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Williams RC, Perry WB, Lambert-Slosarska K, Futcher B, Pellett C, Richardson-O'Neill I, Paterson S, Grimsley JMS, Wade MJ, Weightman AJ, Farkas K, Jones DL. Examining the stability of viral RNA and DNA in wastewater: Effects of storage time, temperature, and freeze-thaw cycles. WATER RESEARCH 2024; 259:121879. [PMID: 38865915 DOI: 10.1016/j.watres.2024.121879] [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: 12/19/2023] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024]
Abstract
Wastewater-based epidemiology (WBE) has been demonstrably successful as a relatively unbiased tool for monitoring levels of SARS-CoV-2 virus circulating in communities during the COVID-19 pandemic. Accumulated biobanks of wastewater samples allow retrospective exploration of spatial and temporal trends for public health indicators such as chemicals, viruses, antimicrobial resistance genes, and the possible emergence of novel human or zoonotic pathogens. We investigated virus resilience to time, temperature, and freeze-thaw cycles, plus the optimal storage conditions to maintain the stability of genetic material (RNA/DNA) of viral +ssRNA (Envelope - E, Nucleocapsid - N and Spike protein - S genes of SARS-CoV-2), dsRNA (Phi6 phage) and circular dsDNA (crAssphage) in wastewater. Samples consisted of (i) processed and extracted wastewater samples, (ii) processed and extracted distilled water samples, and (iii) raw, unprocessed wastewater samples. Samples were stored at -80 °C, -20 °C, 4 °C, or 20 °C for 10 days, going through up to 10 freeze-thaw cycles (once per day). Sample stability was measured using reverse transcription quantitative PCR, quantitative PCR, automated electrophoresis, and short-read whole genome sequencing. Exploring different areas of the SARS-CoV-2 genome demonstrated that the S gene in processed and extracted samples showed greater sensitivity to freeze-thaw cycles than the E or N genes. Investigating surrogate and normalisation viruses showed that Phi6 remains a stable comparison for SARS-CoV-2 in a laboratory setting and crAssphage was relatively resilient to temperature variation. Recovery of SARS-CoV-2 in raw unprocessed samples was significantly greater when stored at 4 °C, which was supported by the sequencing data for all viruses - both time and freeze-thaw cycles negatively impacted sequencing metrics. Historical extracts stored at -80 °C that were re-quantified 12, 14 and 16 months after original quantification showed no major changes. This study highlights the importance of the fast processing and extraction of wastewater samples, following which viruses are relatively robust to storage at a range of temperatures.
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Affiliation(s)
- Rachel C Williams
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
| | - William B Perry
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | | | - Ben Futcher
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK; Department of Oncology, Medical Sciences Division, University of Oxford, Old Road Campus Research Building, Headington, Oxford, OX3 7DQ, UK
| | - Cameron Pellett
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | | | - Steve Paterson
- Centre for Genomic Research, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jasmine M S Grimsley
- UK Health Security Agency, Data Analytics & Surveillance Group, 10 South Colonnade, Canary Wharf, London, E14 4PU, UK; The London Data Company, London, EC2N 2AT, UK
| | - Matthew J Wade
- UK Health Security Agency, Data Analytics & Surveillance Group, 10 South Colonnade, Canary Wharf, London, E14 4PU, UK
| | - Andrew J Weightman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Kata Farkas
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Davey L Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
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Acheampong E, Husain AA, Dudani H, Nayak AR, Nag A, Meena E, Shrivastava SK, McClure P, Tarr AW, Crooks C, Lade R, Gomes RL, Singer A, Kumar S, Bhatnagar T, Arora S, Kashyap RS, Monaghan TM. Population infection estimation from wastewater surveillance for SARS-CoV-2 in Nagpur, India during the second pandemic wave. PLoS One 2024; 19:e0303529. [PMID: 38809825 PMCID: PMC11135679 DOI: 10.1371/journal.pone.0303529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool for predicting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease outbreaks in high-income countries (HICs) with centralized sewage infrastructure. However, few studies have applied WBE alongside epidemic disease modelling to estimate the prevalence of SARS-CoV-2 in low-resource settings. This study aimed to explore the feasibility of collecting untreated wastewater samples from rural and urban catchment areas of Nagpur district, to detect and quantify SARS-CoV-2 using real-time qPCR, to compare geographic differences in viral loads, and to integrate the wastewater data into a modified Susceptible-Exposed-Infectious-Confirmed Positives-Recovered (SEIPR) model. Of the 983 wastewater samples analyzed for SARS-CoV-2 RNA, we detected significantly higher sample positivity rates, 43.7% (95% confidence interval (CI) 40.1, 47.4) and 30.4% (95% CI 24.66, 36.66), and higher viral loads for the urban compared with rural samples, respectively. The Basic reproductive number, R0, positively correlated with population density and negatively correlated with humidity, a proxy for rainfall and dilution of waste in the sewers. The SEIPR model estimated the rate of unreported coronavirus disease 2019 (COVID-19) cases at the start of the wave as 13.97 [95% CI (10.17, 17.0)] times that of confirmed cases, representing a material difference in cases and healthcare resource burden. Wastewater surveillance might prove to be a more reliable way to prepare for surges in COVID-19 cases during future waves for authorities.
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Affiliation(s)
- Edward Acheampong
- Department of Statistics and Actuarial Science, University of Ghana, Legon, Accra, Ghana
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Aliabbas A. Husain
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Hemanshi Dudani
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Amit R. Nayak
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Aditi Nag
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Ekta Meena
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Sandeep K. Shrivastava
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Patrick McClure
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Alexander W. Tarr
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Colin Crooks
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | | | - Rachel L. Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Andrew Singer
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Saravana Kumar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Tarun Bhatnagar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Sudipti Arora
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Rajpal Singh Kashyap
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Tanya M. Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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3
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Robotto A, Olivero C, Pozzi E, Strumia C, Crasà C, Fedele C, Derosa M, Di Martino M, Latino S, Scorza G, Civra A, Lembo D, Quaglino P, Brizio E, Polato D. Efficient wastewater sample filtration improves the detection of SARS-CoV-2 variants: An extensive analysis based on sequencing parameters. PLoS One 2024; 19:e0304158. [PMID: 38787865 PMCID: PMC11125551 DOI: 10.1371/journal.pone.0304158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
During the SARS-CoV-2 pandemic, many countries established wastewater (WW) surveillance to objectively monitor the level of infection within the population. As new variants continue to emerge, it has become clear that WW surveillance is an essential tool for the early detection of variants. The EU Commission published a recommendation suggesting an approach to establish surveillance of SARS-CoV-2 and its variants in WW, besides specifying the methodology for WW concentration and RNA extraction. Therefore, different groups have approached the issue with different strategies, mainly focusing on WW concentration methods, but only a few groups highlighted the importance of prefiltering WW samples and/or purification of RNA samples. Aiming to obtain high-quality sequencing data allowing variants detection, we compared four experimental conditions generated from the treatment of: i) WW samples by WW filtration and ii) the extracted RNA by DNase treatment, purification and concentration of the extracted RNA. To evaluate the best condition, the results were assessed by focusing on several sequencing parameters, as the outcome of SARS-CoV-2 sequencing from WW is crucial for variant detection. Overall, the best sequencing result was obtained by filtering the WW sample. Moreover, the present study provides an overview of some sequencing parameters to consider when optimizing a method for monitoring SARS-CoV-2 variants from WW samples, which can also be applied to any sample preparation methodology.
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Affiliation(s)
- Angelo Robotto
- Environmental Protection Agency of Piedmont (Arpa Piemonte), Torino, Italy
| | - Carlotta Olivero
- Department of Regional Centre of Molecular Biology, Environmental Protection Agency of Piedmont (Arpa Piemonte), La Loggia, Torino, Italy
| | - Elisa Pozzi
- Department of Regional Centre of Molecular Biology, Environmental Protection Agency of Piedmont (Arpa Piemonte), La Loggia, Torino, Italy
| | - Claudia Strumia
- Department of Regional Centre of Molecular Biology, Environmental Protection Agency of Piedmont (Arpa Piemonte), La Loggia, Torino, Italy
| | - Camilla Crasà
- Department of Regional Centre of Molecular Biology, Environmental Protection Agency of Piedmont (Arpa Piemonte), La Loggia, Torino, Italy
| | - Cristina Fedele
- Department of Regional Centre of Molecular Biology, Environmental Protection Agency of Piedmont (Arpa Piemonte), La Loggia, Torino, Italy
| | - Maddalena Derosa
- Department of Regional Centre of Molecular Biology, Environmental Protection Agency of Piedmont (Arpa Piemonte), La Loggia, Torino, Italy
| | - Massimo Di Martino
- Department of Regional Centre of Molecular Biology, Environmental Protection Agency of Piedmont (Arpa Piemonte), La Loggia, Torino, Italy
| | - Stefania Latino
- Department of Regional Centre of Molecular Biology, Environmental Protection Agency of Piedmont (Arpa Piemonte), La Loggia, Torino, Italy
| | - Giada Scorza
- Department of Regional Centre of Molecular Biology, Environmental Protection Agency of Piedmont (Arpa Piemonte), La Loggia, Torino, Italy
| | - Andrea Civra
- Dept. of Clinical and Biological Sciences, University of Turin, Orbassano, Torino, Italy
| | - David Lembo
- Dept. of Clinical and Biological Sciences, University of Turin, Orbassano, Torino, Italy
| | - Paola Quaglino
- Environmental Protection Agency of Piedmont (Arpa Piemonte), Torino, Italy
| | - Enrico Brizio
- Environmental Protection Agency of Piedmont (Arpa Piemonte), Torino, Italy
| | - Denis Polato
- Department of Regional Centre of Molecular Biology, Environmental Protection Agency of Piedmont (Arpa Piemonte), La Loggia, Torino, Italy
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Adams C, Bias M, Welsh RM, Webb J, Reese H, Delgado S, Person J, West R, Shin S, Kirby A. The National Wastewater Surveillance System (NWSS): From inception to widespread coverage, 2020-2022, United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171566. [PMID: 38461979 PMCID: PMC11103741 DOI: 10.1016/j.scitotenv.2024.171566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/12/2024]
Abstract
Wastewater surveillance is a valuable tool that can be used to track infectious diseases in a community. In September 2020, the Centers for Disease Control and Prevention (CDC) established the National Wastewater Surveillance System (NWSS) to coordinate and build the nation's capacity to detect and quantify concentrations of SARS-CoV-2 RNA in U.S. wastewater. This is the first surveillance summary of NWSS, covering September 1, 2020 to December 31, 2022. Through partnerships with state, tribal, local, and territorial health departments, NWSS became a national surveillance platform that can be readily expanded and adapted to meet changing public health needs. Beginning with 209 sampling sites in September 2020, NWSS rapidly expanded to >1500 sites by December 2022, covering ≈47 % of the U.S. population. As of December 2022, >152,000 unique wastewater samples have been collected by NWSS partners, primarily from wastewater treatment plants (WWTPs). WWTPs participating in NWSS tend to be larger than the average U.S. WWTP and serve more populated communities. In December 2022, ≈8 % of the nearly 16,000 U.S. WWTPs were participating in NWSS. NWSS partners used a variety of methods for sampling and testing wastewater samples; however, progress is being made to standardize these methods. In July 2021, NWSS partners started submitting SARS-CoV-2 genome sequencing data to NWSS. In October 2022, NWSS expanded to monkeypox virus testing, with plans to include additional infectious disease targets in the future. Through the rapid implementation and expansion of NWSS, important lessons have been learned. Wastewater surveillance programs should consider both surge and long-term capacities when developing an implementation plan, and early standardization of sampling and testing methods is important to facilitate data comparisons across sites. NWSS has proven to be a flexible and sustainable surveillance system that will continue to be a useful complement to case-based surveillance for guiding public health action.
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Affiliation(s)
- Carly Adams
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA; Epidemic Intelligence Service, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA.
| | - Megan Bias
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Rory M Welsh
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Jenna Webb
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Heather Reese
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Stephen Delgado
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - John Person
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Rachel West
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Soo Shin
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Amy Kirby
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
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5
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Inson JGM, Malla B, Amalin DM, Carvajal TM, Enriquez MLD, Hirai S, Raya S, Rahmani AF, Angga MS, Sthapit N, Shrestha S, Ruti AA, Takeda T, Kitajima M, Alam ZF, Haramoto E. Detection of SARS-CoV-2 and Omicron variant RNA in wastewater samples from Manila, Philippines. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170921. [PMID: 38350577 DOI: 10.1016/j.scitotenv.2024.170921] [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: 11/22/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 02/15/2024]
Abstract
Manila, a highly urbanized city, is listed as one of the top cities with the highest recorded number of coronavirus disease 2019 (COVID-19) cases in the Philippines. This study aimed to detect and quantify the RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the Omicron variant in 51 wastewater samples collected from three locations in Manila, namely Estero de Santa Clara, Estero de Pandacan, which are open drainages, and a sewage treatment plant (STP) at De La Salle University-Manila, between July 2022 and February 2023. Using one-step reverse transcription-quantitative polymerase chain reaction, SARS-CoV-2 and Omicron variant RNA were detected in 78 % (40/51; 4.9 ± 0.5 log10 copies/L) and 60 % (24/40; 4.4 ± 0.3 log10 copies/L) of wastewater samples collected from all sampling sites, respectively. SARS-CoV-2 RNA was detected frequently at Estero de Santa Clara (88 %, 15/17); its highest concentration was at the STP (6.3 log10 copies/L). The Omicron variant RNA was present in the samples collected (4.4 ± 0.3 log10 copies/L) from all sampling sites, with the highest concentration at the STP (4.9 log10 copies/L). Regardless of normalization, using concentrations of pepper mild mottle virus RNA, SARS-CoV-2 RNA concentrations exhibited the highest positive correlation with COVID-19 reported cases in Manila 5 days after the clinical report. These findings revealed that wastewater-based epidemiology may aid in identifying and monitoring of the presence of pathogens in open drainages and STPs in the Philippines. This paper provides the first documentation on SARS-CoV-2 and the Omicron variant in wastewater from Manila.
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Affiliation(s)
- Jessamine Gail M Inson
- Department of Biology, De La Salle University, Manila 1004, Philippines; Environmental Biomonitoring Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Divina M Amalin
- Department of Biology, De La Salle University, Manila 1004, Philippines; Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Thaddeus M Carvajal
- Department of Biology, De La Salle University, Manila 1004, Philippines; Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | | | - Soichiro Hirai
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
| | - Sunayana Raya
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Aulia Fajar Rahmani
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Made Sandhyana Angga
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Niva Sthapit
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Annisa Andarini Ruti
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Tomoko Takeda
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan.
| | - Zeba F Alam
- Department of Biology, De La Salle University, Manila 1004, Philippines; Environmental Biomonitoring Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila 1004, Philippines.
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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Bisen M, Kharga K, Mehta S, Jabi N, Kumar L. Bacteriophages in nature: recent advances in research tools and diverse environmental and biotechnological applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22199-22242. [PMID: 38411907 DOI: 10.1007/s11356-024-32535-3] [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: 11/16/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Bacteriophages infect and replicate within bacteria and play a key role in the environment, particularly in microbial ecosystems and bacterial population dynamics. The increasing recognition of their significance stems from their wide array of environmental and biotechnological uses, which encompass the mounting issue of antimicrobial resistance (AMR). Beyond their therapeutic potential in combating antibiotic-resistant infections, bacteriophages also find vast applications such as water quality monitoring, bioremediation, and nutrient cycling within environmental sciences. Researchers are actively involved in isolating and characterizing bacteriophages from different natural sources to explore their applications. Gaining insights into key aspects such as the life cycle of bacteriophages, their host range, immune interactions, and physical stability is vital to enhance their application potential. The establishment of diverse phage libraries has become indispensable to facilitate their wide-ranging uses. Consequently, numerous protocols, ranging from traditional to cutting-edge techniques, have been developed for the isolation, detection, purification, and characterization of bacteriophages from diverse environmental sources. This review offers an exploration of tools, delves into the methods of isolation, characterization, and the extensive environmental applications of bacteriophages, particularly in areas like water quality assessment, the food sector, therapeutic interventions, and the phage therapy in various infections and diseases.
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Affiliation(s)
- Monish Bisen
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Kusum Kharga
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sakshi Mehta
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Nashra Jabi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
- Cancer Biology Laboratory, Raj Khosla Centre for Cancer Research, Shoolini University, Himachal Pradesh, Solan, 173229, India.
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7
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Olejarz JW, Roster KIO, Kissler SM, Lipsitch M, Grad YH. Optimal environmental testing frequency for outbreak surveillance. Epidemics 2024; 46:100750. [PMID: 38394927 PMCID: PMC10979539 DOI: 10.1016/j.epidem.2024.100750] [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: 09/14/2023] [Revised: 01/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Public health surveillance for pathogens presents an optimization problem: we require enough sampling to identify intervention-triggering shifts in pathogen epidemiology, such as new introductions or sudden increases in prevalence, but not so much that costs due to surveillance itself outweigh those from pathogen-associated illness. To determine this optimal sampling frequency, we developed a general mathematical model for the introduction of a new pathogen that, once introduced, increases in prevalence exponentially. Given the relative cost of infection vs. sampling, we derived equations for the expected combined cost per unit time of disease burden and surveillance for a specified sampling frequency, and thus the sampling frequency for which the expected total cost per unit time is lowest.
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Affiliation(s)
- Jason W Olejarz
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Kirstin I Oliveira Roster
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Computer Science, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Marc Lipsitch
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
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8
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Dehghan Banadaki M, Torabi S, Rockward A, Strike WD, Noble A, Keck JW, Berry SM. Simple SARS-CoV-2 concentration methods for wastewater surveillance in low resource settings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168782. [PMID: 38000737 PMCID: PMC10842712 DOI: 10.1016/j.scitotenv.2023.168782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Wastewater-based epidemiology (WBE) measures pathogens in wastewater to monitor infectious disease prevalence in communities. Due to the high dilution of pathogens in sewage, a concentration method is often required to achieve reliable biomarker signals. However, most of the current concentration methods rely on expensive equipment and labor-intensive processes, which limits the application of WBE in low-resource settings. Here, we compared the performance of four inexpensive and simple concentration methods to detect SARS-CoV-2 in wastewater samples: Solid Fraction, Porcine Gastric Mucin-conjugated Magnetic Beads, Calcium Flocculation-Citrate Dissolution (CFCD), and Nanotrap® Magnetic Beads (NMBs). The NMBs and CFCD methods yielded the highest concentration performance for SARS-CoV-2 (∼16-fold concentration and ∼ 41 % recovery) and require <45 min processing time. CFCD has a relatively low consumable cost (<$2 per four sample replicates). All methods can be performed with basic laboratory equipment and minimal electricity usage which enables further application of WBE in remote areas and low resource settings.
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Affiliation(s)
| | - Soroosh Torabi
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
| | - Alexus Rockward
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States
| | - William D Strike
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States
| | - Ann Noble
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
| | - James W Keck
- WWAMI School of Medicine, University of Alaska Anchorage, United States
| | - Scott M Berry
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States; Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States.
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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.
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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
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10
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Xu X, Deng Y, Ding J, Shi X, Zheng X, Wang D, Yang Y, Liu L, Wang C, Li S, Gu H, Poon LLM, Zhang T. Refining detection methods for emerging SARS-CoV-2 mutants in wastewater: A case study on the Omicron variants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166215. [PMID: 37591380 DOI: 10.1016/j.scitotenv.2023.166215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
COVID-19 is an ongoing public health threat worldwide driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Wastewater surveillance has emerged as a complementary tool to clinical surveillance to control the COVID-19 pandemic. With the emergence of new variants of SARS-CoV-2, accumulated mutations that occurred in the SARS-CoV-2 genome raise new challenges for RT-qPCR diagnosis used in wastewater surveillance. There is a pressing need to develop refined methods for modifying primer/probes to better detect these emerging variants in wastewater. Here, we exemplified this process by focusing on the Omicron variants, for which we have developed and validated a modified detection method. We first modified the primers/probe mismatches of three assays commonly used in wastewater surveillance according to in silico analysis results for the mutations of 882 sequences collected during the fifth-wave outbreak in Hong Kong, and then evaluated them alongside the seven original assays. The results showed that five of seven original assays had better sensitivity for detecting Omicron variants, with the limits of detection (LoDs) ranging from 1.53 to 2.76 copies/μL. UCDC-N1 and Charité-E sets had poor performances, having LoDs higher than 10 copies/μL and false-positive/false-negative results in wastewater testing, probably due to the mismatch and demonstrating the need for modification of primer/probe sequences. The modified assays exhibited higher sensitivity and specificity, along with better reproducibility in detecting 81 wastewater samples. In addition, the sequencing results of six wastewater samples by Illumina also validated the presence of mismatches in the primer/probe binding sites of the three assays. This study highlights the importance of re-configuration of the primer-probe sets and refinements for the sequences to ensure the diagnostic effectiveness of RT-qPCR detection.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Haogao Gu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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11
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Barnes KG, Levy JI, Gauld J, Rigby J, Kanjerwa O, Uzzell CB, Chilupsya C, Anscombe C, Tomkins-Tinch C, Mbeti O, Cairns E, Thole H, McSweeney S, Chibwana MG, Ashton PM, Jere KC, Meschke JS, Diggle P, Cornick J, Chilima B, Jambo K, Andersen KG, Kawalazira G, Paterson S, Nyirenda TS, Feasey N. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems. Nat Commun 2023; 14:7883. [PMID: 38036496 PMCID: PMC10689440 DOI: 10.1038/s41467-023-43047-y] [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: 04/11/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
The COVID-19 pandemic has profoundly impacted health systems globally and robust surveillance has been critical for pandemic control, however not all countries can currently sustain community pathogen surveillance programs. Wastewater surveillance has proven valuable in high-income settings, but less is known about the utility of water surveillance of pathogens in low-income countries. Here we show how wastewater surveillance of SAR-CoV-2 can be used to identify temporal changes and help determine circulating variants quickly. In Malawi, a country with limited community-based COVID-19 testing capacity, we explore the utility of rivers and wastewater for SARS-CoV-2 surveillance. From May 2020-May 2022, we collect water from up to 112 river or defunct wastewater treatment plant sites, detecting SARS-CoV-2 in 8.3% of samples. Peak SARS-CoV-2 detection in water samples predate peaks in clinical cases. Sequencing of water samples identified the Beta, Delta, and Omicron variants, with Delta and Omicron detected well in advance of detection in patients. Our work highlights how wastewater can be used to detect emerging waves, identify variants of concern, and provide an early warning system in settings with no formal sewage systems.
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Affiliation(s)
- Kayla G Barnes
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Joshua I Levy
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jillian Gauld
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan Rigby
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Oscar Kanjerwa
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Christopher B Uzzell
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Chisomo Chilupsya
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Catherine Anscombe
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Christopher Tomkins-Tinch
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Omar Mbeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Herbert Thole
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Shannon McSweeney
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Marah G Chibwana
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Philip M Ashton
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
| | - Khuzwayo C Jere
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - John Scott Meschke
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Peter Diggle
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Jennifer Cornick
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
| | - Benjamin Chilima
- CHICAS, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Kondwani Jambo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Public Health Institute of Malawi, Lilongwe, Malawi
| | - Kristian G Andersen
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Scripps Research Translational Institute, La Jolla, CA, USA
| | - Gift Kawalazira
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Tonney S Nyirenda
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Nicholas Feasey
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
- School of Medicine, University of St Andrews, St Andrews, UK
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12
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Nagelkerke E, Hetebrij WA, Koelewijn JM, Kooij J, van der Drift AMR, van der Beek RFHJ, de Jonge EF, Lodder WJ. PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance. Front Public Health 2023; 11:1141494. [PMID: 38026384 PMCID: PMC10652756 DOI: 10.3389/fpubh.2023.1141494] [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: 01/10/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
Since the start of the COVID-19 pandemic in 2020, wastewater surveillance programs were established, or upscaled, in many countries around the world and have proven to be a cost-effective way of monitoring infectious disease pathogens. Many of these programs use RT-qPCR, and quantify the viral concentrations in samples based on standard curves, by including preparations of a reference material with known nucleic acid or virus concentrations in the RT-qPCR analyses. In high-throughput monitoring programs it is possible to combine data from multiple previous runs, circumventing the need for duplication and resulting in decreased costs and prolonged periods during which the reference material is obtained from the same batch. However, over time, systematic shifts in standard curves are likely to occur. This would affect the reliability and usefulness of wastewater surveillance as a whole. We aim to find an optimal combination of standard curve data to compensate for run-to-run measurement variance while ensuring enough flexibility to capture systematic longitudinal shifts. Based on more than 4000 observations obtained with the CDC N1 and N2 assays, taken as a part of the National Sewage Surveillance program at the Dutch National Institute for Public Health and the Environment, we show that seasonal and long-term shifts in RT-qPCR efficiency and sensitivity occur. We find that in our setting, using five days of standard-curve data to quantify, results in the least error prone curve or best approximation. This results in differences up to 100% in quantified viral loads when averaged out over a nationwide program of >300 treatment plants. Results show that combining standard curves from a limited set of runs can be a valid approach to quantification without obscuring the trends in the viral load of interest.
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Affiliation(s)
- Erwin Nagelkerke
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
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13
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Zhao L, Geng Q, Corchis-Scott R, McKay RM, Norton J, Xagoraraki I. Targeting a free viral fraction enhances the early alert potential of wastewater surveillance for SARS-CoV-2: a methods comparison spanning the transition between delta and omicron variants in a large urban center. Front Public Health 2023; 11:1140441. [PMID: 37546328 PMCID: PMC10400354 DOI: 10.3389/fpubh.2023.1140441] [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: 01/09/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction Wastewater surveillance has proven to be a valuable approach to monitoring the spread of SARS-CoV-2, the virus that causes Coronavirus disease 2019 (COVID-19). Recognizing the benefits of wastewater surveillance as a tool to support public health in tracking SARS-CoV-2 and other respiratory pathogens, numerous wastewater virus sampling and concentration methods have been tested for appropriate applications as well as their significance for actionability by public health practices. Methods Here, we present a 34-week long wastewater surveillance study that covers nearly 4 million residents of the Detroit (MI, United States) metropolitan area. Three primary concentration methods were compared with respect to recovery of SARS-CoV-2 from wastewater: Virus Adsorption-Elution (VIRADEL), polyethylene glycol precipitation (PEG), and polysulfone (PES) filtration. Wastewater viral concentrations were normalized using various parameters (flow rate, population, total suspended solids) to account for variations in flow. Three analytical approaches were implemented to compare wastewater viral concentrations across the three primary concentration methods to COVID-19 clinical data for both normalized and non-normalized data: Pearson and Spearman correlations, Dynamic Time Warping (DTW), and Time Lagged Cross Correlation (TLCC) and peak synchrony. Results It was found that VIRADEL, which captures free and suspended virus from supernatant wastewater, was a leading indicator of COVID-19 cases within the region, whereas PEG and PES filtration, which target particle-associated virus, each lagged behind the early alert potential of VIRADEL. PEG and PES methods may potentially capture previously shed and accumulated SARS-CoV-2 resuspended from sediments in the interceptors. Discussion These results indicate that the VIRADEL method can be used to enhance the early-warning potential of wastewater surveillance applications although drawbacks include the need to process large volumes of wastewater to concentrate sufficiently free and suspended virus for detection. While lagging the VIRADEL method for early-alert potential, both PEG and PES filtration can be used for routine COVID-19 wastewater monitoring since they allow a large number of samples to be processed concurrently while being more cost-effective and with rapid turn-around yielding results same day as collection.
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Affiliation(s)
- Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Robert Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - John Norton
- Great Lakes Water Authority, Detroit, MI, United States
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
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14
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Haque R, Hossain ME, Miah M, Rahman M, Amin N, Rahman Z, Islam MS, Rahman MZ. Monitoring SARS-CoV-2 variants in wastewater of Dhaka City, Bangladesh: approach to complement public health surveillance systems. Hum Genomics 2023; 17:58. [PMID: 37420264 PMCID: PMC10326934 DOI: 10.1186/s40246-023-00505-4] [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: 04/24/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Wastewater-based epidemiological surveillance has been considered a powerful tool for early detection and monitoring of the dynamics of SARS-CoV-2 and its lineages circulating in a community. This study is aimed to investigate the complexity of SARS-CoV-2 infection dynamics in Dhaka city by examining its genetic variants in wastewater. Also, the study seeks to determine a connection between the SARS-CoV-2 variations detected in clinical testing and those found in wastewater samples. RESULTS Out of 504 samples tested in RT-qPCR, 185 (36.7%) tested positive for SARS-CoV-2 viral RNA. The median log10 concentration of SARS-CoV-2 N gene copies/Liter of wastewater (gc/L) was 5.2, and the median log10 concentration of ORF1ab was 4.9. To further reveal the genetic diversity of SARS-CoV-2, ten samples with ORF1ab real-time RT-PCR cycle threshold (Ct) values ranging from 28.78 to 32.13 were subjected to whole genome sequencing using nanopore technology. According to clade classification, sequences from wastewater samples were grouped into 4 clades: 20A, 20B, 21A, 21J, and the Pango lineage, B.1, B.1.1, B.1.1.25, and B.1.617.2, with coverage ranging from 94.2 to 99.8%. Of them, 70% belonged to clade 20B, followed by 10% to clade 20A, 21A, and 21J. Lineage B.1.1.25 was predominant in Bangladesh and phylogenetically related to the sequences from India, the USA, Canada, the UK, and Italy. The Delta variant (B.1.617.2) was first identified in clinical samples at the beginning of May 2021. In contrast, we found that it was circulating in the community and was detected in wastewater in September 2020. CONCLUSION Environmental surveillance is useful for monitoring temporal and spatial trends of existing and emerging infectious diseases and supports evidence-based public health measures. The findings of this study supported the use of wastewater-based epidemiology and provided the baseline data for the dynamics of SARS-CoV-2 variants in the wastewater environment in Dhaka, Bangladesh.
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Affiliation(s)
- Rehnuma Haque
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh.
- Department of Women's and Children's Health, Uppsala University, Akademiska Sjukhuset, 75185, Uppsala, Sweden.
| | - Mohammad Enayet Hossain
- One Health Laboratory, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mojnu Miah
- One Health Laboratory, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Nuhu Amin
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
- Institute for Sustainable Futures, The University of Technology Sydney, 235 Jones St, Ultimo, NSW, 2007, Australia
| | - Ziaur Rahman
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
| | - Md Shariful Islam
- Environmental Interventions Unit, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
- The School of Public Health, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mohammed Ziaur Rahman
- One Health Laboratory, Infectious Diseases Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212, Bangladesh
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15
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Wani H, Menon S, Desai D, D’Souza N, Bhathena Z, Desai N, Rose JB, Shrivastava S. Wastewater-Based Epidemiology of SARS-CoV-2: Assessing Prevalence and Correlation with Clinical Cases. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:131-143. [PMID: 37133676 PMCID: PMC10155169 DOI: 10.1007/s12560-023-09555-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/18/2023] [Indexed: 05/04/2023]
Abstract
Wastewater-based epidemiology has been recognized as a tool to monitor the progress of COVID-19 pandemic worldwide. The study presented herein aimed at quantitating the SARS-CoV-2 RNA in the wastewaters, predicting the number of infected individuals in the catchment areas, and correlating it with the clinically reported COVID-19 cases. Wastewater samples (n = 162) from different treatment stages were collected from three wastewater treatment plants (WWTPs) from Mumbai city during the 2nd surge of COVID-19 (April 2021 to June 2021). SARS-CoV-2 causing COVID-19, was detected in 76.2% and 4.8% of raw and secondary treated (n = 63 each) wastewater samples respectively while all tertiary treated samples (n = 36) were negative. The quantity of SARS-CoV-2 RNA determined as gene copies/100 mL varied among all the three WWTPs under study. The gene copy numbers thus obtained were further used to estimate the number of infected individuals within the population served by these WWTPs using two published methods. A positive correlation (p < 0.05) was observed between the estimated number of infected individuals and clinically confirmed COVID-19 cases reported during the sampling period in two WWTPs. Predicted infected individuals calculated in this study were 100 times higher than the reported COVID-19 cases in all the WWTPs assessed. The study findings demonstrated that the present wastewater treatment technologies at the three WWTPs studied were adequate to remove the virus. However, SARS-CoV-2 genome surveillance with emphasis on monitoring its variants should be implemented as a routine practice to prepare for any future surge in infections.
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Affiliation(s)
- Hima Wani
- Bhavan’s Research Center, Bhavan’s College Campus, Andheri West, Mumbai, Maharashtra 400058 India
| | - Smita Menon
- Bhavan’s Research Center, Bhavan’s College Campus, Andheri West, Mumbai, Maharashtra 400058 India
- Department of Microbiology, Bhavan’s College, Andheri West, Mumbai, Maharashtra 400058 India
| | - Dipen Desai
- Bhavan’s Research Center, Bhavan’s College Campus, Andheri West, Mumbai, Maharashtra 400058 India
| | - Nishita D’Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824 USA
| | - Zarine Bhathena
- Department of Microbiology, Bhavan’s College, Andheri West, Mumbai, Maharashtra 400058 India
| | - Nishith Desai
- Bhavan’s Research Center, Bhavan’s College Campus, Andheri West, Mumbai, Maharashtra 400058 India
| | - Joan B. Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824 USA
| | - Sandhya Shrivastava
- Bhavan’s Research Center, Bhavan’s College Campus, Andheri West, Mumbai, Maharashtra 400058 India
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16
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Rashed AO, Huynh C, Merenda A, Rodriguez-Andres J, Kong L, Kondo T, Razal JM, Dumée LF. Dry-spun carbon nanotube ultrafiltration membranes tailored by anti-viral metal oxide coatings for human coronavirus 229E capture in water. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:110176. [PMID: 37234558 PMCID: PMC10201849 DOI: 10.1016/j.jece.2023.110176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/21/2023] [Accepted: 05/20/2023] [Indexed: 05/28/2023]
Abstract
Although waterborne virus removal may be achieved using separation membrane technologies, such technologies remain largely inefficient at generating virus-free effluents due to the lack of anti-viral reactivity of conventional membrane materials required to deactivating viruses. Here, a stepwise approach towards simultaneous filtration and disinfection of Human Coronavirus 229E (HCoV-229E) in water effluents, is proposed by engineering dry-spun ultrafiltration carbon nanotube (CNT) membranes, coated with anti-viral SnO2 thin films via atomic layer deposition. The thickness and pore size of the engineered CNT membranes were fine-tuned by varying spinnable CNT sheets and their relative orientations on carbon nanofibre (CNF) porous supports to reach thicknesses less than 1 µm and pore size around 28 nm. The nanoscale SnO2 coatings were found to further reduce the pore size down to ∼21 nm and provide more functional groups on the membrane surface to capture the viruses via size exclusion and electrostatic attractions. The synthesized CNT and SnO2 coated CNT membranes were shown to attain a viral removal efficiency above 6.7 log10 against HCoV-229E virus with fast water permeance up to ∼4 × 103 and 3.5 × 103 L.m-2.h-1.bar-1, respectively. Such high performance was achieved by increasing the dry-spun CNT sheets up to 60 layers, orienting successive 30 CNT layers at 45°, and coating 40 nm SnO2 on the synthesized membranes. The current study provides an efficient scalable fabrication scheme to engineer flexible ultrafiltration CNT-based membranes for cost-effective filtration and inactivation of waterborne viruses to outperform the state-of-the-art ultrafiltration membranes.
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Affiliation(s)
- Ahmed O Rashed
- Deakin University, Geelong, Institute for Frontier Materials, 3216 Waurn Ponds, Victoria, Australia
| | - Chi Huynh
- LINTEC OF AMERICA, INC. Nano-Science and Technology Center, 2900 E. Plano Pkwy. Suite 100, Plano, TX 75074, United States
| | - Andrea Merenda
- School of Science, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | | | - Lingxue Kong
- Deakin University, Geelong, Institute for Frontier Materials, 3216 Waurn Ponds, Victoria, Australia
| | - Takeshi Kondo
- LINTEC OF AMERICA, INC. Nano-Science and Technology Center, 2900 E. Plano Pkwy. Suite 100, Plano, TX 75074, United States
| | - Joselito M Razal
- Deakin University, Geelong, Institute for Frontier Materials, 3216 Waurn Ponds, Victoria, Australia
| | - Ludovic F Dumée
- Khalifa University, Department of Chemical Engineering, Abu Dhabi, United Arab Emirates
- Research and Innovation Center on CO2 and Hydrogen, Khalifa University, Abu Dhabi, United Arab Emirates
- Center for Membrane and Advanced Water Technology, Khalifa University, Abu Dhabi, United Arab Emirates
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17
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Chau KK, Goodall T, Bowes M, Easterbrook K, Brett H, Hughes J, Crook DW, Read DS, Walker AS, Stoesser N. High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent. Microb Genom 2023; 9. [PMID: 37145848 DOI: 10.1099/mgen.0.000983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Wastewater-based epidemiology (WBE) for population-level surveillance of antimicrobial resistance (AMR) is gaining significant traction, but the impact of wastewater sampling methods on results is unclear. In this study, we characterized taxonomic and resistome differences between single-timepoint-grab and 24 h composites of wastewater influent from a large UK-based wastewater treatment work [WWTW (population equivalent: 223 435)]. We autosampled hourly influent grab samples (n=72) over three consecutive weekdays, and prepared additional 24 h composites (n=3) from respective grabs. For taxonomic profiling, metagenomic DNA was extracted from all samples and 16S rRNA gene sequencing was performed. One composite and six grabs from day 1 underwent metagenomic sequencing for metagenomic dissimilarity estimation and resistome profiling. Taxonomic abundances of phyla varied significantly across hourly grab samples but followed a repeating diurnal pattern for all 3 days. Hierarchical clustering grouped grab samples into four time periods dissimilar in both 16S rRNA gene-based profiles and metagenomic distances. 24H-composites resembled mean daily phyla abundances and showed low variability of taxonomic profiles. Of the 122 AMR gene families (AGFs) identified across all day 1 samples, single grab samples identified a median of six (IQR: 5-8) AGFs not seen in the composite. However, 36/36 of these hits were at lateral coverage <0.5 (median: 0.19; interquartile range: 0.16-0.22) and potential false positives. Conversely, the 24H-composite identified three AGFs not seen in any grab with higher lateral coverage (0.82; 0.55-0.84). Additionally, several clinically significant human AGFs (bla VIM, bla IMP, bla KPC) were intermittently or completely missed by grab sampling but captured by the 24 h composite. Wastewater influent undergoes significant taxonomic and resistome changes on short timescales potentially affecting interpretation of results based on sampling strategy. Grab samples are more convenient and potentially capture low-prevalence/transient targets but are less comprehensive and temporally variable. Therefore, we recommend 24H-composite sampling where feasible. Further validation and optimization of WBE methods is vital for its development into a robust AMR surveillance approach.
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Affiliation(s)
- Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
| | - T Goodall
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - M Bowes
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - K Easterbrook
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - H Brett
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - J Hughes
- Thames Water, Clearwater Court, Vastern Road, Reading, RG1 8DB, UK
| | - D W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - D S Read
- UK Centre for Ecology & Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - A S Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
| | - N Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford in partnership with Public Health England, Oxford, UK
- Department of Microbiology/Infectious diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, The Joint Research Office, Second Floor, OUH Cowley, Unipart House Business Centre, Garsington Road, Oxford, OX4 2PG, UK
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18
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de Rooij MM, Sikkema RS, Bouwknegt M, de Geus Y, Stanoeva KR, Nieuwenweg S, van Dam AS, Raben C, Dohmen W, Heederik D, Reusken C, Meijer A, Koopmans MP, Franz E, Smit LA. A Comprehensive Sampling Study on SARS-CoV-2 Contamination of Air and Surfaces in a Large Meat Processing Plant Experiencing COVID-19 Clusters in June 2020. J Occup Environ Med 2023; 65:e227-e233. [PMID: 36640441 PMCID: PMC10090283 DOI: 10.1097/jom.0000000000002785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
OBJECTIVE We aimed to assess SARS-CoV-2 contamination of air and surfaces to gain insight into potential occupational exposure in a large meat processing plant experiencing COVID-19 clusters. Methods: Oro-nasopharyngeal SARS-CoV-2 screening was performed in 76 workers. Environmental samples ( n = 275) including air, ventilation systems, sewage, and swabs of high-touch surfaces and workers' hands were tested for SARS-CoV-2 RNA by real-time quantitative polymerase chain reaction. Results: Twenty-seven (35.5%) of the (predominantly asymptomatic) workers tested positive with modest to low viral loads (cycle threshold ≥ 29.7). Six of 203 surface swabs, 1 of 12 personal air samples, and one of four sewage samples tested positive; other samples tested negative. Conclusions: Although one third of workers tested positive, environmental contamination was limited. Widespread SARS-CoV-2 transmission via air and surfaces was considered unlikely within this plant at the time of investigation while strict COVID-19 control measures were already implemented.
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19
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Dehghan Banadaki M, Torabi S, Strike WD, Noble A, Keck JW, Berry SM. Improving wastewater-based epidemiology performance through streamlined automation. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:109595. [PMID: 36875746 PMCID: PMC9970922 DOI: 10.1016/j.jece.2023.109595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/02/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Wastewater-based epidemiology (WBE) has enabled us to describe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in populations. However, implementation of wastewater monitoring of SARS-CoV-2 is limited due to the need for expert staff, expensive equipment, and prolonged processing times. As WBE increases in scope (beyond SARS-CoV-2) and scale (beyond developed regions), there is a need to make WBE processes simpler, cheaper, and faster. We developed an automated workflow based on a simplified method termed exclusion-based sample preparation (ESP). Our automated workflow takes 40 min from raw wastewater to purified RNA, which is several times faster than conventional WBE methods. The total assay cost per sample/replicate is $6.50 which includes consumables and reagents for concentration, extraction, and RT-qPCR quantification. The assay complexity is reduced significantly, as extraction and concentration steps are integrated and automated. The high recovery efficiency of the automated assay (84.5 ± 25.4%) yielded an improved Limit of Detection (LoDAutomated=40 copies/mL) compared to the manual process (LoDManual=206 copies/mL), increasing analytical sensitivity. We validated the performance of the automated workflow by comparing it with the manual method using wastewater samples from several locations. The results from the two methods correlated strongly (r = 0.953), while the automated method was shown to be more precise. In 83% of the samples, the automated method showed lower variation between replicates, which is likely due to higher technical errors in the manual process e.g., pipetting. Our automated wastewater workflow can support the expansion of WBE in the fight against Coronavirus Disease of 2019 (COVID-19) and other epidemics.
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Affiliation(s)
| | - Soroosh Torabi
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
| | - William D Strike
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States
| | - Ann Noble
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
| | - James W Keck
- Department of Family and Community Medicine, College of Medicine, University of Kentucky, United States
| | - Scott M Berry
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States
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20
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Tavazzi S, Cacciatori C, Comero S, Fatta-Kassinos D, Karaolia P, Iakovides IC, Loutsiou P, Gutierrez-Aguirre I, Lengar Z, Bajde I, Tenson T, Kisand V, Laas P, Panksep K, Tammert H, Mariani G, Skejo H, Gawlik BM. Short-term stability of wastewater samples for storage and shipment in the context of the EU Sewage Sentinel System for SARS-CoV-2. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:109623. [PMID: 36890876 PMCID: PMC9979635 DOI: 10.1016/j.jece.2023.109623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
In the context of an EU-wide surveillance system for SARS-CoV-2 in wastewater, recommended by the European Commission, this study aims to provide scientific support to the adequacy of transport and storage conditions of samples both in terms of duration and samples temperature. Three laboratories in Slovenia, Cyprus and Estonia investigated the short-term, one-week, isochronous stability of wastewater samples by RT-qPCR based detection of SARS-CoV-2 genes. The results were tested for statistical significance to determine uncertainty of quantification and shelf-life, at testing temperatures of + 20 °C and - 20 °C, relative to reference at + 4 °C. Samples were collected from three urban wastewater treatment plant influents and analysed respectively for SARS-CoV-2 genes N1, N2 (Laboratory 1), N2, E (Laboratory 2) and N3 (Laboratory 3), with various analytical methods. For a period of 7/8 days at + 20 °C, decreasing trends of measured concentrations were observed for all genes resulting in instability according to the statistical analysis, while at - 20 °C the trend of variation was stable only for N1, N2 (Laboratory 1) and N3 (Laboratory 3). Trends for gene E concentrations at - 20 °C (Laboratory 2) could not be tested statistically for stability because of lack of data. Over a period of just 3 days at + 20 °C, the variation was statistically non-significant indicating stability for genes N1, E and N3 for laboratories 1, 2 and 3, respectively. Nonetheless, the outcome of the study presents evidence to support the choice of the selected temperature at which samples shall be preserved during storage before analysis or transport to the laboratory. The conditions (+4 °C, ∼ few days) chosen for EU wastewater surveillance are in accordance with these results, highlighting the importance of stability testing of environmental samples to determine the short-term analytical uncertainty.
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Affiliation(s)
- S Tavazzi
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - C Cacciatori
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - S Comero
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - D Fatta-Kassinos
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - P Karaolia
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - I C Iakovides
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - P Loutsiou
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | | | - Z Lengar
- National Institute of Biology, Vecna Pot 111, SI-1000 Ljubljana, Slovenia
| | - I Bajde
- National Institute of Biology, Vecna Pot 111, SI-1000 Ljubljana, Slovenia
| | - T Tenson
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - V Kisand
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - P Laas
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - K Panksep
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - H Tammert
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - G Mariani
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - H Skejo
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - B M Gawlik
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
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21
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Rondeau NC, Rose OJ, Alt ER, Ariyan LA, Elikan AB, Everard JL, Schreier AR, Tessler ME, Tulinsky GH, Vo JR, Ray CA, Yang CY, Miranda JJL, Mailloux BJ. Building-Level Detection Threshold of SARS-CoV-2 in Wastewater. Microbiol Spectr 2023; 11:e0292922. [PMID: 36975999 PMCID: PMC10100851 DOI: 10.1128/spectrum.02929-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/25/2023] [Indexed: 03/29/2023] Open
Abstract
We established wastewater surveillance of SARS-CoV-2 in a small, residential, urban college as part of an integrated public health response during the COVID-19 pandemic. Students returned to campus in spring 2021. During the semester, students were required to perform nasal PCR tests twice weekly. At the same time, wastewater monitoring was established in 3 campus dormitory buildings. Two were dedicated dormitories with populations of 188 and 138 students; 1 was an isolation building where students were moved within 2 h of receiving positive test results. Analysis of wastewater from isolation indicated that the amount of viral shedding was highly variable and that viral concentration could not be used to estimate the number of cases at the building level. However, rapid movement of students to isolation enabled determination of predictive power, specificity, and sensitivity from instances in which generally one positive case at a time occurred in a building. Our assay yields effective results with an ~60% positive predictive power, ~90% negative predictive power, and ~90% specificity. Sensitivity, however, is low at ~40%. Detection is improved in the few instances of 2 simultaneous positive cases, with sensitivity of 1 case versus 2 cases increasing from ~20% to 100%. We also measured the appearance of a variant of concern on campus and noted a similarity in timeline with increased prevalence in surrounding New York City. Monitoring SARS-CoV-2 in the sewage outflow of individual buildings can be used with a realistic goal of containing outbreak clusters but not necessarily single cases. IMPORTANCE Diagnostic testing of sewage can detect levels of circulating viruses to help inform public health. Wastewater-based epidemiology has been particularly active during the COVID-19 pandemic to measure the prevalence of SARS-CoV-2. Understanding the technical limitations of diagnostic testing for individual buildings would help inform future surveillance programs. We report our diagnostic and clinical data monitoring of buildings on a college campus in New York City during the spring 2021 semester. Frequent nasal testing, mitigation measures, and public health protocols provided a context in which to study the effectiveness of wastewater-based epidemiology. Our efforts could not consistently detect individual positive COVID-19 cases, but sensitivity is significantly improved in detecting two simultaneous cases. We therefore contend that wastewater surveillance may be more practically suited for the mitigation of outbreak clusters.
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Affiliation(s)
- Nicole C. Rondeau
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
| | - Oliver J. Rose
- Office of Facilities Services, Barnard College, Columbia University, New York, New York, USA
| | - Ellen R. Alt
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
| | - Lina A. Ariyan
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
| | - Annabelle B. Elikan
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
| | - Jenna L. Everard
- Environmental Science Department, Barnard College, Columbia University, New York, New York, USA
| | - Abigail R. Schreier
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
| | - Maya E. Tessler
- Environmental Science Department, Barnard College, Columbia University, New York, New York, USA
| | - Grace H. Tulinsky
- Environmental Science Department, Barnard College, Columbia University, New York, New York, USA
| | - Janet R. Vo
- Environmental Science Department, Barnard College, Columbia University, New York, New York, USA
| | - Caroline A. Ray
- President’s Office, Barnard College, Columbia University, New York, New York, USA
| | - Cynthia Y. Yang
- President’s Office, Barnard College, Columbia University, New York, New York, USA
| | - JJ L. Miranda
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
| | - Brian J. Mailloux
- Environmental Science Department, Barnard College, Columbia University, New York, New York, USA
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22
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Davis A, Keely SP, Brinkman NE, Bohrer Z, Ai Y, Mou X, Chattopadhyay S, Hershey O, Senko J, Hull N, Lytmer E, Quintero A, Lee J. Evaluation of intra- and inter-lab variability in quantifying SARS-CoV-2 in a state-wide wastewater monitoring network. ENVIRONMENTAL SCIENCE : WATER RESEARCH & TECHNOLOGY 2023; 9:1053-1068. [PMID: 37701755 PMCID: PMC10494892 DOI: 10.1039/d2ew00737a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
In December 2019, SARS-CoV-2, the virus that causes coronavirus disease 2019, was first reported and subsequently triggered a global pandemic. Wastewater monitoring, a strategy for quantifying viral gene concentrations from wastewater influents within a community, has served as an early warning and management tool for the spread of SARS-CoV-2 in a community. Ohio built a collaborative statewide wastewater monitoring network that is supported by eight labs (university, government, and commercial laboratories) with unique sample processing workflows. Consequently, we sought to characterize the variability in wastewater monitoring results for network labs. Across seven trials between October 2020 and November 2021, eight participating labs successfully quantified two SARS-CoV-2 RNA targets and human fecal indicator virus targets in wastewater sample aliquots with reproducible results, although recovery efficiencies of spiked surrogates ranged from 3 to 75%. When SARS-CoV-2 gene fragment concentrations were adjusted for recovery efficiency and flow, the proportion of variance between laboratories was minimized, serving as the best model to account for between-lab variance. Another adjustment factor (alone and in different combinations with the above factors) considered to account for sample and measurement variability includes fecal marker normalization. Genetic quantification variability can be attributed to many factors, including the methods, individual samples, and water quality parameters. In addition, statistically significant correlations were observed between SARS-CoV-2 RNA and COVID-19 case numbers, supporting the notion that wastewater surveillance continues to serve as an effective monitoring tool. This study serves as a real-time example of multi-laboratory collaboration for public health preparedness for infectious diseases.
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Affiliation(s)
- Angela Davis
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, 1841 Neil Avenue, Columbus, OH 43210, USA
| | - Scott P Keely
- United States Environmental Protection Agency, Office of Research and Development, USA
| | - Nichole E Brinkman
- United States Environmental Protection Agency, Office of Research and Development, USA
| | | | - Yuehan Ai
- Department of Food Science & Technology, The Ohio State University, USA
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, USA
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, Department of Biology and Department of Geosciences, University of Toledo, USA
| | - Olivia Hershey
- Department of Geosciences and Biology, University of Akron, USA
| | - John Senko
- Department of Geosciences and Biology, University of Akron, USA
| | - Natalie Hull
- Department of Civil, Environmental and Geodetic Engineering and Sustainability Institute, The Ohio State University, USA
| | - Eva Lytmer
- Department of Biological Sciences, Bowling Green State University, USA
| | | | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, 1841 Neil Avenue, Columbus, OH 43210, USA
- Department of Food Science & Technology, The Ohio State University, USA
- Infectious Diseases Institute, The Ohio State University, USA
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23
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Balakrishnan A, Jacob MM, Senthil Kumar P, Kapoor A, Ponnuchamy M, Sivaraman P, Sillanpää M. Strategies for safe management of hospital wastewater during the COVID-19 pandemic. INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY : IJEST 2023; 20:1-16. [PMID: 36817164 PMCID: PMC9925218 DOI: 10.1007/s13762-023-04803-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/18/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Management of hospital wastewater is a challenging task, particularly during the situations like coronavirus 2019 (COVID-19) pandemic. The hospital effluent streams are likely to contain many known and unknown contaminants including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) along with a variety of pollutants arising from pharmaceuticals, life-style chemicals, drugs, radioactive species, and human excreta from the patients. The effluents are a mixed bag of contaminants with some of them capable of infecting through contact. Hence, it is essential to identify appropriate treatment strategies for hospital waste streams. In this work, various pollutants emerging in the context of COVID-19 are examined. A methodical review is conducted on the occurrence and disinfection methods of SARS-CoV-2 in wastewater. An emphasis is given to the necessity of addressing the challenges of handling hospital effluents dynamically involved during the pandemic scenario to ensure human and environmental safety. A comparative evaluation of disinfection strategies makes it evident that the non-contact methods like ultraviolet irradiation, hydrogen peroxide vapor, and preventive approaches such as the usage of antimicrobial surface coating offer promise in reducing the chance of disease transmission. These methods are also highly efficient in comparison with other strategies. Chemical disinfection strategies such as chlorination may lead to further disinfection byproducts, complicating the treatment processes. An overall analysis of various disinfection methods is presented here, including developing methods such as membrane technologies, highlighting the merits and demerits of each of these processes. Finally, the wastewater surveillance adopted during the COVID-19 outbreak is discussed. Supplementary Information The online version contains supplementary material available at 10.1007/s13762-023-04803-1.
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Affiliation(s)
- A. Balakrishnan
- Department of Chemical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha 769008 India
| | - M. M. Jacob
- Department of Chemical Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203 India
| | - P. Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, Chennai 603203 India
- Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, Chennai 603203 India
- School of Engineering, Lebanese American University, Byblos, Lebanon
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413 India
| | - A. Kapoor
- Department of Chemical Engineering, Harcourt Butler Technical University, Kanpur, Uttar Pradesh 208002 India
| | - M. Ponnuchamy
- Department of Chemical Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203 India
| | - P. Sivaraman
- Department of Chemical Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203 India
| | - M. Sillanpää
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451 Saudi Arabia
- School of Resources and Environment, University of Electronic Science and Technology of China (UESTC), NO. 2006, Xiyuan Ave., West High-Tech Zone, Chengdu, Sichuan 611731 People’s Republic of China
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24
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Ash KT, Li Y, Alamilla I, Joyner DC, Williams DE, McKay PJ, Green BM, Iler C, DeBlander SE, North CM, Kara-Murdoch F, Swift CM, Hazen TC. SARS-CoV-2 raw wastewater surveillance from student residences on an urban university campus. Front Microbiol 2023; 14:1101205. [PMID: 36846780 PMCID: PMC9948028 DOI: 10.3389/fmicb.2023.1101205] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
The COVID-19 pandemic brought about an urgent need to monitor the community prevalence of infection and detect the presence of SARS-CoV-2. Testing individual people is the most reliable method to measure the spread of the virus in any given community, but it is also the most expensive and time-consuming. Wastewater-based epidemiology (WBE) has been used since the 1960s when scientists implemented monitoring to measure the effectiveness of the Polio vaccine. Since then, WBE has been used to monitor populations for various pathogens, drugs, and pollutants. In August 2020, the University of Tennessee-Knoxville implemented a SARS-CoV-2 surveillance program that began with raw wastewater surveillance of the student residence buildings on campus, the results of which were shared with another lab group on campus that oversaw the pooled saliva testing of students. Sample collection began at 8 am, and the final RT-qPCR results were obtained by midnight. The previous day's results were presented to the campus administrators and the Student Health Center at 8 am the following morning. The buildings surveyed included all campus dormitories, fraternities, and sororities, 46 buildings in all representing an on-campus community of over 8,000 students. The WBE surveillance relied upon early morning "grab" samples and 24-h composite sampling. Because we only had three Hach AS950 Portable Peristaltic Sampler units, we reserved 24-h composite sampling for the dormitories with the highest population of students. Samples were pasteurized, and heavy sediment was centrifuged and filtered out, followed by a virus concentration step before RNA extraction. Each sample was tested by RT-qPCR for the presence of SARS-CoV-2, using the CDC primers for N Capsid targets N1 and N3. The subsequent pooled saliva tests from sections of each building allowed lower costs and minimized the total number of individual verification tests that needed to be analyzed by the Student Health Center. Our WBE results matched the trend of the on-campus cases reported by the student health center. The highest concentration of genomic copies detected in one sample was 5.06 × 107 copies/L. Raw wastewater-based epidemiology is an efficient, economical, fast, and non-invasive method to monitor a large community for a single pathogen or multiple pathogen targets.
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Affiliation(s)
- K. T. Ash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States,Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
| | - Y. Li
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
| | - I. Alamilla
- Student Health Center, University of Tennessee, Knoxville, TN, United States
| | - D. C. Joyner
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - D. E. Williams
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - P. J. McKay
- Student Health Center, University of Tennessee, Knoxville, TN, United States
| | - B. M. Green
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - C. Iler
- Facilities Services Department, University of Tennessee, Knoxville, TN, United States
| | - S. E. DeBlander
- College of Natural Science, Michigan State University, East Lansing, MI, United States
| | - C. M. North
- Student Health Center, University of Tennessee, Knoxville, TN, United States
| | - F. Kara-Murdoch
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States,Battelle Memorial Institute, Columbus, OH, United States
| | - C. M. Swift
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - T. C. Hazen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States,Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States,Department of Microbiology, University of Tennessee, Knoxville, TN, United States,Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States,*Correspondence: T. C. Hazen, ✉
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25
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Alahdal HM, Ameen F, AlYahya S, Sonbol H, Khan A, Alsofayan Y, Alahmari A. Municipal wastewater viral pollution in Saudi Arabia: effect of hot climate on COVID-19 disease spreading. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:25050-25057. [PMID: 34138435 PMCID: PMC8210523 DOI: 10.1007/s11356-021-14809-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
The viral RNA of SARS-Coronavirus-2 is known to be contaminating municipal wastewater. We aimed to assess if COVID-19 disease is spreading through wastewater. We studied the amount of viral RNA in raw sewage and the efficiency of the sewage treatment to remove the virus. Sewage water was collected before and after the activated sludge process three times during summer 2020 from three different sewage treatment plants. The sewage treatment was efficient in removing SARS-CoV-2 viral RNA. Each sewage treatment plant gathered wastewater from one hospital, of which COVID-19 admissions were used to describe the level of disease occurrence in the area. The presence of SARS-CoV-2 viral RNA-specific target genes (N1, N2, and E) was confirmed using RT-qPCR analysis. However, hospital admission did not correlate significantly with viral RNA. Moreover, viral RNA loads were relatively low, suggesting that sewage might preserve viral RNA in a hot climate only for a short time.
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Affiliation(s)
- Hadil M Alahdal
- Department of Biology, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fuad Ameen
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - Sami AlYahya
- National Center for Biotechnology, King Abdulaziz City for Science & Technology, Riyadh, Saudi Arabia
| | - Hana Sonbol
- Department of Biology, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Anas Khan
- Department of Emergency Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Global Center for Mass Gatherings Medicine, Ministry of Health, P.O. Box 11461, Riyadh, Saudi Arabia
| | - Yousef Alsofayan
- Global Center for Mass Gatherings Medicine, Ministry of Health, P.O. Box 11461, Riyadh, Saudi Arabia
| | - Ahmed Alahmari
- Global Center for Mass Gatherings Medicine, Ministry of Health, P.O. Box 11461, Riyadh, Saudi Arabia
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26
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Galani A, Markou A, Dimitrakopoulos L, Kontou A, Kostakis M, Kapes V, Diamantopoulos MA, Adamopoulos PG, Avgeris M, Lianidou E, Scorilas A, Paraskevis D, Tsiodras S, Dimopoulos MA, Thomaidis N. Delta SARS-CoV-2 variant is entirely substituted by the omicron variant during the fifth COVID-19 wave in Attica region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159062. [PMID: 36181801 PMCID: PMC9519360 DOI: 10.1016/j.scitotenv.2022.159062] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Abstract
Wastewater analysis is the most attractive alternative way for the quantification and variant profiling of SARS-CoV-2. Infection dynamics can be monitored by RT-qPCR assays while NGS can provide evidence for the presence of existing or new emerging SARS-CoV-2 variants. Herein, apart from the infection dynamic in Attica since June 1st, 2021, the monitoring of 9 mutations of the omicron and 4 mutations of the delta SARS-CoV-2 variants, utilizing both novel Nested-Seq and RT-PCR, is reported and the substitution of the delta variant (B.1.617.2) by the omicron variant (B.1.1.529) in Attica, Greece within approximately one month is highlighted. The key difference between the two methodologies is discovery power. RT-PCR can only detect known sequences cost-effectively, while NGS is a hypothesis-free approach that does not require prior knowledge to detect novel genes. Overall, the potential of wastewater genomic surveillance for the early discovery and monitoring of variants important for disease management at the community level is underlined. This is the first study, reporting the SARS-CoV-2 infection dynamic for an extended time period and the first attempt to monitor two of the most severe variants with two different methodologies in Greece.
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Affiliation(s)
- Aikaterini Galani
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Athina Markou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Lampros Dimitrakopoulos
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Aikaterini Kontou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Marios Kostakis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Vasileios Kapes
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece; Laboratory of Clinical Biochemistry - Molecular Diagnostics, Second Department of Pediatrics, "P. & A. Kyriakou" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Sotirios Tsiodras
- Fourth Department of Internal Medicine, School of Medicine, University General Hospital Attikon, National and Kapodistrian University of Athens, Greece
| | | | - Nikolaos Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece.
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27
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Sridhar J, Parit R, Boopalakrishnan G, Rexliene MJ, Praveen R, Viswananathan B. Importance of wastewater-based epidemiology for detecting and monitoring SARS-CoV-2. CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2022; 6:100241. [PMID: 37520919 PMCID: PMC9341170 DOI: 10.1016/j.cscee.2022.100241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 08/01/2023]
Abstract
Coronavirus disease caused by the SARS-CoV-2 virus has emerged as a global challenge in terms of health and disease monitoring. COVID-19 infection is mainly spread through the SARS-CoV-2 infection leading to the development of mild to severe clinical manifestations. The virus binds to its cognate receptor ACE2 which is widely expressed among different tissues in the body. Notably, SARS-CoV-2 shedding in the fecal samples has been reported through the screening of sewage water across various countries. Wastewater screening for the presence of SARS-CoV-2 provides an alternative method to monitor infection threat, variant identification, and clinical evaluation to restrict the virus progression. Multiple cohort studies have reported the application of wastewater treatment approaches and epidemiological significance in terms of virus monitoring. Thus, the manuscript outlines consolidated and systematic information regarding the application of wastewater-based epidemiology in terms of monitoring and managing a viral disease outbreak like COVID-19.
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Affiliation(s)
- Jayavel Sridhar
- Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai, 625021, Tamilnadu, India
| | - Rahul Parit
- Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai, 625021, Tamilnadu, India
| | | | - M Johni Rexliene
- Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai, 625021, Tamilnadu, India
| | - Rajkumar Praveen
- Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai, 625021, Tamilnadu, India
| | - Balaji Viswananathan
- Department of Biotechnology (DDE), Madurai Kamaraj University, Madurai, 625021, Tamilnadu, India
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28
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Karami C, Dargahi A, Vosoughi M, Normohammadi A, Jeddi F, Asghariazar V, Mokhtari A, Sedigh A, Zandian H, Alighadri M. SARS-CoV-2 in municipal wastewater treatment plant, collection network, and hospital wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:85577-85585. [PMID: 34264498 PMCID: PMC8280616 DOI: 10.1007/s11356-021-15374-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/06/2021] [Indexed: 05/08/2023]
Abstract
The current outbreak of coronavirus disease (COVID-19) has led to creating a public health emergency conditions since 2019. COVID-19, which is caused by SARS-CoV-2, is spread via human-to-human transmission by direct contact or droplets. Through conducting this study, we were looking for detecting SARS-CoV-2 in wastewater produced in Iran country (Ardabil, Nir, Khalkhal, and Kowsar) (wastewater collection network, wastewater treatment plant, and hospital wastewater). In this research, samples (n=76) were collected from influent and effluent of municipal and hospital wastewater treatment plants, and some samples were also collected from Ardabil municipal wastewater manholes. The sampling duration included the white (lower risk of COVID-19) and red (high risk of COVID-19) conditions. Samples were stored at -20 °C for further diagnostic tests. The specific primer and probe real-time reverse transcriptase-polymerase chain reaction (real-time PCR) targeting ORF1ab and N genes (nucleoprotein gene) were applied to detect viral genomes of the SARS-CoV-2 virus in the wastewater samples. Out of 76 samples, a total of 15 samples (19.73%) collected from wastewater in Ardabil province (Ardabil, Nir, Khalkhal, and Kowsar), were positive in terms of SARS-CoV-2. Wastewater epidemiology can facilitate detection of the incidence of pathogens through metropolises, measurement of population prevalence without direct testing, and provision of information to the public health system about the efficiency of intervening efforts. Graphical abstract.
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Affiliation(s)
- Chiman Karami
- Department of Microbiology, Parasitology and Immunology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - 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.
- Department of Environmental Health Engineering, School of Public Health, Ardabil University of Medical Sciences, Ardabil, Iran.
| | - Ali Normohammadi
- Department of Environmental Health Engineering, School of Public Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Farhad Jeddi
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Vahid Asghariazar
- Immunology Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Ahamad Mokhtari
- Department of Environmental Health Engineering, School of Public Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Anoshirvan Sedigh
- Department of Environmental Health Engineering, School of Public Health, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hamed Zandian
- Social Determinants of Health Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Morteza Alighadri
- Department of Environmental Health Engineering, School of Public Health, Ardabil University of Medical Sciences, Ardabil, Iran
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29
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Relationship between SARS-CoV-2 in wastewater and clinical data from five wastewater sheds. JOURNAL OF HAZARDOUS MATERIALS ADVANCES 2022; 8:100159. [PMID: 36619827 PMCID: PMC9448702 DOI: 10.1016/j.hazadv.2022.100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 01/17/2023]
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global pandemic starting in 2019 with nearly 500 million confirmed cases as of April 2022. Infection with SARS-CoV-2 is accompanied by shedding of virus in stool, and its presence in wastewater samples has been documented globally. Therefore, monitoring of SARS-CoV-2 in wastewater offers a promising approach to assess the pandemic situation covering pre-symptomatic and asymptomatic cases in areas with limited clinical testing. In this study, the presence of SARS-CoV-2 RNA in wastewater from five wastewater resource recovery facilities (WRRFs), located in two adjacent counties, was investigated and compared with the number of clinical COVID-19 cases during a 2020-2021 outbreak in United States. Statistical correlation analyses of SARS-CoV-2 viral abundance in wastewater and COVID-19 daily vs weekly clinical cases was performed. While a weak correlation on a daily basis was observed, this correlation improved when weekly clinical case data were applied. The viral fecal indicator Pepper Mild Mottle Virus (PMMoV) was furthermore used to assess the effects of normalization and the impact of dilution due to infiltration in the wastewater sheds. Normalization did not improve the correlations with clinical data. However, PMMoV provided important information about infiltration and presence of industrial wastewater discharge in the wastewater sheds. This study showed the utility of WBE to assist in public health responses to COVID-19, emphasizing that routine monitoring of large WRRFs could provide sufficient information for large-scale dynamics.
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Wartell BA, Proano C, Bakalian L, Kaya D, Croft K, McCreary M, Lichtenstein N, Miske V, Arcellana P, Boyer J, Benschoten IV, Anderson M, Crabb A, Gilson S, Gourley A, Wheeler T, Trest B, Bowman G, Kjellerup BV. Implementing wastewater surveillance for SARS-CoV-2 on a university campus: Lessons learned. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2022; 94:e10807. [PMID: 36372781 PMCID: PMC9827968 DOI: 10.1002/wer.10807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Wastewater surveillance, also known as wastewater-based epidemiology (WBE), has been successfully used to detect SARS-CoV-2 and other viruses in sewage in many locations in the United States and globally. This includes implementation of the surveillance on college and university campuses. A two-phase study was conducted during the 2020-2021 academic year to test the feasibility of a WBE system on campus and to supplement the clinical COVID-19 testing performed for the student, staff, and faculty body. The primary objective during the Fall 2020 semester was to monitor a large portion of the on-campus population and to obtain an understanding of the spreading of the SARS-CoV-2 virus. The Spring 2021 objective was focused on selected residence halls and groups of residents on campus, as this was more efficient and relevant for an effective follow-up response. Logistical problems and planning oversights initially occurred but were corrected with improved communication and experience. Many lessons were learned, including effective mapping, site planning, communication, personnel organization, and equipment management, and obtained along the way, thereby paving an opportune guide for future planning efforts. PRACTITIONER POINTS: WBE was successful in the detection of many SARS-CoV-2 variants incl. Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron. Careful planning and contingencies were essential for a successful implementation of a SARS-CoV-2 monitoring program. A surveillance program may be important for detection and monitoring of other public health relevant targets in wastewater incl. bacteria, viruses, fungi and viruses. Diverse lessons were learned incl. effective mapping, site planning, communication, personnel organization, and equipment management, thereby providing a guide for future planning efforts.
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Affiliation(s)
- Brian A. Wartell
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Camila Proano
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Lena Bakalian
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Devrim Kaya
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Kristen Croft
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Michael McCreary
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Naomi Lichtenstein
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Victoria Miske
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Patricia Arcellana
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Jessica Boyer
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Isabelle Van Benschoten
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Marya Anderson
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Andrea Crabb
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Susan Gilson
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Anthony Gourley
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Tim Wheeler
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Brian Trest
- Facilities ManagementUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Glynnis Bowman
- Facilities ManagementUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Birthe V. Kjellerup
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
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31
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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.
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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
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32
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Mousazadeh M, Kabdaşlı I, Khademi S, Sandoval MA, Moussavi SP, Malekdar F, Gilhotra V, Hashemi M, Dehghani MH. A critical review on the existing wastewater treatment methods in the COVID-19 era: What is the potential of advanced oxidation processes in combatting viral especially SARS-CoV-2? JOURNAL OF WATER PROCESS ENGINEERING 2022; 49:103077. [PMID: 35990175 PMCID: PMC9381433 DOI: 10.1016/j.jwpe.2022.103077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 06/01/2023]
Abstract
The COVID-19 epidemic has put the risk of virus contamination in water bodies on the horizon of health authorities. Hence, finding effective ways to remove the virus, especially SARS-CoV-2, from wastewater treatment plants (WWTPs) has emerged as a hot issue in the last few years. Herein, this study first deals with the fate of SARS-CoV-2 genetic material in WWTPs, then critically reviews and compares different wastewater treatment methods for combatting COVID-19 as well as to increase the water quality. This critical review sheds light the efficiency of advanced oxidation processes (AOPs) to inactivate virus, specially SARS-CoV-2 RNA. Although several physicochemical treatment processes (e.g. activated sludge) are commonly used to eliminate pathogens, AOPs are the most versatile and effective virus inactivation methods. For instance, TiO2 is the most known and widely studied photo-catalyst innocuously utilized to degrade pollutants as well as to photo-induce bacterial and virus disinfection due to its high chemical resistance and efficient photo-activity. When ozone is dissolved in water and wastewater, it generates a wide spectrum of the reactive oxygen species (ROS), which are responsible to degrade materials in virus membranes resulting in destroying the cell wall. Furthermore, electrochemical advanced oxidation processes act through direct oxidation when pathogens react at the anode surface or by indirect oxidation through oxidizing species produced in the bulk solution. Consequently, they represent a feasible choice for the inactivation of a wide range of pathogens. Nonetheless, there are some challenges with AOPs which should be addressed for application at industrial-scale.
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Affiliation(s)
- Milad Mousazadeh
- Social Determinants of Health Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
- Department of Environmental Health Engineering, School of Health, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Işık Kabdaşlı
- İstanbul Technical University, Civil Engineering Faculty, Environmental Engineering Department, Ayazağa Campus, 34469 Maslak, İstanbul, Turkey
| | - Sara Khademi
- Health, Safety, and Environment Specialist, North Drilling Company, Ahvaz, Iran
| | - Miguel Angel Sandoval
- Universidad de Santiago de Chile USACH, Facultad de Química y Biología, Departamento de Química de los Materiales, Laboratorio de Electroquímica Medio Ambiental, LEQMA, Casilla 40, Correo 33, Santiago, Chile
- Universidad de Guanajuato, División de Ciencias Naturales y Exactas, Departamento de Ingeniería Química, Noria Alta S/N, 36050, Guanajuato, Guanajuato, Mexico
| | | | - Fatemeh Malekdar
- Department of Foot and Mouth Disease Vaccine Production, Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Vishakha Gilhotra
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Marjan Hashemi
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hadi Dehghani
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Institute for Environmental Research, Center for Solid Waste Research, Tehran University of Medical Sciences, Tehran, Iran
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33
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Masri NZ, Card KG, Caws EA, Babcock A, Powell R, Lowe CJ, Donovan S, Norum S, Lyons S, De Pol S, Kostenchuk L, Dorea C, Lachowsky NJ, Willerth SM, Fyles TM, Buckley HL. Testing specificity and sensitivity of wastewater-based epidemiology for detecting SARS-CoV-2 in four communities on Vancouver Island, Canada. ENVIRONMENTAL ADVANCES 2022; 9:100310. [PMID: 36321068 PMCID: PMC9613784 DOI: 10.1016/j.envadv.2022.100310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/22/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
We report wastewater surveillance of the spread of SARS-CoV-2 based upon 24-h composite influent samples taken weekly from four wastewater treatment plants (WWTP) on Vancouver Island, BC, Canada between January 3, 2021 and July 10, 2021. Samples were analyzed by reverse transcription quantitative polymerase chain reaction targeting the N1 and N2 gene fragments of SARS-CoV-2 and a region of the replication associate protein of the pepper mottle mosaic virus (PMMoV) serving as endemic control. Only a small proportion of samples had quantifiable levels of N1 or N2. Overall case rates are weakly correlated with the concentration (gene copies/L) and with the flux of viral material influent to the WWTP (gene copies/day); the latter accounts for influent flow variations. Poisson multimodal rank correlation accounts for differences between the four WWTP and shows a significant correlation with a significant positive intercept. Receiver operator characteristics (ROC) analysis confirms a cut-off of cases based on amplified/not-amplified experimental data. At the optimal cut point of 19 (N1) or 17 (N2) cases/week/100,000 the sensitivity and specificity is about 75% for N1 and 67% for N2.
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Affiliation(s)
- Nadia Zeina Masri
- Division of Medical Sciences, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | | | - Emmanuelle A Caws
- Department of Civil Engineering and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Canada
| | - Alana Babcock
- Division of Medical Sciences, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | | | | | - Shelley Donovan
- Environmental Monitoring Program, Capital Regional District, Canada
| | | | - Shirley Lyons
- Environmental Monitoring Program, Capital Regional District, Canada
| | | | | | - Caetano Dorea
- Department of Civil Engineering and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Canada
| | - Nathan J Lachowsky
- School of Public Health and Social Policy, University of Victoria, Canada
| | - Stephanie M Willerth
- Department of Mechanical Engineering and Division of Medical Sciences, University of Victoria; Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Canada
- School of Biomedical Engineering, University of British Columbia, Canada
| | | | - Heather L Buckley
- Department of Civil Engineering, Department of Chemistry, and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Canada
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Bergquist R. COVID-19: Past, present and future. GEOSPATIAL HEALTH 2022; 17. [PMID: 36102028 DOI: 10.4081/gh.2022.1147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Not available.
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Reno U, Regaldo L, Ojeda G, Schmuck J, Romero N, Polla W, Kergaravat SV, Gagneten AM. Wastewater-Based Epidemiology: Detection of SARS-CoV-2 RNA in Different Stages of Domestic Wastewater Treatment in Santa Fe, Argentina. WATER, AIR, AND SOIL POLLUTION 2022; 233:372. [PMID: 36090741 PMCID: PMC9440651 DOI: 10.1007/s11270-022-05772-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED The COVID-19 pandemic affected human life at every level. In this study, we analyzed genetic markers (N and ORF1ab, RNA genes) of SARS-CoV-2 in domestic wastewaters (DWW) in San Justo City (Santa Fe, Argentina), using reverse transcription-quantitative real-time PCR. Out of the 30 analyzed samples, 30% were positive for SARS-CoV-2 RNA. Of the total positive samples, 77% correspond to untreated DWW, 23% to pre-chlorination, and no SARS-CoV-2 RNA was registered at the post-chlorination sampling site. The viral loads of N and OFR1ab genes decreased significantly along the treatment process, and the increase in the number of viral copies of the N gene could anticipate, by 6 days, the number of clinical cases in the population. The concentration of chlorine recommended by the WHO (≥ 0.5 mg L-1 after at least 30 min of contact time at pH 8.0) successfully removed SARS-CoV-2 RNA from DWW. The efficiency of wastewater-based epidemiology (WBE) confirms the need to control and increase DWW treatment systems on a regional and global scale. This work could contribute to building a network for WBE to monitor SARS-CoV-2 in wastewaters during the pandemic waves and the epidemic remission phase. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11270-022-05772-w.
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Affiliation(s)
- Ulises Reno
- Ecotoxicology Laboratory, Department of Natural Sciences, Faculty of Humanities and Sciences, National University of Littoral (UNL), 3000 Santa Fe, Argentina
- National Council for Scientific and Technological Research (CONICET), 3000 Santa Fe, Argentina
| | - Luciana Regaldo
- Ecotoxicology Laboratory, Department of Natural Sciences, Faculty of Humanities and Sciences, National University of Littoral (UNL), 3000 Santa Fe, Argentina
- National Council for Scientific and Technological Research (CONICET), 3000 Santa Fe, Argentina
| | - Guillermo Ojeda
- Central Laboratory, Ministry of Health, 3000 Santa Fe, Argentina
| | - Josefina Schmuck
- Ecotoxicology Laboratory, Department of Natural Sciences, Faculty of Humanities and Sciences, National University of Littoral (UNL), 3000 Santa Fe, Argentina
- National Council for Scientific and Technological Research (CONICET), 3000 Santa Fe, Argentina
| | - Natalí Romero
- Ecotoxicology Laboratory, Department of Natural Sciences, Faculty of Humanities and Sciences, National University of Littoral (UNL), 3000 Santa Fe, Argentina
- National Council for Scientific and Technological Research (CONICET), 3000 Santa Fe, Argentina
| | - Wanda Polla
- Ecotoxicology Laboratory, Department of Natural Sciences, Faculty of Humanities and Sciences, National University of Littoral (UNL), 3000 Santa Fe, Argentina
| | - Silvina V. Kergaravat
- Ecotoxicology Laboratory, Department of Natural Sciences, Faculty of Humanities and Sciences, National University of Littoral (UNL), 3000 Santa Fe, Argentina
- National Council for Scientific and Technological Research (CONICET), 3000 Santa Fe, Argentina
| | - Ana María Gagneten
- Ecotoxicology Laboratory, Department of Natural Sciences, Faculty of Humanities and Sciences, National University of Littoral (UNL), 3000 Santa Fe, Argentina
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Mac Mahon J, Criado Monleon AJ, Gill LW, O'Sullivan JJ, Meijer WG. Wastewater-based epidemiology (WBE) for SARS-CoV-2 - A review focussing on the significance of the sewer network using a Dublin city catchment case study. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2022; 86:1402-1425. [PMID: 36178814 DOI: 10.2166/wst.2022.278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Wastewater-based epidemiology (WBE) has been employed by many countries globally since the beginning of the COVID-19 pandemic in order to assess the benefits of this surveillance tool in the context of informing public health measures. WBE has been successfully employed to detect SARS-CoV-2 at wastewater treatment plants for community-wide surveillance, as well as in smaller catchments and institutions for targeted surveillance of COVID-19. In addition, WBE has been successfully used to detect new variants, identify areas of high infection levels, as well as to detect new infection outbreaks. However, due to to the large number of inherent uncertainties in the WBE process, including the inherent intricacies of the sewer network, decay of the virus en route to a monitoring point, levels of recovery from sampling and quantification methods, levels of faecal shedding among the infected population, as well as population normalisation methods, the usefulness of wastewater samples as a means of accurately quantifying SARS-CoV-2 infection levels among a population remains less clear. The current WBE programmes in place globally will help to identify new areas of research aimed at reducing the levels of uncertainty in the WBE process, thus improving WBE as a public health monitoring tool for future pandemics. In the meantime, such programmes can provide valuable comparisons to clinical testing data and other public health metrics, as well being an effective early warning tool for new variants and new infection outbreaks. This review includes a case study of sampled wastewater from the sewer network in Dublin, Ireland, during a peak infection period of COVID-19 in the city, which evaluates the different uncertainties in the WBE process.
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Affiliation(s)
| | | | | | - John J O'Sullivan
- UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin
| | - Wim G Meijer
- UCD School of Biomolecular & Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin
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Investigating the Potential Effects of COVID-19 Pandemic on Intestinal Coccidian Infections. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.3.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
New infectious agents pose a global threat to the healthcare system, and studies are conducted to estimate their health and epidemiological outcomes in the long run. The SARS-CoV-2 virus, which has caused the COVID-19 disease, was formerly assumed to be a respiratory virus; however, it can have serious systemic effects, affecting organs such as the gastrointestinal tract (GIT). Viral RNA was reported in the stool in a subset of patients, indicating another mode of transmission and diagnosis. In COVID-19, prolonged GIT symptoms, especially diarrhea, were associated with reduced diversity and richness of gut microbiota, immunological dysregulation, and delayed viral clearance. Intestinal coccidian parasites are intracellular protozoa that are most typically transmitted to humans by oocysts found in fecally contaminated food and water. Their epidemiological relevance is coupled to opportunistic infections, which cause high morbidity and mortality among immunocompromised individuals. Among immunocompetent people, intestinal coccidia is also involved in acute diarrhea, which is usually self-limiting. Evaluating the available evidence provided an opportunity to carefully consider that; the COVID-19 virus and coccidian protozoan parasites: namely, Cryptosporidium spp., Cyclospora cayetanensis, and Isospora belli, could mutually influence each other from the microbiological, clinical, diagnostic, and elimination aspects. We further systemically highlighted the possible shared pathogenesis mechanisms, transmission routes, clinical manifestations, parasite-driven immune regulation, and intestinal microbiota alteration. Finally, we showed how this might impact developing and developed countries prevention and vaccination strategies. To the best of our knowledge, there is no review that has discussed the reciprocal effect between coccidian parasites and COVID-19 coinfection.
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de Sousa ARV, do Carmo Silva L, de Curcio JS, da Silva HD, Eduardo Anunciação C, Maria Salem Izacc S, Neto FOS, de Paula Silveira Lacerda E. "pySewage": a hybrid approach to predict the number of SARS-CoV-2-infected people from wastewater in Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67260-67269. [PMID: 35524091 PMCID: PMC9075719 DOI: 10.1007/s11356-022-20609-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/30/2022] [Indexed: 05/21/2023]
Abstract
It is well known that the new coronavirus pandemic has global environmental, public health, and economic implications. In this sense, this study aims to monitor SARS-CoV-2 in the largest wastewater treatment plant of Goiânia, which processes wastewater from more than 700,000 inhabitants, and to correlate the molecular and clinical data collected. Influent and effluent samples were collected at Dr. Helio de Seixo Britto's wastewater treatment plant from January to August 2021. Viral concentration was performed with polyethylene glycol before viral RNA extraction. Real-time qPCR (N1 and N2 gene assays) was performed to detect and quantify the viral RNA present in the samples. The results showed that 43.63% of the samples were positive. There is no significant difference between the detection of primers N1 (mean 3.23 log10 genome copies/L, std 0.23) and N2 (mean 2.95 log10 genome copies/L, std 0.29); also, there is no significant difference between the detection of influent and effluent samples. Our molecular data revealed a positive correlation with clinical data, and infection prevalence was higher than clinical data. In addition, we developed a user-friendly web application to predict the number of infected people based on the detection of viral load present in wastewater samples and may be applied as a public policy strategy for monitoring ongoing outbreaks.
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Affiliation(s)
| | - Lívia do Carmo Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Juliana Santana de Curcio
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Hugo Delleon da Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
- Universitary Center of Goiás (UNIGOIÁS), Goiânia, Goiás, Brazil
| | - Carlos Eduardo Anunciação
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Silvia Maria Salem Izacc
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
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Tamáš M, Potocarova A, Konecna B, Klucar Ľ, Mackulak T. Wastewater Sequencing-An Innovative Method for Variant Monitoring of SARS-CoV-2 in Populations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:9749. [PMID: 35955106 PMCID: PMC9367975 DOI: 10.3390/ijerph19159749] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 05/14/2023]
Abstract
The SARS-CoV-2 outbreak has already affected more than 555 million people, and 6.3 million people have died. Due to its high infectivity, it is crucial to track SARS-CoV-2 outbreaks early to prevent the spread of infection. Wastewater monitoring appears to be a powerful and effective tool for managing epidemiological situations. Due to emerging mutations of SARS-CoV-2, there is a need to monitor mutations in order to control the pandemic. Since the sequencing of randomly chosen individuals is time-consuming and expensive, sequencing of wastewater plays an important role in revealing the dynamics of infection in a population. The sampling method used is a crucial factor and significantly impacts the results. Wastewater can be collected as a grab sample or as a 24 h composite sample. Another essential factor is the sample volume, as is the method of transport used. This review discusses different pretreatment procedures and RNA extraction, which may be performed using various methods, such as column-based extraction, TRIzol, or magnetic extraction. Each of the methods has its advantages and disadvantages, which are described accordingly. RT-qPCR is a procedure that confirms the presence of SARS-CoV-2 genes before sequencing. This review provides an overview of currently used methods for preparing wastewater samples, from sampling to sequencing.
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Affiliation(s)
- Michal Tamáš
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 81372 Bratislava, Slovakia
| | - Alena Potocarova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Barbora Konecna
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Ľubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia
| | - Tomas Mackulak
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
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Hyllestad S, Myrmel M, Lomba JAB, Jordhøy F, Schipper SK, Amato E. Effectiveness of environmental surveillance of SARS-CoV-2 as an early warning system during the first year of the COVID-19 pandemic: a systematic review. JOURNAL OF WATER AND HEALTH 2022; 20:1223-1242. [PMID: 36044191 DOI: 10.2166/wh.2022.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Since infected persons shed SARS-CoV-2 in faeces before symptoms appear, environmental surveillance (ES) may serve as an early warning system (EWS) for COVID-19 and new variants of concern. The ES of SARS-CoV-2 has been widely reviewed; however, its effectiveness as an EWS for SARS-CoV-2 in terms of timeliness, sensitivity and specificity has not been systematically assessed. We conducted a systematic review to identify and synthesise evidence on the ES of SARS-CoV-2 as an EWS to evaluate the added value for public health. Of 1,014 studies identified, we considered 29 for a qualitative synthesis of the timeliness of ES as an EWS for COVID-19, while six studies were assessed for the ability to detect new variants and two for both aims. The synthesis indicates ES may serve as an EWS of 1-2 weeks. ES could complement clinical surveillance for SARS-CoV-2; however, its cost-benefit value for public health decisions needs to be assessed based on the stage of the pandemic and resources available. Studies focusing methodological knowledge gaps as well as how to use and interpret ES signals for public health actions are needed, as is the sharing of knowledge within countries/areas with long experience of such surveillance.
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Affiliation(s)
- Susanne Hyllestad
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jose Antonio Baz Lomba
- Department of Environmental Chemistry and Technology, Norwegian Institute for Water Research (NIVA), Oslo, Norway
| | - Fredrik Jordhøy
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Svanhild Kjørsvik Schipper
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Ettore Amato
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
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Rusková M, Bučková M, Achs A, Puškárová A, Wu JH, Kuchta T, Šubr Z, Pangallo D. Useful molecular tools for facing next pandemic events: Effective sample preparation and improved RT-PCR for highly sensitive detection of SARS-CoV-2 in wastewater environment. Int J Hyg Environ Health 2022; 245:114017. [PMID: 35939897 PMCID: PMC9346026 DOI: 10.1016/j.ijheh.2022.114017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/22/2022] [Accepted: 07/27/2022] [Indexed: 10/28/2022]
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Multifaceted Assessment of Wastewater-Based Epidemiology for SARS-CoV-2 in Selected Urban Communities in Davao City, Philippines: A Pilot Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19148789. [PMID: 35886640 PMCID: PMC9324557 DOI: 10.3390/ijerph19148789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023]
Abstract
Over 60 countries have integrated wastewater-based epidemiology (WBE) in their COVID-19 surveillance programs, focusing on wastewater treatment plants (WWTP). In this paper, we piloted the assessment of SARS-CoV-2 WBE as a complementary public health surveillance method in susceptible communities in a highly urbanized city without WWTP in the Philippines by exploring the extraction and detection methods, evaluating the contribution of physico-chemical–anthropogenic factors, and attempting whole-genome sequencing (WGS). Weekly wastewater samples were collected from sewer pipes or creeks in six communities with moderate-to-high risk of COVID-19 transmission, as categorized by the City Government of Davao from November to December 2020. Physico-chemical properties of the wastewater and anthropogenic conditions of the sites were noted. Samples were concentrated using a PEG-NaCl precipitation method and analyzed by RT-PCR to detect the SARS-CoV-2 N, RdRP, and E genes. A subset of nine samples were subjected to WGS using the Minion sequencing platform. SARS-CoV-2 RNA was detected in twenty-two samples (91.7%) regardless of the presence of new cases. Cycle threshold values correlated with RNA concentration and attack rate. The lack of a sewershed map in the sampled areas highlights the need to integrate this in the WBE planning. A combined analysis of wastewater physico-chemical parameters such as flow rate, surface water temperature, salinity, dissolved oxygen, and total dissolved solids provided insights on the ideal sampling location, time, and method for WBE, and their impact on RNA recovery. The contribution of fecal matter in the wastewater may also be assessed through the coliform count and in the context of anthropogenic conditions in the area. Finally, our attempt on WGS detected single-nucleotide polymorphisms (SNPs) in wastewater which included clinically reported and newly identified mutations in the Philippines. This exploratory report provides a contextualized framework for applying WBE surveillance in low-sanitation areas.
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Zhang Y, Zhu K, Huang W, Guo Z, Jiang S, Zheng C, Yu Y. Can wastewater surveillance assist China to cost-effectively prevent the nationwide outbreak of COVID-19? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154719. [PMID: 35331760 PMCID: PMC8935960 DOI: 10.1016/j.scitotenv.2022.154719] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
China has controlled the nationwide spread of COVID-19 since April 2020, but it is still facing an enormous threat of disease resurgence originating from infected international travelers. Taking the rapid transmission and the mutation of SARS-CoV-2 into consideration, the current status would be easily jeopardized if sporadic locally-transmitted individuals are not identified at an early stage. Clinical diagnosis is the gold standard for COVID-19 surveillance, but it is hard to screen presymptomatic or asymptomatic cases in those who have not exhibited symptoms. Since presymptomatic or asymptomatic individuals are infectious, it is urgent to establish a surveillance system based on other tools that can profile the entire population. Infected people including those who are symptomatic, presymptomatic, and asymptomatic shed SARS-CoV-2 RNA in feces and thereby endow wastewater-based epidemiology (WBE) with an early-warning ability for mass COVID-19 surveillance. In the context of China's "COVID-zero" strategy, this work intends to discuss the practical feasibility of WBE applications as an early warning and disease surveillance system in hopes that WBE together with clinical testing would cost-effectively restrain sporadic COVID-19 outbreaks in China.
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Affiliation(s)
- Ying Zhang
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian 350116, China.
| | - Kongquan Zhu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Weiyi Huang
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zhixuan Guo
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Senhua Jiang
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Chujun Zheng
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Yang Yu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong 518055, PR China.
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Barbé L, Schaeffer J, Besnard A, Jousse S, Wurtzer S, Moulin L, Le Guyader FS, Desdouits M. SARS-CoV-2 Whole-Genome Sequencing Using Oxford Nanopore Technology for Variant Monitoring in Wastewaters. Front Microbiol 2022; 13:889811. [PMID: 35756003 PMCID: PMC9218694 DOI: 10.3389/fmicb.2022.889811] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/29/2022] [Indexed: 01/21/2023] Open
Abstract
Since the beginning of the Coronavirus Disease-19 (COVID-19) pandemic, multiple Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) mutations have been reported and led to the emergence of variants of concern (VOC) with increased transmissibility, virulence or immune escape. In parallel, the observation of viral fecal shedding led to the quantification of SARS-CoV-2 genomes in wastewater, providing information about the dynamics of SARS-CoV-2 infections within a population including symptomatic and asymptomatic individuals. Here, we aimed to adapt a sequencing technique initially designed for clinical samples to apply it to the challenging and mixed wastewater matrix, and hence identify the circulation of VOC at the community level. Composite raw sewage sampled over 24 h in two wastewater-treatment plants (WWTPs) from a city in western France were collected weekly and SARS-CoV-2 quantified by RT-PCR. Samples collected between October 2020 and May 2021 were submitted to whole-genome sequencing (WGS) using the primers and protocol published by the ARTIC Network and a MinION Mk1C sequencer (Oxford Nanopore Technologies, Oxford, United Kingdom). The protocol was adapted to allow near-full genome coverage from sewage samples, starting from ∼5% to reach ∼90% at depth 30. This enabled us to detect multiple single-nucleotide variant (SNV) and assess the circulation of the SARS-CoV-2 VOC Alpha, Beta, Gamma, and Delta. Retrospective analysis of sewage samples shed light on the emergence of the Alpha VOC with detection of first co-occurring signature mutations in mid-November 2020 to reach predominance of this variant in early February 2021. In parallel, a mutation-specific qRT-PCR assay confirmed the spread of the Alpha VOC but detected it later than WGS. Altogether, these data show that SARS-CoV-2 sequencing in sewage can be used for early detection of an emerging VOC in a population and confirm its ability to track shifts in variant predominance.
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Affiliation(s)
- Laure Barbé
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Julien Schaeffer
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Alban Besnard
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Sarah Jousse
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | | | - Laurent Moulin
- R&D Laboratory, DRDQE, Eau de Paris, Ivry-sur-Seine, France
| | | | | | - Marion Desdouits
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
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Grego S, Welling CM, Miller GH, Coggan PF, Sellgren KL, Hawkins BT, Ginsburg GS, Ruiz JR, Fisher DA, Stoner BR. A hands-free stool sampling system for monitoring intestinal health and disease. Sci Rep 2022; 12:10859. [PMID: 35760855 PMCID: PMC9237014 DOI: 10.1038/s41598-022-14803-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
Analysis of stool offers simple, non-invasive monitoring for many gastrointestinal (GI) diseases and access to the gut microbiome, however adherence to stool sampling protocols remains a major challenge because of the prevalent dislike of handling one's feces. We present a technology that enables individual stool specimen collection from toilet wastewater for fecal protein and molecular assay. Human stool specimens and a benchtop test platform integrated with a commercial toilet were used to demonstrate reliable specimen collection over a wide range of stool consistencies by solid/liquid separation followed by spray-erosion. The obtained fecal suspensions were used to perform occult blood tests for GI cancer screening and for microbiome 16S rRNA analysis. Using occult blood home test kits, we found overall 90% agreement with standard sampling, 96% sensitivity and 86% specificity. Microbiome analysis revealed no significant difference in within-sample species diversity compared to standard sampling and specimen cross-contamination was below the detection limit of the assay. Furthermore, we report on the use of an analogue turbidity sensor to assess in real time loose stools for tracking of diarrhea. Implementation of this technology in residential settings will improve the quality of GI healthcare by facilitating increased adherence to routine stool monitoring.
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Affiliation(s)
- Sonia Grego
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA.
| | - Claire M Welling
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
| | - Graham H Miller
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
| | - Peter F Coggan
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
| | - Katelyn L Sellgren
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
| | - Brian T Hawkins
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, School of Medicine, Duke University, Durham, NC, USA
| | - Jose R Ruiz
- Division of Gastroenterology, School of Medicine, Duke University, Durham, NC, USA
| | - Deborah A Fisher
- Division of Gastroenterology, School of Medicine, Duke University, Durham, NC, USA
| | - Brian R Stoner
- Electrical and Computer Engineering, Center for Water, Sanitation, Hygiene and Infectious Disease (WaSH-AID), Duke University, Durham, NC, USA
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Kumblathan T, Piroddi N, Hrudey SE, Li XF. Wastewater Based Surveillance of SARS-CoV-2: Challenges and Perspective from a Canadian Inter-laboratory Study. J Environ Sci (China) 2022; 116:229-232. [PMID: 35219421 PMCID: PMC8789553 DOI: 10.1016/j.jes.2022.01.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Nicholas Piroddi
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Steve E Hrudey
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada.
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Alamin M, Tsuji S, Hata A, Hara-Yamamura H, Honda R. Selection of surrogate viruses for process control in detection of SARS-CoV-2 in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153737. [PMID: 35149069 PMCID: PMC8824713 DOI: 10.1016/j.scitotenv.2022.153737] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 05/24/2023]
Abstract
Since SARS-CoV-2 RNA in wastewater is often present at low concentration or under detection limit, ensuring the reliability of detection processes using appropriate process controls is essential. The objective of this study was to evaluate applicability and limitations of candidate surrogate viruses as process controls under combinations of different virus concentration and RNA extraction methods. Detection efficiency of SARS-CoV-2 spiked in wastewater was compared with those of candidate surrogate viruses of bacteriophage ϕ6, pepper mild mottle virus (PMMoV), F-specific coliphage (F-phage), and murine norovirus (MNV). After inactivated SARS-CoV-2 and ϕ6 were spiked in two different wastewaters, the viruses in solid and liquid fractions of wastewater were concentrated by centrifuge and polyethylene glycol (PEG) precipitation, respectively. Viral RNA was extracted by using QIAamp Viral RNA Mini Kit and 3 other commercially available extraction kits, then quantified by reverse transcription-quantitative PCR using CDCN1 assay. Regardless of extraction kits, SARS-CoV-2 was consistently detected with good efficiency from both liquid (11-200%) and solid fractions (7.1-93%). Among the candidate process controls, PMMoV was widely detected at good efficiencies from both liquid and solid fractions regardless of selection of RNA extraction kits. F-phage and MNV also showed good detection efficiencies in most combinations of wastewater fractions and RNA extraction kits. An enveloped virus ɸ6 was found often undetected or to have very low detection efficiency (0.1-4.2%) even when SARS-CoV-2 spiked in wastewater was detected with good efficiency. Consequently, PMMoV is widely applicable as process control for detection of SARS-CoV-2 either in liquid fractions concentrated by PEG precipitation, or in solid fractions concentrated by centrifuge.
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Affiliation(s)
- Md Alamin
- Graduate School of Natural Science and Technology, Kanazawa University, Japan
| | - Shohei Tsuji
- School of Environmental Design, Kanazawa University, Japan
| | - Akihiko Hata
- Faculty of Engineering, Toyama Prefectural University, Japan
| | | | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Japan.
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Nourbakhsh S, Fazil A, Li M, Mangat CS, Peterson SW, Daigle J, Langner S, Shurgold J, D’Aoust P, Delatolla R, Mercier E, Pang X, Lee BE, Stuart R, Wijayasri S, Champredon D. A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities. Epidemics 2022; 39:100560. [PMID: 35462206 PMCID: PMC8993419 DOI: 10.1016/j.epidem.2022.100560] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/07/2022] [Accepted: 04/03/2022] [Indexed: 02/03/2023] Open
Abstract
The COVID-19 pandemic has stimulated wastewater-based surveillance, allowing public health to track the epidemic by monitoring the concentration of the genetic fingerprints of SARS-CoV-2 shed in wastewater by infected individuals. Wastewater-based surveillance for COVID-19 is still in its infancy. In particular, the quantitative link between clinical cases observed through traditional surveillance and the signals from viral concentrations in wastewater is still developing and hampers interpretation of the data and actionable public-health decisions. We present a modelling framework that includes both SARS-CoV-2 transmission at the population level and the fate of SARS-CoV-2 RNA particles in the sewage system after faecal shedding by infected persons in the population. Using our mechanistic representation of the combined clinical/wastewater system, we perform exploratory simulations to quantify the effect of surveillance effectiveness, public-health interventions and vaccination on the discordance between clinical and wastewater signals. We also apply our model to surveillance data from three Canadian cities to provide wastewater-informed estimates for the actual prevalence, the effective reproduction number and incidence forecasts. We find that wastewater-based surveillance, paired with this model, can complement clinical surveillance by supporting the estimation of key epidemiological metrics and hence better triangulate the state of an epidemic using this alternative data source.
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Affiliation(s)
- Shokoofeh Nourbakhsh
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Aamir Fazil
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Michael Li
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Chand S. Mangat
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Shelley W. Peterson
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jade Daigle
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Stacie Langner
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jayson Shurgold
- Antimicrobial Resistance Division, Infectious Diseases Prevention and Control Branch, Public Health Agency of Canada, Ottawa, ON, Canada
| | - Patrick D’Aoust
- University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
| | - Robert Delatolla
- University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
| | - Elizabeth Mercier
- University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
| | - Xiaoli Pang
- Public Health Laboratory, Alberta Precision Laboratory, Edmonton, AB, Canada,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Bonita E. Lee
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | | | - Shinthuja Wijayasri
- Toronto Public Health, Toronto, ON, Canada,Canadian Field Epidemiology Program, Emergency Management, Public Health Agency of Canada, Canada
| | - David Champredon
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada,Corresponding author
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Zarza E, Diego-García E, García LV, Castro R, Mejía G, Herrera D, Cuevas R, Palomeque Á, Iša P, Guillén K. Monitoring SARS-CoV-2 in the Wastewater and Rivers of Tapachula, a Migratory Hub in Southern Mexico. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:199-211. [PMID: 35508751 PMCID: PMC9067545 DOI: 10.1007/s12560-022-09523-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/20/2022] [Indexed: 05/11/2023]
Abstract
The COVID-19 pandemic has been monitored by applying different strategies, including SARS-CoV-2 detection with clinical testing or through wastewater-based epidemiology (WBE). We used the latter approach to follow SARS-CoV-2 dispersion in Tapachula city, located in Mexico's tropical southern border region. Tapachula is a dynamic entry point for people seeking asylum in Mexico or traveling to the USA. Clinical testing facilities for SARS-CoV-2 monitoring are limited in the city. A total of eighty water samples were collected from urban and suburban rivers and sewage and a wastewater treatment plant over 4 months in Tapachula. We concentrated viral particles with a PEG-8000-based method, performed RNA extraction, and detected SARS-CoV-2 particles through RT-PCR. We considered the pepper mild mottle virus as a fecal water pollution biomarker and analytical control. SARS-CoV-2 viral loads (N1 and N2 markers) were quantified and correlated with official regional statistics of COVID-19 bed occupancy and confirmed cases (r > 91%). Our results concluded that WBE proved a valuable tool for tracing and tracking the COVID-19 pandemic in tropical countries with similar water temperatures (21-29 °C). Monitoring SARS-CoV-2 through urban and suburban river water sampling would be helpful in places lacking a wastewater treatment plant or water bodies with sewage discharges.
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Affiliation(s)
- Eugenia Zarza
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
- Investigadoras CONACyT- El Colegio de la Frontera Sur, Av. Insurgentes Sur 1582, Col. Crédito Constructor, Benito Juárez, 03940, Mexico City, Mexico
| | - Elia Diego-García
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
- Investigadoras CONACyT- El Colegio de la Frontera Sur, Av. Insurgentes Sur 1582, Col. Crédito Constructor, Benito Juárez, 03940, Mexico City, Mexico
| | - Luz Verónica García
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - Ricardo Castro
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - Gamaliel Mejía
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - David Herrera
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - Raúl Cuevas
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - Ángeles Palomeque
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Karina Guillén
- El Colegio de la Frontera Sur (ECOSUR), Grupo Académico de Biotecnología Ambiental, Carretera Antiguo Aeropuerto Km 2.5, 30700, Tapachula, Chiapas, Mexico.
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Several major issues concerning the environmental transmission and risk prevention of SARS-CoV-2. SCIENCE CHINA EARTH SCIENCES 2022; 65:1047-1056. [PMID: 35578665 PMCID: PMC9097562 DOI: 10.1007/s11430-021-9918-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/11/2022] [Accepted: 03/03/2022] [Indexed: 11/03/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is the most serious infectious disease pandemic in the world in a century, and has had a serious impact on the health, safety, and social and economic development of all mankind. Since the earth entered the “Anthropocene”, human activities have become the most important driving force of the evolution of the earth system. At the same time, the epidemic frequency of major human infectious diseases worldwide has been increasing, with more than 70% of novel diseases having zoonotic origins. The review of several major epidemics in human history shows that there is a common rule, i.e., changes in the natural environment have an important and profound impact on the occurrence and development of epidemics. Therefore, the impact of the natural environment on the current COVID-19 pandemic and its mechanisms have become scientific issues that need to be resolved urgently. From the perspective of the natural environment, this study systematically investigated several major issues concerning the environmental transmission and risk prevention of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). From a macroscopic temporal and spatial scale, the research focus on understand the impact of the destruction of the natural environment and global changes on the outbreak of infectious diseases; the threat of zoonotic diseases to human health; the regularity for virus diffusion, migration and mutation in environmental media; the mechanisms of virus transmission from animals and environmental media to humans; and environmental safety, secondary risk prevention and control of major epidemics. Suggestions were made for future key research directions and issues that need attention, with a view to providing a reference for the prevention and control of the global coronavirus disease 2019, and to improving the ability of response to major public health emergencies.
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