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Solomon T, Idris O, Nwaubani D, Baral R, Sherchan SP. Comparative analysis of membrane filter diameters for detection of selected viruses in wastewater samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:173973. [PMID: 38876339 DOI: 10.1016/j.scitotenv.2024.173973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Wastewater serves as a valuable source of information as it contains biological markers that have been shed by infected individuals and from other biological organisms such as plants and animals. Wastewater has been proven to indicate the presence of emerging pathogens in a community before the manifestation of clinical symptoms. Several methods of concentration and nucleic acid extraction have been employed all around the world without a unified method. One such method involves the use of the adsorption extraction method (AE-method), which involves the use of electronegative membrane filters of different pore sizes. The membrane filters also differ by diameter, but no study has been reported on the effect of diameter on capture efficiency. This study was aimed at evaluating the comparative capture efficiency of two different membrane filter diameters of 45 and 90 mm with pore sizes of 0.45 μm for the detection of indicator and pathogenic viruses. Primary influent samples were obtained from two wastewater treatment plants in Baltimore, Maryland, between April 27 and June 29, 2023. A total of twenty samples were processed using 45- and 90-mm membrane filters. Nucleic acids were extracted from the filters using the QIAmp Viral RNA Mini Kit and assayed for four different targets: PMMoV, Norovirus (GI and GII), and CrAssphage by RT-qPCR. The result showed that 45 mm membrane filters had a higher combined mean capture efficiency in log10 gene copies per liter (gc/l) for crAssphage (7.40) than 90 mm membrane filters (7.10). Similarly, the 45-mm filter had higher mean capture efficiency for Norovirus GI (4.67) than the 90-mm filter (1.84) and likewise for Norovirus GII (2.14, 1.04). On the contrary, 90-mm membrane filters were observed to have better capture of PMMoV (6.84) compared to 45-mm membrane filters (6.69). This result therefore implies that 45-mm membrane filters could be more efficient for wastewater surveillance studies through the AE method for indicator viruses like CrAssphage and human disease-causing viruses like Norovirus.
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Affiliation(s)
- Tamunobelema Solomon
- Center of Research Excellence in Wastewater based epidemiology, Morgan State University, Baltimore, MD 21251, United States of America; BioEnvironmental Science Program, Morgan State University, Baltimore, MD 21251, United States of America
| | - Oladele Idris
- BioEnvironmental Science Program, Morgan State University, Baltimore, MD 21251, United States of America
| | - Daniel Nwaubani
- BioEnvironmental Science Program, Morgan State University, Baltimore, MD 21251, United States of America
| | - Rakshya Baral
- BioEnvironmental Science Program, Morgan State University, Baltimore, MD 21251, United States of America
| | - Samendra P Sherchan
- Center of Research Excellence in Wastewater based epidemiology, Morgan State University, Baltimore, MD 21251, United States of America; BioEnvironmental Science Program, Morgan State University, Baltimore, MD 21251, United States of America.
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Gogoi G, Singh SD, Kalyan E, Koch D, Gogoi P, Kshattry S, Mahanta HJ, Imran M, Pandey R, Bharali P. An interpretative review of the wastewater-based surveillance of the SARS-CoV-2: where do we stand on its presence and concern? Front Microbiol 2024; 15:1338100. [PMID: 38318336 PMCID: PMC10839012 DOI: 10.3389/fmicb.2024.1338100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has been used for monitoring infectious diseases like polio, hepatitis, etc. since the 1940s. It is also being used for tracking the SARS-CoV-2 at the population level. This article aims to compile and assess the information for the qualitative and quantitative detection of the SARS-CoV-2 in wastewater. Based on the globally published studies, we highlight the importance of monitoring SARS-CoV-2 presence/detection in the wastewater and concurrently emphasize the development of early surveillance techniques. SARS-CoV-2 RNA sheds in the human feces, saliva, sputum and mucus that ultimately reaches to the wastewater and brings viral RNA into it. For the detection of the virus in the wastewater, different detection techniques have been optimized and are in use. These are based on serological, biosensor, targeted PCR, and next generation sequencing for whole genome sequencing or targeted amplicon sequencing. The presence of the SARS-CoV-2 RNA in wastewater could be used as a potential tool for early detection and devising the strategies for eradication of the virus before it is spread in the community. Additionally, with the right and timely understanding of viral behavior in the environment, an accurate and instructive model that leverages WBE-derived data may be created. This might help with the creation of technological tools and doable plans of action to lessen the negative effects of current viral epidemics or future potential outbreaks on public health and the economy. Further work toward whether presence of viral load correlates with its ability to induce infection, still needs evidence. The current increasing incidences of JN.1 variant is a case in point for continued early detection and surveillance, including wastewater.
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Affiliation(s)
- Gayatri Gogoi
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sarangthem Dinamani Singh
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Emon Kalyan
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Devpratim Koch
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pronami Gogoi
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Suman Kshattry
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Hridoy Jyoti Mahanta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Md Imran
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Rajesh Pandey
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Pankaj Bharali
- Center for Infectious Diseases, Biological Science and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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3
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Baz Lomba JA, Pires J, Myrmel M, Arnø JK, Madslien EH, Langlete P, Amato E, Hyllestad S. Effectiveness of environmental surveillance of SARS-CoV-2 as an early-warning system: Update of a systematic review during the second year of the pandemic. JOURNAL OF WATER AND HEALTH 2024; 22:197-234. [PMID: 38295081 PMCID: wh_2023_279 DOI: 10.2166/wh.2023.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The aim of this updated systematic review was to offer an overview of the effectiveness of environmental surveillance (ES) of SARS-CoV-2 as a potential early-warning system (EWS) for COVID-19 and new variants of concerns (VOCs) during the second year of the pandemic. An updated literature search was conducted to evaluate the added value of ES of SARS-CoV-2 for public health decisions. The search for studies published between June 2021 and July 2022 resulted in 1,588 publications, identifying 331 articles for full-text screening. A total of 151 publications met our inclusion criteria for the assessment of the effectiveness of ES as an EWS and early detection of SARS-CoV-2 variants. We identified a further 30 publications among the grey literature. ES confirms its usefulness as an EWS for detecting new waves of SARS-CoV-2 infection with an average lead time of 1-2 weeks for most of the publication. ES could function as an EWS for new VOCs in areas with no registered cases or limited clinical capacity. Challenges in data harmonization and variant detection require standardized approaches and innovations for improved public health decision-making. ES confirms its potential to support public health decision-making and resource allocation in future outbreaks.
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Affiliation(s)
- Jose Antonio Baz Lomba
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway E-mail:
| | - João Pires
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway; ECDC fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jorunn Karterud Arnø
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Elisabeth Henie Madslien
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Petter Langlete
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Ettore Amato
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Susanne Hyllestad
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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Ampuero M, Martínez-Valdebenito C, Ferrés M, Soto-Rifo R, Gaggero A. Monkeypox Virus in Wastewater Samples from Santiago Metropolitan Region, Chile. Emerg Infect Dis 2023; 29:2358-2361. [PMID: 37877805 PMCID: PMC10617339 DOI: 10.3201/eid2911.230096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
Sewage surveillance provides useful epidemiologic and public health information on viral infections at the population level. We detected monkeypox virus DNA from sewage samples covering 85% of the population in Santiago Metropolitan Region Chile. We also isolated infective viruses from those samples. Wastewater surveillance could complement clinical surveillance for monkeypox virus.
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López-Peñalver RS, Cañas-Cañas R, Casaña-Mohedo J, Benavent-Cervera JV, Fernández-Garrido J, Juárez-Vela R, Pellín-Carcelén A, Gea-Caballero V, Andreu-Fernández V. Predictive potential of SARS-CoV-2 RNA concentration in wastewater to assess the dynamics of COVID-19 clinical outcomes and infections. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 886:163935. [PMID: 37164095 PMCID: PMC10164651 DOI: 10.1016/j.scitotenv.2023.163935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
Coronavirus disease 2019 - caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) -, has triggered a worldwide pandemic resulting in 665 million infections and over 6.5 million deaths as of December 15, 2022. The development of different epidemiological tools have helped predict new outbreaks and assess the behavior of clinical variables in different health contexts. In this study, we aimed to monitor concentrations of SARS-CoV-2 in wastewater as a tool to predict the progression of clinical variables during Waves 3, 5, and 6 of the pandemic in the Spanish city of Xátiva from September 2020 to March 2022. We estimated SARS-CoV-2 RNA concentrations in 195 wastewater samples using the RT-PCR Diagnostic Panel validated by the Center for Disease Control and Prevention. We also compared the trends of several clinical variables (14-day cumulative incidence, positive cases, hospital cases and stays, critical cases and stays, primary care visits, and deaths) for each study wave against wastewater SARS-CoV-2 RNA concentrations using Pearson's product-moment correlations, a two-sided Mann-Whitney U test, and a cross-correlation analysis. We found strong correlations between SARS-CoV-2 concentrations with 14-day cumulative incidence and positive cases over time. Wastewater RNA concentrations showed strong correlations with these variables one and two weeks in advance. There were significant correlations with hospitalizations and critical care during Wave 3 and Wave 6; cross-correlations were stronger for hospitalization stays one week before during Wave 6. No association between vaccination percentages and wastewater viral concentrations was observed. Our findings support wastewater SARS-CoV-2 concentrations as a potential surveillance tool to anticipate infection and epidemiological data such as 14-day cumulative incidence, hospitalizations, and critical care stays. Public health authorities could use this epidemiological tool on a similar population as an aid for health care decision-making during an epidemic outbreak.
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Affiliation(s)
- Raimundo Seguí López-Peñalver
- Faculty of Health Sciences, Valencian International University (VIU), 46002, Valencia, Spain; Global Omnium, Valencia, Spain
| | | | - Jorge Casaña-Mohedo
- Faculty of Health Sciences, Valencian International University (VIU), 46002, Valencia, Spain; Faculty of Health Sciences, Universidad Católica de Valencia San Vicente Mártir, 46001, Valencia, Spain
| | | | - Julio Fernández-Garrido
- Consellería de Sanidad Universal y Salud Pública, Generalitat Valenciana, Department of Nursing, University of Valencia, 46001 Jaume Roig St, Valencia, Spain
| | - Raúl Juárez-Vela
- Faculty of Health Sciences, La Rioja University, 26006 Logroño, Spain
| | - Ana Pellín-Carcelén
- Faculty of Health Sciences, Valencian International University (VIU), 46002, Valencia, Spain
| | - Vicente Gea-Caballero
- Faculty of Health Sciences, Valencian International University (VIU), 46002, Valencia, Spain
| | - Vicente Andreu-Fernández
- Faculty of Health Sciences, Valencian International University (VIU), 46002, Valencia, Spain; Biosanitary Research Institute, Valencian International University (VIU), 46002, Valencia, Spain.
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Cimmino C, Rodrigues Capítulo L, Lerman A, Silva A, Von Haften G, Comino AP, Cigoy L, Scagliola M, Poncet V, Caló G, Uez O, Berón CM. Presence of SARS-CoV-2 in urban effluents in south-east Buenos Aires, Argentina, May 2020 to March 2022. Rev Panam Salud Publica 2023; 47:e94. [PMID: 37324201 PMCID: PMC10261580 DOI: 10.26633/rpsp.2023.94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/14/2023] [Indexed: 06/17/2023] Open
Abstract
Objectives To implement and evaluate the use of wastewater sampling for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in two coastal districts of Buenos Aires Province, Argentina. Methods In General Pueyrredon district, 400 mL of wastewater samples were taken with an automatic sampler for 24 hours, while in Pinamar district, 20 L in total (2.2 L at 20-minute intervals) were taken. Samples were collected once a week. The samples were concentrated based on flocculation using polyaluminum chloride. RNA purification and target gene amplification and detection were performed using reverse transcription polymerase chain reaction for clinical diagnosis of human nasopharyngeal swabs. Results In both districts, the presence of SARS-CoV-2 was detected in wastewater. In General Pueyrredon, SARS-CoV-2 was detected in epidemiological week 28, 2020, which was 20 days before the start of an increase in coronavirus virus disease 2019 (COVID-19) cases in the first wave (epidemiological week 31) and 9 weeks before the maximum number of laboratory-confirmed COVID-19 cases was recorded. In Pinamar district, the virus genome was detected in epidemiological week 51, 2020 but it was not possible to carry out the sampling again until epidemiological week 4, 2022, when viral circulation was again detected. Conclusions It was possible to detect SARS-CoV-2 virus genome in wastewater, demonstrating the usefulness of the application of wastewater epidemiology for long-term SARS-CoV-2 detection and monitoring.
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Affiliation(s)
- Carlos Cimmino
- Instituto Nacional de Epidemiología “Dr. Juan H. Jara”Mar del PlataArgentinaInstituto Nacional de Epidemiología “Dr. Juan H. Jara”, Mar del Plata, Argentina.
| | - Leandro Rodrigues Capítulo
- Centro de Estudios Integrales de la Dinámica ExógenaUniversidad Nacional de La PlataLa PlataArgentinaCentro de Estudios Integrales de la Dinámica Exógena, Universidad Nacional de La Plata, La Plata, Argentina.
| | - Andrea Lerman
- Instituto Nacional de Epidemiología “Dr. Juan H. Jara”Mar del PlataArgentinaInstituto Nacional de Epidemiología “Dr. Juan H. Jara”, Mar del Plata, Argentina.
| | - Andrea Silva
- Instituto Nacional de Epidemiología “Dr. Juan H. Jara”Mar del PlataArgentinaInstituto Nacional de Epidemiología “Dr. Juan H. Jara”, Mar del Plata, Argentina.
| | - Gabriela Von Haften
- Obras Sanitarias Sociedad de EstadoMar del PlataArgentinaObras Sanitarias Sociedad de Estado, Mar del Plata, Argentina.
| | - Ana P. Comino
- Obras Sanitarias Sociedad de EstadoMar del PlataArgentinaObras Sanitarias Sociedad de Estado, Mar del Plata, Argentina.
| | - Luciana Cigoy
- Obras Sanitarias Sociedad de EstadoMar del PlataArgentinaObras Sanitarias Sociedad de Estado, Mar del Plata, Argentina.
| | - Marcelo Scagliola
- Obras Sanitarias Sociedad de EstadoMar del PlataArgentinaObras Sanitarias Sociedad de Estado, Mar del Plata, Argentina.
| | - Verónica Poncet
- Instituto Nacional de Epidemiología “Dr. Juan H. Jara”Mar del PlataArgentinaInstituto Nacional de Epidemiología “Dr. Juan H. Jara”, Mar del Plata, Argentina.
| | - Gonzalo Caló
- Instituto de Investigaciones en Biodiversidad y Biotecnología and FIBAMar del PlataArgentinaInstituto de Investigaciones en Biodiversidad y Biotecnología and FIBA, Mar del Plata, Argentina.
| | - Osvaldo Uez
- Instituto Nacional de Epidemiología “Dr. Juan H. Jara”Mar del PlataArgentinaInstituto Nacional de Epidemiología “Dr. Juan H. Jara”, Mar del Plata, Argentina.
| | - Corina M. Berón
- Instituto de Investigaciones en Biodiversidad y Biotecnología and FIBAMar del PlataArgentinaInstituto de Investigaciones en Biodiversidad y Biotecnología and FIBA, Mar del Plata, Argentina.
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7
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Lopez Marin MA, Zdenkova K, Bartackova J, Cermakova E, Dostalkova A, Demnerova K, Vavruskova L, Novakova Z, Sykora P, Rumlova M, Bartacek J. Monitoring COVID-19 spread in selected Prague's schools based on the presence of SARS-CoV-2 RNA in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:161935. [PMID: 36731569 PMCID: PMC9886433 DOI: 10.1016/j.scitotenv.2023.161935] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/13/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
The COVID-19 pandemic has demanded a broad range of techniques to better monitor its extent. Owing to its consistency, non-invasiveness, and cost effectiveness, wastewater-based epidemiology has emerged as a relevant approach to monitor the pandemic's course. In this work, we analyzed the extent of the COVID-19 pandemic in five primary schools in Prague, the Czech Republic, and how different preventive measures impact the presence of SARS-CoV-2 RNA copy numbers in wastewaters. Copy numbers were measured by reverse transcription-multiplex quantitative real-time PCR. These copy numbers were compared to the number of infected individuals in each school identified through regular clinical tests. Each school had a different monitoring regime and subsequent application of preventive measures to thwart the spread of COVID-19. The schools that constantly identified and swiftly quarantined infected individuals exhibited persistently low amounts of SARS-CoV-2 RNA copies in their wastewaters. In one school, a consistent monitoring of infected individuals, coupled with a delayed action to quarantine, allowed for the estimation of a linear model to predict the number of infected individuals based on the presence of SARS-CoV-2 RNA in the wastewater. The results show the importance of case detection and quarantining to stop the spread of the pandemic and its impact on the presence of SARS-CoV-2 RNA in wastewaters. This work also shows that wastewater-based epidemiological models can be reliably used even in small water catchments, but difficulties arise to fit models due to the nonconstant input of viral particles into the wastewater systems.
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Affiliation(s)
- Marco A Lopez Marin
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - K Zdenkova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czechia.
| | - J Bartackova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - E Cermakova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czechia
| | - A Dostalkova
- Department of Biotechnology, University of Chemistry and Technology Prague, Czechia
| | - K Demnerova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czechia
| | | | - Z Novakova
- Prazske vodovody a kanalizace, a.s., Czechia
| | - P Sykora
- Prazske vodovody a kanalizace, a.s., Czechia
| | - M Rumlova
- Department of Biotechnology, University of Chemistry and Technology Prague, Czechia
| | - J Bartacek
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
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Lessa CLS, Hodel KVS, Gonçalves MDS, Machado BAS. Dengue as a Disease Threatening Global Health: A Narrative Review Focusing on Latin America and Brazil. Trop Med Infect Dis 2023; 8:tropicalmed8050241. [PMID: 37235289 DOI: 10.3390/tropicalmed8050241] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Arboviruses constitute the largest known group of viruses. These viruses are the etiological agents of pathologies known as arboviruses, with dengue being one of the most prevalent. Dengue has resulted in important socioeconomic burdens placed on different countries around the world, including those in Latin America, especially Brazil. Thus, this work intends to carry out a narrative-based review of the literature, conducted using a study of the secondary data developed through a survey of scientific literature databases, and to present the situation of dengue, particularly its distribution in these localities. Our findings from the literature demonstrate the difficulties that managers face in controlling the spread of and planning a response against dengue, pointing to the high cost of the disease for public coffers, rendering the resources that are already limited even scarcer. This can be associated with the different factors that affect the spread of the disease, including ecological, environmental, and social factors. Thus, in order to combat the disease, it is expected that targeted and properly coordinated public policies need to be adopted not only in specific localities, but also globally.
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Affiliation(s)
- Carlos Letacio Silveira Lessa
- Postgraduate Program in Industrial Management and Technology, SENAI CIMATEC University Center, Salvador 41650-010, Brazil
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador 40296-710, Brazil
| | - Katharine Valéria Saraiva Hodel
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC University Center, Salvador 41650-010, Brazil
| | - Marilda de Souza Gonçalves
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador 40296-710, Brazil
- Anemia Research Laboratory, Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Federal University of Bahia, Salvador 40170-115, Brazil
| | - Bruna Aparecida Souza Machado
- Postgraduate Program in Industrial Management and Technology, SENAI CIMATEC University Center, Salvador 41650-010, Brazil
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC University Center, Salvador 41650-010, Brazil
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Prado T, Rey-Benito G, Miagostovich MP, Sato MIZ, Rajal VB, Filho CRM, Pereira AD, Barbosa MRF, Mannarino CF, da Silva AS. Wastewater-based epidemiology for preventing outbreaks and epidemics in Latin America - Lessons from the past and a look to the future. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161210. [PMID: 36581294 DOI: 10.1016/j.scitotenv.2022.161210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Wastewater-based epidemiology (WBE) is an approach with the potential to complement clinical surveillance systems. Using WBE, it is possible to carry out an early warning of a possible outbreak, monitor spatial and temporal trends of infectious diseases, produce real-time results and generate representative epidemiological information in a territory, especially in areas of social vulnerability. Despite the historical uses of this approach, particularly in the Global Polio Eradication Initiative, and for other pathogens, it was during the COVID-19 pandemic that occurred an exponential increase in environmental surveillance programs for SARS-CoV-2 in wastewater, with many experiences and developments in the field of public health using data for decision making and prioritizing actions to control the pandemic. In Latin America, WBE was applied in heterogeneous contexts and with emphasis on populations that present many socio-environmental inequalities, a condition shared by all Latin American countries. This manuscript addresses the concepts and applications of WBE in public health actions, as well as different experiences in Latin American countries, and discusses a model to implement this surveillance system at the local or national level. We emphasize the need to implement this sentinel surveillance system in countries that want to detect the early entry and spread of new pathogens and monitor outbreaks or epidemics of infectious agents in their territories as a complement of public health surveillance systems.
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Affiliation(s)
- Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil.
| | - Gloria Rey-Benito
- Pan American Health Organization (PAHO/WHO), 525 23rd St NW, Washington, DC 20037, United States of America.
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Maria Inês Zanoli Sato
- Department of Environmental Analysis, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil
| | - Veronica Beatriz Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Facultad de Ingeniería, UNSa, Av. Bolivia 5150, Salta 4400, Argentina; Singapore Centre for Environmental Life Science Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Cesar Rossas Mota Filho
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Alyne Duarte Pereira
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Mikaela Renata Funada Barbosa
- Department of Environmental Analysis, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil
| | - Camille Ferreira Mannarino
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Agnes Soares da Silva
- Pan American Health Organization (PAHO/WHO), 525 23rd St NW, Washington, DC 20037, United States of America.
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Lucansky V, Samec M, Burjanivova T, Lukacova E, Kolkova Z, Holubekova V, Turyova E, Hornakova A, Zaborsky T, Podlesniy P, Reizigova L, Dankova Z, Novakova E, Pecova R, Calkovska A, Halasova E. Comparison of the methods for isolation and detection of SARS-CoV-2 RNA in municipal wastewater. Front Public Health 2023; 11:1116636. [PMID: 36960362 PMCID: PMC10028190 DOI: 10.3389/fpubh.2023.1116636] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/17/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction Coronavirus SARS-CoV-2 is a causative agent responsible for the current global pandemic situation known as COVID-19. Clinical manifestations of COVID-19 include a wide range of symptoms from mild (i.e., cough, fever, dyspnea) to severe pneumonia-like respiratory symptoms. SARS-CoV-2 has been demonstrated to be detectable in the stool of COVID-19 patients. Waste-based epidemiology (WBE) has been shown as a promising approach for early detection and monitoring of SARS-CoV-2 in the local population performed via collection, isolation, and detection of viral pathogens from environmental sources. Methods In order to select the optimal protocol for monitoring the COVID-19 epidemiological situation in region Turiec, Slovakia, we (1) compared methods for SARS-CoV-2 separation and isolation, including virus precipitation by polyethylene glycol (PEG), virus purification via ultrafiltration (Vivaspin®) and subsequent isolation by NucleoSpin RNA Virus kit (Macherey-Nagel), and direct isolation from wastewater (Zymo Environ Water RNA Kit); (2) evaluated the impact of water freezing on SARS- CoV-2 separation, isolation, and detection; (3) evaluated the role of wastewater filtration on virus stability; and (4) determined appropriate methods including reverse transcription-droplet digital PCR (RT-ddPCR) and real-time quantitative polymerase chain reaction (RT-qPCR) (targeting the same genes, i.e., RdRp and gene E) for quantitative detection of SARS-CoV-2 in wastewater samples. Results (1) Usage of Zymo Environ Water RNA Kit provided superior quality of isolated RNA in comparison with both ultracentrifugation and PEG precipitation. (2) Freezing of wastewater samples significantly reduces the RNA yield. (3) Filtering is counterproductive when Zymo Environ Water RNA Kit is used. (4) According to the specificity and sensitivity, the RT-ddPCR outperforms RT-qPCR. Discussion The results of our study suggest that WBE is a valuable early warning alert and represents a non-invasive approach to monitor viral pathogens, thus protects public health on a regional and national level. In addition, we have shown that the sensitivity of testing the samples with a nearer detection limit can be improved by selecting the appropriate combination of enrichment, isolation, and detection methods.
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Affiliation(s)
- Vincent Lucansky
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
| | - Marek Samec
- Department of Pathophysiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Tatiana Burjanivova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Eva Lukacova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Kolkova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
| | - Veronika Holubekova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
| | - Eva Turyova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Hornakova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
| | - Tibor Zaborsky
- RÚVZ (Regional Office of Public Health), Martin, Slovakia
| | - Petar Podlesniy
- Centro Investigacion Biomedica en Red Enfermedades Neurodegenerativas (CiberNed), Madrid, Spain
| | - Lenka Reizigova
- Center for Microbiology and Infection Prevention, Department of Laboratory Medicine, Faculty of Health Care and Social Work, Trnava University, Trnava, Slovakia
| | - Zuzana Dankova
- Biobank for Cancer and Rare Diseases, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
| | - Elena Novakova
- Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Renata Pecova
- Department of Pathophysiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Calkovska
- Department of Physiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Erika Halasova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
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11
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Othman I, Helmi A, Slama I, Hamdi R, Mastouri M, Aouni M. Evaluation of three viral concentration methods for detection and quantification of SARS-CoV-2 in wastewater. JOURNAL OF WATER AND HEALTH 2023; 21:354-360. [PMID: 37338315 PMCID: wh_2023_264 DOI: 10.2166/wh.2023.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Wastewater-based epidemiology (WBE) could be useful as an early warning system for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic spread. Viruses are highly diluted in wastewater. Therefore, a virus concentration step is needed for SARS-CoV-2 wastewater detection. We tested the efficiency of three wastewater viral concentration methods: ultrafiltration (UF), electronegative membrane filtration and aluminum hydroxide adsorption-elution. We spiked wastewater with inactivated SARS-CoV-2 and we collected 20 other wastewater samples from five sites in Tunisia. Samples were concentrated by the three methods and SARS-CoV-2 was quantified by reverse transcription digital PCR (RT-dPCR). The most efficient method was UF with a mean SARS-CoV-2 recovery of 54.03 ± 8.25. Moreover, this method provided significantly greater mean concentration and virus detection ability (95%) than the two other methods. The second-most efficient method used electronegative membrane filtration with a mean SARS-CoV-2 recovery of 25.59 ± 5.04% and the least efficient method was aluminum hydroxide adsorption-elution. This study suggests that the UF method provides rapid and straightforward recovery of SARS-CoV-2 in wastewater.
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Affiliation(s)
- Ines Othman
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia E-mail:
| | - Amna Helmi
- Directorate of Milieu Hygiene and Environmental Protection at the Health Ministry, Tunis, Tunisia
| | - Ichrak Slama
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia E-mail:
| | - Rawand Hamdi
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia E-mail:
| | - Maha Mastouri
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia E-mail: ; Fattouma Bourguiba University Hospital, Laboratory of Microbiology, Monastir, Tunisia
| | - Mahjoub Aouni
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia E-mail:
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12
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Evaluation of SARS-CoV-2 concentrations in wastewater and river water samples. CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2022; 6. [PMID: 37520921 PMCID: PMC9055419 DOI: 10.1016/j.cscee.2022.100214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
There are only a few established methods to determine the concentration of encapsulated viruses, such as SARS-CoV-2, in water matrices, limiting the application of wastewater-based epidemiology (WBE)—an important tool for public health research. The present study compared four methods that are commonly used to concentrate non-encapsulated enteric viruses for determining SARS-CoV-2 concentration in wastewater and wastewater-enriched river water samples. The four methods tested were electronegative membrane with Mg+2 addition, aluminum hydroxide-based precipitation, polyethylene glycol (PEG) 8000 precipitation, and ultrafiltration (with porosity of 10 and 50 kDa). Prior to the concentration step, filtration or centrifugation was performed to remove suspended particles from the samples (pretreatment). To evaluate the recovery efficiency (%), samples of SARS-CoV-2 from nasopharyngeal swabs obtained from RT-qPCR-positive patients were used as spiked samples. The second part of the analysis involved the quantification of the SARS-CoV-2 copy number in analytes without SARS-CoV-2-spiked samples. Among the tested methods, pretreatment via centrifugation followed by ultrafiltration with a 50-kDa cut-off was found the most efficient method for wastewater samples with spiked samples (54.3 or 113.01% efficiency). For the wastewater-enriched river samples with spiked samples, pretreatment via centrifugation followed by filtration using an electronegative membrane was the most efficient method (110.8% and 95.9% for N1 and N2 markers, respectively). However, ultrafiltration of the raw river water samples using 10 or 50 kDa cut-off filters and PEG 8000 precipitation showed the best concentration efficiency based on copy number, regardless of the pretreatment approach or sample type (values ranging from 3 × 105 to 6.7 × 103). The effectiveness of the concentration method can vary depending on the type of sample and concentration method. We consider that this study will contribute to more widespread use of WBE for the environmental surveillance of SARS-CoV-2.
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13
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Stephens N, Béen F, Savic D. An Analysis of SARS-CoV-2 in Wastewater to Evaluate the Effectiveness of Nonpharmaceutical Interventions against COVID-19 in The Netherlands. ACS ES&T WATER 2022; 2:2158-2166. [PMID: 37552733 PMCID: PMC9199439 DOI: 10.1021/acsestwater.2c00071] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 05/07/2023]
Abstract
Wastewater-based epidemiology (WBE) is increasingly being recognized as a powerful tool for detecting and monitoring SARS-CoV-2 trends at a population level. This study looked to extend the use of WBE to explore the effectiveness of nonpharmaceutical interventions (NPIs) that have been used in response to COVID-19 and compare the results to the effect of such interventions on COVID-19 hospitalizations. A data-driven approach demonstrated that trends of SARS-CoV-2 RNA in wastewater, from Amsterdam and Utrecht (The Netherlands), precede hospitalizations by at least 3-9 days. Additionally, the effect of NPIs can be seen in wastewater and hospitalizations after 20 and 24 days, respectively. Changepoint analysis indicated that the closure of schools and universities significantly reduced the level of SARS-CoV-2 RNA in wastewater and COVID-19 hospitalizations. Regression modeling suggested the stay-at-home policy is an effective intervention for reducing the level of SARS-CoV-2 RNA in wastewater, whereas the closure of workplaces significantly reduced hospitalizations in both Dutch cities. This study demonstrates how WBE can be used to inform public health decisions and anticipate future strain on healthcare facilities in major cities but also indicates a need for higher temporal resolution of wastewater sampling.
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Affiliation(s)
- Natalie Stephens
- Department of Engineering, Mathematics and Physical
Sciences, University of Exeter, Stocker Road, Exeter EX4 4PY,
United Kingdom
| | - Frederic Béen
- KWR Water Research
Institute, Groningeghaven 7, 430 BB Nieuwegein, The
Netherlands
| | - Dragan Savic
- KWR Water Research
Institute, Groningeghaven 7, 430 BB Nieuwegein, The
Netherlands
- Centre for Water Systems, University of
Exeter, Stocker Road, Exeter EX4 4PY, United
Kingdom
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14
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Mousazadeh M, Kabdaşlı I, Khademi S, Sandoval MA, Moussavi SP, Malekdar F, Gilhotra V, Hashemi M, Dehghani MH. A critical review on the existing wastewater treatment methods in the COVID-19 era: What is the potential of advanced oxidation processes in combatting viral especially SARS-CoV-2? JOURNAL OF WATER PROCESS ENGINEERING 2022; 49:103077. [PMID: 35990175 PMCID: PMC9381433 DOI: 10.1016/j.jwpe.2022.103077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 06/01/2023]
Abstract
The COVID-19 epidemic has put the risk of virus contamination in water bodies on the horizon of health authorities. Hence, finding effective ways to remove the virus, especially SARS-CoV-2, from wastewater treatment plants (WWTPs) has emerged as a hot issue in the last few years. Herein, this study first deals with the fate of SARS-CoV-2 genetic material in WWTPs, then critically reviews and compares different wastewater treatment methods for combatting COVID-19 as well as to increase the water quality. This critical review sheds light the efficiency of advanced oxidation processes (AOPs) to inactivate virus, specially SARS-CoV-2 RNA. Although several physicochemical treatment processes (e.g. activated sludge) are commonly used to eliminate pathogens, AOPs are the most versatile and effective virus inactivation methods. For instance, TiO2 is the most known and widely studied photo-catalyst innocuously utilized to degrade pollutants as well as to photo-induce bacterial and virus disinfection due to its high chemical resistance and efficient photo-activity. When ozone is dissolved in water and wastewater, it generates a wide spectrum of the reactive oxygen species (ROS), which are responsible to degrade materials in virus membranes resulting in destroying the cell wall. Furthermore, electrochemical advanced oxidation processes act through direct oxidation when pathogens react at the anode surface or by indirect oxidation through oxidizing species produced in the bulk solution. Consequently, they represent a feasible choice for the inactivation of a wide range of pathogens. Nonetheless, there are some challenges with AOPs which should be addressed for application at industrial-scale.
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Affiliation(s)
- Milad Mousazadeh
- Social Determinants of Health Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
- Department of Environmental Health Engineering, School of Health, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Işık Kabdaşlı
- İstanbul Technical University, Civil Engineering Faculty, Environmental Engineering Department, Ayazağa Campus, 34469 Maslak, İstanbul, Turkey
| | - Sara Khademi
- Health, Safety, and Environment Specialist, North Drilling Company, Ahvaz, Iran
| | - Miguel Angel Sandoval
- Universidad de Santiago de Chile USACH, Facultad de Química y Biología, Departamento de Química de los Materiales, Laboratorio de Electroquímica Medio Ambiental, LEQMA, Casilla 40, Correo 33, Santiago, Chile
- Universidad de Guanajuato, División de Ciencias Naturales y Exactas, Departamento de Ingeniería Química, Noria Alta S/N, 36050, Guanajuato, Guanajuato, Mexico
| | | | - Fatemeh Malekdar
- Department of Foot and Mouth Disease Vaccine Production, Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Vishakha Gilhotra
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Marjan Hashemi
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hadi Dehghani
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Institute for Environmental Research, Center for Solid Waste Research, Tehran University of Medical Sciences, Tehran, Iran
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15
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Acosta N, Bautista MA, Waddell BJ, McCalder J, Beaudet AB, Man L, Pradhan P, Sedaghat N, Papparis C, Bacanu A, Hollman J, Krusina A, Southern DA, Williamson T, Li C, Bhatnagar S, Murphy S, Chen J, Kuzma D, Clark R, Meddings J, Hu J, Cabaj JL, Conly JM, Dai X, Lu X, Chekouo T, Ruecker NJ, Achari G, Ryan MC, Frankowski K, Hubert CRJ, Parkins MD. Longitudinal SARS-CoV-2 RNA wastewater monitoring across a range of scales correlates with total and regional COVID-19 burden in a well-defined urban population. WATER RESEARCH 2022; 220:118611. [PMID: 35661506 PMCID: PMC9107283 DOI: 10.1016/j.watres.2022.118611] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 04/13/2022] [Accepted: 05/13/2022] [Indexed: 05/03/2023]
Abstract
Wastewater-based epidemiology (WBE) is an emerging surveillance tool that has been used to monitor the ongoing COVID-19 pandemic by tracking SARS-CoV-2 RNA shed into wastewater. WBE was performed to monitor the occurrence and spread of SARS-CoV-2 from three wastewater treatment plants (WWTP) and six neighborhoods in the city of Calgary, Canada (population 1.44 million). A total of 222 WWTP and 192 neighborhood samples were collected from June 2020 to May 2021, encompassing the end of the first-wave (June 2020), the second-wave (November end to December 2020) and the third-wave of the COVID-19 pandemic (mid-April to May 2021). Flow-weighted 24-hour composite samples were processed to extract RNA that was then analyzed for two SARS-CoV-2-specific regions of the nucleocapsid gene, N1 and N2, using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Using this approach SARS-CoV-2 RNA was detected in 98.06% (406/414) of wastewater samples. SARS-CoV-2 RNA abundance was compared to clinically diagnosed COVID-19 cases organized by the three-digit postal code of affected individuals' primary residences, enabling correlation analysis at neighborhood, WWTP and city-wide scales. Strong correlations were observed between N1 & N2 gene signals in wastewater and new daily cases for WWTPs and neighborhoods. Similarly, when flow rates at Calgary's three WWTPs were used to normalize observed concentrations of SARS-CoV-2 RNA and combine them into a city-wide signal, this was strongly correlated with regionally diagnosed COVID-19 cases and clinical test percent positivity rate. Linked census data demonstrated disproportionate SARS-CoV-2 in wastewater from areas of the city with lower socioeconomic status and more racialized communities. WBE across a range of urban scales was demonstrated to be an effective mechanism of COVID-19 surveillance.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - María A Bautista
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Barbara J Waddell
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Janine McCalder
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada; Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Alexander Buchner Beaudet
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada; Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Lawrence Man
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Puja Pradhan
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada; Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Navid Sedaghat
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada; Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Chloe Papparis
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada; Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Andra Bacanu
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada; Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Jordan Hollman
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada; Department of Geosciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Alexander Krusina
- Department of Medicine, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
| | - Danielle A Southern
- Department of Medicine, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
| | - Tyler Williamson
- Department of Community Health Sciences, University of Calgary, 3280 Hospital Drive NW, Calgary, Alberta, T2N 4Z6, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, 3280 Hospital Dr NW, Calgary, Alberta, T2N 4Z6, Canada
| | - Carmen Li
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Srijak Bhatnagar
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Sean Murphy
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Jianwei Chen
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Darina Kuzma
- Advancing Canadian Water Assets, University of Calgary, 3131 210 Ave SE, Calgary, Alberta, T0L 0×0, Canada
| | - Rhonda Clark
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada; Advancing Canadian Water Assets, University of Calgary, 3131 210 Ave SE, Calgary, Alberta, T0L 0×0, Canada
| | - Jon Meddings
- Department of Medicine, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
| | - Jia Hu
- Department of Community Health Sciences, University of Calgary, 3280 Hospital Drive NW, Calgary, Alberta, T2N 4Z6, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, 3280 Hospital Dr NW, Calgary, Alberta, T2N 4Z6, Canada; Provincial Population & Public Health, Alberta Health Services, 3030 Hospital Drive NW, Calgary, Alberta, T2N 4W4, Canada
| | - Jason L Cabaj
- Department of Community Health Sciences, University of Calgary, 3280 Hospital Drive NW, Calgary, Alberta, T2N 4Z6, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, 3280 Hospital Dr NW, Calgary, Alberta, T2N 4Z6, Canada; Provincial Population & Public Health, Alberta Health Services, 3030 Hospital Drive NW, Calgary, Alberta, T2N 4W4, Canada
| | - John M Conly
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada; Department of Medicine, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, 3280 Hospital Dr NW, Calgary, Alberta, T2N 4Z6, Canada; Infection Prevention and Control, Alberta Health Services, 1403 29th Street NW, Calgary, Alberta, T2N 2T9, Canada; Department of Pathology and Laboratory Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada; Snyder Institute for Chronic Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
| | - Xiaotian Dai
- Department of Mathematics and Statistics, University of Calgary, 2500 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Xuewen Lu
- Department of Mathematics and Statistics, University of Calgary, 2500 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Thierry Chekouo
- Department of Mathematics and Statistics, University of Calgary, 2500 Hospital Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Norma J Ruecker
- Water Quality Services, City of Calgary, 625 25 Ave SE, Calgary, Alberta, T2G 4k8, Canada
| | - Gopal Achari
- Department of Civil Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - M Cathryn Ryan
- Department of Geosciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, 3131 210 Ave SE, Calgary, Alberta, T0L 0×0, Canada
| | - Casey R J Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada; Department of Medicine, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada; Snyder Institute for Chronic Diseases, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada.
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16
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Spiliotis K, Koutsoumaris CC, Reppas AI, Papaxenopoulou LA, Starke J, Hatzikirou H. Optimal vaccine roll-out strategies including social distancing for pandemics. iScience 2022; 25:104575. [PMID: 35720194 PMCID: PMC9197569 DOI: 10.1016/j.isci.2022.104575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 03/05/2022] [Accepted: 06/07/2022] [Indexed: 12/14/2022] Open
Abstract
Non-pharmacological interventions (NPIs), principally social distancing, in combination with effective vaccines, aspire to develop a protective immunity shield against pandemics and particularly against the COVID-19 pandemic. In this study, an agent-based network model with small-world topology is employed to find optimal policies against pandemics, including social distancing and vaccination strategies. The agents' states are characterized by a variation of the SEIR model (susceptible, exposed, infected, recovered). To explore optimal policies, an equation-free method is proposed to solve the inverse problem of calibrating an agent's infection rate with respect to the vaccination efficacy. The results show that prioritizing the first vaccine dose in combination with mild social restrictions, is sufficient to control the pandemic, with respect to the number of deaths. Moreover, for the same mild number of social contacts, we find an optimal vaccination ratio of 0.85 between older people of ages > 65 compared to younger ones.
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Affiliation(s)
| | - Constantinos Chr. Koutsoumaris
- Department of Research, Development and Innovation Statistics, National Documentation Centre, 48 Vas. Konstantinou St, Athens 11635, Greece
| | - Andreas I. Reppas
- Universität Berlin and Humboldt- Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Lito A. Papaxenopoulou
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, 38106 Braunschweig, Germany
| | - Jens Starke
- Institute of Mathematics, University of Rostock, 18057 Rostock, Germany
| | - Haralampos Hatzikirou
- Centre for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Straße 46, 01062 Dresden, Germany
- Mathematics Department, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates
- Corresponding author
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17
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Masachessi G, Castro G, Cachi AM, Marinzalda MDLÁ, Liendo M, Pisano MB, Sicilia P, Ibarra G, Rojas RM, López L, Barbás G, Cardozo D, Ré VE, Nates SV. Wastewater based epidemiology as a silent sentinel of the trend of SARS-CoV-2 circulation in the community in central Argentina. WATER RESEARCH 2022; 219:118541. [PMID: 35584586 PMCID: PMC9066365 DOI: 10.1016/j.watres.2022.118541] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/30/2022] [Accepted: 05/01/2022] [Indexed: 05/08/2023]
Abstract
Monitoring wastewater for the traces of viruses allows effective surveillance of entire communities, including symptomatic and asymptomatic infected individuals, providing information on whether a specific pathogen is circulating in a population. In the context of the COVID-19 pandemic, 261 wastewater samples from six communities of the province of Córdoba, Argentina were analyzed. From mid-May 2020 to the end of August 2021, raw sewage samples were collected from the central network pipe that enters into the Wastewater Treatment Plants (WWTP) in Córdoba city and five communities in the Punilla Valley. SARS-CoV-2 was concentrated by using the polyethylene glycol-6000 precipitation method. Viral genomes were extracted from concentrated samples, and N- and E-SARS-CoV-2 genes were detected by using real time RT-PCR. Wastewater samples that resulted positive for SARS-CoV-2 genome detection were subjected to viral variants of concern (VOCs) identification by real time RT-PCR. Overall, just by using the identification of the N gene or E gene, the rates of viral genome detection were 43.4% (86/198) and 51.5% (102/198) respectively, and by using both methodologies (positivity criterion: detection of N and / or E gene), the detection rate was 71.2% (141/198). Thereby, the optimal strategy to study the SARS-CoV-2 genome in wastewater would be the use of the combined detection of both genes. Detection of SARS-CoV-2 variants in wastewater reflected their circulation in the community, showing no VOCs detection in the first COVID-19 wave and their co-circulation with Gamma, Alpha and Delta VOCs during 2021. Therefore, SARS-CoV-2 Wastewater Based Epidemiology (WBE) described the introduction, permanence and/or the co-circulation of viral variants in the community. In geographical areas with a stable population, SARS-CoV-2 WBE could be used as an early warning sign of new COVID-19 cases, whereas in localities with a low number of inhabitants and high tourist influx, WBE may only be useful to reflect the circulation of the virus in the community. Overall, the monitoring of SARS-CoV-2 in wastewater can become a silent sentinel of the trend of viral circulation in the community, providing supplementary information for clinical surveillance to support public health measures.
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Affiliation(s)
- Gisela Masachessi
- Instituto de Virología Dr. J. M. Vanella, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, Córdoba X5000, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina.
| | - Gonzalo Castro
- Departamento Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, T. Cáceres de Allende 421, Córdoba X5000HVE, Argentina
| | - Ariana Mariela Cachi
- Instituto Nacional de Medicina Aeronáutica y Espacial, FAA, Av. Fuerza Aérea Argentina Km 6 1/2 S/N B.0 Civico, Córdoba X5010, Argentina; Facultad de la Fuerza Aérea, Universidad de la Defensa Nacional, Av. Fuerza Aerea Argentina 5011, Córdoba X5000, Argentina
| | - María de Los Ángeles Marinzalda
- Instituto Nacional de Medicina Aeronáutica y Espacial, FAA, Av. Fuerza Aérea Argentina Km 6 1/2 S/N B.0 Civico, Córdoba X5010, Argentina; Facultad de la Fuerza Aérea, Universidad de la Defensa Nacional, Av. Fuerza Aerea Argentina 5011, Córdoba X5000, Argentina
| | - Matías Liendo
- Instituto de Virología Dr. J. M. Vanella, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, Córdoba X5000, Argentina
| | - María Belén Pisano
- Instituto de Virología Dr. J. M. Vanella, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, Córdoba X5000, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
| | - Paola Sicilia
- Departamento Laboratorio Central, Ministerio de Salud de la Provincia de Córdoba, T. Cáceres de Allende 421, Córdoba X5000HVE, Argentina
| | - Gustavo Ibarra
- Planta Municipal de tratamiento de efluente cloacales Bajo Grande-Laboratorio de análisis fisicoquímicos, bacteriológicos EDAR Bajo Grande, Cam. Chacra de la Merced 901, Córdoba X5000, Argentina
| | - Ricardo Manuel Rojas
- Cooperativa Integral Regional de Provisión de Servicios Públicos, Vivienda y Consumo Limitada (COOPI), Moreno 78, Villa Carlos Paz, X5152 Córdoba, Argentina
| | - Laura López
- Área de Epidemiología, Ministerio de Salud de la Provincia de Córdoba, Av. Vélez Sarsfield 2311 Ciudad Universitaria, Córdoba X5016 GCH, Argentina
| | - Gabriela Barbás
- Secretaría de Prevención y Promoción de la Salud, Ministerio de Salud de la Provincia de Córdoba, Av. Vélez Sarsfield 2311 Ciudad Universitaria, Córdoba X5016 GCH, Argentina
| | - Diego Cardozo
- Ministerio de Salud de la Provincia de Córdoba, Argentina Av. Vélez Sarsfield 2311 Ciudad Universitaria, Córdoba X5016 GCH, Argentina
| | - Viviana Elisabeth Ré
- Instituto de Virología Dr. J. M. Vanella, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, Córdoba X5000, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
| | - Silvia Viviana Nates
- Instituto de Virología Dr. J. M. Vanella, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n, Ciudad Universitaria, Córdoba X5000, Argentina
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Bar-Or I, Indenbaum V, Weil M, Elul M, Levi N, Aguvaev I, Cohen Z, Levy V, Azar R, Mannasse B, Shirazi R, Bucris E, Mor O, Sela Brown A, Sofer D, Zuckerman NS, Mendelson E, Erster O. National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel. Viruses 2022; 14:1229. [PMID: 35746700 PMCID: PMC9227326 DOI: 10.3390/v14061229] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
In this report, we describe a national-scale monitoring of the SARS-CoV-2 (SC-2) variant dynamics in Israel, using multiple-time sampling of 13 wastewater treatment plants. We used a combination of inclusive and selective quantitative PCR assays that specifically identify variants A19/A20 or B.1.1.7 and tested each sample for the presence and relative viral RNA load of each variant. We show that between December 2020 and March 2021, a complete shift in the SC-2 variant circulation was observed, where the B.1.1.7 replaced the A19 in all examined test points. We further show that the normalized viral load (NVL) values and the average new cases per week reached a peak in January 2021 and then decreased gradually in almost all test points, in parallel with the progression of the national vaccination campaign, during February-March 2021. This study demonstrates the importance of monitoring SC-2 variant by using a combination of inclusive and selective PCR tests on a national scale through wastewater sampling, which is far more amendable for high-throughput monitoring compared with sequencing. This approach may be useful for real-time dynamics surveillance of current and future variants, such as the Omicron (BA.1, BA.2) and other variants.
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Affiliation(s)
- Itay Bar-Or
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Victoria Indenbaum
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Merav Weil
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Michal Elul
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Nofar Levi
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Irina Aguvaev
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Zvi Cohen
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Virginia Levy
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Roberto Azar
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Batya Mannasse
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Rachel Shirazi
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Efrat Bucris
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
- Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Alin Sela Brown
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Danit Sofer
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Ella Mendelson
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
- Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Oran Erster
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
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19
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Jiang SC, Bischel HN, Goel R, Rosso D, Sherchan S, Whiteson KL, Yan T, Solo-Gabriele HM. Integrating Virus Monitoring Strategies for Safe Non-potable Water Reuse. WATER 2022; 14:1187. [PMID: 37622131 PMCID: PMC10448804 DOI: 10.3390/w14081187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Wastewater reclamation and reuse have the potential to supplement water supplies, offering resiliency in times of drought and helping meet increased water demands associated with population growth. Non-potable water reuse represents the largest potential reuse market. Yet economic constraints for new water reuse infrastructure and safety concerns due to microbial water quality, and especially viral pathogen exposure, limit widespread implementation of water reuse. Cost-effective, real-time methods to measure or indicate viral quality of recycled water would do much to instill greater confidence in the practice. This manuscript discusses advancements in monitoring and modeling of viral health risks in the context of water reuse. First, we describe the current wastewater reclamation processes and treatment technologies with an emphasis on virus removal. Second, we review technologies for the measurement of viruses, both culture- and molecular-based, along with their advantages and disadvantages. We introduce promising viral surrogates and specific pathogenic viruses that can serve as indicators of viral risk for water reuse. We suggest metagenomic analyses for viral screening and flow cytometry for quantification of virus-like particles as new approaches to complement more traditional methods. Third, we describe modeling to assess health risks through quantitative microbial risk assessments (QMRAs), the most common strategy to couple data on virus concentrations with human exposure scenarios. We then explore the potential of artificial neural networks (ANNs) to incorporate suites of data from wastewater treatment processes, water quality parameters, and viral surrogates. We recommend ANNs as a means to utilize existing water quality data, alongside new complementary measures of viral quality, to achieve cost-effective strategies to assess risks associated with infectious human viruses in recycled water. Given the review, we conclude that technologies are ready for identifying and implementing viral surrogates for health risk reduction in the next decade. Incorporating modeling with monitoring data would likely result in more robust assessment of water reuse risk.
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Affiliation(s)
- Sunny C Jiang
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697, USA
- Water-Energy Nexus Center, 844G Engineering Tower, University of California, Irvine, CA 92697-2175
| | - Heather N Bischel
- Department of Civil & Environmental Engineering, University of California, Davis CA 95616
| | - Ramesh Goel
- Department of Civil & Environmental Engineering, University of Utah, Salt Lake City, Utah 84112
| | - Diego Rosso
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697, USA
- Water-Energy Nexus Center, 844G Engineering Tower, University of California, Irvine, CA 92697-2175
| | - Samendra Sherchan
- Department of Environmental Health sciences, Tulane university, New Orleans, LA 70112
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Tao Yan
- Department of Civil and Environmental Engineering, and Water Resources Research Center, University of Hawaii at Manoa, HI 96822, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, FL, 33146, USA
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20
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Pechlivanis N, Tsagiopoulou M, Maniou MC, Togkousidis A, Mouchtaropoulou E, Chassalevris T, Chaintoutis SC, Petala M, Kostoglou M, Karapantsios T, Laidou S, Vlachonikola E, Chatzidimitriou A, Papadopoulos A, Papaioannou N, Dovas CI, Argiriou A, Psomopoulos F. Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater and a use-case in the metropolitan area of Thessaloniki, Greece. Sci Rep 2022; 12:2659. [PMID: 35177697 PMCID: PMC8854625 DOI: 10.1038/s41598-022-06625-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/28/2022] [Indexed: 12/17/2022] Open
Abstract
The COVID-19 pandemic represents an unprecedented global crisis necessitating novel approaches for, amongst others, early detection of emerging variants relating to the evolution and spread of the virus. Recently, the detection of SARS-CoV-2 RNA in wastewater has emerged as a useful tool to monitor the prevalence of the virus in the community. Here, we propose a novel methodology, called lineagespot, for the monitoring of mutations and the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing (NGS). Our proposed method was tested and evaluated using NGS data produced by the sequencing of 14 wastewater samples from the municipality of Thessaloniki, Greece, covering a 6-month period. The results showed the presence of SARS-CoV-2 variants in wastewater data. lineagespot was able to record the evolution and rapid domination of the Alpha variant (B.1.1.7) in the community, and allowed the correlation between the mutations evident through our approach and the mutations observed in patients from the same area and time periods. lineagespot is an open-source tool, implemented in R, and is freely available on GitHub and registered on bio.tools.
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Affiliation(s)
- Nikolaos Pechlivanis
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.,Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece
| | - Maria Tsagiopoulou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Maria Christina Maniou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Anastasis Togkousidis
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Evangelia Mouchtaropoulou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Taxiarchis Chassalevris
- School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece
| | - Serafeim C Chaintoutis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece
| | - Maria Petala
- Department of Civil Engineering, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece
| | - Margaritis Kostoglou
- Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece
| | - Thodoris Karapantsios
- Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece
| | - Stamatia Laidou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.,Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece
| | - Elisavet Vlachonikola
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.,Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Agis Papadopoulos
- EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636, Thessaloníki, Greece
| | - Nikolaos Papaioannou
- School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece
| | - Chrysostomos I Dovas
- School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.,Department of Food Science and Nutrition, University of the Aegean, Myrina, 81400, Lemnos, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.
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Shivalkar S, Pingali MS, Verma A, Singh A, Singh V, Paital B, Das D, Varadwaj PK, Samanta SK. Outbreak of COVID-19: A Detailed Overview and Its Consequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1353:23-45. [PMID: 35137366 DOI: 10.1007/978-3-030-85113-2_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION After the outbreak from Wuhan City of China, COVID-19, caused by SARS-CoV-2, has become a pandemic worldwide in a very short span of time. The high transmission rate and pathogenicity of this virus have made COVID-19 a major public health concern globally. Basically, the emergence of SARS-CoV-2 is the third introduction of a highly infectious human epidemic coronavirus in the twenty-first century. Various research groups have claimed bats to be the natural host of SARS-CoV-2. However, the intermediate host and mode of transmission from bat to humans are not revealed yet. The COVID-19 cost hundreds and thousands of lives and millions are facing the consequences. The objective of this chapter was to analyze the outbreak of COVID-19 and problems faced globally. METHODS All published relevant literature from scientific sources and reputed news channels are considered to write the current review. RESULTS Generally, elder persons and more particularly people with underlying medical conditions are found to be highly vulnerable to severe infection and prone to fatal outcomes. Unfortunately, there is no specific treatment with clinically approved drugs or vaccines to treat this disease. Several research groups have been investigating the efficacies of several antiviral and repurposed drugs. Currently, most of the SARS-COV-2 vaccines are at the preclinical or clinical stage of development. The latest research progress on the epidemiology, clinical characteristics, pathogenesis, diagnosis, and current status of therapeutic intervention indicates that still a specific drug or vaccine needs to come up for the effective treatment of the pandemic COVID-19. It is observed that various aspects of social life, economic status, and healthcare systems are majorly affected by this pandemic. CONCLUSION It is concluded that the outbreak of COVID-19 has severely affected each and every field, such as social, scientific, industrial, transport, and medical sectors. Irrespective of tremendous efforts globally, few vaccines are now available for the prevention of the disease. Specific drug is not available publicly for the treatment of COVID-19. Prevention of air pollution that can aggravate COVID-19 has been suggested. Therefore, as of now, social distancing and sanitization practices are the only options available for the prevention of the disease for many.
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Affiliation(s)
- Saurabh Shivalkar
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, India
| | - M Shivapriya Pingali
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, India
| | - Arushi Verma
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, India
| | - Anirudh Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, India
| | - Vishal Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, India
| | - Biswaranjan Paital
- Reodx Regulation Laboratory, Department of Zoology, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India.
| | - Debashis Das
- Department of Botany, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, India.
| | - Sintu Kumar Samanta
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, India.
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22
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Kalkal A, Allawadhi P, Kumar P, Sehgal A, Verma A, Pawar K, Pradhan R, Paital B, Packirisamy G. Sensing and 3D printing technologies in personalized healthcare for the management of health crises including the COVID-19 outbreak. SENSORS INTERNATIONAL 2022; 3:100180. [PMID: 35601184 PMCID: PMC9107332 DOI: 10.1016/j.sintl.2022.100180] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 01/12/2023] Open
Abstract
A major threat that has surrounded human civilization since the beginning of the year 2020 is the outbreak of coronavirus disease 2019 (COVID-19). It has been declared a pandemic by the World Health Organization and significantly affected populations globally, causing medical and economic despair. Healthcare chains across the globe have been under grave stress owing to shortages of medical equipments necessary to address a pandemic. Furthermore, personal protective equipment supplies, mandatory for healthcare staff for treating severely ill patients, have been in short supply. To address the necessary requisites during the pandemic, several researchers, hospitals, and industries collaborated to meet the demand for these medical equipments in an economically viable manner. In this context, 3D printing technologies have provided enormous potential in creating personalized healthcare equipment, including face masks, face shields, rapid detection kits, testing swabs, biosensors, and various ventilator components. This has been made possible by capitalizing on centralized large-scale manufacturing using 3D printing and local distribution of verified and tested computer-aided design files. The primary focus of this study is, "How 3D printing is helpful in developing these equipments, and how it can be helpful in the development and deployment of various sensing and point-of-care-testing (POCTs) devices for the commercialization?" Further, the present study also takes care of patient safety by implementing novel 3D printed health equipment used for COVID-19 patients. Moreover, the study helps identify and highlight the efforts made by various organizations toward the usage of 3D printing technologies, which are helpful in combating the ongoing pandemic.
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Affiliation(s)
- Ashish Kalkal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Prince Allawadhi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Pramod Kumar
- Institute Instrumentation Center, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Abhishek Sehgal
- Department of Chemical Engineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Ashmit Verma
- Divyasampark iHUB Roorkee for Devices, Materials and Technology Foundation, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Kaustubh Pawar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Rangadhar Pradhan
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Biswaranjan Paital
- Redox Regulation Laboratory, Department of Zoology, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, 751003, India
| | - Gopinath Packirisamy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
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23
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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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