemic has highlighted problems in evaluating the epidemiological scope of the disease using classical surveillance approaches, due to a lack of diagnostic capacity, and their application to only a small proportion of the population. As in previous pandemics, statistics, particularly the proportion of the population infected, are believed to be widely underestimated. Furthermore, analysis of only clinical samples cannot predict outbreaks in a timely manner or easily capture asymptomatic carriers. Threfore, community-scale surveillance, including wastewater-based epidemiology, can bridge the broader community and the clinic, becoming a valuable indirect epidemiological prediction tool for SARS-CoV-2 and other pandemic viruses. This article summarizes current knowledge and discusses the critical factors for implementing wastewater-based epidemiology of COVID-19.
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Affiliation(s)
- David Polo
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain.
| | - Marcos Quintela-Baluja
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom
| | - Davey L Jones
- Environment Centre Wales, Bangor University, Bangor, Gwynedd, LL57 2UW, United Kingdom; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Andrew C Singer
- UK Centre for Ecology & Hydrology. Wallingford, Oxfordshire, OX10 8BB, United Kingdom
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain.
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25
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McCall C, Wu H, Miyani B, Xagoraraki I. Identification of multiple potential viral diseases in a large urban center using wastewater surveillance. WATER RESEARCH 2020; 184:116160. [PMID: 32738707 PMCID: PMC7342010 DOI: 10.1016/j.watres.2020.116160] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/27/2020] [Accepted: 07/05/2020] [Indexed: 05/08/2023]
Abstract
Viruses are linked to a multitude of human illnesses and can disseminate widely in urbanized environments causing global adverse impacts on communities and healthcare infrastructures. Wastewater-based epidemiology was employed using metagenomics and quantitative polymerase chain reaction (qPCR) assays to identify enteric and non-enteric viruses collected from a large urban area for potential public health monitoring and outbreak analysis. Untreated wastewater samples were collected from November 2017 to February 2018 (n = 54) to evaluate the diversity of human viral pathogens in collected samples. Viruses were classified into virus types based on primary transmission routes and reviewed against viral associated diseases reported in the catchment area. Metagenomics detected the presence of viral pathogens that cause clinically significant diseases reported within the study area during the sampling year. Detected viruses belong to the Adenoviridae, Astroviridae, Caliciviridae, Coronaviridae, Flaviviridae, Hepeviridae, Herpesviridae, Matonaviridae, Papillomaviridae, Parvoviridae, Picornaviridae, Poxviridae, Retroviridae, and Togaviridae families. Furthermore, concentrations of adenovirus, norovirus GII, sapovirus, hepatitis A virus, human herpesvirus 6, and human herpesvirus 8 were measured in wastewater samples and compared to metagenomic findings to confirm detected viral genus. Hepatitis A virus obtained the greatest average viral load (1.86 × 107 genome copies/L) in wastewater samples compared to other viruses quantified using qPCR with a 100% detection rate in metagenomic samples. Average concentration of sapovirus (1.36 × 106 genome copies/L) was significantly greater than norovirus GII (2.94 × 104 genome copies/L) indicating a higher burden within the study area. Findings obtained from this study aid in evaluating the utility of wastewater-based epidemiology for identification and routine monitoring of various viruses in large communities. This methodology has the potential to improve public health responses to large scale outbreaks and viral pandemics.
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Affiliation(s)
- Camille McCall
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Huiyun Wu
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Brijen Miyani
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA.
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26
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Kuodi P, Patterson J, Silal S, Hussey GD, Kagina BM. Characterisation of the environmental presence of hepatitis A virus in low-income and middle-income countries: a systematic review and meta-analysis. BMJ Open 2020; 10:e036407. [PMID: 32988941 PMCID: PMC7523219 DOI: 10.1136/bmjopen-2019-036407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE To characterise the environmental presence of hepatitis A virus (HAV) in low- and middle-income countries (LMICs). DESIGN Systematic review and meta-analysis. DATA SOURCES EBSCOhost, PubMed, Scopus, ScienceDirect, Clinical Key and Web of Science were searched. Grey literature was sourced by searching the following electronic databases: Open Grey, National Health Research Database and Mednar. ELIGIBILITY CRITERIA FOR INCLUDING STUDIES Cross-sectional and ecological studies reporting HAV environmental presence and conducted in LMICs between January 2005 and May 2019, irrespective of language of publication. DATA EXTRACTION AND DATA SYNTHESIS Relevant data were extracted from articles meeting the inclusion criteria, and two reviewers independently assessed the studies for risk of bias. High heterogeneity of the extracted data led to the results being reported narratively. RESULTS A total of 2092 records were retrieved, of which 33 met the inclusion criteria. 21 studies were conducted in Tunisia, India and South Africa, and the rest were from Philippines, Pakistan, Morocco, Chad, Mozambique, Kenya and Uganda. In Tunisian raw sewage samples, the prevalence of HAV ranged from 12% to 68%, with an estimated average detection rate of 50% (95% CI 25 to 75), whereas HAV detection in treated sewage in Tunisia ranged from 23% to 65%, with an estimated average detection rate of 38% (95% CI 20 to 57). The prevalence of HAV detection in South African treated sewage and surface water samples ranged from 4% to 37% and from 16% to 76%, with an estimated average detection rates of 15% (95% CI 1 to 29) and 51% (95% CI 21 to 80), respectively. Over the review period, the estimated average detection rate of environmental HAV presence appeared to have declined by 10%. CONCLUSION The quality of included studies was fair, but sampling issues and paucity of data limited the strength of the review findings. PROSPERO REGISTRATION NUMBER CRD42019119592.
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Affiliation(s)
- Paul Kuodi
- Faculty of Health Sciences, Department of Public Health, Lira University, Lira, Uganda
- School of Public Health and Family Medicine, University of Cape Town, Rondebosch, South Africa
| | - Jenna Patterson
- School of Public Health and Family Medicine, University of Cape Town, Rondebosch, South Africa
- Vaccines for Africa Initiative, University of Cape Town Faculty of Health Sciences, Cape Town, South Africa
| | - Sheetal Silal
- Department of Statistical Sciences, University of Cape Town, Rondebosch, South Africa
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gregory D Hussey
- Vaccines for Africa Initiative, University of Cape Town Faculty of Health Sciences, Cape Town, South Africa
| | - Benjamin M Kagina
- School of Public Health and Family Medicine, University of Cape Town, Rondebosch, South Africa
- Vaccines for Africa Initiative, University of Cape Town Faculty of Health Sciences, Cape Town, South Africa
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27
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Muirhead A, Zhu K, Brown J, Basu M, Brinton MA, Costa F, Hayat MJ, Stauber C. Zika Virus RNA Persistence in Sewage. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2020; 7:659-664. [PMID: 37293193 PMCID: PMC10249660 DOI: 10.1021/acs.estlett.0c00535] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite substantial advances in knowledge and understanding about Zika virus (ZIKV), limitations in surveillance for this mainly asymptomatic infection constrain attempts to characterize the epidemiological distribution of the virus. Monitoring of fecal waste streams including sewage offers opportunities to track the spread of arboviruses such as ZIKV, known to be present in fecal waste and urine. To demonstrate the feasibility of ZIKV RNA detection in sewage, we examined viral RNA decay in sewage from a local wastewater treatment plant. We added ZIKV (MEX 1-44) to unpasteurized sewage and stored the samples at 4°C, 25°C or 35°C for one month. We extracted nucleic acids from the mixture using a QiaAmp Minelute Virus Spin Kit and measured ZIKV RNA using a TaqPath Zika Virus Kit. We found no appreciable decline in ZIKV RNA detection at 4°C during the month. We estimate that 90% decay of detectable ZIKV RNA occurred after 21 days at 25°C and after 8.5 days at 35°C. Our preliminary work suggests ZIKV RNA can remain detectable in sewage over a range of temperatures and that sewage provides a cost-effective, community diagnostic tool that deserves further investigation as a novel epidemiologic surveillance approach.
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Affiliation(s)
- Aaron Muirhead
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
| | - Kevin Zhu
- Civil and Environmental Engineering, School of Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joe Brown
- Civil and Environmental Engineering, School of Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mausaumi Basu
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, USA
| | - Margo A Brinton
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, USA
| | - Federico Costa
- Institute of Collective Health, Federal University of Bahia, Salvador, Bahia, BR
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia, BR
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Matthew J Hayat
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
| | - Christine Stauber
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
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28
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Salvador D, Neto C, Benoliel MJ, Caeiro MF. Assessment of the Presence of Hepatitis E virus in Surface Water and Drinking Water in Portugal. Microorganisms 2020; 8:E761. [PMID: 32438739 PMCID: PMC7285264 DOI: 10.3390/microorganisms8050761] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/13/2022] Open
Abstract
Hepatitis E virus (HEV) is a non-enveloped single-stranded positive-sense RNA virus, belonging to the Hepeviridae family, resistant to environmental conditions, and transmitted by the consumption of contaminated water. This virus is responsible for both sporadic and epidemic outbreaks, leading to thousands of infections per year in several countries, and is thus considered an emerging disease in Europe and Asia. This study refers to a survey in Portugal during 2019, targeting the detection and eventual quantification of enteric viruses in samples from surface and drinking water. Samples positive for HEV RNA were recurrently found by reverse transcription quantitative PCR (RT-qPCR), in both types of matrix. The infectivity of these samples was evaluated in cultured Vero E6 cells and RNA from putative viruses produced in cultures evidencing cytopathic effects and was subjected to RT-qPCR targeting HEV genomic RNA. Our results evidenced the existence of samples positive either for HEV RNA (77.8% in surface water and 66.7% in drinking water) or for infectious HEV (23.0% in surface water and 27.7% in drinking water). These results highlight the need for effective virological control of water for human consumption and activities.
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Affiliation(s)
- Daniel Salvador
- Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Avenida Prof. Egas Moniz, Edifício Egas Moniz, Piso 0, Ala C, 1649-028 Lisboa, Portugal;
- Direção de Laboratório e Controlo da Qualidade da Água (LAB) da Empresa Portuguesa das Águas Livres (EPAL), Avenida de Berlim, 15, 1800-031 Lisboa, Portugal; (C.N.); (M.J.B.)
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Centro de Estudos do Ambiente e do Mar (CESAM), Edifício C2—Piso 2, Campo Grande, 1749-016 Lisboa, Portugal
| | - Célia Neto
- Direção de Laboratório e Controlo da Qualidade da Água (LAB) da Empresa Portuguesa das Águas Livres (EPAL), Avenida de Berlim, 15, 1800-031 Lisboa, Portugal; (C.N.); (M.J.B.)
| | - Maria João Benoliel
- Direção de Laboratório e Controlo da Qualidade da Água (LAB) da Empresa Portuguesa das Águas Livres (EPAL), Avenida de Berlim, 15, 1800-031 Lisboa, Portugal; (C.N.); (M.J.B.)
| | - Maria Filomena Caeiro
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa, Centro de Estudos do Ambiente e do Mar (CESAM), Edifício C2—Piso 2, Campo Grande, 1749-016 Lisboa, Portugal
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29
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Brown J, Cumming O. Stool-Based Pathogen Detection Offers Advantages as an Outcome Measure for Water, Sanitation, and Hygiene Trials. Am J Trop Med Hyg 2020; 102:260-261. [PMID: 31701856 PMCID: PMC7008332 DOI: 10.4269/ajtmh.19-0639] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Most health impact trials of water, sanitation, and hygiene use caregiver-reported diarrhea in children as the primary outcome; this measure is known to be subject to considerable bias, especially when used in unblinded trials. Detection of enteric pathogens in stool or fecal waste via multiplex molecular methods may offer advantages over—and is complementary to—caregiver-reported diarrhea because these measures are objective, on the causal pathway from exposures of interest to disease outcomes, and increasingly feasible in high-burden countries.
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Affiliation(s)
- Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Oliver Cumming
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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30
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Environmental and Adaptive Changes Necessitate a Paradigm Shift for Indicators of Fecal Contamination. Microbiol Spectr 2020. [DOI: 10.1128/microbiolspec.erv-0001-2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
ABSTRACT
Changes in the occurrence, distribution, and seasonal variation of waterborne pathogens due to global climate change may increase the risk of human exposure to these microorganisms, thus heightening the need for more reliable surveillance systems. Routine monitoring of drinking water supplies and recreational waters is performed using fecal indicator microorganisms, such as
Escherichia coli
,
Enterococcus
spp., and coliphages. However, the presence and numbers of these indicators, especially
E. coli
and
Enterococcus
spp., do not correlate well with those of other pathogens, especially enteric viruses, which are a major cause of waterborne outbreaks associated with contaminated water and food, and recreational use of lakes, ponds, rivers, and estuarine waters. For that reason, there is a growing need for a surveillance system that can detect and quantify viral pathogens directly in water sources to reduce transmission of pathogens associated with fecal transmission. In this review, we present an updated overview of relevant waterborne enteric viruses that we believe should be more commonly screened to better evaluate water quality and to determine the safety of water use and reuse and of epidemiological data on viral outbreaks. We also discuss current methodologies that are available to detect and quantify these viruses in water resources. Finally, we highlight challenges associated with virus monitoring. The information presented in this review is intended to aid in the assessment of human health risks due to contact with water sources, especially since current environmental and adaptive changes may be creating the need for a paradigm shift for indicators of fecal contamination.
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31
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Ibrahim C, Hammami S, Pothier P, Khelifi N, Hassen A. The performance of biological and tertiary wastewater treatment procedures for rotaviruses A removal. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:5718-5729. [PMID: 31177419 PMCID: PMC7223008 DOI: 10.1007/s11356-019-05487-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 05/14/2019] [Indexed: 05/19/2023]
Abstract
Enteric viruses, generally found in sewage, are recognized as the main cause of waterborne and foodborne public health outbreaks. Among leading enteric viruses, the Rotavirus A (RVA) detection in wastewater appeared to be a novel approach to monitor the emergence of these viruses in some countries where the viral gastroenteritis surveillance is almost absent such as in Tunisia. The RVA detection and quantification in an industrial sewage purification plant of Charguia I (Tunis, Tunisia) were achieved to evaluate the performance of activated sludge procedures coupled to a macrofiltration monolamp ultraviolet irradiation type C (UV-C254) disinfection reactor. This UV-C254 system was preceded by a fiberglass cartridge filter system with an average porosity of 45 μm to clarify the water and thus increase its UV transmittance. A total of 140 composite sewage samples was collected from this line of treatment and analyzed for RVA detection. The detection and the viral load quantification of RVA were performed using real-time reverse transcription polymerase chain reaction (RT-PCR). The virological results showed in general that RVA were detected at high frequency of 98% (137/140). In fact, the RVA detection rates at the exit of the two studied wastewater treatment were about 100% at the exit of the activated sludge procedure. It means that all wastewater sampled at this last step of treatment was positive for RVA detection. On the other hand, 92.5% of the wastewater samples taken at the exit of the monolamp UV-C254 reactor were positive for the RVA. However, the RVA quantification results expressed as viral load showed a significant reduction in the means of RVA viral loads at the exit of the biological activated sludge procedure and the tertiary UV-C254 treatment, showing in general an improved treated wastewater virological quality. Therefore, the RVA load removal rates recorded at the two successive stages of treatment, the activated sludge and the UV-C254 treatment, were around 85% and 73%, respectively, as compared to the one with 100% registered for the raw wastewater. In addition, good physical-chemical and bacteriological qualities of the treated sewage were found at the exit of the two considered wastewater treatment procedures. The present investigation represents the first Tunisian environmental report showing the good effectiveness and performance of the biological and the tertiary treatments for RVA removal. Therefore, an improved and an optimized tertiary disinfection treatment was needed since it could be a good means for getting better viral water quality and for minimizing the transmission and dissemination of human infectious viral diseases.
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Affiliation(s)
- Chourouk Ibrahim
- Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Centre of Research and Water Technologies (CERTE), 8020 Techno Park of Borj Cédria, Borj Cédria, Tunisia
- Faculty of Mathematical, Physical and Natural Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Salah Hammami
- National School of Veterinary Medicine at Sidi-Thabet, IRESA, University of Manouba, 2020 Tunis, Tunisia
| | - Pierre Pothier
- National Reference Centre for Enteric Viruses, Laboratory of Virology, University Hospital of Dijon, 21070 Dijon, France
| | - Nesserine Khelifi
- Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Centre of Research and Water Technologies (CERTE), 8020 Techno Park of Borj Cédria, Borj Cédria, Tunisia
| | - Abdennaceur Hassen
- Laboratory of Treatment and Valorization of Water Rejects (LTVRH), Centre of Research and Water Technologies (CERTE), 8020 Techno Park of Borj Cédria, Borj Cédria, Tunisia
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O'Brien E, Xagoraraki I. A water-focused one-health approach for early detection and prevention of viral outbreaks. One Health 2019; 7:100094. [PMID: 31080867 PMCID: PMC6501061 DOI: 10.1016/j.onehlt.2019.100094] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
Despite consistent efforts to protect public health there is still a heavy burden of viral disease, both in the United States and abroad. In addition to conventional medical treatment, there is a need for a holistic approach for early detection and prevention of viral outbreaks at a population level. One-Health is a relatively new integrative approach to the solving of global health challenges. A key component to the One-Health approach is the notion that human health, animal health, and environmental health are all innately interrelated. One-Health interventions, initiated by veterinary doctors, have proven to be effective in controlling outbreaks, but thus far the applications focus on zoonotic viruses transmitted from animals to humans. Environmental engineers and environmental scientists hold a critical role in the further development of One-Health approaches that include water-related transport and transmission of human, animal, and zoonotic viruses. In addition to waterborne viruses, the proposed approach is applicable to a wide range of viruses that are found in human excrement since contaminated water-based surveillance systems may be used for early detection of viral disease. This paper proposes a greater One-Health based framework that involves water-related pathways. The first step in the proposed framework is the identification of critical exposure pathways of viruses in the water environment. Identification of critical pathways informs the second and third steps, which include water-based surveillance systems for early detection at a population level and implementation of intervention approaches to block the critical pathways of exposure.
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Affiliation(s)
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
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Abstract
The immense global burden of infectious disease outbreaks and the need to establish prediction and prevention systems have been recognized by the World Health Organization (WHO), the National Institutes of Health (NIH), the United States Agency of International Development (USAID), the Bill and Melinda Gates Foundation, and the international scientific community. Despite multiple efforts, this infectious burden is still increasing. For example, it has been reported that between 1.5 and 12 million people die each year from waterborne diseases and diarrheal diseases are listed within the top 15 leading causes of death worldwide. Rapid population growth, climate change, natural disasters, immigration, globalization, and the corresponding sanitation and waste management challenges are expected to intensify the problem in the years to come.
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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