1
|
Morecchiato F, Coppi M, Niccolai C, Antonelli A, Di Gloria L, Calà P, Mancuso F, Ramazzotti M, Lotti T, Lubello C, Rossolini GM. Evaluation of different molecular systems for detection and quantification of SARS-CoV-2 RNA from wastewater samples. J Virol Methods 2024; 328:114956. [PMID: 38796134 DOI: 10.1016/j.jviromet.2024.114956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
Wastewater-based epidemiology has proved to be a suitable approach for tracking the spread of epidemic agents including SARS-CoV-2 RNA. Different protocols have been developed for quantitative detection of SARS-CoV-2 RNA from wastewater samples, but little is known on their performance. In this study we compared three protocols based on Reverse Transcription Real Time-PCR (RT-PCR) and one based on Droplet Digital PCR (ddPCR) for SARS-CoV-2 RNA detection from 35 wastewater samples. Overall, SARS-CoV-2 RNA was detected by at least one method in 85.7 % of samples, while 51.4 %, 22.8 % and 8.6 % resulted positive with two, three or all four methods, respectively. Protocols based on commercial RT-PCR assays and on Droplet Digital PCR showed an overall higher sensitivity vs. an in-house assay. The use of more than one system, targeting different genes, could be helpful to increase detection sensitivity.
Collapse
Affiliation(s)
- Fabio Morecchiato
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Claudia Niccolai
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Leandro Di Gloria
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50, Firenze (FI) 50134, Italy
| | - Piergiuseppe Calà
- Tuscany Region, Department of Prevention Local Health Authority Tuscany Center, Via S. Salvi, 12, Firenze (FI) 50135, Italy
| | - Fabrizio Mancuso
- Ingegnerie Toscane - Area R&D, Via Bellatalla, 1, Pisa (PI) 56121, Italy
| | - Matteo Ramazzotti
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50, Firenze (FI) 50134, Italy
| | - Tommaso Lotti
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3, Firenze (FI) 50139, Italy
| | - Claudio Lubello
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3, Firenze (FI) 50139, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy.
| |
Collapse
|
2
|
van der Drift AMR, Haver A, Kloosterman A, van der Beek RFHJ, Nagelkerke E, Eggink D, Laros JFJ, Nrs C, van Dissel JT, de Roda Husman AM, Lodder WJ. Long-term wastewater monitoring of SARS-CoV-2 viral loads and variants at the major international passenger hub Amsterdam Schiphol Airport: A valuable addition to COVID-19 surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 937:173535. [PMID: 38802021 DOI: 10.1016/j.scitotenv.2024.173535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Wastewater-based epidemiological surveillance at municipal wastewater treatment plants has proven to play an important role in COVID-19 surveillance. Considering international passenger hubs contribute extensively to global transmission of viruses, wastewater surveillance at this type of location may be of added value as well. The aim of this study is to explore the potential of long-term wastewater surveillance at a large passenger hub as an additional tool for public health surveillance during different stages of a pandemic. Here, we present an analysis of SARS-CoV-2 viral loads in airport wastewater by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) from the beginning of the COVID-19 pandemic in Feb 2020, and an analysis of SARS-CoV-2 variants by whole-genome next-generation sequencing from Sep 2020, both until Sep 2022, in the Netherlands. Results are contextualized using (inter)national measures and data sources such as passenger numbers, clinical surveillance data and national wastewater surveillance data. Our findings show that wastewater surveillance was possible throughout the study period, irrespective of measures, as viral loads were detected and quantified in 98.6 % (273/277) of samples. Emergence of SARS-CoV-2 variants, identified in 91.0 % (161/177) of sequenced samples, coincided with increases in viral loads. Furthermore, trends in viral load and variant detection in airport wastewater closely followed, and in some cases preceded, trends in national daily average viral load in wastewater and variants detected in clinical surveillance. Wastewater-based epidemiology at a large international airport is a valuable addition to classical COVID-19 surveillance and the developed expertise can be applied in pandemic preparedness plans for other (emerging) pathogens in the future.
Collapse
Affiliation(s)
- Anne-Merel R van der Drift
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; Institute for Risk Assessment Science (IRAS), Utrecht University (UU), Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Auke Haver
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Astrid Kloosterman
- Centre for Environmental Safety and Security (M&V), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721, MA, Bilthoven, the Netherlands
| | - Rudolf F H J van der Beek
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Erwin Nagelkerke
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Dirk Eggink
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Applied Evolutionary Biology, 1105 AZ Amsterdam, the Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics (HG), Leiden University Medical Center (LUMC); Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Department of BioInformatics and computational services (BIR), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721, MA, Bilthoven, the Netherlands
| | - Consortium Nrs
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Jaap T van Dissel
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; Department of Infectious Diseases, Leiden University Medical Center (LUMC); Albinusdreef 2, 2333, ZA, Leiden, the Netherlands
| | - Ana Maria de Roda Husman
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; Institute for Risk Assessment Science (IRAS), Utrecht University (UU), Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Willemijn J Lodder
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands.
| |
Collapse
|
3
|
Rashid SA, Rajendiran S, Nazakat R, Mohammad Sham N, Khairul Hasni NA, Anasir MI, Kamel KA, Muhamad Robat R. A scoping review of global SARS-CoV-2 wastewater-based epidemiology in light of COVID-19 pandemic. Heliyon 2024; 10:e30600. [PMID: 38765075 PMCID: PMC11098849 DOI: 10.1016/j.heliyon.2024.e30600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Recently, wastewater-based epidemiology (WBE) research has experienced a strong impetus during the Coronavirus disease 2019 (COVID-19) pandemic. However, a few technical issues related to surveillance strategies, such as standardized procedures ranging from sampling to testing protocols, need to be resolved in preparation for future infectious disease outbreaks. This review highlights the study characteristics, potential use of WBE and overview of methods, as well as methods utilized to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including its variant in wastewater. A literature search was performed electronically in PubMed and Scopus according to PRISMA guidelines for relevant peer-reviewed articles published between January 2020 and March 2022. The search identified 588 articles, out of which 221 fulfilled the necessary criteria and are discussed in this review. Most global WBE studies were conducted in North America (n = 75, 34 %), followed by Europe (n = 68, 30.8 %), and Asia (n = 43, 19.5 %). The review also showed that most of the application of WBE observed were to correlate SARS-CoV-2 ribonucleic acid (RNA) trends in sewage with epidemiological data (n = 90, 40.7 %). The techniques that were often used globally for sample collection, concentration, preferred matrix recovery control and various sample types were also discussed. Overall, this review provided a framework for researchers specializing in WBE to apply strategic approaches to their research questions in achieving better functional insights. In addition, areas that needed more in-depth analysis, data collection, and ideas for new initiatives were identified.
Collapse
Affiliation(s)
- Siti Aishah Rashid
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Sakshaleni Rajendiran
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Raheel Nazakat
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Noraishah Mohammad Sham
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Nurul Amalina Khairul Hasni
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Mohd Ishtiaq Anasir
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Khayri Azizi Kamel
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Rosnawati Muhamad Robat
- Occupational & Environmental Health Unit, Public Health Division, Selangor State Health Department, Ministry of Health Malaysia, Malaysia
| |
Collapse
|
4
|
Krogsgaard LW, Benedetti G, Gudde A, Richter SR, Rasmussen LD, Midgley SE, Qvesel AG, Nauta M, Bahrenscheer NS, von Kappelgaard L, McManus O, Hansen NC, Pedersen JB, Haimes D, Gamst J, Nørgaard LS, Jørgensen ACU, Ejegod DM, Møller SS, Clauson-Kaas J, Knudsen IM, Franck KT, Ethelberg S. Results from the SARS-CoV-2 wastewater-based surveillance system in Denmark, July 2021 to June 2022. WATER RESEARCH 2024; 252:121223. [PMID: 38310802 DOI: 10.1016/j.watres.2024.121223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/01/2023] [Accepted: 01/28/2024] [Indexed: 02/06/2024]
Abstract
The microbiological analysis of wastewater samples is increasingly used for the surveillance of SARS-CoV-2 globally. We described the setup process of the national SARS-CoV-2 wastewater-based surveillance system in Denmark, presented its main results during the first year of activities, from July 2021 to June 2022, and discussed their operational significance. The Danish SARS-CoV-2 wastewater-based surveillance system was designed to cover 85 % of the population in Denmark and it entailed taking three weekly samples from 230 sites. Samples were RT-qPCR tested for SARS-CoV-2 RNA, targeting the genetic markers N1, N2 and RdRp, and for two faecal indicators, Pepper Mild Mottle Virus and crAssphage. We calculated the weekly SARS-CoV-2 RNA concentration in the wastewater from each sampling site and monitored it in view of the results from individual testing, at the national and regional levels. We attempted to use wastewater results to identify potential local outbreaks, and we sequenced positive wastewater samples using Nanopore sequencing to monitor the circulation of viral variants in Denmark. The system reached its full implementation by October 2021 and covered up to 86.4 % of the Danish population. The system allowed for monitoring of the national and regional trends of SARS-CoV-2 infections in Denmark. However, the system contribution to the identification of potential local outbreaks was limited by the extensive information available from clinical testing. The sequencing of wastewater samples identified relevant variants of concern, in line with results from sequencing of human samples. Amidst the COVID-19 pandemic, Denmark implemented a nationwide SARS-CoV-2 wastewater-based surveillance system that integrated routine surveillance from individual testing. Today, while testing for COVID-19 at the community level has been discontinued, the system is on the frontline to monitor the occurrence and spread of SARS-CoV-2 in Denmark.
Collapse
Affiliation(s)
- Lene Wulff Krogsgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Guido Benedetti
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark.
| | - Aina Gudde
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Stine Raith Richter
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Lasse Dam Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Sofie Elisabeth Midgley
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Amanda Gammelby Qvesel
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Maarten Nauta
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Naja Stolberg Bahrenscheer
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Lene von Kappelgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Oliver McManus
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, Gustav III: s Boulevard 40, 16973 Solna, Sweden
| | - Nicco Claudio Hansen
- Test Centre Denmark, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Jan Bryla Pedersen
- Department of Finance, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Danny Haimes
- Danish Patient Safety Authority, Islands Brygge 67, 2300 Copenhagen, Denmark
| | - Jesper Gamst
- Eurofins Environment, Ladelundvej 85, 6600 Vejen, Denmark
| | | | | | | | | | - Jes Clauson-Kaas
- HOFOR - Greater Copenhagen Utility, Ørestads Boulevard 35, 2300 Copenhagen, Denmark
| | - Ida Marie Knudsen
- HOFOR - Greater Copenhagen Utility, Ørestads Boulevard 35, 2300 Copenhagen, Denmark
| | - Kristina Træholt Franck
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; Department of Public Health, Global Health Section, University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen, Denmark
| |
Collapse
|
5
|
Norese C, Nicosia E, Cortese K, Gentili V, Rizzo R, Rizzo S, Grasselli E, De Negri Atanasio G, Gagliani MC, Tiso M, Zinni M, Pulliero A, Izzotti A. SARS-CoV-2 presence in recreational seawater and evaluation of intestine permeability: experimental evidence of low impact on public health. Front Public Health 2024; 12:1326453. [PMID: 38500723 PMCID: PMC10944960 DOI: 10.3389/fpubh.2024.1326453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/13/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction Coastal seawater pollution poses a public health risk due to the potential ingestion of contaminated water during recreational activities. Wastewater-based epidemiology has revealed the abundant presence of SARS-CoV-2 in seawater emitted from wastewater outlets. The objective of this research was to investigate the impact of seawater on SARS-CoV-2 infectivity to assess the safety of recreational activities in seawater. Methods Wild SARS-CoV-2 was collected from oral swabs of COVID-19 affected patients and incubated for up to 90 min using the following solutions: (a) standard physiological solution (control), (b) reconstructed seawater (3.5% NaCl), and (c) authentic seawater (3.8%). Samples were then exposed to two different host systems: (a) Vero E6 cells expressing the ACE2 SARS-CoV-2 receptor and (b) 3D multi-tissue organoids reconstructing the human intestine. The presence of intracellular virus inside the host systems was determined using plaque assay, quantitative real-time PCR (qPCR), and transmission electron microscopy. Results Ultrastructural examination of Vero E6 cells revealed the presence of virus particles at the cell surface and in replicative compartments inside cells treated with seawater and/or reconstituted water only for samples incubated up to 2 min. After a 90-min incubation, the presence of the virus and its infectivity in Vero E6 cells was reduced by 90%. Ultrastructural analysis performed in 3D epi-intestinal tissue did not reveal intact viral particles or infection signs, despite the presence of viral nucleic acid detected by qPCR. Indeed, viral genes (Orf1ab and N) were found in the intestinal luminal epithelium but not in the enteric capillaries. These findings suggest that the intestinal tissue is not a preferential entry site for SARS-CoV-2 in the human body. Additionally, the presence of hypertonic saline solution did not increase the susceptibility of the intestinal epithelium to virus penetration; rather, it neutralized its infectivity. Conclusion Our results indicate that engaging in recreational activities in a seawater environment does not pose a significant risk for COVID-19 infection, despite the possible presence of viral nucleic acid deriving from degraded and fragmented viruses.
Collapse
Affiliation(s)
- Clelia Norese
- DIMES, Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Elena Nicosia
- Regione Liguria, Environmental Department, Ligurian Region, Genoa, Italy
| | - Katia Cortese
- DIMES, Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Valentina Gentili
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Roberta Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
- LTTA, Clinical Research Center, University of Ferrara, Ferrara, Italy
| | - Sabrina Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Elena Grasselli
- Department of Earth, Environmental, and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Giulia De Negri Atanasio
- Department of Earth, Environmental, and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | | | - Micaela Tiso
- MICAMO, Spin-Off Department of Earth Sciences, University of Genoa, Genoa, Italy
| | - Matteo Zinni
- MICAMO, Spin-Off Department of Earth Sciences, University of Genoa, Genoa, Italy
| | | | - Alberto Izzotti
- DIMES, Department of Experimental Medicine, University of Genoa, Genoa, Italy
- HSM, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| |
Collapse
|
6
|
Corrin T, Rabeenthira P, Young KM, Mathiyalagan G, Baumeister A, Pussegoda K, Waddell LA. A scoping review of human pathogens detected in untreated human wastewater and sludge. JOURNAL OF WATER AND HEALTH 2024; 22:436-449. [PMID: 38421635 PMCID: wh_2024_326 DOI: 10.2166/wh.2024.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Wastewater monitoring is an approach to identify the presence or abundance of pathogens within a population. The objective of this scoping review (ScR) was to identify and characterize research on human pathogens and antimicrobial resistance detected in untreated human wastewater and sludge. A search was conducted up to March 2023 and standard ScR methodology was followed. This ScR included 1,722 articles, of which 56.5% were published after the emergence of COVID-19. Viruses and bacteria were commonly investigated, while research on protozoa, helminths, and fungi was infrequent. Articles prior to 2019 were dominated by research on pathogens transmitted through fecal-oral or waterborne pathways, whereas more recent articles have explored the detection of pathogens transmitted through other pathways such as respiratory and vector-borne. There was variation in sampling, samples, and sample processing across studies. The current evidence suggests that wastewater monitoring could be applied to a range of pathogens as a public health tool to detect an emerging pathogen and understand the burden and spread of disease to inform decision-making. Further development and refinement of the methods to identify and interpret wastewater signals for different prioritized pathogens are needed to develop standards on when, why, and how to monitor effectively.
Collapse
Affiliation(s)
- Tricia Corrin
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, Ontario N1H 7M7, Canada E-mail:
| | - Prakathesh Rabeenthira
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, 110 Stone Road, Guelph, Ontario N1G 3W4, Canada
| | - Kaitlin M Young
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, Ontario N1H 7M7, Canada
| | - Gajuna Mathiyalagan
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, 110 Stone Road, Guelph, Ontario N1G 3W4, Canada
| | - Austyn Baumeister
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, Ontario N1H 7M7, Canada
| | - Kusala Pussegoda
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, Ontario N1H 7M7, Canada
| | - Lisa A Waddell
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, 370 Speedvale Avenue West, Guelph, Ontario N1H 7M7, Canada
| |
Collapse
|
7
|
La Rosa G, Mancini P, Iaconelli M, Veneri C, Bonanno Ferraro G, Del Giudice C, Suffredini E, Muratore A, Ferrara F, Lucentini L, Martuzzi M, Piccioli A. Tracing the footprints of SARS-CoV-2 in oceanic waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167343. [PMID: 37751837 DOI: 10.1016/j.scitotenv.2023.167343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023]
Abstract
The detection of SARS-CoV-2 in water environments has predominantly focused on wastewater, neglecting its presence in oceanic waters. This study aimed to fill this knowledge gap by investigating the occurrence of SARS-CoV-2 in remote sea and oceanic waters, at large distances from the coastline. Forty-three 500-liter samples were collected between May 2022 and January 2023 from the Atlantic Ocean, the Mediterranean Sea, the Arctic region, the Persian Gulf and the Red Sea. Using molecular detection methods including real-time RT-qPCR and nested PCR followed by sequencing, we successfully detected SARS-CoV-2 RNA in 7 of the 43 marine water samples (16.3 %), and specifically in samples taken from the Atlantic Ocean and the Mediterranean Sea. The estimated concentrations of SARS-CoV-2 genome copies in the positive samples ranged from 6 to 470 per 100 l. The presence of mutations characteristic of the Omicron variant was identified in these samples by amplicon sequencing. These findings provide evidence of the unforeseen presence of SARS-CoV-2 in marine waters even at distances of miles from the coastline and in open ocean waters. It is important to consider that these findings only display the occurrence of SARS-CoV-2 RNA, and further investigations are required to assess if infectious virus can be present in the marine environment.
Collapse
Affiliation(s)
- Giuseppina La Rosa
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy.
| | - P Mancini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - G Bonanno Ferraro
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - C Del Giudice
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - A Muratore
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - F Ferrara
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - L Lucentini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - M Martuzzi
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - A Piccioli
- Office of the Director General, Istituto Superiore di Sanità, Rome, Italy
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Wilhelm A, Schoth J, Meinert-Berning C, Bastian D, Blum H, Elsinga G, Graf A, Heijnen L, Ho J, Kluge M, Krebs S, Stange C, Uchaikina A, Dolny R, Wurzbacher C, Drewes JE, Medema G, Tiehm A, Ciesek S, Teichgräber B, Wintgens T, Weber FA, Widera M. Interlaboratory comparison using inactivated SARS-CoV-2 variants as a feasible tool for quality control in COVID-19 wastewater monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166540. [PMID: 37634730 DOI: 10.1016/j.scitotenv.2023.166540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Wastewater-based SARS-CoV-2 epidemiology (WBE) has proven as an excellent tool to monitor pandemic dynamics supporting individual testing strategies. WBE can also be used as an early warning system for monitoring the emergence of novel pathogens or viral variants. However, for a timely transmission of results, sophisticated sample logistics and analytics performed in decentralized laboratories close to the sampling sites are required. Since multiple decentralized laboratories commonly use custom in-house workflows for sample purification and PCR-analysis, comparative quality control of the analytical procedures is essential to report reliable and comparable results. In this study, we performed an interlaboratory comparison at laboratories specialized for PCR and high-throughput-sequencing (HTS)-based WBE analysis. Frozen reserve samples from low COVID-19 incidence periods were spiked with different inactivated authentic SARS-CoV-2 variants in graduated concentrations and ratios. Samples were sent to the participating laboratories for analysis using laboratory specific methods and the reported viral genome copy numbers and the detection of viral variants were compared with the expected values. All PCR-laboratories reported SARS-CoV-2 genome copy equivalents (GCE) for all spiked samples with a mean intra- and inter-laboratory variability of 19 % and 104 %, respectively, largely reproducing the spike-in scheme. PCR-based genotyping was, in dependence of the underlying PCR-assay performance, able to predict the relative amount of variant specific substitutions even in samples with low spike-in amount. The identification of variants by HTS, however, required >100 copies/ml wastewater and had limited predictive value when analyzing at a genome coverage below 60 %. This interlaboratory test demonstrates that despite highly heterogeneous isolation and analysis procedures, overall SARS-CoV-2 GCE and mutations were determined accurately. Hence, decentralized SARS-CoV-2 wastewater monitoring is feasible to generate comparable analysis results. However, since not all assays detected the correct variant, prior evaluation of PCR and sequencing workflows as well as sustained quality control such as interlaboratory comparisons are mandatory for correct variant detection.
Collapse
Affiliation(s)
- Alexander Wilhelm
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany
| | - Jens Schoth
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | | | - Daniel Bastian
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Goffe Elsinga
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Leo Heijnen
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Johannes Ho
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Mariana Kluge
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Claudia Stange
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Anna Uchaikina
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Regina Dolny
- Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074 Aachen, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Andreas Tiehm
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Sandra Ciesek
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany; German Center for Infection Research (DZIF), 38124 Braunschweig, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D 60595 Frankfurt am Main, Germany
| | - Burkhard Teichgräber
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | - Thomas Wintgens
- Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074 Aachen, Germany
| | - Frank-Andreas Weber
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany
| | - Marek Widera
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany.
| |
Collapse
|
10
|
Lau M, King BJ, Keegan A, Drigo B, Donner E, Monis P. Comparison of kits for SARS-CoV-2 extraction in liquid and passive samples. Lett Appl Microbiol 2023; 76:ovad136. [PMID: 38066699 DOI: 10.1093/lambio/ovad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/19/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
Abstract
Effective extraction and detection of viral nucleic acids from sewage are fundamental components of a successful SARS-CoV-2 sewage surveillance programme. As there is no standard method employed in sewage surveillance, understanding the performance of different extraction kits in the recovery of SARS-CoV-2 and the impact that PCR inhibitors have on quantification is essential to minimize data discrepancies caused by sample extraction. Three commercial nucleic acid extraction kits: the RNeasy PowerSoil Total RNA Kit (PS), the RNeasy PowerMicrobiome Kit (PMB), and the MagMAX™ Microbiome Ultra Nucleic Acid Isolation Kit (MM), with minor modifications, were evaluated. Their efficacy in recovering viral ribonucleic acid and removal of PCR inhibitors was assessed using two South Australian wastewater matrices-one from a major metropolitan site and one from a regional centre. Both had SARS-CoV-2 present due to active COVID-19 cases in these communities. Overall, the MM kit had a higher recovery of SARS-CoV-2 from the samples tested, followed by PMB and PS. The PMB kit performance was strongly influenced by the sample matrix when compared to the MM kit. It is recommended to assess the performance of extraction kits using different local wastewater matrices to ensure the accuracy and reliability of monitoring results to avoid false reporting.
Collapse
Affiliation(s)
- Melody Lau
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
| | - Brendon J King
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
| | - Alexandra Keegan
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
- UniSA STEM, University of South Australia, Adelaide, SA 5001, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
- Cooperative Research Centre for Solving Antimicrobial resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, SA 5001, Australia
| | - Paul Monis
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
| |
Collapse
|
11
|
Kagami K, Kitajima M, Takahashi H, Teshima T, Ishiguro N. Association of wastewater SARS-CoV-2 load with confirmed COVID-19 cases at a university hospital in Sapporo, Japan during the period from February 2021 to February 2023. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165457. [PMID: 37499823 DOI: 10.1016/j.scitotenv.2023.165457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Accepted: 07/08/2023] [Indexed: 07/29/2023]
Abstract
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been used to monitor trends in SARS-CoV-2 prevalence in a community without being influenced by clinical testing resources or healthcare-seeking behaviors. Since the rate of mortality from COVID-19 is higher in elderly patients with comorbidities, it is important to protect hospitalized patients from nosocomial infections caused by SARS-CoV-2. SARS-CoV-2 dissemination within a hospital ward was mostly mediated by healthcare workers (HCWs) and patients. HCWs need to understand the occurrence of COVID-19 and reflect this in their infection control measures. The aim of the present study was to determine the potential of SARS-CoV-2 RNA in wastewater as a leading indicator of confirmed COVID-19 cases at a university hospital. The trend of the geometric mean RNA concentrations in wastewater collected in Sapporo corresponded well with that of the number of newly confirmed COVID-19 cases at Hokkaido University Hospital between February 15, 2021 and February 26, 2023 (Pearson's r = 0.8823, p < 0.0001). Our results showed that monitoring SARS-CoV-2 RNA in municipal wastewater was useful for estimating the number of COVID-19 patients in healthcare facilities in the city.
Collapse
Affiliation(s)
- Keisuke Kagami
- Department of Infection Control and Prevention, Hokkaido University Hospital, Kita-ku, Sapporo, Hokkaido, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Kita-ku, Sapporo, Hokkaido, Japan
| | - Hisashi Takahashi
- Sewerage & Rivers Bureau, Sapporo City, Toyohira-ku, Sapporo, Hokkaido, Japan
| | - Takanori Teshima
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Kita-ku, Sapporo, Hokkaido, Japan; Department of Hematology, Hokkaido University Faculty of Medicine, Kita-ku, Sapporo, Hokkaido, Japan
| | - Nobuhisa Ishiguro
- Department of Infection Control and Prevention, Hokkaido University Hospital, Kita-ku, Sapporo, Hokkaido, Japan.
| |
Collapse
|
12
|
Voidarou C, Rozos G, Stavropoulou E, Giorgi E, Stefanis C, Vakadaris G, Vaou N, Tsigalou C, Kourkoutas Y, Bezirtzoglou E. COVID-19 on the spectrum: a scoping review of hygienic standards. Front Public Health 2023; 11:1202216. [PMID: 38026326 PMCID: PMC10646607 DOI: 10.3389/fpubh.2023.1202216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
The emergence of COVID-19 in Wuhan, China, rapidly escalated into a worldwide public health crisis. Despite numerous clinical treatment endeavors, initial defenses against the virus primarily relied on hygiene practices like mask-wearing, meticulous hand hygiene (using soap or antiseptic solutions), and maintaining social distancing. Even with the subsequent advent of vaccines and the commencement of mass vaccination campaigns, these hygiene measures persistently remain in effect, aiming to curb virus transmission until the achievement of herd immunity. In this scoping review, we delve into the effectiveness of these measures and the diverse transmission pathways, focusing on the intricate interplay within the food network. Furthermore, we explore the virus's pathophysiology, considering its survival on droplets of varying sizes, each endowed with distinct aerodynamic attributes that influence disease dispersion dynamics. While respiratory transmission remains the predominant route, the potential for oral-fecal transmission should not be disregarded, given the protracted presence of viral RNA in patients' feces after the infection period. Addressing concerns about food as a potential viral vector, uncertainties shroud the virus's survivability and potential to contaminate consumers indirectly. Hence, a meticulous and comprehensive hygienic strategy remains paramount in our collective efforts to combat this pandemic.
Collapse
Affiliation(s)
| | - Georgios Rozos
- Veterinary Directorate, South Aegean Region, Ermoupolis, Greece
| | - Elisavet Stavropoulou
- Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland
| | - Elpida Giorgi
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christos Stefanis
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Georgios Vakadaris
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Natalia Vaou
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christina Tsigalou
- Laboratory of Hygiene and Environmental Protection, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Yiannis Kourkoutas
- Laboratory of Applied Microbiology and Biotechnology, Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eugenia Bezirtzoglou
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| |
Collapse
|
13
|
Diamond MB, Yee E, Bhinge M, Scarpino SV. Wastewater surveillance facilitates climate change-resilient pathogen monitoring. Sci Transl Med 2023; 15:eadi7831. [PMID: 37851828 DOI: 10.1126/scitranslmed.adi7831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Traditional disease surveillance systems are ill-equipped to handle climate change-driven shifts in pathogen dynamics. If paired with wastewater surveillance, a cost-effective and scalable approach for generating high-resolution health data, such next-generation systems can enable effective resource allocation and delivery of targeted interventions.
Collapse
Affiliation(s)
| | | | | | - Samuel V Scarpino
- Department of Health Sciences Northeastern University, Boston, MA 02115, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| |
Collapse
|
14
|
Saied AA, Metwally AA, Dhawan M, Chandran D, Chakraborty C, Dhama K. Wastewater surveillance strategy as an early warning system for detecting cryptic spread of pandemic viruses. QJM 2023; 116:741-744. [PMID: 37307065 DOI: 10.1093/qjmed/hcad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 06/13/2023] Open
Affiliation(s)
- A A Saied
- National Food Safety Authority (NFSA), Aswan Branch, Aswan 81511, Egypt
- Ministry of Tourism and Antiquities, Aswan Office, Aswan 81511, Egypt
| | - A A Metwally
- Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Aswan University, Aswan 81528, Egypt
| | - M Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India
- Trafford College, Altrincham, Manchester WA14 5PQ, UK
| | - D Chandran
- Department of Veterinary Sciences and Animal Husbandry, Amrita School of Agricultural Sciences, Amrita VishwaVidyapeetham University, Coimbatore 642109, Tamil Nadu, India
| | - C Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata 700126, West Bengal, India
| | - K Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, Izatnagar 243122, Uttar Pradesh, India
| |
Collapse
|
15
|
Flood MT, Sharp J, Bruggink J, Cormier M, Gomes B, Oldani I, Zimmy L, Rose JB. Understanding the efficacy of wastewater surveillance for SARS-CoV-2 in two diverse communities. PLoS One 2023; 18:e0289343. [PMID: 37535602 PMCID: PMC10399835 DOI: 10.1371/journal.pone.0289343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023] Open
Abstract
During the COVID-19 pandemic, wastewater-based surveillance has been shown to be a useful tool for monitoring the spread of disease in communities and the emergence of new viral variants of concern. As the pandemic enters its fourth year and clinical testing has declined, wastewater offers a consistent non-intrusive way to monitor community health in the long term. This study sought to understand how accurately wastewater monitoring represented the actual burden of disease between communities. Two communities varying in size and demographics in Michigan were monitored for SARS-CoV-2 in wastewater between March of 2020 and February of 2022. Additionally, each community was monitored for SARS-CoV-2 variants of concern from December 2020 to February 2022. Wastewater results were compared with zipcode and county level COVID-19 case data to determine which scope of clinical surveillance was most correlated with wastewater loading. Pearson r correlations were highest in the smaller of the two communities (population of 25,000) for N1 GC/person/day with zipcode level case data, and date of the onset of symptoms (r = 0.81). A clear difference was seen with more cases and virus signals in the wastewater of the larger community (population 110,000) when examined based on vaccine status, which reached only 50%. While wastewater levels of SARS-CoV-2 had a lower correlation to cases in the larger community, the information was still seen as valuable in supporting public health actions and further data including vaccination status should be examined in the future.
Collapse
Affiliation(s)
- Matthew T Flood
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America
| | - Josh Sharp
- Department of Biology, Northern Michigan University, Marquette, Michigan, United States of America
| | - Jennifer Bruggink
- Department of Biology, Northern Michigan University, Marquette, Michigan, United States of America
| | - Molly Cormier
- Department of Biology, Northern Michigan University, Marquette, Michigan, United States of America
| | - Bailey Gomes
- Department of Biology, Northern Michigan University, Marquette, Michigan, United States of America
| | - Isabella Oldani
- Department of Biology, Northern Michigan University, Marquette, Michigan, United States of America
| | - Lauren Zimmy
- Department of Biology, Northern Michigan University, Marquette, Michigan, United States of America
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America
| |
Collapse
|
16
|
Ng WY, Thoe W, Yang R, Cheung WP, Chen CK, To KH, Pak KM, Leung HW, Lai WK, Wong TK, Lau TK, Au KW, Xu XQ, Zheng XW, Deng Y, Lau YK, To CK, Peiris M, Leung GM, Zhang T, Yang M, An W, Chen W, Wang C, Chui HK. The city-wide full-scale interactive application of sewage surveillance programme for assisting real-time COVID-19 pandemic control - A case study in Hong Kong. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162661. [PMID: 36898549 PMCID: PMC9991928 DOI: 10.1016/j.scitotenv.2023.162661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
The paper discusses the implementation of Hong Kong's tailor-made sewage surveillance programme led by the Government, which has demonstrated how an efficient and well-organized sewage surveillance system can complement conventional epidemiological surveillance to facilitate the planning of intervention strategies and actions for combating COVID-19 pandemic in real-time. This included the setting up of a comprehensive sewerage network-based SARS-CoV-2 virus surveillance programme with 154 stationary sites covering 6 million people (or 80 % of the total population), and employing an intensive monitoring programme to take samples from each stationary site every 2 days. From 1 January to 22 May 2022, the daily confirmed case count started with 17 cases per day on 1 January to a maximum of 76,991 cases on 3 March and dropped to 237 cases on 22 May. During this period, a total of 270 "Restriction-Testing Declaration" (RTD) operations at high-risk residential areas were conducted based on the sewage virus testing results, where over 26,500 confirmed cases were detected with a majority being asymptomatic. In addition, Compulsory Testing Notices (CTN) were issued to residents, and the distribution of Rapid Antigen Test kits was adopted as alternatives to RTD operations in areas of moderate risk. These measures formulated a tiered and cost-effective approach to combat the disease in the local setting. Some ongoing and future enhancement efforts to improve efficacy are discussed from the perspective of wastewater-based epidemiology. Forecast models on case counts based on sewage virus testing results were also developed with R2 of 0.9669-0.9775, which estimated that up to 22 May 2022, around 2,000,000 people (~67 % higher than the total number of 1,200,000 reported to the health authority, due to various constraints or limitations) had potentially contracted the disease, which is believed to be reflecting the real situation occurring in a highly urbanized metropolis like Hong Kong.
Collapse
Affiliation(s)
- Wai-Yin Ng
- Environmental Protection Department, Hong Kong SAR Government, China
| | - Wai Thoe
- Environmental Protection Department, Hong Kong SAR Government, China
| | - Rong Yang
- Environmental Protection Department, Hong Kong SAR Government, China
| | - Wai-Ping Cheung
- Environmental Protection Department, Hong Kong SAR Government, China
| | - Che-Kong Chen
- Environmental Protection Department, Hong Kong SAR Government, China
| | - King-Ho To
- Environmental Protection Department, Hong Kong SAR Government, China
| | - Kan-Ming Pak
- Drainage Service Department, Hong Kong SAR Government, China
| | - Hon-Wan Leung
- Drainage Service Department, Hong Kong SAR Government, China
| | - Wai-Kwan Lai
- Drainage Service Department, Hong Kong SAR Government, China
| | - Tsz-Kin Wong
- Drainage Service Department, Hong Kong SAR Government, China
| | - Tat-Kwong Lau
- Drainage Service Department, Hong Kong SAR Government, China
| | - Ka-Wing Au
- Centre for Health Protection, Department of Health, Hong Kong SAR Government, China
| | - Xiao-Qing Xu
- Department of Civil Engineering, The University of Hong Kong, China
| | - Xia-Wan Zheng
- Department of Civil Engineering, The University of Hong Kong, China
| | - Yu Deng
- Department of Civil Engineering, The University of Hong Kong, China
| | - Yan-Kin Lau
- CMA Industrial Development Foundation Limited, Hong Kong, China
| | - Chi-Kai To
- CMA Industrial Development Foundation Limited, Hong Kong, China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, China
| | | | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, China
| | - Min Yang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wei An
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wenxiu Chen
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chen Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ho-Kwong Chui
- Environmental Protection Department, Hong Kong SAR Government, China; Hong Kong University of Science and Technology, China.
| |
Collapse
|
17
|
Keshaviah A, Diamond MB, Wade MJ, Scarpino SV. Wastewater monitoring can anchor global disease surveillance systems. Lancet Glob Health 2023; 11:e976-e981. [PMID: 37202030 DOI: 10.1016/s2214-109x(23)00170-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/28/2023] [Accepted: 03/27/2023] [Indexed: 05/20/2023]
Abstract
To inform the development of global wastewater monitoring systems, we surveyed programmes in 43 countries. Most programmes monitored predominantly urban populations. In high-income countries (HICs), composite sampling at centralised treatment plants was most common, whereas grab sampling from surface waters, open drains, and pit latrines was more typical in low-income and middle-income countries (LMICs). Almost all programmes analysed samples in-country, with an average processing time of 2·3 days in HICs and 4·5 days in LMICs. Whereas 59% of HICs regularly monitored wastewater for SARS-CoV-2 variants, only 13% of LMICs did so. Most programmes share their wastewater data internally, with partnering organisations, but not publicly. Our findings show the richness of the existing wastewater monitoring ecosystem. With additional leadership, funding, and implementation frameworks, thousands of individual wastewater initiatives can coalesce into an integrated, sustainable network for disease surveillance-one that minimises the risk of overlooking future global health threats.
Collapse
Affiliation(s)
| | | | - Matthew J Wade
- Analytics & Data Science Directorate, UK Health Security Agency, London, UK
| | - Samuel V Scarpino
- Institute for Experiential AI, Network Science Institute, Department of Health Sciences, and Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA; Santa Fe Institute, Santa Fe, NM, USA; Vermont Complex Systems Center, University of Vermont, Burlington, VT, USA.
| |
Collapse
|
18
|
van Boven M, Hetebrij WA, Swart A, Nagelkerke E, van der Beek RF, Stouten S, Hoogeveen RT, Miura F, Kloosterman A, van der Drift AMR, Welling A, Lodder WJ, de Roda Husman AM. Patterns of SARS-CoV-2 circulation revealed by a nationwide sewage surveillance programme, the Netherlands, August 2020 to February 2022. Euro Surveill 2023; 28:2200700. [PMID: 37347416 PMCID: PMC10288829 DOI: 10.2807/1560-7917.es.2023.28.25.2200700] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/16/2023] [Indexed: 06/23/2023] Open
Abstract
BackgroundSurveillance of SARS-CoV-2 in wastewater offers a near real-time tool to track circulation of SARS-CoV-2 at a local scale. However, individual measurements of SARS-CoV-2 in sewage are noisy, inherently variable and can be left-censored.AimWe aimed to infer latent virus loads in a comprehensive sewage surveillance programme that includes all sewage treatment plants (STPs) in the Netherlands and covers 99.6% of the Dutch population.MethodsWe applied a multilevel Bayesian penalised spline model to estimate time- and STP-specific virus loads based on water flow-adjusted SARS-CoV-2 qRT-PCR data for one to four sewage samples per week for each of the more than 300 STPs.ResultsThe model captured the epidemic upsurges and downturns in the Netherlands, despite substantial day-to-day variation in the measurements. Estimated STP virus loads varied by more than two orders of magnitude, from ca 1012 virus particles per 100,000 persons per day in the epidemic trough in August 2020 to almost 1015 per 100,000 in many STPs in January 2022. The timing of epidemics at the local level was slightly shifted between STPs and municipalities, which resulted in less pronounced peaks and troughs at the national level.ConclusionAlthough substantial day-to-day variation is observed in virus load measurements, wastewater-based surveillance of SARS-CoV-2 that is performed at high sampling frequency can track long-term progression of an epidemic at a local scale in near real time.
Collapse
Affiliation(s)
- Michiel van Boven
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Wouter A Hetebrij
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Arno Swart
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Erwin Nagelkerke
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Rudolf Fhj van der Beek
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sjors Stouten
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Rudolf T Hoogeveen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Fuminari Miura
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Center for Marine Environmental Studies (CMES), Ehime University, Ehime, Japan
| | - Astrid Kloosterman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Centre for Environmental Safety and Security, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Anne-Merel R van der Drift
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Anne Welling
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Willemijn J Lodder
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ana Maria de Roda Husman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Institute for Risk Assessment Science (IRAS), Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
19
|
Rogawski McQuade ET, Blake IM, Brennhofer SA, Islam MO, Sony SSS, Rahman T, Bhuiyan MH, Resha SK, Wettstone EG, Hughlett L, Reagan C, Elwood SE, Mira Y, Mahmud AS, Hosan K, Hoque MR, Alam MM, Rahman M, Shirin T, Haque R, Taniuchi M. Real-time sewage surveillance for SARS-CoV-2 in Dhaka, Bangladesh versus clinical COVID-19 surveillance: a longitudinal environmental surveillance study (December, 2019-December, 2021). THE LANCET. MICROBE 2023; 4:e442-e451. [PMID: 37023782 PMCID: PMC10069819 DOI: 10.1016/s2666-5247(23)00010-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 04/05/2023]
Abstract
BACKGROUND Clinical surveillance for COVID-19 has typically been challenging in low-income and middle-income settings. From December, 2019, to December, 2021, we implemented environmental surveillance in a converging informal sewage network in Dhaka, Bangladesh, to investigate SARS-CoV-2 transmission across different income levels of the city compared with clinical surveillance. METHODS All sewage lines were mapped, and sites were selected with estimated catchment populations of more than 1000 individuals. We analysed 2073 sewage samples, collected weekly from 37 sites, and 648 days of case data from eight wards with varying socioeconomic statuses. We assessed the correlations between the viral load in sewage samples and clinical cases. FINDINGS SARS-CoV-2 was consistently detected across all wards (low, middle, and high income) despite large differences in reported clinical cases and periods of no cases. The majority of COVID-19 cases (26 256 [55·1%] of 47 683) were reported from Ward 19, a high-income area with high levels of clinical testing (123 times the number of tests per 100 000 individuals compared with Ward 9 [middle-income] in November, 2020, and 70 times the number of tests per 100 000 individuals compared with Ward 5 [low-income] in November, 2021), despite containing only 19·4% of the study population (142 413 of 734 755 individuals). Conversely, a similar quantity of SARS-CoV-2 was detected in sewage across different income levels (median difference in high-income vs low-income areas: 0·23 log10 viral copies + 1). The correlation between the mean sewage viral load (log10 viral copies + 1) and the log10 clinical cases increased with time (r = 0·90 in July-December, 2021 and r=0·59 in July-December, 2020). Before major waves of infection, viral load quantity in sewage samples increased 1-2 weeks before the clinical cases. INTERPRETATION This study demonstrates the utility and importance of environmental surveillance for SARS-CoV-2 in a lower-middle-income country. We show that environmental surveillance provides an early warning of increases in transmission and reveals evidence of persistent circulation in poorer areas where access to clinical testing is limited. FUNDING Bill & Melinda Gates Foundation.
Collapse
Affiliation(s)
- Elizabeth T Rogawski McQuade
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA; Department of Epidemiology, Emory University, Atlanta, GA, USA
| | - Isobel M Blake
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK
| | - Stephanie A Brennhofer
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | | | - Erin G Wettstone
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Lauren Hughlett
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Claire Reagan
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Sarah E Elwood
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Ayesha S Mahmud
- Department of Demography, University of California at Berkeley, Berkeley, CA, USA
| | - Kawsar Hosan
- a2i, Dhaka, Bangladesh; Department of Economics, Jahangirnagar University, Dhaka, Bangladesh
| | | | | | - Mahbubur Rahman
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research, Dhaka, Bangladesh
| | | | - Mami Taniuchi
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA; Department of Civil and Environmental Engineering Systems and Environment, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
20
|
Schill R, Nelson KL, Harris-Lovett S, Kantor RS. The dynamic relationship between COVID-19 cases and SARS-CoV-2 wastewater concentrations across time and space: Considerations for model training data sets. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162069. [PMID: 36754324 PMCID: PMC9902279 DOI: 10.1016/j.scitotenv.2023.162069] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
During the COVID-19 pandemic, wastewater-based surveillance has been used alongside diagnostic testing to monitor infection rates. With the decline in cases reported to public health departments due to at-home testing, wastewater data may serve as the primary input for epidemiological models, but training these models is not straightforward. We explored factors affecting noise and bias in the ratio between wastewater and case data collected in 26 sewersheds in California from October 2020 to March 2022. The strength of the relationship between wastewater and case data appeared dependent on sampling frequency and population size, but was not increased by wastewater normalization to flow rate or case count normalization to testing rates. Additionally, the lead and lag times between wastewater and case data varied over time and space, and the ratio of log-transformed individual cases to wastewater concentrations changed over time. This ratio decreased between the Epsilon/Alpha and Delta variant surges of COVID-19 and increased during the Omicron BA.1 variant surge, and was also related to the diagnostic testing rate. Based on this analysis, we present a framework of scenarios describing the dynamics of the case to wastewater ratio to aid in data handling decisions for ongoing modeling efforts.
Collapse
Affiliation(s)
- Rebecca Schill
- TUM School of Engineering and Design, Technical University of Munich, Germany
| | - Kara L Nelson
- Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | | | - Rose S Kantor
- Civil and Environmental Engineering, University of California, Berkeley, CA, USA.
| |
Collapse
|
21
|
Duarte MF, de Andrade IA, Silva JMF, de Melo FL, Machado AM, Inoue-Nagata AK, Nagata T. Metagenomic analyses of plant virus sequences in sewage water for plant viruses monitoring. TROPICAL PLANT PATHOLOGY 2023; 48:1-9. [PMID: 37362078 PMCID: PMC10147536 DOI: 10.1007/s40858-023-00575-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/25/2023] [Indexed: 06/28/2023]
Abstract
Frequent monitoring of emerging viruses of agricultural crops is one of the most important missions for plant virologists. A fast and precise identification of potential harmful viruses may prevent the occurrence of serious epidemics. Nowadays, high-throughput sequencing (HTS) technologies became an accessible and powerful tool for this purpose. The major discussion of this strategy resides in the process of sample collection, which is usually laborious, costly and nonrepresentative. In this study, we assessed the use of sewage water samples for monitoring the widespread, numerous, and stable plant viruses using HTS analysis and RT-qPCR. Plant viruses belonged to 12 virus families were found, from which Virgaviridae, Solemoviridae, Tymoviridae, Alphaflexiviridae, Betaflexiviridae, Closteroviridae and Secoviridae were the most abundant ones with more than 20 species. Additionally, we detected one quarantine virus in Brazil and a new tobamovirus species. To assess the importance of the processed foods as virus release origins to sewage, we selected two viruses, the tobamovirus pepper mild mottle virus (PMMoV) and the carlavirus garlic common latent virus (GarCLV), to detect in processed food materials by RT-qPCR. PMMoV was detected in large amount in pepper-based processed foods and in sewage samples, while GarCLV was less frequent in dried and fresh garlic samples, and in the sewage samples. This suggested a high correlation of virus abundance in sewage and processed food sources. The potential use of sewage for a virus survey is discussed in this study. Supplementary Information The online version contains supplementary material available at 10.1007/s40858-023-00575-8.
Collapse
Affiliation(s)
| | | | | | | | - Ana Maria Machado
- Companhia de Saneamento Ambiental Do DF, ETE-Norte, Brasília, DF 70800-130 Brazil
| | | | | |
Collapse
|
22
|
Kisand V, Laas P, Palmik-Das K, Panksep K, Tammert H, Albreht L, Allemann H, Liepkalns L, Vooro K, Ritz C, Hauryliuk V, Tenson T. Prediction of COVID-19 positive cases, a nation-wide SARS-CoV-2 wastewater-based epidemiology study. WATER RESEARCH 2023; 231:119617. [PMID: 36682239 PMCID: PMC9845016 DOI: 10.1016/j.watres.2023.119617] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Taking advantage of Estonia's small size and population, we have employed wastewater-based epidemiology approach to monitor the spread of SARS-CoV-2, releasing weekly nation-wide updates. In this study we report results obtained between August 2020 and December 2021. Weekly 24 h composite samples were collected from wastewater treatment plants of larger towns already covered 65% of the total population that was complemented up to 40 additional grab samples from smaller towns/villages and the specific sites of concern. The N3 gene abundance was quantified by RT-qPCR. The N3 gene copy number (concentration) in wastewater fluctuated in accordance with the SARS-CoV-2 spread within the total population, with N3 abundance starting to increase 1.25 weeks (9 days) (95% CI: [1.10, 1.41]) before a rise in COVID-19 positive cases. Statistical model between the load of virus in wastewater and number of infected people validated with the Alpha variant wave (B.1.1.17) could be used to predict the order of magnitude in incidence numbers in Delta wave (B.1.617.2) in fall 2021. Targeted testing of student dormitories, retirement and nursing homes and prisons resulted in successful early discovery of outbreaks. We put forward a SARS-CoV-2 Wastewater Index (SARS2-WI) indicator of normalized virus load as COVID-19 infection metric to complement the other metrics currently used in disease control and prevention: dynamics of effective reproduction number (Re), 7-day mean of new cases, and a sum of new cases within last 14 days. In conclusion, an efficient surveillance system that combines analysis of composite and grab samples was established in Estonia. There is considerable discussion how the viral load in wastewater correlates with the number of infected people. Here we show that this correlation can be found. Moreover, we confirm that an increased signal in wastewater is observed before the increase in the number of infections. The surveillance system helped to inform public health policy and place direct interventions during the COVID-19 pandemic in Estonia via early warning of epidemic spread in various regions of the country.
Collapse
Affiliation(s)
- Veljo Kisand
- Institute of Technology, University of Tartu, Estonia.
| | - Peeter Laas
- Institute of Technology, University of Tartu, Estonia
| | | | | | - Helen Tammert
- Institute of Technology, University of Tartu, Estonia
| | | | - Hille Allemann
- Estonian Environmental Research Centre, Tallinn, Estonia
| | | | - Katri Vooro
- Estonian Environmental Research Centre, Tallinn, Estonia
| | - Christian Ritz
- Department of Population Health and Morbidity, National Institute of Public Health, University of Southern Denmark, Denmark
| | - Vasili Hauryliuk
- Institute of Technology, University of Tartu, Estonia; Department of Experimental Medical Science, Lund University, Sweden
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Estonia.
| |
Collapse
|
23
|
Helm B, Geissler M, Mayer R, Schubert S, Oertel R, Dumke R, Dalpke A, El-Armouche A, Renner B, Krebs P. Regional and temporal differences in the relation between SARS-CoV-2 biomarkers in wastewater and estimated infection prevalence - Insights from long-term surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159358. [PMID: 36240928 PMCID: PMC9554318 DOI: 10.1016/j.scitotenv.2022.159358] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Wastewater-based epidemiology provides a conceptual framework for the evaluation of the prevalence of public health related biomarkers. In the context of the Coronavirus disease-2019, wastewater monitoring emerged as a complementary tool for epidemic management. In this study, we evaluated data from six wastewater treatment plants in the region of Saxony, Germany. The study period lasted from February to December 2021 and covered the third and fourth regional epidemic waves. We collected 1065 daily composite samples and analyzed SARS-CoV-2 RNA concentrations using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Regression models quantify the relation between RNA concentrations and disease prevalence. We demonstrated that the relation is site and time specific. Median loads per diagnosed case differed by a factor of 3-4 among sites during both waves and were on average 45 % higher during the third wave. In most cases, log-log-transformed data achieved better regression performance than non-transformed data and local calibration outperformed global models for all sites. The inclusion of lag/lead time, discharge and detection probability improved model performance in all cases significantly, but the importance of these components was also site and time specific. In all cases, models with lag/lead time and log-log-transformed data obtained satisfactory goodness-of-fit with adjusted coefficients of determination higher than 0.5. Back-estimation of testing efficiency from wastewater data confirmed state-wide prevalence estimation from individual testing statistics, but revealed pronounced differences throughout the epidemic waves and among the different sites.
Collapse
Affiliation(s)
- Björn Helm
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany.
| | - Michael Geissler
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Robin Mayer
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany
| | - Sara Schubert
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; Institute of Hydrobiology, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany
| | - Reinhard Oertel
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Roger Dumke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Alexander Dalpke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; University Heidelberg, Institute of Medical Microbiology and Hygiene, Heidelberg, Germany
| | - Ali El-Armouche
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany; Institute of Pharmacology and Toxicology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Bertold Renner
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Peter Krebs
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany
| |
Collapse
|
24
|
Gitter A, Oghuan J, Godbole AR, Chavarria CA, Monserrat C, Hu T, Wang Y, Maresso AW, Hanson BM, Mena KD, Wu F. Not a waste: Wastewater surveillance to enhance public health. FRONTIERS IN CHEMICAL ENGINEERING 2023. [DOI: 10.3389/fceng.2022.1112876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Domestic wastewater, when collected and evaluated appropriately, can provide valuable health-related information for a community. As a relatively unbiased and non-invasive approach, wastewater surveillance may complement current practices towards mitigating risks and protecting population health. Spurred by the COVID-19 pandemic, wastewater programs are now widely implemented to monitor viral infection trends in sewersheds and inform public health decision-making. This review summarizes recent developments in wastewater-based epidemiology for detecting and monitoring communicable infectious diseases, dissemination of antimicrobial resistance, and illicit drug consumption. Wastewater surveillance, a quickly advancing Frontier in environmental science, is becoming a new tool to enhance public health, improve disease prevention, and respond to future epidemics and pandemics.
Collapse
|
25
|
Maryam S, Ul Haq I, Yahya G, Ul Haq M, Algammal AM, Saber S, Cavalu S. COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2. Front Cell Infect Microbiol 2023; 12:978643. [PMID: 36683701 PMCID: PMC9854263 DOI: 10.3389/fcimb.2022.978643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.
Collapse
Affiliation(s)
- Sajida Maryam
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Ihtisham Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
- Department of Physical Chemistry and Polymers Technology, Silesian University of Technology, Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Gliwice, Poland
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mehboob Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Abdelazeem M Algammal
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| |
Collapse
|
26
|
Amman F, Markt R, Endler L, Hupfauf S, Agerer B, Schedl A, Richter L, Zechmeister M, Bicher M, Heiler G, Triska P, Thornton M, Penz T, Senekowitsch M, Laine J, Keszei Z, Klimek P, Nägele F, Mayr M, Daleiden B, Steinlechner M, Niederstätter H, Heidinger P, Rauch W, Scheffknecht C, Vogl G, Weichlinger G, Wagner AO, Slipko K, Masseron A, Radu E, Allerberger F, Popper N, Bock C, Schmid D, Oberacher H, Kreuzinger N, Insam H, Bergthaler A. Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale. Nat Biotechnol 2022; 40:1814-1822. [PMID: 35851376 DOI: 10.1038/s41587-022-01387-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/07/2022] [Indexed: 01/14/2023]
Abstract
SARS-CoV-2 surveillance by wastewater-based epidemiology is poised to provide a complementary approach to sequencing individual cases. However, robust quantification of variants and de novo detection of emerging variants remains challenging for existing strategies. We deep sequenced 3,413 wastewater samples representing 94 municipal catchments, covering >59% of the population of Austria, from December 2020 to February 2022. Our system of variant quantification in sewage pipeline designed for robustness (termed VaQuERo) enabled us to deduce the spatiotemporal abundance of predefined variants from complex wastewater samples. These results were validated against epidemiological records of >311,000 individual cases. Furthermore, we describe elevated viral genetic diversity during the Delta variant period, provide a framework to predict emerging variants and measure the reproductive advantage of variants of concern by calculating variant-specific reproduction numbers from wastewater. Together, this study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without extensive individual monitoring.
Collapse
Affiliation(s)
- Fabian Amman
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Rudolf Markt
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Lukas Endler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Sebastian Hupfauf
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Schedl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Lukas Richter
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | | | - Martin Bicher
- dwh GmbH, Vienna, Austria.,Institute for Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Georg Heiler
- Complexity Science Hub, Vienna, Austria.,Institute of Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Petr Triska
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Matthew Thornton
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Martin Senekowitsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jan Laine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Zsofia Keszei
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Peter Klimek
- Complexity Science Hub, Vienna, Austria.,Section for Science of Complex Systems, Medical University of Vienna, Vienna, Austria
| | - Fabiana Nägele
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Markus Mayr
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Beatrice Daleiden
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Steinlechner
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Harald Niederstätter
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Petra Heidinger
- Austrian Centre of Industrial Biotechnology GmbH, Graz, Austria
| | - Wolfgang Rauch
- Department of Infrastructure, Universität Innsbruck, Innsbruck, Austria
| | | | - Gunther Vogl
- Institut für Lebensmittelsicherheit, Veterinärmedizin und Umwelt des Landes Kärnten, Klagenfurt am Wörthersee, Austria
| | - Günther Weichlinger
- Abteilung 12 - Wasserwirtschaft, Amt der Kärntner Landesregierung, Klagenfurt am Wörthersee, Austria
| | | | - Katarzyna Slipko
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Amandine Masseron
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Elena Radu
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria.,Ştefan S. Nicolau Institute of Virology, Bucharest, Romania
| | | | - Niki Popper
- dwh GmbH, Vienna, Austria.,Institute for Information Systems Engineering, Technische Universität Wien, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Daniela Schmid
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, Austria
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, Technische Universität Wien, Vienna, Austria
| | - Heribert Insam
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Institute of Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
27
|
Pang X, Gao T, Ellehoj E, Li Q, Qiu Y, Maal-Bared R, Sikora C, Tipples G, Diggle M, Hinshaw D, Ashbolt NJ, Talbot J, Hrudey SE, Lee BE. Wastewater-Based Surveillance Is an Effective Tool for Trending COVID-19 Prevalence in Communities: A Study of 10 Major Communities for 17 Months in Alberta. ACS ES&T WATER 2022; 2:2243-2254. [PMID: 36380772 PMCID: PMC9514327 DOI: 10.1021/acsestwater.2c00143] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
The correlations between SARS-CoV-2 RNA levels in wastewater from 12 wastewater treatment plants and new COVID-19 cases in the corresponding sewersheds of 10 communities were studied over 17 months. The analysis from the longest continuous surveillance reported to date revealed that SARS-CoV-2 RNA levels correlated well with temporal changes of COVID-19 cases in each community. The strongest correlation was found during the third wave (r = 0.97) based on the population-weighted SARS-CoV-2 RNA levels in wastewater. Different correlations were observed (r from 0.51 to 0.86) in various sizes of communities. The population in the sewershed had no observed effects on the strength of the correlation. Fluctuation of SARS-CoV-2 RNA levels in wastewater mirrored increases and decreases of COVID-19 cases in the corresponding community. Since the viral shedding to sewers from all infected individuals is included, wastewater-based surveillance provides an unbiased and no-discriminate estimation of the prevalence of COVID-19 compared with clinical testing that was subject to testing-seeking behaviors and policy changes. Wastewater-based surveillance on SARS-CoV-2 represents a temporal trend of COVID-19 disease burden and is an effective and supplementary monitoring when the number of COVID-19 cases reaches detectable thresholds of SARS-CoV-2 RNA in wastewater of treatment facilities serving various sizes of populations.
Collapse
Affiliation(s)
- Xiaoli Pang
- Department
of Laboratory Medicine and Pathology, School of Public Health, Department of Medicine, and Department of
Pediatrics, University of Alberta, Edmonton, Alberta T6G 2E2, Canada
- Alberta
Precision Laboratories, Edmonton, Alberta T6G 2J2, Canada
| | - Tiejun Gao
- Department
of Laboratory Medicine and Pathology, School of Public Health, Department of Medicine, and Department of
Pediatrics, University of Alberta, Edmonton, Alberta T6G 2E2, Canada
| | - Erik Ellehoj
- Ellehoj
Redmond Consulting, Edmonton, Alberta T6G 0Y4, Canada
| | - Qiaozhi Li
- Department
of Laboratory Medicine and Pathology, School of Public Health, Department of Medicine, and Department of
Pediatrics, University of Alberta, Edmonton, Alberta T6G 2E2, Canada
| | - Yuanyuan Qiu
- Department
of Laboratory Medicine and Pathology, School of Public Health, Department of Medicine, and Department of
Pediatrics, University of Alberta, Edmonton, Alberta T6G 2E2, Canada
| | | | - Christopher Sikora
- Department
of Laboratory Medicine and Pathology, School of Public Health, Department of Medicine, and Department of
Pediatrics, University of Alberta, Edmonton, Alberta T6G 2E2, Canada
| | - Graham Tipples
- Department
of Laboratory Medicine and Pathology, School of Public Health, Department of Medicine, and Department of
Pediatrics, University of Alberta, Edmonton, Alberta T6G 2E2, Canada
- Alberta
Precision Laboratories, Edmonton, Alberta T6G 2J2, Canada
| | - Mathew Diggle
- Alberta
Precision Laboratories, Edmonton, Alberta T6G 2J2, Canada
| | - Deena Hinshaw
- Department
of Laboratory Medicine and Pathology, School of Public Health, Department of Medicine, and Department of
Pediatrics, University of Alberta, Edmonton, Alberta T6G 2E2, Canada
| | | | - James Talbot
- Department
of Laboratory Medicine and Pathology, School of Public Health, Department of Medicine, and Department of
Pediatrics, University of Alberta, Edmonton, Alberta T6G 2E2, Canada
| | - Steve E. Hrudey
- Department
of Laboratory Medicine and Pathology, School of Public Health, Department of Medicine, and Department of
Pediatrics, University of Alberta, Edmonton, Alberta T6G 2E2, Canada
| | - Bonita E. Lee
- Department
of Laboratory Medicine and Pathology, School of Public Health, Department of Medicine, and Department of
Pediatrics, University of Alberta, Edmonton, Alberta T6G 2E2, Canada
| |
Collapse
|
28
|
Wilhelm A, Schoth J, Meinert-Berning C, Agrawal S, Bastian D, Orschler L, Ciesek S, Teichgräber B, Wintgens T, Lackner S, Weber FA, Widera M. Wastewater surveillance allows early detection of SARS-CoV-2 omicron in North Rhine-Westphalia, Germany. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157375. [PMID: 35850355 PMCID: PMC9287496 DOI: 10.1016/j.scitotenv.2022.157375] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 05/25/2023]
Abstract
Wastewater-based epidemiology (WBE) has demonstrated its importance to support SARS-CoV-2 epidemiology complementing individual testing strategies. Due to their immune-evasive potential and the resulting significance for public health, close monitoring of SARS-CoV-2 variants of concern (VoC) is required to evaluate the regulation of early local countermeasures. In this study, we demonstrate a rapid workflow for wastewater-based early detection and monitoring of the newly emerging SARS-CoV-2 VoCs Omicron in the end of 2021 at the municipal wastewater treatment plant (WWTP) Emschermuendung (KLEM) in the Federal State of North-Rhine-Westphalia (NRW, Germany). Initially, available primers detecting Omicron-related mutations were rapidly validated in a central laboratory. Subsequently, RT-qPCR analysis of purified SARS-CoV-2 RNA was performed in a decentral PCR laboratory in close proximity to KLEM. This decentralized approach enabled the early detection of K417N present in Omicron in samples collected on 8th December 2021 and the detection of further mutations (N501Y, Δ69/70) in subsequent biweekly sampling campaigns. The presence of Omicron in wastewater was confirmed by next generation sequencing (NGS) in a central laboratory with samples obtained on 14th December 2021. Moreover, the relative increase of the mutant fraction of Omicron was quantitatively monitored over time by dPCR in a central PCR laboratory starting on 12th December 2021 confirming Omicron as the dominant variant by the end of 2021. In conclusions, WBE plays a crucial role in surveillance of SARS-CoV-2 variants and is suitable as an early warning system to identify variant emergence. In particular, the successive workflow using RT-qPCR, RT-dPCR and NGS demonstrates the strength of WBE as a versatile tool to monitor variant spreading.
Collapse
Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany
| | - Jens Schoth
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | | | - Shelesh Agrawal
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Water and Environmental Biotechnology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Daniel Bastian
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15- 17, D-52056 Aachen, Germany
| | - Laura Orschler
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Water and Environmental Biotechnology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany; German Center for Infection Research (DZIF), 38124 Braunschweig, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor Stern Kai 7, D-60595 Frankfurt am Main, Germany
| | - Burkhard Teichgräber
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | - Thomas Wintgens
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15- 17, D-52056 Aachen, Germany; Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074, Aachen, Germany
| | - Susanne Lackner
- Department of Civil and Environmental Engineering Sciences, Institute IWAR, Water and Environmental Biotechnology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Frank-Andreas Weber
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15- 17, D-52056 Aachen, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany.
| |
Collapse
|
29
|
Cutrupi F, Cadonna M, Manara S, Postinghel M, La Rosa G, Suffredini E, Foladori P. The wave of the SARS-CoV-2 Omicron variant resulted in a rapid spike and decline as highlighted by municipal wastewater surveillance. ENVIRONMENTAL TECHNOLOGY & INNOVATION 2022; 28:102667. [PMID: 35615435 PMCID: PMC9122782 DOI: 10.1016/j.eti.2022.102667] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 05/10/2023]
Abstract
This paper highlights the extraordinarily rapid spread of SARS-CoV-2 loads in wastewater that during the Omicron wave in December 2021-February 2022, compared with the profiles acquired in 2020-21 with 410 samples from two wastewater treatment plants (Trento+suburbs, 132,500 inhabitants). Monitoring of SARS-CoV-2 in wastewater focused on: (i) 3 samplings/week and analysis, (ii) normalization to calculate genomic units (GU) inh-1 d-1; (iii) calculation of a 7-day moving average to smooth daily fluctuations; (iv) comparison with the 'current active cases'/100,000 inh progressively affected by the mass vaccination. The time profiles of SARS-CoV-2 in wastewater matched the waves of active cases. In February-April 2021, a viral load of 1.0E+07 GU inh-1 d - 1 corresponded to 700 active cases/100,000 inh. In July-September 2021, although the low current active cases, sewage revealed an appreciable SARS-CoV-2 circulation (in this period 2.2E+07 GU inh-1 d-1 corresponded to 90 active cases/100,000 inh). Omicron was not detected in wastewater until mid-December 2021. The Omicron spread caused a 5-6 fold increase of the viral load in two weeks, reaching the highest peak (2.0-2.2E+08 GU inh-1 d-1 and 4500 active cases/100,000 inh) during the pandemic. In this period, wastewater surveillance anticipated epidemiological data by about 6 days. In winter 2021-22, despite the 4-7 times higher viral loads in wastewater, hospitalizations were 4 times lower than in winter 2020-21 due to the vaccination coverage >80%. The Omicron wave demonstrated that SARS-CoV-2 monitoring of wastewater anticipated epidemiological data, confirming its importance in long-term surveillance.
Collapse
Affiliation(s)
- Francesca Cutrupi
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, via Mesiano 77, 38123 Trento, Italy
| | - Maria Cadonna
- ADEP, Agenzia per la Depurazione (Wastewater Treatment Agency), Autonomous Province of Trento, via Gilli 3, 38121 Trento, Italy
| | - Serena Manara
- Department of Cellular Computational and Integrative Biology-CIBIO, Via Sommarive 9, 38123 Trento, Italy
| | - Mattia Postinghel
- ADEP, Agenzia per la Depurazione (Wastewater Treatment Agency), Autonomous Province of Trento, via Gilli 3, 38121 Trento, Italy
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Foladori
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, via Mesiano 77, 38123 Trento, Italy
| |
Collapse
|
30
|
Dargahi A, Vosoughi M, Normohammadi A, Sedigh A, Gholizadeh H, Sadeghi H, Karami C, Jeddi F. Investigating SARS-CoV-2 RNA in five municipal wastewater treatment plants, hospital wastewater and wastewater collection networks during the COVID-19 pandemic in Ardabil Province, Iran. APPLIED WATER SCIENCE 2022; 12:256. [PMID: 36277855 PMCID: PMC9579531 DOI: 10.1007/s13201-022-01773-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Since 2019, the outbreak of coronavirus with acute respiratory symptoms has caused an epidemic worldwide. Transmission of the disease through respiratory droplets was announced as the main mode of transmission in 2020. But in this study, we discussed the method of indirect transmission of the virus through sewage. In this study, effluents related to urban and hospital wastewater treatment plants in 5 regions of Ardabil Province (northwest of Iran) were investigated. In this research, 120 samples were kept in pre-test conditions (temperature -20 degrees Celsius). To identify the viral genome, special primer and chain reaction probe targeting ORF1ab and N (nucleoprotein gene) genes were used. Out of a total of 120 samples, a total of 3 samples were positive. Wastewater epidemiology (WBE) can be considered as a cost-effective method in the diagnosis and prediction of pathogenic agents. And be considered an effective method for decision-making in order to protect the health of citizens.
Collapse
Affiliation(s)
- Abdollah Dargahi
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mehdi Vosoughi
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Ali Normohammadi
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Environmental Health Engineering, School of Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Anoshirvan Sedigh
- Department of Environmental Health Engineering, School of Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Helia Gholizadeh
- Department of Environmental Health Engineering, School of Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hadi Sadeghi
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Environmental Health Engineering, School of Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Chiman Karami
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Microbiology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Farhad Jeddi
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| |
Collapse
|
31
|
Wernike K, Drewes S, Mehl C, Hesse C, Imholt C, Jacob J, Ulrich RG, Beer M. No Evidence for the Presence of SARS-CoV-2 in Bank Voles and Other Rodents in Germany, 2020–2022. Pathogens 2022; 11:pathogens11101112. [PMID: 36297169 PMCID: PMC9610409 DOI: 10.3390/pathogens11101112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Rodentia is the most speciose mammalian order, found across the globe, with some species occurring in close proximity to humans. Furthermore, rodents are known hosts for a variety of zoonotic pathogens. Among other animal species, rodents came into focus when the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) spread through human populations across the globe, initially as laboratory animals to study the viral pathogenesis and to test countermeasures. Under experimental conditions, some rodent species including several cricetid species are susceptible to SARS-CoV-2 infection and a few of them can transmit the virus to conspecifics. To investigate whether SARS-CoV-2 is also spreading in wild rodent populations in Germany, we serologically tested samples of free-ranging bank voles (Myodes glareolus, n = 694), common voles (Microtus arvalis, n = 2), house mice (Mus musculus, n = 27), brown or Norway rats (Rattus norvegicus, n = 97) and Apodemus species (n = 8) for antibodies against the virus. The samples were collected from 2020 to 2022 in seven German federal states. All but one sample tested negative by a multispecies ELISA based on the receptor-binding domain (RBD) of SARS-CoV-2. The remaining sample, from a common vole collected in 2021, was within the inconclusive range of the RBD-ELISA, but this result could not be confirmed by a surrogate virus neutralization test as the sample gave a negative result in this test. These results indicate that SARS-CoV-2 has not become highly prevalent in wild rodent populations in Germany.
Collapse
Affiliation(s)
- Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
- Correspondence:
| | - Stephan Drewes
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
| | - Calvin Mehl
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
- German Centre for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 17493 Greifswald-Insel Riems, Germany
| | - Christin Hesse
- Rodent Research, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, 48161 Münster, Germany
| | - Christian Imholt
- Rodent Research, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, 48161 Münster, Germany
| | - Jens Jacob
- Rodent Research, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, 48161 Münster, Germany
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
- German Centre for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 17493 Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
| |
Collapse
|
32
|
de Araújo JC, Mota VT, Teodoro A, Leal C, Leroy D, Madeira C, Machado EC, Dias MF, Souza CC, Coelho G, Bressani T, Morandi T, Freitas GTO, Duarte A, Perdigão C, Tröger F, Ayrimoraes S, de Melo MC, Laguardia F, Reis MTP, Mota C, Chernicharo CAL. Long-term monitoring of SARS-CoV-2 RNA in sewage samples from specific public places and STPs to track COVID-19 spread and identify potential hotspots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155959. [PMID: 35588823 DOI: 10.2139/ssrn.4055085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 05/21/2023]
Abstract
Coronavirus pandemic started in March 2020 and since then has caused millions of deaths worldwide. Wastewater-based epidemiology (WBE) can be used as an epidemiological surveillance tool to track SARS-CoV-2 dissemination and provide warning of COVID-19 outbreaks. Considering that there are public places that could be potential hotspots of infected people that may reflect the local epidemiological situation, the presence of SARS-CoV-2 RNA was analyzed by RT-qPCR for approximately 16 months in sewage samples from five public places located in the metropolitan area of Belo Horizonte, MG, Brazil: the sewage treatment plant of Confins International Airport (AIR), the main interstate bus terminal (BUS), an upscale shopping centre (SHC1), a popular shopping centre (SHC2) and a university institute (UNI). The results were compared to those of the influent sewage of the two main sewage treatment plants of Belo Horizonte (STP1 and STP2). Viral monitoring in the STPs proved to be an useful regional surveillance tool, reflecting the trends of COVID-19 cases. However, the viral concentrations in the samples from the selected public places were generally much lower than those of the municipal STPs, which may be due to the behaviour of the non-infected or asymptomatic people, who are likely to visit these places relatively more than the symptomatic infected ones. Among these places, the AIR samples presented the highest viral concentrations and concentration peaks were observed previously to local outbreaks. Therefore, airport sewage monitoring can provide an indication of the regional epidemiological situation. For the other places, particularly the UNI, the results suggested a greater potential to detect the infection and trace cases especially among employees and regular attendees. Taken together, the results indicate that for a regular and permanent sentinel sewage surveillance the sewage from STPs, AIR and UNI could be monitored.
Collapse
Affiliation(s)
- Juliana Calábria de Araújo
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil.
| | - Vera Tainá Mota
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Amanda Teodoro
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Cíntia Leal
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Deborah Leroy
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Camila Madeira
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Elayne C Machado
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Marcela F Dias
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Cassia C Souza
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Gabriela Coelho
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Thiago Bressani
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Thiago Morandi
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Gabriel Tadeu O Freitas
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Alyne Duarte
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | | | - Flávio Tröger
- National Agency for Water and Sanitation (ANA), Brazil
| | | | | | | | | | - César Mota
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Carlos A L Chernicharo
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| |
Collapse
|
33
|
de Araújo JC, Mota VT, Teodoro A, Leal C, Leroy D, Madeira C, Machado EC, Dias MF, Souza CC, Coelho G, Bressani T, Morandi T, Freitas GTO, Duarte A, Perdigão C, Tröger F, Ayrimoraes S, de Melo MC, Laguardia F, Reis MTP, Mota C, Chernicharo CAL. Long-term monitoring of SARS-CoV-2 RNA in sewage samples from specific public places and STPs to track COVID-19 spread and identify potential hotspots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155959. [PMID: 35588823 PMCID: PMC9110006 DOI: 10.1016/j.scitotenv.2022.155959] [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: 03/10/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 05/21/2023]
Abstract
Coronavirus pandemic started in March 2020 and since then has caused millions of deaths worldwide. Wastewater-based epidemiology (WBE) can be used as an epidemiological surveillance tool to track SARS-CoV-2 dissemination and provide warning of COVID-19 outbreaks. Considering that there are public places that could be potential hotspots of infected people that may reflect the local epidemiological situation, the presence of SARS-CoV-2 RNA was analyzed by RT-qPCR for approximately 16 months in sewage samples from five public places located in the metropolitan area of Belo Horizonte, MG, Brazil: the sewage treatment plant of Confins International Airport (AIR), the main interstate bus terminal (BUS), an upscale shopping centre (SHC1), a popular shopping centre (SHC2) and a university institute (UNI). The results were compared to those of the influent sewage of the two main sewage treatment plants of Belo Horizonte (STP1 and STP2). Viral monitoring in the STPs proved to be an useful regional surveillance tool, reflecting the trends of COVID-19 cases. However, the viral concentrations in the samples from the selected public places were generally much lower than those of the municipal STPs, which may be due to the behaviour of the non-infected or asymptomatic people, who are likely to visit these places relatively more than the symptomatic infected ones. Among these places, the AIR samples presented the highest viral concentrations and concentration peaks were observed previously to local outbreaks. Therefore, airport sewage monitoring can provide an indication of the regional epidemiological situation. For the other places, particularly the UNI, the results suggested a greater potential to detect the infection and trace cases especially among employees and regular attendees. Taken together, the results indicate that for a regular and permanent sentinel sewage surveillance the sewage from STPs, AIR and UNI could be monitored.
Collapse
Affiliation(s)
- Juliana Calábria de Araújo
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil.
| | - Vera Tainá Mota
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Amanda Teodoro
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Cíntia Leal
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Deborah Leroy
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Camila Madeira
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Elayne C Machado
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Marcela F Dias
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Cassia C Souza
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Gabriela Coelho
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Thiago Bressani
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Thiago Morandi
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Gabriel Tadeu O Freitas
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Alyne Duarte
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | | | - Flávio Tröger
- National Agency for Water and Sanitation (ANA), Brazil
| | | | | | | | | | - César Mota
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Carlos A L Chernicharo
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| |
Collapse
|
34
|
Brogna C, Brogna B, Bisaccia DR, Giuliano M, Montano L, Cristoni S, Petrillo M, Piscopo M. SARS-CoV-2: Reinfection after 18 Months of a Previous Case with Multiple Negative Nasopharyngeal Swab Tests and Positive Fecal Molecular Test. Medicina (B Aires) 2022; 58:medicina58050642. [PMID: 35630059 PMCID: PMC9148128 DOI: 10.3390/medicina58050642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
This short communication describes the reinfection after nearly 18 months of the same patient who was previously infected with coronavirus disease 2019 (COVID-19) and who showed multiple negative real-time quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) results by nasal swabs for severe acute respiratory syndrome coronavirus (SARS-CoV-2) but positive results on a fecal sample. We previously noted how, in the presence of symptoms suggestive of pneumonia, visible on a chest computed tomography (CT) scan and confirmed by fecal molecular testing, it was possible to draw the diagnosis of SARS-CoV-2 infection. One year later, the same patient was again affected by SARS-CoV-2. This time, the first antigenic nasal swab showed readily positive results. However, the patient’s clinical course appeared to be more attenuated, showing no signs of pulmonary involvement in the radiographic examinations performed. This case shows a novelty in the pulmonary radiological evaluation of new SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Carlo Brogna
- Department of Research, Craniomed Group Facility SRL, 83038 Montemiletto, Italy;
- Correspondence: (C.B.); (B.B.)
| | - Barbara Brogna
- Department of Radiology, Moscati Hospital, Contrada Amoretta, 83100 Avellino, Italy
- Correspondence: (C.B.); (B.B.)
| | | | - Marino Giuliano
- Marsanconsulting Srl Public Health Company, Via dei Fiorentini, 80133 Napoli, Italy;
| | - Luigi Montano
- Andrology Unit and Service of LifeStyle Medicine in Uro-Andrology, Local Health Authority (ASL), 84124 Salerno, Italy;
| | | | | | - Marina Piscopo
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy;
| |
Collapse
|
35
|
Dzinamarira T, Murewanhema G, Iradukunda PG, Madziva R, Herrera H, Cuadros DF, Tungwarara N, Chitungo I, Musuka G. Utilization of SARS-CoV-2 Wastewater Surveillance in Africa-A Rapid Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:969. [PMID: 35055789 PMCID: PMC8775514 DOI: 10.3390/ijerph19020969] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/04/2022] [Accepted: 01/13/2022] [Indexed: 02/06/2023]
Abstract
Wastewater-based epidemiology for SARS-CoV-2 RNA detection in wastewater is desirable for understanding COVID-19 in settings where financial resources and diagnostic facilities for mass individual testing are severely limited. We conducted a rapid review to map research evidence on the utilization of SARS-CoV-2 wastewater surveillance in Africa. We searched PubMed, Google Scholar, and the World Health Organization library databases for relevant reports, reviews, and primary observational studies. Eight studies met the inclusion criteria. Narrative synthesis of the findings from included primary studies revealed the testing methodologies utilized and that detected amount of SARS-CoV-2 viral RNA correlated with the number of new cases in the studied areas. The included reviews revealed the epidemiological significance and environmental risks of SARS-CoV-2 wastewater. Wastewater surveillance data at the community level can be leveraged for the rapid assessment of emerging threats and aid pandemic preparedness. Our rapid review revealed a glaring gap in the primary literature on SARS-CoV-2 wastewater surveillance on the continent, and accelerated and adequate investment into research is urgently needed to address this gap.
Collapse
Affiliation(s)
- Tafadzwa Dzinamarira
- School of Health Systems & Public Health, University of Pretoria, Pretoria 0002, South Africa
- ICAP at Columbia University, Harare, Zimbabwe;
| | - Grant Murewanhema
- Unit of Obstetrics and Gynaecology, Department of Primary Health Care Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | - Patrick Gad Iradukunda
- London School of Hygiene and Tropical Medicine, University of London, London WC1E 7HU, UK;
| | - Roda Madziva
- School of Sociology and Social Policy, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Helena Herrera
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2UP, UK;
| | - Diego F. Cuadros
- Department of Geography and Geographic Information Science, University of Cincinnati, Cincinnati, OH 45221, USA;
| | - Nigel Tungwarara
- Department of Health Studies, University of South Africa, Pretoria 0002, South Africa;
| | - Itai Chitungo
- Chemical Pathology Unit, Department of Laboratory Diagnostic and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | | |
Collapse
|
36
|
Mancusi A, Capuano F, Girardi S, Di Maro O, Suffredini E, Di Concilio D, Vassallo L, Cuomo MC, Tafuro M, Signorelli D, Pierri A, Pizzolante A, Cerino P, La Rosa G, Proroga YTR, Pierri B. Detection of SARS-CoV-2 RNA in Bivalve Mollusks by Droplet Digital RT-PCR (dd RT-PCR). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:943. [PMID: 35055765 PMCID: PMC8776039 DOI: 10.3390/ijerph19020943] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/12/2022]
Abstract
Bivalve shellfish are readily contaminated by human pathogens present in waters impacted by municipal sewage, and the detection of SARS-CoV-2 in feces of infected patients and in wastewater has drawn attention to the possible presence of the virus in bivalves. The aim of this study was to collect data on SARS-CoV-2 prevalence in bivalve mollusks from harvesting areas of Campania region. A total of 179 samples were collected between September 2019 and April 2021 and were tested using droplet digital RT-PCR (dd RT-PCR) and real-time RT-PCR. Combining results obtained with different assays, SARS-CoV-2 presence was detected in 27/179 (15.1%) of samples. A median viral concentration of 1.1 × 102 and 1.4 × 102 g.c./g was obtained using either Orf1b nsp14 or RdRp/gene E, respectively. Positive results were unevenly distributed among harvesting areas and over time, positive samples being more frequent after January 2021. Partial sequencing of the spike region was achieved for five samples, one of which displaying mutations characteristic of the Alpha variant (lineage B.1.1.7). This study confirms that bivalve mollusks may bioaccumulate SARS-CoV-2 to detectable levels and that they may represent a valuable approach to track SARS-CoV-2 in water bodies and to monitor outbreak trends and viral diversity.
Collapse
Affiliation(s)
- Andrea Mancusi
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (F.C.); (S.G.); (O.D.M.)
| | - Federico Capuano
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (F.C.); (S.G.); (O.D.M.)
| | - Santa Girardi
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (F.C.); (S.G.); (O.D.M.)
| | - Orlandina Di Maro
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (F.C.); (S.G.); (O.D.M.)
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Denise Di Concilio
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Lucia Vassallo
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Maria Concetta Cuomo
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Maria Tafuro
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Daniel Signorelli
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Andrea Pierri
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Antonio Pizzolante
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Pellegrino Cerino
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Yolande Thérèse Rose Proroga
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (F.C.); (S.G.); (O.D.M.)
| | - Biancamaria Pierri
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| |
Collapse
|
37
|
Detection of Enterovirus D68 in Wastewater Samples from the UK between July and November 2021. Viruses 2022; 14:v14010143. [PMID: 35062346 PMCID: PMC8781944 DOI: 10.3390/v14010143] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 02/06/2023] Open
Abstract
Infection with enterovirus D68 (EV-D68) has been linked with severe neurological disease such as acute flaccid myelitis (AFM) in recent years. However, active surveillance for EV-D68 is lacking, which makes full assessment of this association difficult. Although a high number of EV-D68 infections were expected in 2020 based on the EV-D68's known biannual circulation patterns, no apparent increase in EV-D68 detections or AFM cases was observed during 2020. We describe an upsurge of EV-D68 detections in wastewater samples from the United Kingdom between July and November 2021 mirroring the recently reported rise in EV-D68 detections in clinical samples from various European countries. We provide the first publicly available 2021 EV-D68 sequences showing co-circulation of EV-D68 strains from genetic clade D and sub-clade B3 as in previous years. Our results show the value of environmental surveillance (ES) for the early detection of circulating and clinically relevant human viruses. The use of a next-generation sequencing (NGS) approach helped us to estimate the prevalence of EV-D68 viruses among EV strains from other EV serotypes and to detect EV-D68 minor variants. The utility of ES at reducing gaps in virus surveillance for EV-D68 and the possible impact of nonpharmaceutical interventions introduced to control the COVID-19 pandemic on EV-D68 transmission dynamics are discussed.
Collapse
|
38
|
"Five Keys to Safer Food" and COVID-19. Nutrients 2021; 13:nu13124491. [PMID: 34960042 PMCID: PMC8705606 DOI: 10.3390/nu13124491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
On 11 March 2020, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) and, up to 18:37 a.m. on 9 December 2021, it has produced 268,440,530 cases and 5,299,511 deaths. This disease, in some patients, included pneumonia and shortness of breath, being transmitted through droplets and aerosols. To date, there is no scientific literature to justify transmission directly from foods. In this review, we applied the precautionary principle for the home and the food industry using the known "Five Keys to Safer Food" manual developed by the World Health Organization (WHO) and extended punctually in its core information from five keys, in the light of new COVID-19 evidence, to guarantee a possible food safety tool.
Collapse
|