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Barbé L, Schaeffer J, Besnard A, Jousse S, Wurtzer S, Moulin L, Le Guyader FS, Desdouits M. SARS-CoV-2 Whole-Genome Sequencing Using Oxford Nanopore Technology for Variant Monitoring in Wastewaters. Front Microbiol 2022; 13:889811. [PMID: 35756003 PMCID: PMC9218694 DOI: 10.3389/fmicb.2022.889811] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/29/2022] [Indexed: 01/21/2023] Open
Abstract
Since the beginning of the Coronavirus Disease-19 (COVID-19) pandemic, multiple Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) mutations have been reported and led to the emergence of variants of concern (VOC) with increased transmissibility, virulence or immune escape. In parallel, the observation of viral fecal shedding led to the quantification of SARS-CoV-2 genomes in wastewater, providing information about the dynamics of SARS-CoV-2 infections within a population including symptomatic and asymptomatic individuals. Here, we aimed to adapt a sequencing technique initially designed for clinical samples to apply it to the challenging and mixed wastewater matrix, and hence identify the circulation of VOC at the community level. Composite raw sewage sampled over 24 h in two wastewater-treatment plants (WWTPs) from a city in western France were collected weekly and SARS-CoV-2 quantified by RT-PCR. Samples collected between October 2020 and May 2021 were submitted to whole-genome sequencing (WGS) using the primers and protocol published by the ARTIC Network and a MinION Mk1C sequencer (Oxford Nanopore Technologies, Oxford, United Kingdom). The protocol was adapted to allow near-full genome coverage from sewage samples, starting from ∼5% to reach ∼90% at depth 30. This enabled us to detect multiple single-nucleotide variant (SNV) and assess the circulation of the SARS-CoV-2 VOC Alpha, Beta, Gamma, and Delta. Retrospective analysis of sewage samples shed light on the emergence of the Alpha VOC with detection of first co-occurring signature mutations in mid-November 2020 to reach predominance of this variant in early February 2021. In parallel, a mutation-specific qRT-PCR assay confirmed the spread of the Alpha VOC but detected it later than WGS. Altogether, these data show that SARS-CoV-2 sequencing in sewage can be used for early detection of an emerging VOC in a population and confirm its ability to track shifts in variant predominance.
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Affiliation(s)
- Laure Barbé
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Julien Schaeffer
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Alban Besnard
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Sarah Jousse
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | | | - Laurent Moulin
- R&D Laboratory, DRDQE, Eau de Paris, Ivry-sur-Seine, France
| | | | - Marion Desdouits
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
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Kumblathan T, Piroddi N, Hrudey SE, Li XF. Wastewater Based Surveillance of SARS-CoV-2: Challenges and Perspective from a Canadian Inter-laboratory Study. J Environ Sci (China) 2022; 116:229-232. [PMID: 35219421 PMCID: PMC8789553 DOI: 10.1016/j.jes.2022.01.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Nicholas Piroddi
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Steve E Hrudey
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada.
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53
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Alamin M, Tsuji S, Hata A, Hara-Yamamura H, Honda R. Selection of surrogate viruses for process control in detection of SARS-CoV-2 in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153737. [PMID: 35149069 PMCID: PMC8824713 DOI: 10.1016/j.scitotenv.2022.153737] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 05/24/2023]
Abstract
Since SARS-CoV-2 RNA in wastewater is often present at low concentration or under detection limit, ensuring the reliability of detection processes using appropriate process controls is essential. The objective of this study was to evaluate applicability and limitations of candidate surrogate viruses as process controls under combinations of different virus concentration and RNA extraction methods. Detection efficiency of SARS-CoV-2 spiked in wastewater was compared with those of candidate surrogate viruses of bacteriophage ϕ6, pepper mild mottle virus (PMMoV), F-specific coliphage (F-phage), and murine norovirus (MNV). After inactivated SARS-CoV-2 and ϕ6 were spiked in two different wastewaters, the viruses in solid and liquid fractions of wastewater were concentrated by centrifuge and polyethylene glycol (PEG) precipitation, respectively. Viral RNA was extracted by using QIAamp Viral RNA Mini Kit and 3 other commercially available extraction kits, then quantified by reverse transcription-quantitative PCR using CDCN1 assay. Regardless of extraction kits, SARS-CoV-2 was consistently detected with good efficiency from both liquid (11-200%) and solid fractions (7.1-93%). Among the candidate process controls, PMMoV was widely detected at good efficiencies from both liquid and solid fractions regardless of selection of RNA extraction kits. F-phage and MNV also showed good detection efficiencies in most combinations of wastewater fractions and RNA extraction kits. An enveloped virus ɸ6 was found often undetected or to have very low detection efficiency (0.1-4.2%) even when SARS-CoV-2 spiked in wastewater was detected with good efficiency. Consequently, PMMoV is widely applicable as process control for detection of SARS-CoV-2 either in liquid fractions concentrated by PEG precipitation, or in solid fractions concentrated by centrifuge.
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Affiliation(s)
- Md Alamin
- Graduate School of Natural Science and Technology, Kanazawa University, Japan
| | - Shohei Tsuji
- School of Environmental Design, Kanazawa University, Japan
| | - Akihiko Hata
- Faculty of Engineering, Toyama Prefectural University, Japan
| | | | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Japan.
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54
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Nourbakhsh S, Fazil A, Li M, Mangat CS, Peterson SW, Daigle J, Langner S, Shurgold J, D'Aoust P, Delatolla R, Mercier E, Pang X, Lee BE, Stuart R, Wijayasri S, Champredon D. A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities. Epidemics 2022; 39:100560. [PMID: 35462206 PMCID: PMC8993419 DOI: 10.1016/j.epidem.2022.100560] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/07/2022] [Accepted: 04/03/2022] [Indexed: 02/03/2023] Open
Abstract
The COVID-19 pandemic has stimulated wastewater-based surveillance, allowing public health to track the epidemic by monitoring the concentration of the genetic fingerprints of SARS-CoV-2 shed in wastewater by infected individuals. Wastewater-based surveillance for COVID-19 is still in its infancy. In particular, the quantitative link between clinical cases observed through traditional surveillance and the signals from viral concentrations in wastewater is still developing and hampers interpretation of the data and actionable public-health decisions. We present a modelling framework that includes both SARS-CoV-2 transmission at the population level and the fate of SARS-CoV-2 RNA particles in the sewage system after faecal shedding by infected persons in the population. Using our mechanistic representation of the combined clinical/wastewater system, we perform exploratory simulations to quantify the effect of surveillance effectiveness, public-health interventions and vaccination on the discordance between clinical and wastewater signals. We also apply our model to surveillance data from three Canadian cities to provide wastewater-informed estimates for the actual prevalence, the effective reproduction number and incidence forecasts. We find that wastewater-based surveillance, paired with this model, can complement clinical surveillance by supporting the estimation of key epidemiological metrics and hence better triangulate the state of an epidemic using this alternative data source.
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Affiliation(s)
- Shokoofeh Nourbakhsh
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Aamir Fazil
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Michael Li
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Chand S Mangat
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Shelley W Peterson
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jade Daigle
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Stacie Langner
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jayson Shurgold
- Antimicrobial Resistance Division, Infectious Diseases Prevention and Control Branch, Public Health Agency of Canada, Ottawa, ON, Canada
| | - Patrick D'Aoust
- University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
| | - Robert Delatolla
- University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
| | - Elizabeth Mercier
- University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
| | - Xiaoli Pang
- Public Health Laboratory, Alberta Precision Laboratory, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | | | - Shinthuja Wijayasri
- Toronto Public Health, Toronto, ON, Canada; Canadian Field Epidemiology Program, Emergency Management, Public Health Agency of Canada, Canada
| | - David Champredon
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada.
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Zarza E, Diego-García E, García LV, Castro R, Mejía G, Herrera D, Cuevas R, Palomeque Á, Iša P, Guillén K. Monitoring SARS-CoV-2 in the Wastewater and Rivers of Tapachula, a Migratory Hub in Southern Mexico. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:199-211. [PMID: 35508751 PMCID: PMC9067545 DOI: 10.1007/s12560-022-09523-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/20/2022] [Indexed: 05/11/2023]
Abstract
The COVID-19 pandemic has been monitored by applying different strategies, including SARS-CoV-2 detection with clinical testing or through wastewater-based epidemiology (WBE). We used the latter approach to follow SARS-CoV-2 dispersion in Tapachula city, located in Mexico's tropical southern border region. Tapachula is a dynamic entry point for people seeking asylum in Mexico or traveling to the USA. Clinical testing facilities for SARS-CoV-2 monitoring are limited in the city. A total of eighty water samples were collected from urban and suburban rivers and sewage and a wastewater treatment plant over 4 months in Tapachula. We concentrated viral particles with a PEG-8000-based method, performed RNA extraction, and detected SARS-CoV-2 particles through RT-PCR. We considered the pepper mild mottle virus as a fecal water pollution biomarker and analytical control. SARS-CoV-2 viral loads (N1 and N2 markers) were quantified and correlated with official regional statistics of COVID-19 bed occupancy and confirmed cases (r > 91%). Our results concluded that WBE proved a valuable tool for tracing and tracking the COVID-19 pandemic in tropical countries with similar water temperatures (21-29 °C). Monitoring SARS-CoV-2 through urban and suburban river water sampling would be helpful in places lacking a wastewater treatment plant or water bodies with sewage discharges.
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Affiliation(s)
- Eugenia Zarza
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
- Investigadoras CONACyT- El Colegio de la Frontera Sur, Av. Insurgentes Sur 1582, Col. Crédito Constructor, Benito Juárez, 03940, Mexico City, Mexico
| | - Elia Diego-García
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
- Investigadoras CONACyT- El Colegio de la Frontera Sur, Av. Insurgentes Sur 1582, Col. Crédito Constructor, Benito Juárez, 03940, Mexico City, Mexico
| | - Luz Verónica García
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - Ricardo Castro
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - Gamaliel Mejía
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - David Herrera
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - Raúl Cuevas
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - Ángeles Palomeque
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Karina Guillén
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico.
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56
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Several major issues concerning the environmental transmission and risk prevention of SARS-CoV-2. SCIENCE CHINA EARTH SCIENCES 2022; 65:1047-1056. [PMID: 35578665 PMCID: PMC9097562 DOI: 10.1007/s11430-021-9918-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/11/2022] [Accepted: 03/03/2022] [Indexed: 11/03/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is the most serious infectious disease pandemic in the world in a century, and has had a serious impact on the health, safety, and social and economic development of all mankind. Since the earth entered the “Anthropocene”, human activities have become the most important driving force of the evolution of the earth system. At the same time, the epidemic frequency of major human infectious diseases worldwide has been increasing, with more than 70% of novel diseases having zoonotic origins. The review of several major epidemics in human history shows that there is a common rule, i.e., changes in the natural environment have an important and profound impact on the occurrence and development of epidemics. Therefore, the impact of the natural environment on the current COVID-19 pandemic and its mechanisms have become scientific issues that need to be resolved urgently. From the perspective of the natural environment, this study systematically investigated several major issues concerning the environmental transmission and risk prevention of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). From a macroscopic temporal and spatial scale, the research focus on understand the impact of the destruction of the natural environment and global changes on the outbreak of infectious diseases; the threat of zoonotic diseases to human health; the regularity for virus diffusion, migration and mutation in environmental media; the mechanisms of virus transmission from animals and environmental media to humans; and environmental safety, secondary risk prevention and control of major epidemics. Suggestions were made for future key research directions and issues that need attention, with a view to providing a reference for the prevention and control of the global coronavirus disease 2019, and to improving the ability of response to major public health emergencies.
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57
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Alhama J, Maestre JP, Martín MÁ, Michán C. Monitoring COVID-19 through SARS-CoV-2 quantification in wastewater: progress, challenges and prospects. Microb Biotechnol 2022; 15:1719-1728. [PMID: 34905659 PMCID: PMC9151337 DOI: 10.1111/1751-7915.13989] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/13/2022] Open
Abstract
Wastewater-Based Epidemiology (WBE) is widely used to monitor the progression of the current SARS-CoV-2 pandemic at local levels. In this review, we address the different approaches to the steps needed for this surveillance: sampling wastewaters (WWs), concentrating the virus from the samples and quantifying them by qPCR, focusing on the main limitations of the methodologies used. Factors that can influence SARS-CoV-2 monitoring in WWs include: (i) physical parameters as temperature that can hamper the detection in warm seasons and tropical regions, (ii) sampling methodologies and timetables, being composite samples and Moore swabs the less variable and more sensitive approaches, (iii) virus concentration methodologies that need to be feasible and practicable in simpler laboratories and (iv) detection methodologies that should tend to use faster and cost-effective procedures. The efficiency of WW treatments and the use of WWs for SARS-CoV-2 variants detection are also addressed. Furthermore, we discuss the need for the development of common standardized protocols, although these must be versatile enough to comprise variations among target communities. WBE screening of risk populations will allow for the prediction of future outbreaks, thus alerting authorities to implement early action measurements.
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Affiliation(s)
- José Alhama
- Department of Biochemistry and Molecular BiologyUniversidad de CórdobaCampus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo OchoaCórdoba14071Spain
| | - Juan P. Maestre
- Department of Civil, Architectural, and Environmental EngineeringThe University of Texas at Austin301 E. Dean Keeton St., Stop C1786AustinTX78712USA
| | - M. Ángeles Martín
- Department of Inorganic Chemistry and Chemical EngineeringArea of Chemical EngineeringUniversidad de CórdobaInstitute of Fine Chemistry and Nanochemistry (IUNAN)Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Marie CurieCórdoba14071Spain
| | - Carmen Michán
- Department of Biochemistry and Molecular BiologyUniversidad de CórdobaCampus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo OchoaCórdoba14071Spain
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58
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Peinado B, Martínez-García L, Martínez F, Nozal L, Sánchez MB. Improved methods for the detection and quantification of SARS-CoV-2 RNA in wastewater. Sci Rep 2022; 12:7201. [PMID: 35504966 PMCID: PMC9063616 DOI: 10.1038/s41598-022-11187-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/12/2022] [Indexed: 12/15/2022] Open
Abstract
Since the start of the COVID-19 pandemic, different methods have been used to detect the presence of genetic material of SARS-CoV-2 in wastewater. The use of wastewater for SARS-CoV-2 RNA detection and quantification showed different problems, associated to the complexity of the matrix and the lack of standard methods used to analyze the presence of an enveloped virus, such as coronavirus. Different strategies for the concentration process were selected to carry out the detection and quantification of SARS-CoV-2 RNA in wastewater: (a) aluminum hydroxide adsorption-precipitation, (b) pre-treatment with glycine buffer and precipitation with polyethylene-glycol (PEG) and (c) ultrafiltration (Centricon). Our results showed that the reduction of organic matter, using the pre-treatment with glycine buffer before the concentration with Centricon or aluminum hydroxide adsorption-precipitation, improved the recovery percentage of the control virus, Mengovirus (MgV) (8.37% ± 5.88 n = 43; 6.97% ± 6.51 n = 20, respectively), and the detection of SARS-CoV-2 in comparison with the same methodology without a pre-treatment. For the concentration with Centricon, the use of 100 mL of wastewater, instead of 200 mL, increased the MgV recovery, and allowed a positive detection of SARS-CoV-2 with N1 and N2 targets. The quantity of SARS-CoV-2 RNA detected in wastewater did not show a direct correlation with the number of confirmed cases, but the study of its upwards or downwards trend over time enabled the detection of an increase of epidemiological data produced in September 2020, January 2021 and April 2021.
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Affiliation(s)
- Beatriz Peinado
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Spain
| | - Lorena Martínez-García
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Spain
| | - Francisco Martínez
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Spain
| | - Leonor Nozal
- Center of Applied Chemistry and Biotechnology (CQAB), University of Alcala and General Foundation of Alcala University (FGUA), A-II km 33.600, 28805, Alcalá de Henares, Madrid, Spain
| | - Maria Blanca Sánchez
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805, Alcalá de Henares, Spain.
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Agrawal S, Orschler L, Schubert S, Zachmann K, Heijnen L, Tavazzi S, Gawlik BM, de Graaf M, Medema G, Lackner S. Prevalence and circulation patterns of SARS-CoV-2 variants in European sewage mirror clinical data of 54 European cities. WATER RESEARCH 2022; 214:118162. [PMID: 35193077 PMCID: PMC8817224 DOI: 10.1016/j.watres.2022.118162] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 05/04/2023]
Abstract
For community-level monitoring, the European Commission under the EU Sewage Sentinel System recommends wastewater-based SARS-CoV-2 surveillance. Tracking SARS-CoV-2 variants in a community is pivotal for appropriate public health response. Genome sequencing of SARS-CoV-2 in wastewater samples for tracking variants is challenging, often resulting in low coverage genome sequences, thereby impeding the detection of the SARS-CoV-2 mutations. Therefore, we aimed at high-coverage SARS-CoV-2 genome sequences from sewage samples which we successfully accomplished. This first pan-European surveillance compared the mutation profiles associated with the variants of concerns: B.1.1.7, P.1, B.1.351 and B.1.617.2 across 20 European countries, including 54 municipalities. The results highlight that SARS-CoV-2 variants detected in the wastewater samples mirror the variants profiles reported in clinical data. This study demonstrated that >98% coverage of SARS-CoV-2 genomic sequences is possible and can be used to track SARS-CoV-2 mutations in wastewater to support identifying variants circulating in a city at the community level.
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Affiliation(s)
- Shelesh Agrawal
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Water and Environmental Biotechnology, Technical University of Darmstadt, Darmstadt, Germany.
| | - Laura Orschler
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Water and Environmental Biotechnology, Technical University of Darmstadt, Darmstadt, Germany
| | - Selina Schubert
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Water and Environmental Biotechnology, Technical University of Darmstadt, Darmstadt, Germany
| | - Kira Zachmann
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Water and Environmental Biotechnology, Technical University of Darmstadt, Darmstadt, Germany
| | - Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherland
| | - Simona Tavazzi
- European Commission, Joint Research Centre, Ispra, VA, Italy
| | | | - Miranda de Graaf
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherland
| | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherland
| | - Susanne Lackner
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Chair of Water and Environmental Biotechnology, Technical University of Darmstadt, Darmstadt, Germany
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60
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Song W, Zhang T, Lin H, Yang Y, Zhao G, Huang X. Conventional and Microfluidic Methods for the Detection of Nucleic Acid of SARS-CoV-2. MICROMACHINES 2022; 13:636. [PMID: 35457940 PMCID: PMC9031662 DOI: 10.3390/mi13040636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 12/23/2022]
Abstract
Nucleic acid testing (NAT) played a crucial role in containing the spread of SARS-CoV-2 during the epidemic. The gold standard technique, the quantitative real-time polymerase chain reaction (qRT-PCR) technique, is currently used by the government and medical boards to detect SARS-CoV-2. Due to the limitations of this technology, it is not capable of meeting the needs of large-scale rapid detection. To solve this problem, many new techniques for detecting nucleic acids of SARS-CoV-2 have been reported. Therefore, a review that systematically and comprehensively introduces and compares various detection technologies is needed. In this paper, we not only review the traditional NAT but also provide an overview of microfluidic-based NAT technologies and summarize and discuss the characteristics and development prospects of these techniques.
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Affiliation(s)
| | | | | | | | | | - Xiaowen Huang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China; (W.S.); (T.Z.); (H.L.); (Y.Y.); (G.Z.)
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61
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Li L, Mazurowski L, Dewan A, Carine M, Haak L, Guarin TC, Dastjerdi NG, Gerrity D, Mentzer C, Pagilla KR. Longitudinal monitoring of SARS-CoV-2 in wastewater using viral genetic markers and the estimation of unconfirmed COVID-19 cases. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152958. [PMID: 35016937 PMCID: PMC8743272 DOI: 10.1016/j.scitotenv.2022.152958] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 05/18/2023]
Abstract
In this study, wastewater-based surveillance was carried out to establish the correlation between SARS-CoV-2 viral RNA concentrations in wastewater and the incidence of corona virus disease 2019 (COVID-19) from clinical testing. The influent wastewater of three major water reclamation facilities (WRFs) in Northern Nevada, serving a population of 390,750, was monitored for SARS-CoV-2 viral RNA gene markers, N1 and N2, from June 2020 through September 2021. A total of 614 samples were collected and analyzed. The SARS-CoV-2 concentrations in wastewater were observed to peak twice during the study period. A moderate correlation trend between coronavirus disease 2019 (COVID-19) incidence data from clinical testing and SARS-CoV-2 viral RNA concentrations in wastewater was observed (Spearman r = 0.533). This correlation improved when using weekly average SARS-CoV-2 marker concentrations of wastewater and clinical case data (Spearman r = 0.790), presumably by mitigating the inherent variability of the environmental dataset and the effects of clinical testing artifacts (e.g., reporting lags). The research also demonstrated the value of wastewater-based surveillance as an early warning signal for early detection of trends in COVID-19 incidence. This was accomplished by identifying that the reported clinical cases had a stronger correlation to SARS-CoV-2 wastewater monitoring data when they were estimated to lag 7-days behind the wastewater data. The results aided local decision makers in developing strategies to manage COVID-19 in the region and provide a framework for how wastewater-based surveillance can be applied across localities to enhance the public health monitoring of the ongoing pandemic.
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Affiliation(s)
- Lin Li
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV 89557, USA
| | - Lauren Mazurowski
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV 89557, USA
| | - Aimee Dewan
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV 89557, USA
| | - Madeline Carine
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV 89557, USA
| | - Laura Haak
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV 89557, USA
| | - Tatiana C Guarin
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV 89557, USA
| | | | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Casey Mentzer
- Truckee Meadows Water Reclamation Facility, Sparks, NV 89502, USA
| | - Krishna R Pagilla
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV 89557, USA.
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Ahmed W, Bivins A, Metcalfe S, Smith WJM, Verbyla ME, Symonds EM, Simpson SL. Evaluation of process limit of detection and quantification variation of SARS-CoV-2 RT-qPCR and RT-dPCR assays for wastewater surveillance. WATER RESEARCH 2022; 213:118132. [PMID: 35152136 PMCID: PMC8812148 DOI: 10.1016/j.watres.2022.118132] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/21/2022] [Accepted: 01/29/2022] [Indexed: 05/21/2023]
Abstract
Effective wastewater surveillance of SARS-CoV-2 RNA requires the rigorous characterization of the limit of detection resulting from the entire sampling process - the process limit of detection (PLOD). Yet to date, no studies have gone beyond quantifying the assay limit of detection (ALOD) for RT-qPCR or RT-dPCR assays. While the ALOD is the lowest number of gene copies (GC) associated with a 95% probability of detection in a single PCR reaction, the PLOD represents the sensitivity of the method after considering the efficiency of all processing steps (e.g., sample handling, concentration, nucleic acid extraction, and PCR assays) to determine the number of GC in the wastewater sample matrix with a specific probability of detection. The primary objective of this study was to estimate the PLOD resulting from the combination of primary concentration and extraction with six SARS-CoV-2 assays: five RT-qPCR assays (US CDC N1 and N2, China CDC N and ORF1ab (CCDC N and CCDC ORF1ab), and E_Sarbeco RT-qPCR, and one RT-dPCR assay (US CDC N1 RT-dPCR) using two models (exponential survival and cumulative Gaussian). An adsorption extraction (AE) concentration method (i.e., virus adsorption on membrane and the RNA extraction from the membrane) was used to concentrate gamma-irradiated SARS-CoV-2 seeded into 36 wastewater samples. Overall, the US CDC N1 RT-dPCR and RT-qPCR assays had the lowest ALODs (< 10 GC/reaction) and PLODs (<3,954 GC/50 mL; 95% probability of detection) regardless of the seeding level and model used. Nevertheless, consistent amplification and detection rates decreased when seeding levels were < 2.32 × 103 GC/50 mL even for US CDC N1 RT-qPCR and RT-dPCR assays. Consequently, when SARS-CoV-2 RNA concentrations are expected to be low, it may be necessary to improve the positive detection rates of wastewater surveillance by analyzing additional field and RT-PCR replicates. To the best of our knowledge, this is the first study to assess the SARS-CoV-2 PLOD for wastewater and provides important insights on the analytical limitations for trace detection of SARS-CoV-2 RNA in wastewater.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN, 46556, USA
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Matthew E Verbyla
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, CA, USA
| | - Erin M Symonds
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
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63
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Chau KK, Barker L, Budgell EP, Vihta KD, Sims N, Kasprzyk-Hordern B, Harriss E, Crook DW, Read DS, Walker AS, Stoesser N. Systematic review of wastewater surveillance of antimicrobial resistance in human populations. ENVIRONMENT INTERNATIONAL 2022; 162:107171. [PMID: 35290866 PMCID: PMC8960996 DOI: 10.1016/j.envint.2022.107171] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 01/23/2022] [Accepted: 02/28/2022] [Indexed: 05/05/2023]
Abstract
OBJECTIVES We systematically reviewed studies using wastewater for AMR surveillance in human populations, to determine: (i) evidence of concordance between wastewater-human AMR prevalence estimates, and (ii) methodological approaches which optimised identifying such an association, and which could be recommended as standard. We used Lin's concordance correlation coefficient (CCC) to quantify concordance between AMR prevalence estimates in wastewater and human compartments (where CCC = 1 reflects perfect concordance), and logistic regression to identify study features (e.g. sampling methods) associated with high agreement studies (defined as >70% of within-study wastewater-human AMR prevalence comparisons within ±10%). RESULTS Of 8,867 records and 441 full-text methods reviewed, 33 studies were included. AMR prevalence data was extractable from 24 studies conducting phenotypic-only (n = 7), genotypic-only (n = 1) or combined (n = 16) AMR detection. Overall concordance of wastewater-human AMR prevalence estimates was reasonably high for both phenotypic (CCC = 0.85 [95% CI 0.8-0.89]) and genotypic approaches (CCC = 0.88 (95% CI 0.84-0.9)) despite diverse study designs, bacterial species investigated and phenotypic/genotypic targets. No significant relationships between methodological approaches and high agreement studies were identified using logistic regression; however, this was limited by inconsistent reporting of study features, significant heterogeneity in approaches and limited sample size. Based on a secondary, descriptive synthesis, studies conducting composite sampling of wastewater influent, longitudinal sampling >12 months, and time-/location-matched sampling of wastewater and human compartments generally had higher agreement. CONCLUSION Wastewater-based surveillance of AMR appears promising, with high overall concordance between wastewater and human AMR prevalence estimates in studies irrespective of heterogenous approaches. However, our review suggests future work would benefit from: time-/location-matched sampling of wastewater and human populations, composite sampling of influent, and sampling >12 months for longitudinal studies. Further research and clear and consistent reporting of study methods is required to identify optimal practice.
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Affiliation(s)
- K K Chau
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - L Barker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - E P Budgell
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - K D Vihta
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - N Sims
- Department of Chemistry, Faculty of Science, University of Bath, Bath BA2 7AY, United Kingdom.
| | - B Kasprzyk-Hordern
- Department of Chemistry, Faculty of Science, University of Bath, Bath BA2 7AY, United Kingdom.
| | - E Harriss
- Bodleian Healthcare Libraries, University of Oxford, Oxford OX3 9DU, United Kingdom.
| | - D W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - D S Read
- UK Centre for Ecology & Hydrology, Wallingford OX10 8BB, United Kingdom.
| | - A S Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford OX4 2PG, United Kingdom.
| | - N Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
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64
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Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden. ENVIRONMENTS 2022. [DOI: 10.3390/environments9030039] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The detection of SARS-CoV-2 RNA fragments in feces has paved the way for wastewater-based epidemiology to contribute to COVID-19 mitigation measures, with its use in a public health context still under development. As a way to facilitate data comparison, this paper explores the impact of using alternative normalization approaches (wastewater treatment plant (WWTP) flow, population size estimates (derived using total nitrogen (TN), total phosphorus (TP) and census data) and pepper mild mottle virus (PMMoV)) on the relationship between viral wastewater data and clinical case numbers. Influent wastewater samples were collected at two WWTPs in Luleå, northern Sweden, between January and March 2021. TN and TP were determined upon sample collection, with RNA analysis undertaken on samples after one freeze–thaw cycle. The strength of the correlation between normalization approaches and clinical cases differed between WWTPs (r ≤ 0.73 or r ≥ 0.78 at the larger WWTP and r ≤ 0.23 or r ≥ 0.43 at the smaller WWTP), indicating that the use of wastewater as an epidemiological tool is context-dependent. Depending on the normalization approach utilized, time-shifted analyses imply that wastewater data on SARS-CoV-2 RNA pre-dated a rise in clinical cases by 0–2 and 5–8 days, for the lager and smaller WWTPs, respectively. SARS-CoV-2 viral loads normalized to the population or PMMoV better reflect the number of clinical cases when comparing wastewater data between sewer catchments.
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65
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Qiu Y, Yu J, Pabbaraju K, Lee BE, Gao T, Ashbolt NJ, Hrudey SE, Diggle M, Tipples G, Maal-Bared R, Pang X. Validating and optimizing the method for molecular detection and quantification of SARS-CoV-2 in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:151434. [PMID: 34742974 PMCID: PMC8568330 DOI: 10.1016/j.scitotenv.2021.151434] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 05/18/2023]
Abstract
Wastewater surveillance of SARS-CoV-2 has become a promising tool to estimate population-level changes in community infections and the prevalence of COVID-19 disease. Although many studies have reported the detection and quantification of SARS-CoV-2 in wastewater, remarkable variation remains in the methodology. In this study, we validated a molecular testing method by concentrating viruses from wastewater using ultrafiltration and detecting SARS-CoV-2 using one-step RT-qPCR assay. The following parameters were optimized including sample storage condition, wastewater pH, RNA extraction and RT-qPCR assay by quantification of SARS-CoV-2 or spiked human coronavirus strain 229E (hCoV-229E). Wastewater samples stored at 4 °C after collection showed significantly enhanced detection of SARS-CoV-2 with approximately 2-3 PCR-cycle threshold (Ct) values less when compared to samples stored at -20 °C. Pre-adjustment of the wastewater pH to 9.6 to aid virus desorption followed by pH readjustment to neutral after solid removal significantly increased the recovery of spiked hCoV-229E. Of the five commercially available RNA isolation kits evaluated, the MagMAX-96 viral RNA isolation kit showed the best recovery of hCoV-229E (50.1 ± 20.1%). Compared with two-step RT-qPCR, one-step RT-qPCR improved sensitivity for SARS-CoV-2 detection. Salmon DNA was included for monitoring PCR inhibition and pepper mild mottle virus (PMMoV), a fecal indicator indigenous to wastewater, was used to normalize SARS-CoV-2 levels in wastewater. Our method for molecular detection of SARS-CoV-2 in wastewater provides a useful tool for public health surveillance of COVID-19.
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Affiliation(s)
- Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Jiaao Yu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kanti Pabbaraju
- Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Calgary, Alberta, Canada
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Tiejun Gao
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Nicholas J Ashbolt
- Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Steve E Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Mathew Diggle
- Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, Alberta, Canada
| | - Graham Tipples
- Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, Alberta, Canada
| | | | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, Alberta, Canada.
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66
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Evaluation of Pre-Analytical and Analytical Methods for Detecting SARS-CoV-2 in Municipal Wastewater Samples in Northern Italy. WATER 2022. [DOI: 10.3390/w14050833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
(1) Background: The surveillance of SARS-CoV-2 RNA in urban wastewaters allows one to monitor the presence of the virus in a population, including asymptomatic and symptomatic individuals, capturing the real circulation of this pathogen. The aim of this study was to evaluate the performance of different pre-analytical and analytical methods for identifying the presence of SARS-CoV-2 in untreated municipal wastewaters samples by conducting an inter-laboratory proficiency test. (2) Methods: three methods of concentration, namely, (A) Dextran and PEG-6000 two-phase separation, (B) PEG-8000 precipitation without a chloroform purification step and (C) PEG-8000 precipitation with a chloroform purification step were combined with three different protocols of RNA extraction by using commercial kits and were tested by using two primers/probe sets in three different master mixes. (3) Results: PEG-8000 precipitation without chloroform treatment showed the best performance in the SARS-CoV-2 recovery; no major differences were observed among the protocol of RNA extraction and the one-step real-time RT-PCR master mix kits. The highest analytic sensitivity was observed by using primers/probe sets targeting the N1/N3 fragments of SARS-CoV-2. (4) Conclusions: PEG-8000 precipitation in combination with real-time RT-PCR targeting the N gene (two fragments) was the best performing workflow for the detection of SARS-CoV-2 RNA in municipal wastewaters.
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67
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Twigg C, Wenk J. Review and Meta‐Analysis: SARS‐CoV‐2 and Enveloped Virus Detection in Feces and Wastewater. CHEMBIOENG REVIEWS 2022. [PMCID: PMC9083821 DOI: 10.1002/cben.202100039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Detection and quantification of viruses supplies key information on their spread and allows risk assessment for public health. In wastewater, existing detection methods have been focusing on non‐enveloped enteric viruses due to enveloped virus transmission, such as coronaviruses, by the fecal‐oral route being less likely. Since the beginning of the SARS‐CoV‐2 pandemic, interest and importance of enveloped virus detection in wastewater has increased. Here, quantitative studies on SARS‐CoV‐2 occurrence in feces and raw wastewater and other enveloped viruses via quantitative real‐time reverse transcription polymerase chain reaction (RT‐qPCR) during the early stage of the pandemic until April 2021 are reviewed, including statistical evaluation of the positive detection rate and efficiency throughout the detection process involving concentration, extraction, and amplification stages. Optimized and aligned sampling protocols and concentration methods for enveloped viruses, along with SARS‐CoV‐2 surrogates, in wastewater environments may improve low and variable recovery rates providing increased detection efficiency and comparable data on viral load measured across different studies.
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Affiliation(s)
- Charlotte Twigg
- University of Bath Department of Chemical Engineering and Water Innovation and Research Centre (WIRC@Bath) Claverton Down BA2 7AY Bath Somerset United Kingdom
| | - Jannis Wenk
- University of Bath Department of Chemical Engineering and Water Innovation and Research Centre (WIRC@Bath) Claverton Down BA2 7AY Bath Somerset United Kingdom
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68
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Thongpradit S, Prasongtanakij S, Srisala S, Kumsang Y, Chanprasertyothin S, Boonkongchuen P, Pitidhammabhorn D, Manomaipiboon P, Somchaiyanon P, Chandanachulaka S, Hirunrueng T, Ongphiphadhanakul B. A Simple Method to Detect SARS-CoV-2 in Wastewater at Low Virus Concentration. JOURNAL OF ENVIRONMENTAL AND PUBLIC HEALTH 2022; 2022:4867626. [PMID: 35242195 PMCID: PMC8888108 DOI: 10.1155/2022/4867626] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/15/2022]
Abstract
Background Since its initial appearance in December 2019, coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally. Wastewater surveillance has been demonstrated as capable of identifying infection clusters early. The purpose of this study was to investigate a quick and simple method to detect SARS-CoV-2 in wastewater in Thailand during the early stages of the second outbreak wave when the prevalence of the disease and the virus concentration in wastewater were low. Methods Wastewater samples were collected from a hospital caring for patients with COVID-19 and from 35 markets, two of which were associated with recently reported COVID-19 cases. Then, samples were concentrated by membrane filtering prior to SARS-CoV-2 detection by RT-qPCR. Results SARS-CoV-2 RNA was detected in the wastewater samples from the hospital; the Ct values for the N, ORF1ab, and S genes progressively increased as the number of patients admitted to the treatment floor decreased. Notably, the ORF1ab and S genes were still detectable in wastewater even when only one patient with COVID-19 remained at the hospital. SARS-CoV-2 RNA was detected in the wastewater samples from fresh market where COVID-19 cases were reported. Conclusions Our findings suggest that wastewater surveillance for SARS-CoV-2 is sensitive and can detect the virus even in places with a high ambient temperature and relatively low prevalence of COVID-19.
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Affiliation(s)
- Supranee Thongpradit
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Salaya, Thailand
| | - Somsak Prasongtanakij
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Salaya, Thailand
| | - Supanart Srisala
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Salaya, Thailand
| | - Yothin Kumsang
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Salaya, Thailand
| | | | - Pairoj Boonkongchuen
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Salaya, Samut Prakan, Thailand
| | - Dhanesh Pitidhammabhorn
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Salaya, Samut Prakan, Thailand
| | | | | | | | | | - Boonsong Ongphiphadhanakul
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Salaya, Thailand
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Salaya, Thailand
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69
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Castiglioni S, Schiarea S, Pellegrinelli L, Primache V, Galli C, Bubba L, Mancinelli F, Marinelli M, Cereda D, Ammoni E, Pariani E, Zuccato E, Binda S. SARS-CoV-2 RNA in urban wastewater samples to monitor the COVID-19 pandemic in Lombardy, Italy (March-June 2020). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150816. [PMID: 34627901 PMCID: PMC8497959 DOI: 10.1016/j.scitotenv.2021.150816] [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: 08/05/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 04/15/2023]
Abstract
Wastewater-based viral surveillance was proposed as a promising approach to monitor the circulation of SARS-CoV-2 in the general population. The aim of this study was to develop an analytical method to detect SARS-CoV-2 RNA in urban wastewater, and apply it to follow the trends of epidemic in the framework of a surveillance network in the Lombardy region (Northern Italy). This area was the first hotspot of COVID-19 in Europe and was severely affected. Composite 24 h samples were collected weekly in eight cities from end-March to mid-June 2020 (first peak of the pandemic). The method developed and optimized, involved virus concentration using PEG centrifugation, and one-step real-time RT-PCR for analysis. SARS-CoV-2 RNA was identified in 65 (61%) out of 107 samples, and the viral concentrations (up to 2.1 E + 05 copies/L) were highest in March-April. By mid-June, wastewater samples tested negative in all the cities corresponding to the very low number of cases recorded in the same period. Viral loads were calculated considering the wastewater daily flow rate and the population served by each wastewater treatment plant, and were used for inter- city comparison. The highest viral loads were found in Brembate, Ranica and Lodi corresponding to the hotspots of the first peak of pandemic. The pattern of decrease of SARS-CoV-2 in wastewater was closely comparable to the decline of active COVID-19 cases in the population, reflecting the effect of lock-down. This study tested wastewater surveillance of SARS-CoV-2 to follow the pandemic trends in one of most affected areas worldwide, demonstrating that it can integrate ongoing virological surveillance of COVID-19, providing information from both symptomatic and asymptomatic individuals, and monitoring the effect of health interventions.
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Affiliation(s)
- Sara Castiglioni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy.
| | - Silvia Schiarea
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Valeria Primache
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Laura Bubba
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Federica Mancinelli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy
| | | | | | | | - Elena Pariani
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Ettore Zuccato
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Environmental Sciences, Via Mario Negri 2, 20156 Milan, Italy
| | - Sandro Binda
- Department of Biomedical Sciences of Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
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70
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Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 34818780 DOI: 10.20944/preprints202104.0481.v1] [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] [Indexed: 05/05/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:149877. [PMID: 34818780 PMCID: PMC8386095 DOI: 10.1016/j.scitotenv.2021.149877] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 05/18/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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Anand U, Li X, Sunita K, Lokhandwala S, Gautam P, Suresh S, Sarma H, Vellingiri B, Dey A, Bontempi E, Jiang G. SARS-CoV-2 and other pathogens in municipal wastewater, landfill leachate, and solid waste: A review about virus surveillance, infectivity, and inactivation. ENVIRONMENTAL RESEARCH 2022; 203:111839. [PMID: 34358502 PMCID: PMC8332740 DOI: 10.1016/j.envres.2021.111839] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/15/2021] [Accepted: 08/02/2021] [Indexed: 05/18/2023]
Abstract
This review discusses the techniques available for detecting and inactivating of pathogens in municipal wastewater, landfill leachate, and solid waste. In view of the current COVID-19 pandemic, SARS-CoV-2 is being given special attention, with a thorough examination of all possible transmission pathways linked to the selected waste matrices. Despite the lack of works focused on landfill leachate, a systematic review method, based on cluster analysis, allows to analyze the available papers devoted to sewage sludge and wastewater, allowing to focalize the work on technologies able to detect and treat pathogens. In this work, great attention is also devoted to infectivity and transmission mechanisms of SARS-CoV-2. Moreover, the literature analysis shows that sewage sludge and landfill leachate seem to have a remote chance to act as a virus transmission route (pollution-to-human transmission) due to improper collection and treatment of municipal wastewater and solid waste. However due to the incertitude about virus infectivity, these possibilities cannot be excluded and need further investigation. As a conclusion, this paper shows that additional research is required not only on the coronavirus-specific disinfection, but also the regular surveillance or monitoring of viral loads in sewage sludge, wastewater, and landfill leachate. The disinfection strategies need to be optimized in terms of dosage and potential adverse impacts like antimicrobial resistance, among many other factors. Finally, the presence of SARS-CoV-2 and other pathogenic microorganisms in sewage sludge, wastewater, and landfill leachate can hamper the possibility to ensure safe water and public health in economically marginalized countries and hinder the realization of the United Nations' sustainable development goals (SDGs).
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Xuan Li
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Kumari Sunita
- Department of Botany, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - Snehal Lokhandwala
- Department of Environmental Science & Technology, Shroff S.R. Rotary Institute of Chemical Technology, UPL University of Sustainable Technology, Ankleshwar, Gujarat, 393135, India
| | - Pratibha Gautam
- Department of Environmental Science & Technology, Shroff S.R. Rotary Institute of Chemical Technology, UPL University of Sustainable Technology, Ankleshwar, Gujarat, 393135, India
| | - S Suresh
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, 462 003, Madhya Pradesh, India
| | - Hemen Sarma
- Department of Botany, Nanda Nath Saikia College, Dhodar Ali, Titabar, 785630, Assam, India
| | - Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, 641-046, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123, Brescia, Italy.
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia.
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73
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Sojobi AO, Zayed T. Impact of sewer overflow on public health: A comprehensive scientometric analysis and systematic review. ENVIRONMENTAL RESEARCH 2022; 203:111609. [PMID: 34216613 DOI: 10.1016/j.envres.2021.111609] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 05/09/2023]
Abstract
Sewer overflow (SO), which has attracted global attention, poses serious threat to public health and ecosystem. SO impacts public health via consumption of contaminated drinking water, aerosolization of pathogens, food-chain transmission, and direct contact with fecally-polluted rivers and beach sediments during recreation. However, no study has attempted to map the linkage between SO and public health including Covid-19 using scientometric analysis and systematic review of literature. Results showed that only few countries were actively involved in SO research in relation to public health. Furthermore, there are renewed calls to scale up environmental surveillance to safeguard public health. To safeguard public health, it is important for public health authorities to optimize water and wastewater treatment plants and improve building ventilation and plumbing systems to minimize pathogen transmission within buildings and transportation systems. In addition, health authorities should formulate appropriate policies that can enhance environmental surveillance and facilitate real-time monitoring of sewer overflow. Increased public awareness on strict personal hygiene and point-of-use-water-treatment such as boiling drinking water will go a long way to safeguard public health. Ecotoxicological studies and health risk assessment of exposure to pathogens via different transmission routes is also required to appropriately inform the use of lockdowns, minimize their socio-economic impact and guide evidence-based welfare/social policy interventions. Soft infrastructures, optimized sewer maintenance and prescreening of sewer overflow are recommended to reduce stormwater burden on wastewater treatment plant, curtail pathogen transmission and marine plastic pollution. Comprehensive, integrated surveillance and global collaborative efforts are important to curtail on-going Covid-19 pandemic and improve resilience against future pandemics.
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Affiliation(s)
| | - Tarek Zayed
- Department of Building and Real Estate, The Hong Kong Polytechnic University, Hong Kong, China.
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74
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Mainardi PH, Bidoia ED. Challenges and emerging perspectives of an international SARS-CoV-2 epidemiological surveillance in wastewater. AN ACAD BRAS CIENC 2021; 93:e20210163. [PMID: 34878048 DOI: 10.1590/0001-3765202120210163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/23/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 is a new type of coronavirus capable to infect humans and cause the severe acute respiratory syndrome COVID-19, a disease that has been causing huge impacts across the Earth. COVID-19 patients, including mild, pre-symptomatic and asymptomatic cases, were often seen to contain infectious fragments of SARS-CoV-2 in feces and urine samples. Therefore, studies to detect the new coronavirus in wastewater, which collect and concentrate human excreta, have been extremely useful as a viral tracking tool in communities. This type of monitoring, in addition to serve as a non-invasive early warning of COVID-19 outbreaks, would provide better predictions about the SARS-CoV-2 spread and strongly contribute to maintenance the global health. Although current methods to detect viruses in wastewater, based on molecular RT-PCR and RT-qPCR techniques, were considered as reliable and provided accurate qualitative and quantitative results, they have been facing considerable challenges concerning the SARS-CoV-2 surveillance. In this review, the methods used to detect the SARS-CoV-2 in wastewater and the challenges to implement an international viral monitoring network were described. The article also addressed the emerging perspectives associated with the SARS-CoV-2 epidemiological surveillance in this environment and the importance of a worldwide collaboration to generate and disseminate the detection results.
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Affiliation(s)
- Pedro H Mainardi
- Universidade Estadual Paulista Júlio de Mesquita Filho /UNESP, Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Av. 24A, 1515, Bela Vista, 13506900 Rio Claro, SP, Brazil
| | - Ederio D Bidoia
- Universidade Estadual Paulista Júlio de Mesquita Filho /UNESP, Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Av. 24A, 1515, Bela Vista, 13506900 Rio Claro, SP, Brazil
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Zahedi A, Monis P, Deere D, Ryan U. Wastewater-based epidemiology-surveillance and early detection of waterborne pathogens with a focus on SARS-CoV-2, Cryptosporidium and Giardia. Parasitol Res 2021; 120:4167-4188. [PMID: 33409629 PMCID: PMC7787619 DOI: 10.1007/s00436-020-07023-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022]
Abstract
Waterborne diseases are a major global problem, resulting in high morbidity and mortality, and massive economic costs. The ability to rapidly and reliably detect and monitor the spread of waterborne diseases is vital for early intervention and preventing more widespread disease outbreaks. Pathogens are, however, difficult to detect in water and are not practicably detectable at acceptable concentrations that need to be achieved in treated drinking water (which are of the order one per million litre). Furthermore, current clinical-based surveillance methods have many limitations such as the invasive nature of the testing and the challenges in testing large numbers of people. Wastewater-based epidemiology (WBE), which is based on the analysis of wastewater to monitor the emergence and spread of infectious disease at a population level, has received renewed attention in light of the current coronavirus disease 2019 (COVID-19) pandemic. The present review will focus on the application of WBE for the detection and surveillance of pathogens with a focus on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the waterborne protozoan parasites Cryptosporidium and Giardia. The review highlights the benefits and challenges of WBE and the future of this tool for community-wide infectious disease surveillance.
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Affiliation(s)
- Alireza Zahedi
- Harry Butler Institute, Murdoch University, Perth, Australia
| | - Paul Monis
- South Australian Water Corporation, Adelaide, Australia
| | - Daniel Deere
- Water Futures and Water Research Australia, Sydney, Australia
| | - Una Ryan
- Harry Butler Institute, Murdoch University, Perth, Australia.
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76
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Sangkham S. A review on detection of SARS-CoV-2 RNA in wastewater in light of the current knowledge of treatment process for removal of viral fragments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113563. [PMID: 34488114 PMCID: PMC8373619 DOI: 10.1016/j.jenvman.2021.113563] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/02/2021] [Accepted: 08/17/2021] [Indexed: 05/05/2023]
Abstract
The entire globe is affected by the novel disease of coronavirus 2019 (COVID-19 or 2019-nCoV), which is formally recognised as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The World Health Organisation (WHO) announced this disease as a global pandemic. The presence of SARS-CoV-2 RNA in unprocessed wastewater has become a cause of worry due to these emerging pathogens in the process of wastewater treatment, as reported in the present study. This analysis intends to interpret the fate, environmental factors and route of transmission of SARS-CoV-2, along with its eradication by treating the wastewater for controlling and preventing its further spread. Different recovery estimations of the virus have been depicted by the detection of SARS-CoV-2 RNA in wastewater through the viral concentration techniques. Most frequently used viral concentration techniques include polyethylene glycol (PEG) precipitation, ultrafiltration, electronegative membrane, and ultracentrifugation, after which the detection and quantification of SARS-CoV-2 RNA are done in wastewater samples through quantitative reverse transcription-polymerase chain reaction (RT-qPCR). The wastewater treatment plant (WWTP) holds the key responsibility of eliminating pathogens prior to the discharge of wastewater into surface water bodies. The removal of SARS-CoV-2 RNA at the treatment stage is dependent on the operations of wastewater treatment systems during the outbreak of the virus; particularly, in the urban and extensively populated regions. Efficient primary, secondary and tertiary methods of wastewater treatment and disinfection can reduce or inactivate SARS-CoV-2 RNA before being drained out. Nonetheless, further studies regarding COVID-19-related disinfectants, environment conditions and viral concentrations in each treatment procedure, implications on the environment and regular monitoring of transmission need to be done urgently. Hence, monitoring the SARS-CoV-2 RNA in samples of wastewater under the procedure of wastewater-based epidemiology (WBE) supplement the real-time data pertaining to the investigation of the COVID-19 pandemic in the community, regional and national levels.
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Affiliation(s)
- Sarawut Sangkham
- Department of Environmental Health, School of Public Health, University of Phayao, Muang District, Phayao, 56000, Thailand.
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77
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Navarro A, Gómez L, Sanseverino I, Niegowska M, Roka E, Pedraccini R, Vargha M, Lettieri T. SARS-CoV-2 detection in wastewater using multiplex quantitative PCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:148890. [PMID: 34298359 PMCID: PMC8278834 DOI: 10.1016/j.scitotenv.2021.148890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 05/03/2023]
Abstract
A multiplex reverse transcription quantitative PCR (RT-qPCR)-based method was designed for the simultaneous detection of different SARS-CoV-2 genes. In this study, we used three target genes encoding for the nucleocapsid 1 and 3 (N1, N3), and the spike (S) proteins, all commonly used in the detection of SARS-CoV-2 in human and environmental samples. The performance of the multiplex assay, compared to the single assay was assessed for the standard calibration curve, required for absolute quantification, and then, for the real environmental samples to detect SARS-CoV-2. For this latter, four environmental samples were collected at a local wastewater treatment plant (WWTP). The results showed that the cycle threshold (Ct) values of the multiplex were comparable to the values obtained by the singleplex PCR. The amplification of the three target genes indicated the presence of SARS-CoV-2 in the four water samples with an increasing trend in February and these results were confirmed in the multiplex approach, showing the robustness of this method and its applicability for the relative abundance analysis among the samples. Overall, both the laboratory and field work results demonstrated that the multiplex PCR assay developed in this study could provide a method for SARS-CoV-2 detection as robust as the single qPCR, but faster and cost-effective, reducing by three times the number of reactions, and consequently the handling time and reagents.
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Affiliation(s)
- Anna Navarro
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Livia Gómez
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Isabella Sanseverino
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Magdalena Niegowska
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Eszter Roka
- Department of Public Health Laboratory, National Public Health Centre, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | | | - Marta Vargha
- Department of Public Health Laboratory, National Public Health Centre, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - Teresa Lettieri
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy.
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78
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Kim DY, Shinde SK, Lone S, Palem RR, Ghodake GS. COVID-19 Pandemic: Public Health Risk Assessment and Risk Mitigation Strategies. J Pers Med 2021; 11:1243. [PMID: 34945715 PMCID: PMC8707584 DOI: 10.3390/jpm11121243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022] Open
Abstract
A newly emerged respiratory viral disease called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is also known as pandemic coronavirus disease (COVID-19). This pandemic has resulted an unprecedented global health crisis and devastating impact on several sectors of human lives and economies. Fortunately, the average case fatality ratio for SARS-CoV-2 is below 2%, much lower than that estimated for MERS (34%) and SARS (11%). However, COVID-19 has a much higher transmissibility rate, as evident from the constant increase in the count of infections worldwide. This article explores the reasons behind how COVID-19 was able to cause a global pandemic crisis. The current outbreak scenario and causes of rapid global spread are examined using recent developments in the literature, epidemiological features relevant to public health awareness, and critical perspective of risk assessment and mitigation strategies. Effective pandemic risk mitigation measures have been established and amended against COVID-19 diseases, but there is still much scope for upgrading execution and coordination among authorities in terms of organizational leadership's commitment and diverse range of safety measures, including administrative control measures, engineering control measures, and personal protective equipment (PPE). The significance of containment interventions against the COVID-19 pandemic is now well established; however, there is a need for its effective execution across the globe, and for the improvement of the performance of risk mitigation practices and suppression of future pandemic crises.
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Affiliation(s)
- Dae-Young Kim
- Department of Biological and Environmental Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Korea; (D.-Y.K.); (S.K.S.)
| | - Surendra Krushna Shinde
- Department of Biological and Environmental Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Korea; (D.-Y.K.); (S.K.S.)
| | - Saifullah Lone
- Interdisciplinary Division for Renewable Energy and Advanced Materials (iDREAM), National Institute of Technology (NIT), Srinagar 190006, India;
| | - Ramasubba Reddy Palem
- Department of Medical Biotechnology, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Korea;
| | - Gajanan Sampatrao Ghodake
- Department of Biological and Environmental Science, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Korea; (D.-Y.K.); (S.K.S.)
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79
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Kumblathan T, Liu Y, Uppal GK, Hrudey SE, Li XF. Wastewater-Based Epidemiology for Community Monitoring of SARS-CoV-2: Progress and Challenges. ACS ENVIRONMENTAL AU 2021; 1:18-31. [PMID: 37579255 PMCID: PMC8340581 DOI: 10.1021/acsenvironau.1c00015] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Wastewater-based epidemiology (WBE) is useful for the surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in communities, complementing clinical diagnostic testing of individuals. In this Review, we summarize recent progress and highlight remaining challenges in monitoring SARS-CoV-2 RNA in wastewater systems for community and environmental surveillance. Very low concentrations of viral particles and RNA present in the complicated wastewater and sewage sample matrix require efficient sample processing and sensitive detection. We discuss advantages and limitations of available methods for wastewater sample processing, including collection, separation, enrichment, RNA extraction, and purification. Efficient extraction of the viral RNA and removal of interfering sample matrices are critical to the subsequent reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for sensitive detection of SARS-CoV-2 in wastewater. We emphasize the importance of implementing appropriate controls and method validation, which include the use of surrogate viruses for assessing extraction efficiency and normalization against measurable chemical and biological components in wastewater. Critical analysis of the published studies reveals imperative research needs for the development, validation, and standardization of robust and sensitive methods for quantitative detection of viral RNA and proteins in wastewater for WBE.
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Affiliation(s)
| | | | - Gursharan K. Uppal
- Division of Analytical and
Environmental Toxicology, Department of Laboratory Medicine and Pathology,
Faculty of Medicine and Dentistry, University
of Alberta, Edmonton, AB, Canada T6G 2G3
| | - Steve E. Hrudey
- Division of Analytical and
Environmental Toxicology, Department of Laboratory Medicine and Pathology,
Faculty of Medicine and Dentistry, University
of Alberta, Edmonton, AB, Canada T6G 2G3
| | - Xing-Fang Li
- Division of Analytical and
Environmental Toxicology, Department of Laboratory Medicine and Pathology,
Faculty of Medicine and Dentistry, University
of Alberta, Edmonton, AB, Canada T6G 2G3
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80
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Tomasino MP, Semedo M, Vieira E Moreira P, Ferraz E, Rocha A, Carvalho MF, Magalhães C, Mucha AP. SARS-CoV-2 RNA detected in urban wastewater from Porto, Portugal: Method optimization and continuous 25-week monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148467. [PMID: 34465065 PMCID: PMC8221651 DOI: 10.1016/j.scitotenv.2021.148467] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 05/20/2023]
Abstract
Research on the emerging COVID-19 pandemic is demonstrating that wastewater infrastructures can be used as public health observatories of virus circulation in human communities. Important efforts are being organized worldwide to implement sewage-based surveillance of SARS-CoV-2 that can be used for preventive or early warning purposes, informing preparedness and response measures. However, its successful implementation requires important and iterative methodological improvements, as well as the establishment of standardized methods. The aim of this study was to develop a continuous monitoring protocol for SARS-CoV-2 in wastewater, that could be used to model virus circulation within the communities, complementing the current clinical surveillance. Specific objectives included (1) optimization and validation of a method for virus quantification; (2) monitoring the time-evolution of SARS-CoV-2 in wastewater from two wastewater treatment plants (WWTPs) in the city of Porto, Portugal. Untreated wastewater samples were collected weekly from the two WWTPs between May 2020 and March 2021, encompassing two COVID-19 incidence peaks in the region (mid-November 2020 and mid-January 2021). In the first stage of this study, we compared, optimized and selected a sampling and analysis protocol that included virus concentration through centrifugation, RNA extraction from both liquid and solid fractions and quantification by reverse transcription quantitative PCR (RT-qPCR). In the second stage, we used the selected methodology to track SARS-CoV-2 in the collected wastewater over time. SARS-CoV-2 RNA was detected in 39 and 37 out of 48 liquid and solid fraction samples of untreated wastewater, respectively. The copy numbers varied throughout the study between 0 and 0.15 copies/ng RNA and a good fit was observed between the SARS-CoV-2 RNA concentration in the untreated wastewater and the COVID-19 temporal trends in the study region. We also analyzed eight samples from the treated effluent and found no SARS-CoV-2 RNA detection after tertiary treatment and UV disinfection. In agreement with the recent literature, the results from this study support the use of wastewater-based surveillance to complement clinical testing and evaluate temporal and spatial trends of the current pandemic.
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Affiliation(s)
- Maria Paola Tomasino
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Miguel Semedo
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal.
| | | | - Elza Ferraz
- AEdPorto - Empresa de Águas e Energia do Município do Porto, EM, Porto, Portugal
| | - Adelaide Rocha
- AEdPorto - Empresa de Águas e Energia do Município do Porto, EM, Porto, Portugal
| | - Maria F Carvalho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal; ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Catarina Magalhães
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal; FCUP - Faculty of Sciences, University of Porto, Porto, Portugal
| | - Ana P Mucha
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal; FCUP - Faculty of Sciences, University of Porto, Porto, Portugal
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81
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Rafiee M, Isazadeh S, Mohseni-Bandpei A, Mohebbi SR, Jahangiri-Rad M, Eslami A, Dabiri H, Roostaei K, Tanhaei M, Amereh F. Moore swab performs equal to composite and outperforms grab sampling for SARS-CoV-2 monitoring in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148205. [PMID: 34102442 PMCID: PMC8170911 DOI: 10.1016/j.scitotenv.2021.148205] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) approaches to detect SARS-CoV-2 in municipal wastewater can provide unique information on the incidence or prevalence of COVID-19 in community. However, there are several technical challenges coupled with sewage sampling for SARS-CoV-2, including intermittent shedding of viruses, sampling time, volume, and frequency. Sampling schemes thus may need to be tailored to reach out highly sensitive, accurate, and reliable results. Herein, we compared the accuracy and threshold cycle (Ct) profiles of SARS-CoV-2 in Moore swabs, composite (16-h), and grab samples taken from sewage manholes (n = 17) at the Middle Eastern city of Tehran, Iran, on two occasions (November 2020 and May 2021). Samples were concentrated by polyethylene glycol precipitation and the corresponding Ct values for CDC 'N' and 'ORF1ab' assays were derived by means of real time RT-qPCR. Overall, the Moore swabs performed equal to samples composited over 16 h for qualitative monitoring, and 34/34 (100%) were positive for SARS-CoV-2. The 'N' assay showed the highest detection frequency as compared to 'ORF1ab'. The mean Moore swab Ct profiles were more consistent with 16 h composite sampling as compared with corresponding grab samples, providing hints as to the best sampling protocol to adopt when planning a sewage monitoring campaign particularly under WBE. Furthermore, our analyses on local differences showed somewhat higher virus copy numbers in the southern areas. The experimental design of this study revealed that the Moore swab and composite samples are more sensitive than grab samples, suggesting that the collection of grab samples may be inappropriate for characterizing total number of viral RNA copies in sewage samples. Given the transiently presence of human host-restricted infections such as SARS-CoV-2 and the simplicity and affordability of Moore swab, the method is well suited for disease surveillance in resource poor regions struggling with limited capacity for clinical testing.
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Affiliation(s)
- Mohammad Rafiee
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Siavash Isazadeh
- Environmental Research and Development, American Water Works, Delran, NJ, USA
| | - Anoushiravan Mohseni-Bandpei
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Jahangiri-Rad
- Water Purification Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Akbar Eslami
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Dabiri
- Department of Medical Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Kasra Roostaei
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Tanhaei
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Amereh
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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82
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Preparing for COVID-2x: Urban Planning Needs to Regard Urological Wastewater as an Invaluable Communal Public Health Asset and Not as a Burden. URBAN SCIENCE 2021. [DOI: 10.3390/urbansci5040075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Prior to the COVID-19 pandemic, the analysis of urological wastewater had been a matter of academic curiosity and community-wide big-picture studies looking at drug use or the presence of select viruses such as Hepatitis. The COVID-19 pandemic saw systematic testing of urological wastewater emerge as a significant early detection tool for the presence of SARS-CoV-2 in a community. Even though the pandemic still rages in all continents, it is time to consider the post-pandemic world. This paper posits that urban planners should treat urological wastewater as a communal public health asset and that future sewer design should allow for stratified multi-order sampling.
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83
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Abstract
The 2019 coronavirus disease (COVID-19), an airborne infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a global pandemic. SARS-CoV-2 relies on the angiotensin-converting enzyme 2 receptor for cellular entry and the abundance of this receptor in the gastrointestinal (GI) tract may help explain the GI manifestations, including dysgeusia, nausea, vomiting, diarrhea, and abdominal pain, present in over 40% of infected patients. GI tract involvement also raises the concern for oral-fecal transmission which is poorly understood. Outcome studies in COVID-19 patients with preexisting liver disease and inflammatory bowel disease show predominantly mild transaminase elevations and no increased risk from the use of biological agents in inflammatory bowel disease patients. High-dose corticosteroids, however, should be avoided. As endoscopic procedures are aerosol-generating, modifications to clinical practice is necessary to minimize the spread of COVID-19. We have reviewed current literature to describe the impact of COVID-19 in gastroenterology and hepatology as well as targets of future research.
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84
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Sanchez-Galan JE, Ureña G, Escovar LF, Fabrega-Duque JR, Coles A, Kurt Z. Challenges to detect SARS-CoV-2 on environmental media, the need and strategies to implement the detection methodologies in wastewaters. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2021; 9:105881. [PMID: 34221893 PMCID: PMC8239206 DOI: 10.1016/j.jece.2021.105881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/15/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Understanding risks, putting in place preventative methods to seamlessly continue daily activities are essential tools to fight a pandemic. All social, commercial and leisure activities have an impact on the environmental media. Therefore, to accurately predict the fate and behavior of viruses in the environment, it is necessary to understand and analyze available detection methods, possible transmission pathways and preventative techniques. The aim of this review is to critically analyze and summarize the research done regarding SARS-COV-2 virus detection, focusing on sampling and laboratory detection methods in environmental media. Special attention will be given to wastewater and sewage sludge. This review has summarized the survival of the virus on surfaces to estimate the risk carried by different environmental media (water, wastewater, air and soil) in order to explain which communities are under higher risk. The critical analysis concludes that the detection of SARS-CoV-2 with current technologies and sampling strategies would reveal the presence of the virus. This information could be used to design systematic sampling points throughout the sewage systems when available, taking into account peak flows and more importantly economic factors on when to sample. Such approaches will provide clues for potential future viral outbreak, saving financial resources by reducing testing necessities for viral detection, hence contributing for more appropriate confinement policies by governments and could be further used to define more precisely post-pandemic or additional waves measures if/ when needed.
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Affiliation(s)
- Javier E Sanchez-Galan
- Facultad de Ingeniería de Sistemas Computacionales (FISC), Universidad Tecnológica de Panamá, Panama
- Grupo de Investigación en Biotecnología, Bioinformática y Biología de Sistemas (GIBBS), Universidad Tecnológica de Panamá, Panama
- Institute of Scientific Research and High Technology Services, Panama City, Panama
| | - Grimaldo Ureña
- Grupo de Investigación en Biotecnología, Bioinformática y Biología de Sistemas (GIBBS), Universidad Tecnológica de Panamá, Panama
- Theoretical Evolutionary Genetics Laboratory, University of Houston, Houston, TX, USA
| | | | - Jose R Fabrega-Duque
- Centro de Investigaciones Hidráulicas e Hidrotécnicas (CIHH), Universidad Tecnologica de Panama, Panama
| | - Alexander Coles
- Centro de Investigaciones Hidráulicas e Hidrotécnicas (CIHH), Universidad Tecnologica de Panama, Panama
| | - Zohre Kurt
- Grupo de Investigación en Biotecnología, Bioinformática y Biología de Sistemas (GIBBS), Universidad Tecnológica de Panamá, Panama
- Urban Risk Center, Florida State University-Panama, Panama
- Institute of Scientific Research and High Technology Services, Panama City, Panama
- Department of Environmental Engineering, Middle East Technical University, Ankara, Turkey
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85
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Lazuka A, Arnal C, Soyeux E, Sampson M, Lepeuple AS, Deleuze Y, Pouradier Duteil S, Lacroix S. COVID-19 wastewater based epidemiology: long-term monitoring of 10 WWTP in France reveals the importance of the sampling context. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 84:1997-2013. [PMID: 34695026 DOI: 10.2166/wst.2021.418] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
SARS-CoV-2 wastewater-based epidemiology (WBE) has been advanced as a relevant indicator of distribution of COVID-19 in communities, supporting classical testing and tracing epidemiological approaches. An extensive sampling campaign, including ten municipal wastewater treatment plants, has been conducted in different cities of France over a 20-week period, encompassing the second peak of COVID-19 outbreak in France. A well-recognised ultrafiltration - RNA extraction - RT-qPCR protocol was used and qualified, showing 5.5 +/- 0.5% recovery yield on heat-inactivated SARS-CoV-2. Importantly the whole, solid and liquid, fraction of wastewater was used for virus concentration in this study. Campaign results showed medium- to strong- correlation between SARS-CoV-2 WBE data and COVID-19 prevalence. To go further, statistical relationships between WWTP inlet flow rate and rainfall were studied and taken into account for each WWTP in order to calculate contextualized SARS-CoV-2 loads. This metric presented improved correlation strengths with COVID-19 prevalence for WWTP particularly submitted and sensitive to rain. Such findings highlighted that SARS-CoV-2 WBE data ultimately require to be contextualized for relevant interpretation.
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Affiliation(s)
- A Lazuka
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - C Arnal
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - E Soyeux
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - M Sampson
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - A-S Lepeuple
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - Y Deleuze
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - S Pouradier Duteil
- Veolia Eau France, 30 rue Madeleine Vionnet, 93300, Aubervilliers, France
| | - S Lacroix
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
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86
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Kabdaşlı I, Tünay O. Concentration techniques tailored for the detection of SARS-CoV-2 genetic material in domestic wastewater and treatment plant sludge: A review. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2021; 9:106296. [PMID: 34485054 PMCID: PMC8405238 DOI: 10.1016/j.jece.2021.106296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 05/06/2023]
Abstract
Upon the outbreak of COVID-19 pandemic, detection and quantification of SARS-CoV-2 genetic material in domestic wastewater have led to an increase in the efforts to define and implement the wastewater-based epidemiology (WBE). This application provides valuable information to define local contamination monitoring, emergence of COVID-19 and its variants and many other aspects to cope with and control the pandemic. WBE surveillance, however, requires several consecutive steps such as sampling, pretreatment and concentration of samples, and detection and quantification of SARS-CoV-2 genetic material in wastewater. In this review paper, the literature regarding to all these applications reviewed considering their advantages, disadvantages as well as their applicability. A specific emphasis was placed on the last step, detection and quantification since it covers the most critical procedure for concentrating the virus before measurement. Evaluation of the existing data indicating ultrafiltration, polyethylene glycol (PEG) precipitation and electronegative membrane filtration (ENMF) were the most promising techniques for concentration. The ongoing studies are proposed to be continued within the context of standard methods. Future research needs are delineated and suggestions are made for details.
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Affiliation(s)
- Işık Kabdaşlı
- İstanbul Technical University, Civil Engineering Faculty, Environmental Engineering Department, Ayazağa Campus, Sarıyer, İstanbul 34469, Republic of Turkey
| | - Olcay Tünay
- İstanbul Technical University, Civil Engineering Faculty, Environmental Engineering Department, Ayazağa Campus, Sarıyer, İstanbul 34469, Republic of Turkey
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87
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Pulicharla R, Kaur G, Brar SK. A year into the COVID-19 pandemic: Rethinking of wastewater monitoring as a preemptive approach. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2021; 9:106063. [PMID: 34307017 PMCID: PMC8282934 DOI: 10.1016/j.jece.2021.106063] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/29/2021] [Accepted: 07/13/2021] [Indexed: 05/10/2023]
Abstract
Under the current pandemic situation caused by the novel coronavirus SARS-CoV-2, wastewater monitoring has been increasingly investigated as a surveillance tool for community-wide disease prevalence. After a year into the pandemic, this review critically discusses the real progress made in the detection of SARS-CoV-2 using wastewater monitoring. The limitations and the key challenges faced in improving the detection methods are highlighted. As per the literature, the complex nature of the wastewater matrix poses problems in processing the samples and achieving high sensitivity at low loads of viral RNA using the current detection methods. Furthermore, in the absence of a gold standard analytical method for wastewater, the validation of the generated data for use in wastewater-based epidemiological modeling of the disease becomes practically difficult. However, research is advancing in adopting clinical methods to the wastewater by using appropriate processing controls, and recovery methods. Besides, the technological advances made by the industry including the development of PCR kits with improved detection limits, easy-to-use viral RNA concentration methods, ability to detect the coronavirus variants, and artificial intelligence and advanced data modeling for continuous and remote monitoring greatly help to debottleneck some of these problems. Currently, these technologies are limited to healthcare systems, however, their use for wastewater monitoring is expected to provide opportunities for wide-scale applications of wastewater-based epidemiology (WBE). Moreover, the data from wastewater monitoring act as the initial checkpoint for human health even before the appearance of symptoms, hence WBE needs more attention to manage current and future infectious transmissions.
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Affiliation(s)
- Rama Pulicharla
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario M3J 1P3, Canada
| | - Guneet Kaur
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario M3J 1P3, Canada
| | - Satinder K Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario M3J 1P3, Canada
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88
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Markt R, Mayr M, Peer E, Wagner AO, Lackner N, Insam H. Detection and Stability of SARS-CoV-2 Fragments in Wastewater: Impact of Storage Temperature. Pathogens 2021; 10:1215. [PMID: 34578246 PMCID: PMC8471725 DOI: 10.3390/pathogens10091215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/02/2022] Open
Abstract
SARS-CoV-2 wastewater epidemiology suffers from uncertainties concerning sample storage. We show the effect of the storage of wastewater on the detectable SARS-CoV-2 load. Storage at 4 °C for up to 9 days had no significant effect, while storage at -20 °C led to a significant reduction in gene copy numbers.
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Affiliation(s)
- Rudolf Markt
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria; (M.M.); (E.P.); (A.O.W.); (N.L.); (H.I.)
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89
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Markt R, Mayr M, Peer E, Wagner AO, Lackner N, Insam H. Detection and Stability of SARS-CoV-2 Fragments in Wastewater: Impact of Storage Temperature. Pathogens 2021; 10. [PMID: 34578246 DOI: 10.1101/2021.02.22.21250768] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 05/21/2023] Open
Abstract
SARS-CoV-2 wastewater epidemiology suffers from uncertainties concerning sample storage. We show the effect of the storage of wastewater on the detectable SARS-CoV-2 load. Storage at 4 °C for up to 9 days had no significant effect, while storage at -20 °C led to a significant reduction in gene copy numbers.
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Affiliation(s)
- Rudolf Markt
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Markus Mayr
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Evelyn Peer
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Andreas O Wagner
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Lackner
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, 6020 Innsbruck, Austria
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90
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Bivins A, Kaya D, Bibby K, Simpson SL, Bustin SA, Shanks OC, Ahmed W. Variability in RT-qPCR assay parameters indicates unreliable SARS-CoV-2 RNA quantification for wastewater surveillance. WATER RESEARCH 2021; 203:117516. [PMID: 34412018 DOI: 10.20944/preprints202106.0320.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/17/2021] [Accepted: 07/30/2021] [Indexed: 05/19/2023]
Abstract
Due to the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has become an important tool for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within communities. In particular, reverse transcription-quantitative PCR (RT-qPCR) has been used to generate large datasets aimed at detecting and quantifying SARS-CoV-2 RNA in wastewater. Although RT-qPCR is rapid and sensitive, there is no standard method yet, there are no certified quantification standards, and experiments are conducted using different assays, reagents, instruments, and data analysis protocols. These variations can induce errors in quantitative data reports, thereby potentially misleading interpretations, and conclusions. We review the SARS-CoV-2 wastewater surveillance literature focusing on variability of RT-qPCR data as revealed by inconsistent standard curves and associated parameters. We find that variation in these parameters and deviations from best practices, as described in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines suggest a frequent lack of reproducibility and reliability in quantitative measurements of SARS-CoV-2 RNA in wastewater.
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Affiliation(s)
- Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Devrim Kaya
- School of Chemical, Biological, & Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Stephen A Bustin
- Medical Technology Research Center, Faculty of Health, Education and Social Care, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK
| | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH, 45268, USA
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park 4102, QLD, Australia.
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91
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Bivins A, Kaya D, Bibby K, Simpson SL, Bustin SA, Shanks OC, Ahmed W. Variability in RT-qPCR assay parameters indicates unreliable SARS-CoV-2 RNA quantification for wastewater surveillance. WATER RESEARCH 2021; 203:117516. [PMID: 34412018 PMCID: PMC8341816 DOI: 10.1016/j.watres.2021.117516] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/17/2021] [Accepted: 07/30/2021] [Indexed: 05/18/2023]
Abstract
Due to the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has become an important tool for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within communities. In particular, reverse transcription-quantitative PCR (RT-qPCR) has been used to generate large datasets aimed at detecting and quantifying SARS-CoV-2 RNA in wastewater. Although RT-qPCR is rapid and sensitive, there is no standard method yet, there are no certified quantification standards, and experiments are conducted using different assays, reagents, instruments, and data analysis protocols. These variations can induce errors in quantitative data reports, thereby potentially misleading interpretations, and conclusions. We review the SARS-CoV-2 wastewater surveillance literature focusing on variability of RT-qPCR data as revealed by inconsistent standard curves and associated parameters. We find that variation in these parameters and deviations from best practices, as described in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines suggest a frequent lack of reproducibility and reliability in quantitative measurements of SARS-CoV-2 RNA in wastewater.
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Affiliation(s)
- Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Devrim Kaya
- School of Chemical, Biological, & Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Stephen A Bustin
- Medical Technology Research Center, Faculty of Health, Education and Social Care, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK
| | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH, 45268, USA
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park 4102, QLD, Australia.
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92
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Pillay L, Amoah ID, Deepnarain N, Pillay K, Awolusi OO, Kumari S, Bux F. Monitoring changes in COVID-19 infection using wastewater-based epidemiology: A South African perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147273. [PMID: 33965818 PMCID: PMC8062404 DOI: 10.1016/j.scitotenv.2021.147273] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 05/17/2023]
Abstract
Monitoring of COVID-19 infections within communities via wastewater-based epidemiology could provide a cost-effective alternative to clinical testing. This approach, however, still requires improvement for its efficient application. In this paper, we present the use of wastewater-based epidemiology in monitoring COVID-19 infection dynamics in the KwaZulu-Natal province of South Africa, focusing on four wastewater treatment plants for 14 weeks. The SARS-CoV-2 viral load in influent wastewater was determined using droplet digital PCR, and the number of people infected was estimated using published models as well as using a modified model to improve efficiency. On average, viral loads ranged between 0 and 2.73 × 105 copies/100 ml, 0-1.52 × 105 copies/100 ml, 3 × 104-7.32 × 105 copies/100 ml and 1.55 × 104-4.12 × 105 copies/100 ml in the four wastewater treatment plants studied. The peak in viral load corresponded to the reported COVID-19 infections within the districts where these catchments are located. In addition, we also observed that easing of lockdown restrictions by authorities corresponded with an increase in viral load in the untreated wastewater. Estimation of infection numbers based on the viral load showed that a higher number of people could potentially be infected, compared to the number of cases reported based on clinical testing. The findings reported in this paper contribute to the field of wastewater-based epidemiology for COVID-19 surveillance, whilst highlighting some of the challenges associated with this approach, especially in developing countries.
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Affiliation(s)
- Leanne Pillay
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Isaac Dennis Amoah
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Nashia Deepnarain
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Kriveshin Pillay
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Oluyemi Olatunji Awolusi
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.
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93
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Revilla Pacheco C, Terán Hilares R, Colina Andrade G, Mogrovejo-Valdivia A, Pacheco Tanaka DA. Emerging contaminants, SARS-COV-2 and wastewater treatment plants, new challenges to confront: A short review. BIORESOURCE TECHNOLOGY REPORTS 2021; 15:100731. [PMID: 34124614 PMCID: PMC8183098 DOI: 10.1016/j.biteb.2021.100731] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022]
Abstract
The current pandemic caused by SARS-CoV-2 has put public health at risk, being wastewater-based epidemiology (WBE) a potential tool in the detection, prevention, and treatment of present and possible future outbreaks, since this virus enters wastewater through various sources such as feces, vomit, and sputum. Thus, advanced technologies such as advanced oxidation processes (AOP), membrane technology (MT) are identified through a systematic literature review as an alternative option for the destruction and removal of emerging contaminants (drugs and personal care products) released mainly by infected patients. The objectives of this review are to know the implications that the new COVID-19 outbreak is generating and will generate in water compartments, as well as the new challenges faced by wastewater treatment plants due to the change in a load of contaminants and the solutions proposed based on the aforementioned technologies to be applied to preserve public health and the environment.
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Affiliation(s)
- Claudia Revilla Pacheco
- Laboratorio de Tecnología de Membranas, Universidad Católica de Santa María - UCSM, Urb. San José, San José S/N, Yanahuara, Arequipa, Peru
| | - Ruly Terán Hilares
- Laboratorio de Tecnología de Membranas, Universidad Católica de Santa María - UCSM, Urb. San José, San José S/N, Yanahuara, Arequipa, Peru
| | - Gilberto Colina Andrade
- Laboratorio de Tecnología de Membranas, Universidad Católica de Santa María - UCSM, Urb. San José, San José S/N, Yanahuara, Arequipa, Peru
| | - Alejandra Mogrovejo-Valdivia
- Laboratorio de Tecnología de Membranas, Universidad Católica de Santa María - UCSM, Urb. San José, San José S/N, Yanahuara, Arequipa, Peru
| | - David Alfredo Pacheco Tanaka
- Laboratorio de Tecnología de Membranas, Universidad Católica de Santa María - UCSM, Urb. San José, San José S/N, Yanahuara, Arequipa, Peru
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94
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A rapid and simple protocol for concentration of SARS-CoV-2 from sewage. J Virol Methods 2021; 297:114272. [PMID: 34454988 PMCID: PMC8388153 DOI: 10.1016/j.jviromet.2021.114272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/21/2022]
Abstract
The aim of this study was to set up a simple protocol to concentrate SARS-CoV-2 from sewage, which can be implemented in laboratories with minimal equipment resources. The method avoids the need for extensive purification steps and reduces the concentration of potential inhibitors of RT-qPCR contained in sewage. The concentration method consists of a single step, in which a small volume (40 mL) of sewage sample is incubated with polyaluminum chloride (PAC)(0.00045 N Al3+ final concentration). Virus particles adsorbed to the precipitate are collected by low-speed centrifugation, after which the recovered pellet is resuspended with a saline buffer. PAC-concentrated samples are stable for at least one week at 4 °C. Therefore, they may be sent refrigerated to a diagnosis center for RNA extraction and RT-qPCR for SARS-CoV-2 RNA detection if the lab does not have such capabilities. The PAC concentration method produced an average shift of 4.5-units in quantification cycle (Cq) values compared to non-concentrated samples, indicating a 25-fold increase in detection sensitivity. The lower detection limit corresponded approximately to 100 viral copies per ml. Kappa index indicated substantial agreement between PAC and polyethylene glycol (PEG) precipitation protocols (k = 0.688, CI 0.457-0.919). This low-cost concentration protocol could be useful to aid in the monitoring of community circulation of SARS-CoV-2, especially in low- and middle-income countries, which do not have massive access to support from specialized labs for sewage surveillance.
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95
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Wurtz N, Revol O, Jardot P, Giraud-Gatineau A, Houhamdi L, Soumagnac C, Annessi A, Lacoste A, Colson P, Aherfi S, Scola BL. Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France. Pathogens 2021. [PMID: 34451505 DOI: 10.3390/pathogens10081042.pmid:34451505;pmcid:pmc8401729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the "UK variant" in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.
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Affiliation(s)
- Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Revol
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Priscilla Jardot
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Audrey Giraud-Gatineau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Linda Houhamdi
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | | | | | | | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
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96
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Wurtz N, Revol O, Jardot P, Giraud-Gatineau A, Houhamdi L, Soumagnac C, Annessi A, Lacoste A, Colson P, Aherfi S, Scola BL. Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France. Pathogens 2021; 10:1042. [PMID: 34451505 PMCID: PMC8401729 DOI: 10.3390/pathogens10081042] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the "UK variant" in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.
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Affiliation(s)
- Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Revol
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Priscilla Jardot
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Audrey Giraud-Gatineau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Linda Houhamdi
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Christophe Soumagnac
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Alexandre Annessi
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Alexandre Lacoste
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
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97
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Gibas C, Lambirth K, Mittal N, Juel MAI, Barua VB, Roppolo Brazell L, Hinton K, Lontai J, Stark N, Young I, Quach C, Russ M, Kauer J, Nicolosi B, Chen D, Akella S, Tang W, Schlueter J, Munir M. Implementing building-level SARS-CoV-2 wastewater surveillance on a university campus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 782:146749. [PMID: 33838367 DOI: 10.1101/2020.12.31.20248843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/20/2021] [Accepted: 03/21/2021] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic has been a source of ongoing challenges and presents an increased risk of illness in group environments, including jails, long-term care facilities, schools, and residential college campuses. Early reports that the SARS-CoV-2 virus was detectable in wastewater in advance of confirmed cases sparked widespread interest in wastewater-based epidemiology (WBE) as a tool for mitigation of COVID-19 outbreaks. One hypothesis was that wastewater surveillance might provide a cost-effective alternative to other more expensive approaches such as pooled and random testing of groups. In this paper, we report the outcomes of a wastewater surveillance pilot program at the University of North Carolina at Charlotte, a large urban university with a substantial population of students living in on-campus dormitories. Surveillance was conducted at the building level on a thrice-weekly schedule throughout the university's fall residential semester. In multiple cases, wastewater surveillance enabled the identification of asymptomatic COVID-19 cases that were not detected by other components of the campus monitoring program, which also included in-house contact tracing, symptomatic testing, scheduled testing of student athletes, and daily symptom reporting. In the context of all cluster events reported to the University community during the fall semester, wastewater-based testing events resulted in the identification of smaller clusters than were reported in other types of cluster events. Wastewater surveillance was able to detect single asymptomatic individuals in dorms with resident populations of 150-200. While the strategy described was developed for COVID-19, it is likely to be applicable to mitigation of future pandemics in universities and other group-living environments.
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Affiliation(s)
- Cynthia Gibas
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America; Bioinformatics Research Center, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America.
| | - Kevin Lambirth
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America.
| | - Neha Mittal
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Md Ariful Islam Juel
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Visva Bharati Barua
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Lauren Roppolo Brazell
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Keshawn Hinton
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Jordan Lontai
- Department of Geography and Earth Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Nicholas Stark
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Isaiah Young
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Cristine Quach
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Morgan Russ
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Jacob Kauer
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Bridgette Nicolosi
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Don Chen
- Department of Engineering Technology and Construction Management, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Srinivas Akella
- Department of Computer Science, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Wenwu Tang
- Department of Geography and Earth Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America; Center for Applied Geographic Information Systems, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Jessica Schlueter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America; Bioinformatics Research Center, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Mariya Munir
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
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98
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Mousazadeh M, Ashoori R, Paital B, Kabdaşlı I, Frontistis Z, Hashemi M, Sandoval MA, Sherchan S, Das K, Emamjomeh MM. Wastewater Based Epidemiology Perspective as a Faster Protocol for Detecting Coronavirus RNA in Human Populations: A Review with Specific Reference to SARS-CoV-2 Virus. Pathogens 2021; 10:1008. [PMID: 34451472 PMCID: PMC8401392 DOI: 10.3390/pathogens10081008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/21/2022] Open
Abstract
Wastewater-based epidemiology (WBE) has a long history of identifying a variety of viruses from poliovirus to coronaviruses, including novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The presence and detection of SARS-CoV-2 in human feces and its passage into the water bodies are significant public health challenges. Hence, the hot issue of WBE of SARS-CoV-2 in the coronavirus respiratory disease (COVID-19) pandemic is a matter of utmost importance (e.g., SARS-CoV-1). The present review discusses the background, state of the art, actual status, and prospects of WBE, as well as the detection and quantification protocols of SARS-CoV-2 in wastewater. The SARS-CoV-2 detection studies have been performed in different water matrixes such as influent and effluent of wastewater treatment plants, suburban pumping stations, hospital wastewater, and sewer networks around the globe except for Antarctica. The findings revealed that all WBE studies were in accordance with clinical and epidemiological data, which correlates the presence of SARS-CoV-2 ribonucleic acid (RNA) with the number of new daily positive cases officially reported. This last was confirmed via Reverse Transcriptase-quantitative Polymerase Chain Reaction (RT-qPCR) testing which unfortunately is not suitable for real-time surveillance. In addition, WBE concept may act as a faster protocol to alert the public health authorities to take administrative orders (possible re-emerging infections) due to the impracticality of testing all citizens in a short time with limited diagnostic facilities. A comprehensive and integrated review covering all steps starting from sampling to molecular detection of SARS-CoV-2 in wastewater has been made to guide for the development well-defined and reliable protocols.
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Affiliation(s)
- Milad Mousazadeh
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran;
- Department of Environmental Health Engineering, School of Health, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Razieh Ashoori
- Department of Environmental Health Engineering, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran;
| | - Biswaranjan Paital
- Redox Regulation Laboratory, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar 751003, India;
| | - Işık Kabdaşlı
- Environmental Engineering Department, Civil Engineering Faculty, Ayazağa Campus, İstanbul Technical University, İstanbul 34469, Turkey;
| | - Zacharias Frontistis
- Department of Chemical Engineering, University of Western Macedonia, 50132 Kozani, Greece;
| | - Marjan Hashemi
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran;
| | - Miguel A. Sandoval
- Laboratorio de Electroquímica Medio Ambiental LEQMA, Departamento de Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile USACH, Casilla 40, Correo 33, Santiago 9170022, Chile;
- Departamento de Ingeniería Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Samendra Sherchan
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 7011, USA;
| | - Kabita Das
- Department of Philosophy, Utkal University, Bhubaneswar 751004, India;
| | - Mohammad Mahdi Emamjomeh
- Social Determinants of Health Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
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99
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Khanna S. Microbiota restoration for recurrent Clostridioides difficile: Getting one step closer every day! J Intern Med 2021; 290:294-309. [PMID: 33856727 DOI: 10.1111/joim.13290] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/27/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Clostridioides difficile infection (CDI) is an urgent health threat being the most common healthcare-associated infection, and its management is a clinical conundrum. Over 450 000 infections are seen in the United States with similar incidence seen in the rest of the developed world. The majority of infections seen are mild-moderate with fulminant disease and mortality being rare complications seen in the elderly and in those with comorbidities. The most common complication of CDI is recurrent infection with rates as high as 60% after three or more infections. A dilemma in the management of primary and recurrent CDI is testing due to the high sensitivity of the nucleic acid amplification tests such as the polymerase chain reaction, which leads to clinical false positives if patients are not chosen carefully (with symptoms) before testing. A newer testing regimen involving a 2-step strategy is emerging using glutamate dehydrogenase as a screening strategy followed by enzyme immunoassay for the C. difficile toxin. Microbiota restoration therapies are the cornerstone of management of recurrent CDI to prevent future recurrences. The most common modality of microbiota restoration is faecal microbiota transplantation, which has been tainted with heterogeneity and adverse events such as serious infectious transmission. The success rates for recurrence prevention from microbiota restoration therapies are over 90% compared with less than 50% of recurrence prevention with courses of antibiotics. This has led to development and emergence of standardized microbiota restoration therapies in capsule and enema forms. Capsule-based therapies include CP101 (positive phase II results), RBX7455 (positive phase I results), SER-109 (positive phase III results) and VE303 (ongoing phase II trial). Enema-based therapy includes RBX2660 (positive phase III data). This review summarizes the principles of management and diagnosis of CDI and focuses on emerging and existing data on faecal microbiota transplantation and standardized microbiota restoration therapies.
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Affiliation(s)
- S Khanna
- From the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
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100
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Ji B, Zhao Y, Wei T, Kang P. Water science under the global epidemic of COVID-19: Bibliometric tracking on COVID-19 publication and further research needs. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2021; 9:105357. [PMID: 33747765 PMCID: PMC7959687 DOI: 10.1016/j.jece.2021.105357] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 05/05/2023]
Abstract
There are overwhelming increases of studies and over 200,000 publications related to all the aspects of COVID-19. Among them, 262 papers were published by authors from 67 countries regarding COVID-19 with water science and technology. Although the transmission routes of SARS-CoV-2 in water cycle have not been proved, the water and wastewater play an important role in the control of COVID-19 pandemic. Accordingly, it is scholarly relevant and interesting to look into publications of COVID-19 in water science and technology to track the investigations for moving forward in the years to come. It is believed that, through the literature survey, the question on what we know and what we do not know about COVID-19 so far can be clear, thus providing useful information for helping curbing the epidemic from water sector. This forms the basis of the current study. As such, a bibliometric analysis was conducted. It reveals that wastewater-based epidemiology (WBE) has recently gained global attention with the source and survival characteristics of coronavirus in the aquatic environment; the methodology of virus detection; the water hygiene; and the impact of the COVID-19 pandemic on the water ecosystem being the main topics in 2020. Various studies have shown that drinking water is safety whereas wastewater may be a potential risk during this pandemic. From the perspective of the water cycle, the scopes for further research needs are discussed and proposed, which could enhance the important role and value of water science in warning, monitoring, and predicting COVID-19 during epidemic outbreaks.
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Affiliation(s)
- Bin Ji
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, PR China
- Department of Municipal and Environmental Engineering, Faculty of Water Resources and Hydroelectric Engineering, Xi'an University of Technology, Xi'an 710048, PR China
| | - Yaqian Zhao
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, PR China
- Department of Municipal and Environmental Engineering, Faculty of Water Resources and Hydroelectric Engineering, Xi'an University of Technology, Xi'an 710048, PR China
| | - Ting Wei
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, PR China
- Chemical Engineering Department, University of Alcalá, Madrid, Spain
| | - Peiying Kang
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an 710048, PR China
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