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Nagarkar M, Keely SP, Jahne M, Wheaton E, Hart C, Smith B, Garland J, Varughese EA, Braam A, Wiechman B, Morris B, Brinkman NE. SARS-CoV-2 monitoring at three sewersheds of different scales and complexity demonstrates distinctive relationships between wastewater measurements and COVID-19 case data. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151534. [PMID: 34780821 PMCID: PMC8590472 DOI: 10.1016/j.scitotenv.2021.151534] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 05/18/2023]
Abstract
Wastewater monitoring of SARS-CoV-2 presents a means of tracking COVID-19 community infection dynamics on a broader geographic scale. However, accounting for environmental and sample-processing losses may be necessary for wastewater measurements to readily inform our understanding of infection prevalence. Here, we present measurements of the SARS-CoV-2 N1 and N2 gene targets from weekly wastewater samples at three sites in Hamilton County, Ohio, during an increase and subsequent decline of COVID-19 infections. The concentration of N1 or N2 RNA in wastewater, measured over the course of six months, ranged from below the detection limit to over 104 gene copies/l, and correlated with case data at two wastewater treatment plants, but not at a sub-sewershed-level sampling site. We also evaluated the utility of a broader range of variables than has been reported consistently in previous work, in improving correlations of SARS-CoV-2 concentrations with case data. These include a spiked matrix recovery control (OC43), flow-normalization, and assessment of fecal loading using endogenous fecal markers (HF183, PMMoV, crAssphage). We found that adjusting for recovery, flow, and fecal indicators increased these correlations for samples from a larger sewershed (serving ~488,000 people) with greater industrial and stormwater inputs, but raw N1/N2 concentrations corresponded better with case data at a smaller, residential-oriented sewershed. Our results indicate that the optimal adjustment factors for correlating wastewater and clinical case data moving forward may not be generalizable to all sewersheds.
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Affiliation(s)
- M Nagarkar
- Office of Research and Development, United States Environmental Protection Agency, 26 W Martin Luther King Dr, Cincinnati, OH, USA.
| | - S P Keely
- Office of Research and Development, United States Environmental Protection Agency, 26 W Martin Luther King Dr, Cincinnati, OH, USA.
| | - M Jahne
- Office of Research and Development, United States Environmental Protection Agency, 26 W Martin Luther King Dr, Cincinnati, OH, USA.
| | - E Wheaton
- Office of Research and Development, United States Environmental Protection Agency, 26 W Martin Luther King Dr, Cincinnati, OH, USA.
| | - C Hart
- Office of Research and Development, United States Environmental Protection Agency, 26 W Martin Luther King Dr, Cincinnati, OH, USA.
| | - B Smith
- Office of Research and Development, United States Environmental Protection Agency, 26 W Martin Luther King Dr, Cincinnati, OH, USA.
| | - J Garland
- Office of Research and Development, United States Environmental Protection Agency, 26 W Martin Luther King Dr, Cincinnati, OH, USA.
| | - E A Varughese
- Office of Research and Development, United States Environmental Protection Agency, 26 W Martin Luther King Dr, Cincinnati, OH, USA.
| | - A Braam
- APTIM Corp., 4171 Essen Lane, Baton Rouge, LA 70809.
| | - B Wiechman
- APTIM Corp., 4171 Essen Lane, Baton Rouge, LA 70809.
| | - B Morris
- Pegasus Technical Services Inc., 26 W Martin Luther King Dr, Cincinnati, OH, USA.
| | - N E Brinkman
- Office of Research and Development, United States Environmental Protection Agency, 26 W Martin Luther King Dr, Cincinnati, OH, USA.
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52
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Oh C, Kim K, Araud E, Wang L, Shisler JL, Nguyen TH. A novel approach to concentrate human and animal viruses from wastewater using receptors-conjugated magnetic beads. WATER RESEARCH 2022; 212:118112. [PMID: 35091223 DOI: 10.1016/j.watres.2022.118112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023]
Abstract
Viruses are present at low concentrations in wastewater; therefore, an effective method for concentrating virus particles is necessary for accurate wastewater-based epidemiology (WBE). We designed a novel approach to concentrate human and animal viruses from wastewater using porcine gastric mucin-conjugated magnetic beads (PGM-MBs). We systematically evaluated the performances of the PGM-MBs method (sensitivity, specificity, and robustness to environmental inhibitors) with six viral species, including Tulane virus (a surrogate for human norovirus), rotavirus, adenovirus, porcine coronavirus (transmissible gastroenteritis virus or TGEV), and two human coronaviruses (NL63 and SARS-CoV-2) in influent wastewater and raw sewage samples. We determined the multiplication factor (the ratio of genome concentration of the final solution to that of the initial solution) for the PGM-MBs method, which ranged from 1.3 to 64.0 depending on the viral species. Because the recovery efficiency was significantly higher when calculated with virus titers than it was with genome concentration, the PGM-MBs method could be an appropriate tool for assessing the risk to humans who are inadvertently exposed to wastewater contaminated with infectious viruses. Furthermore, PCR inhibitors were not concentrated by PGM-MBs, suggesting that this tool will be successful for use with environmental samples. In addition, the PGM-MBs method is cost-effective (0.5 USD/sample) and has a fast turnaround time (3 h from virus concentration to genome quantification). Thus, this method can be implemented in high throughput facilities. Because of its strong performance, intrinsic characteristics of targeting the infectious virus, robustness to wastewater, and adaptability to high throughput systems, the PGM-MBs method can be successfully applied to WBE and ultimately provides valuable public health information.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, United States.
| | - Kyukyoung Kim
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, United States
| | - Elbashir Araud
- Holonyak Micro & Nanotechnology Lab, University of Illinois at Urbana-Champaign
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, United States
| | - Joanna L Shisler
- Department of Microbiology, University of Illinois at Urbana-Champaign, United States
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, United States; Institute of Genomic Biology, University of Illinois at Urbana-Champaign, United States
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53
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FERCHICHI S, FATNASSI N, DHAOUADI A, ATTIA EL HILI H. [The hazards of SARS-COV-2 for aquatic ecosystems]. MEDECINE TROPICALE ET SANTE INTERNATIONALE 2022; 2:mtsi.v2i1.2022.228. [PMID: 35685840 PMCID: PMC9128476 DOI: 10.48327/mtsi.v2i1.2022.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 02/14/2022] [Indexed: 11/24/2022]
Abstract
Introduction The current COVID-19 pandemic is due to a new emerging coronavirus SARS-CoV-2, belonging to the Coronaviridae family and to the Orthocoronavirinae subfamily. This virus was first reported in December 2019 in China. Although reported by several countries in several animal species, COVID-19 is a disease transmitted from human to human. Moreover, SARS-CoV-2 virus and its RNA were detected in body excretions besides saliva, such as urine and fecal matter discharged into sewage. Bibliographic review Within this framework, this article aims to synthesize the bibliographical reviews on SARS-CoV-2 in aquatic environment. It will underline the generalities on SARS-CoV-2, the possible sources of potential contaminations of SARS-CoV-2 in water environment, the viability of SARS-CoV-2 in aquatic environment, the receptive species and the impacts of SARS-CoV-2 on the aquatic ecosystems. Conclusion We compile key information about SARS-CoV-2 that are considered important to remember and highlight the importance of further research in this area in order to assess the hazards of SARS-CoV-2 on aquatic ecosystems.
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Affiliation(s)
- Salma FERCHICHI
- Centre national de veille zoosanitaire, 33 avenue Charles Nicolle, Tunis, Tunisie
| | - Naouel FATNASSI
- Centre national de veille zoosanitaire, 33 avenue Charles Nicolle, Tunis, Tunisie
| | - Anissa DHAOUADI
- Centre national de veille zoosanitaire, 33 avenue Charles Nicolle, Tunis, Tunisie
| | - Hédia ATTIA EL HILI
- Centre national de veille zoosanitaire, 33 avenue Charles Nicolle, Tunis, Tunisie
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54
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Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden. ENVIRONMENTS 2022. [DOI: 10.3390/environments9030039] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The detection of SARS-CoV-2 RNA fragments in feces has paved the way for wastewater-based epidemiology to contribute to COVID-19 mitigation measures, with its use in a public health context still under development. As a way to facilitate data comparison, this paper explores the impact of using alternative normalization approaches (wastewater treatment plant (WWTP) flow, population size estimates (derived using total nitrogen (TN), total phosphorus (TP) and census data) and pepper mild mottle virus (PMMoV)) on the relationship between viral wastewater data and clinical case numbers. Influent wastewater samples were collected at two WWTPs in Luleå, northern Sweden, between January and March 2021. TN and TP were determined upon sample collection, with RNA analysis undertaken on samples after one freeze–thaw cycle. The strength of the correlation between normalization approaches and clinical cases differed between WWTPs (r ≤ 0.73 or r ≥ 0.78 at the larger WWTP and r ≤ 0.23 or r ≥ 0.43 at the smaller WWTP), indicating that the use of wastewater as an epidemiological tool is context-dependent. Depending on the normalization approach utilized, time-shifted analyses imply that wastewater data on SARS-CoV-2 RNA pre-dated a rise in clinical cases by 0–2 and 5–8 days, for the lager and smaller WWTPs, respectively. SARS-CoV-2 viral loads normalized to the population or PMMoV better reflect the number of clinical cases when comparing wastewater data between sewer catchments.
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Qiu Y, Yu J, Pabbaraju K, Lee BE, Gao T, Ashbolt NJ, Hrudey SE, Diggle M, Tipples G, Maal-Bared R, Pang X. Validating and optimizing the method for molecular detection and quantification of SARS-CoV-2 in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:151434. [PMID: 34742974 PMCID: PMC8568330 DOI: 10.1016/j.scitotenv.2021.151434] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 05/18/2023]
Abstract
Wastewater surveillance of SARS-CoV-2 has become a promising tool to estimate population-level changes in community infections and the prevalence of COVID-19 disease. Although many studies have reported the detection and quantification of SARS-CoV-2 in wastewater, remarkable variation remains in the methodology. In this study, we validated a molecular testing method by concentrating viruses from wastewater using ultrafiltration and detecting SARS-CoV-2 using one-step RT-qPCR assay. The following parameters were optimized including sample storage condition, wastewater pH, RNA extraction and RT-qPCR assay by quantification of SARS-CoV-2 or spiked human coronavirus strain 229E (hCoV-229E). Wastewater samples stored at 4 °C after collection showed significantly enhanced detection of SARS-CoV-2 with approximately 2-3 PCR-cycle threshold (Ct) values less when compared to samples stored at -20 °C. Pre-adjustment of the wastewater pH to 9.6 to aid virus desorption followed by pH readjustment to neutral after solid removal significantly increased the recovery of spiked hCoV-229E. Of the five commercially available RNA isolation kits evaluated, the MagMAX-96 viral RNA isolation kit showed the best recovery of hCoV-229E (50.1 ± 20.1%). Compared with two-step RT-qPCR, one-step RT-qPCR improved sensitivity for SARS-CoV-2 detection. Salmon DNA was included for monitoring PCR inhibition and pepper mild mottle virus (PMMoV), a fecal indicator indigenous to wastewater, was used to normalize SARS-CoV-2 levels in wastewater. Our method for molecular detection of SARS-CoV-2 in wastewater provides a useful tool for public health surveillance of COVID-19.
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Affiliation(s)
- Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Jiaao Yu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kanti Pabbaraju
- Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Calgary, Alberta, Canada
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Tiejun Gao
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Nicholas J Ashbolt
- Faculty of Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Steve E Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Mathew Diggle
- Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, Alberta, Canada
| | - Graham Tipples
- Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, Alberta, Canada
| | | | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, Alberta, Canada.
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56
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Twigg C, Wenk J. Review and Meta‐Analysis: SARS‐CoV‐2 and Enveloped Virus Detection in Feces and Wastewater. CHEMBIOENG REVIEWS 2022. [PMCID: PMC9083821 DOI: 10.1002/cben.202100039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Detection and quantification of viruses supplies key information on their spread and allows risk assessment for public health. In wastewater, existing detection methods have been focusing on non‐enveloped enteric viruses due to enveloped virus transmission, such as coronaviruses, by the fecal‐oral route being less likely. Since the beginning of the SARS‐CoV‐2 pandemic, interest and importance of enveloped virus detection in wastewater has increased. Here, quantitative studies on SARS‐CoV‐2 occurrence in feces and raw wastewater and other enveloped viruses via quantitative real‐time reverse transcription polymerase chain reaction (RT‐qPCR) during the early stage of the pandemic until April 2021 are reviewed, including statistical evaluation of the positive detection rate and efficiency throughout the detection process involving concentration, extraction, and amplification stages. Optimized and aligned sampling protocols and concentration methods for enveloped viruses, along with SARS‐CoV‐2 surrogates, in wastewater environments may improve low and variable recovery rates providing increased detection efficiency and comparable data on viral load measured across different studies.
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Affiliation(s)
- Charlotte Twigg
- University of Bath Department of Chemical Engineering and Water Innovation and Research Centre (WIRC@Bath) Claverton Down BA2 7AY Bath Somerset United Kingdom
| | - Jannis Wenk
- University of Bath Department of Chemical Engineering and Water Innovation and Research Centre (WIRC@Bath) Claverton Down BA2 7AY Bath Somerset United Kingdom
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57
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Sangsanont J, Rattanakul S, Kongprajug A, Chyerochana N, Sresung M, Sriporatana N, Wanlapakorn N, Poovorawan Y, Mongkolsuk S, Sirikanchana K. SARS-CoV-2 RNA surveillance in large to small centralized wastewater treatment plants preceding the third COVID-19 resurgence in Bangkok, Thailand. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151169. [PMID: 34699826 PMCID: PMC8540006 DOI: 10.1016/j.scitotenv.2021.151169] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 05/07/2023]
Abstract
Wastewater surveillance for SARS-CoV-2 RNA has been a successful indicator of COVID-19 outbreaks in populations prior to clinical testing. However, this has been mostly conducted in high-income countries, which means there is a dearth of performance investigations in low- and middle-income countries with different socio-economic settings. This study evaluated the applicability of SARS-CoV-2 RNA monitoring in wastewater (n = 132) to inform COVID-19 infection in the city of Bangkok, Thailand using CDC N1 and N2 RT-qPCR assays. Wastewater influents (n = 112) and effluents (n = 20) were collected from 19 centralized wastewater treatment plants (WWTPs) comprising four large, four medium, and 11 small WWTPs during seven sampling events from January to April 2021 prior to the third COVID-19 resurgence that was officially declared in April 2021. The CDC N1 assay showed higher detection rates and mostly lower Ct values than the CDC N2. SARS-CoV-2 RNA was first detected at the first event when new reported cases were low. Increased positive detection rates preceded an increase in the number of newly reported cases and increased over time with the reported infection incidence. Wastewater surveillance (both positive rates and viral loads) showed strongest correlation with daily new COVID-19 cases at 22-24 days lag (Spearman's Rho = 0.85-1.00). Large WWTPs (serving 432,000-580,000 of the population) exhibited similar trends of viral loads and new cases to those from all 19 WWTPs, emphasizing that routine monitoring of the four large WWTPs could provide sufficient information for the city-scale dynamics. Higher sampling frequency at fewer sites, i.e., at the four representative WWTPs, is therefore suggested especially during the subsiding period of the outbreak to indicate the prevalence of COVID-19 infection, acting as an early warning of COVID-19 resurgence.
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Affiliation(s)
- Jatuwat Sangsanont
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Water Science and Technology for Sustainable Environmental Research Group, Chulalongkorn University, Bangkok 10330, Thailand
| | - Surapong Rattanakul
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Montakarn Sresung
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Nonnarit Sriporatana
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok 10400, Thailand.
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58
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Kevill JL, Pellett C, Farkas K, Brown MR, Bassano I, Denise H, McDonald JE, Malham SK, Porter J, Warren J, Evens NP, Paterson S, Singer AC, Jones DL. A comparison of precipitation and filtration-based SARS-CoV-2 recovery methods and the influence of temperature, turbidity, and surfactant load in urban wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:151916. [PMID: 34826466 PMCID: PMC8610557 DOI: 10.1016/j.scitotenv.2021.151916] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/09/2021] [Accepted: 11/19/2021] [Indexed: 05/09/2023]
Abstract
Wastewater-based epidemiology (WBE) has become a complimentary surveillance tool during the SARS-CoV-2 pandemic. Viral concentration methods from wastewater are still being optimised and compared, whilst viral recovery under different wastewater characteristics and storage temperatures remains poorly understood. Using urban wastewater samples, we tested three viral concentration methods; polyethylene glycol precipitation (PEG), ammonium sulphate precipitation (AS), and CP select™ InnovaPrep® (IP) ultrafiltration. We found no major difference in SARS-CoV-2 and faecal indicator virus (crAssphage) recovery from wastewater samples (n = 46) using these methods, PEG slightly (albeit non-significantly), outperformed AS and IP for SARS-CoV-2 detection, as a higher genome copies per litre (gc/l) was recorded for a larger proportion of samples. Next generation sequencing of 8 paired samples revealed non-significant differences in the quality of data between AS and IP, though IP data quality was slightly better and less variable. A controlled experiment assessed the impact of wastewater suspended solids (turbidity; 0-400 NTU), surfactant load (0-200 mg/l), and storage temperature (5-20 °C) on viral recovery using the AS and IP methods. SARS-CoV-2 recoveries were >20% with AS and <10% with IP in turbid samples, whilst viral recoveries for samples with additional surfactant were between 0-18% for AS and 0-5% for IP. Turbidity and sample storage temperature combined had no significant effect on SARS-CoV-2 recovery (p > 0.05), whilst surfactant and storage temperature combined were significant negative correlates (p < 0.001 and p < 0.05, respectively). In conclusion, our results show that choice of methodology had small effect on viral recovery of SARS-CoV-2 and crAssphage in wastewater samples within this study. In contrast, sample turbidity, storage temperature, and surfactant load did affect viral recovery, highlighting the need for careful consideration of the viral concentration methodology used when working with wastewater samples.
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Affiliation(s)
- Jessica L Kevill
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| | - Cameron Pellett
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Mathew R Brown
- Joint Biosecurity Centre, Department of Health and Social Care, London WC1B 4DA, UK; School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Irene Bassano
- Joint Biosecurity Centre, Department of Health and Social Care, London WC1B 4DA, UK; Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK
| | - Hubert Denise
- Joint Biosecurity Centre, Department of Health and Social Care, London WC1B 4DA, UK
| | - James E McDonald
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Jonathan Porter
- Environment Agency National Laboratory Service, Exeter, Devon EX6 8PE, UK
| | - Jonathan Warren
- Environment Agency National Laboratory Service, Exeter, Devon EX6 8PE, UK
| | - Nicholas P Evens
- Environment Agency National Laboratory Service, Exeter, Devon EX6 8PE, UK
| | - Steve Paterson
- Centre of Genomics Research & NERC Environmental Omics Facility, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Davey L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6105, Australia
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59
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The Detection of SARS-CoV-2 in the Environment: Lessons from Wastewater. WATER 2022. [DOI: 10.3390/w14040599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Wastewater has historically been an important source of enteric pathogens, as well as a source of unconventational or unexpected pathogens, including those present in the respiratory tract, saliva, urine, and blood. This is the case with SARS-CoV-2, the causative agent of the most recent pandemic. SARS-CoV-2 has been identified in wastewater across various geographical regions prior to, and during, the report of cases. The detection of SARS-CoV-2 in wastewater is usually performed using molecular techniques targeting specific genomic regions. High-throughput sequencing techniques, both untargeted and targeted or amplicon-based, are also being applied in combination with molecular techniques for the detection of SARS-CoV-2 variants to determine the genetic diversity and phylogenetic relatedness. The identification of SARS-CoV-2 in wastewater has a number of epidemiological, biological, and ecological applications, which can be incorporated into future outbreaks, epidemics, or pandemics.
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60
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Zhang S, Li X, Shi J, Sivakumar M, Luby S, O'Brien J, Jiang G. Analytical performance comparison of four SARS-CoV-2 RT-qPCR primer-probe sets for wastewater samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150572. [PMID: 34582851 PMCID: PMC8464025 DOI: 10.1016/j.scitotenv.2021.150572] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 05/18/2023]
Abstract
Current studies have confirmed the feasibility of SARS-CoV-2 RNA detection by RT-qPCR assays in wastewater samples as an effective surveillance tool of COVID-19 prevalence in a community. Analytical performance of various RT-qPCR assays has been compared against wastewater samples based on the positive ratio. However, there is no systematic comparison work has been conducted for both analytical sensitivity and quantitative reliability against wastewater, which are essential factors for WBE. In this study, the detection performance of four RT-qPCR primer-probe sets, including CCDC-N, CDC-N1, N-Sarbeco, and E-Sarbeco, was systematically evaluated with pure synthetized plasmids, spiked wastewater mocks and raw wastewater samples. In addition to confirm RT-qPCR results, Nanopore sequencing was employed to delineate at molecular level for the analytical sensitivity and reproducibility of those primer-probe sets. CCDC-N showed high sensitivity and the broadest linearity range for wastewater samples. It was thus recommended to be the most efficient tool in the quantitative analysis of SARS-CoV-2 in wastewater. CDC-N1 had the highest sensitivity for real wastewater and thus would be suitable for the screening of wastewater for the presence of SARS-CoV-2. When applying the primer-probe sets to wastewater samples collected from different Australian catchments, increased active clinical cases were observed with the augment of SARS-CoV-2 RNA quantified by RT-qPCR in wastewater in low prevalence communities.
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Affiliation(s)
- Shuxin Zhang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Xuan Li
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Jiahua Shi
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Muttucumaru Sivakumar
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Stephen Luby
- Woods Institute for the Environment, Stanford University, United States
| | - Jake O'Brien
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Australia
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia.
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61
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Barbosa MRF, Garcia SC, Bruni ADC, Machado FS, de Oliveira RX, Dropa M, da Costa AC, Leal E, Brandão CJ, da Silva RLO, Iko BY, Kondo VKM, de Araújo RS, da Silveira VB, de Andrade TM, Nunes DR, Janini LMR, Braconi CT, Maricato JT, Sato MIZ. One-year surveillance of SARS-CoV-2 in wastewater from vulnerable urban communities in metropolitan São Paulo, Brazil. JOURNAL OF WATER AND HEALTH 2022; 20:471-490. [PMID: 36366999 DOI: 10.2166/wh.2022.210] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The current COVID-19 pandemic has emphasized the vulnerability of communities living in the urban outskirts and informal settlements. The lack of reliable COVID-19 case data highlights the importance and application of wastewater-based epidemiology. This study aimed to monitor the COVID-19 trends in four vulnerable urban communities (slums and low-income neighborhoods) in metropolitan São Paulo by assessing the SARS-CoV-2 RNA viral load in wastewater. We analyzed 160 samples from May 2020 to June 2021 with weekly or fortnightly samplings. The samples were ultracentrifuged with glycine elution and quantified by N1/N2 SARS-CoV-2 RT-qPCR. The results of positivity were 100% (Paraisópolis, Heliópolis and Cidade Tiradentes) and 76.9% (Vila Brasilândia). The new case numbers of COVID-19, counted from the onset of symptoms, positively correlated with SARS-CoV-2 N1 viral loads from the two largest communities (p<0.001). SARS-CoV-2 infectivity was tested in Vero E6 cells after concentration with the two techniques, ultrafiltration (Centricon® Plus-70 10 kDa) and sucrose cushion ultracentrifugation, but none of the evaluated samples presented positive results. Next-generation sequencing (NGS) analysis from samples collected in March and August 2021 revealed the presence of the clade 20 J (lineage P.1) belonging to the most prevalent circulating variant in the country. Our results showed that wastewater surveillance data can be used as complementary indicators to monitor the dynamics and temporal trends of COVID-19. The infectivity test results strengthened the evidence of low risk of infection associated with SARS-CoV-2 in wastewater.
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Affiliation(s)
- Mikaela Renata Funada Barbosa
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Suzi Cristina Garcia
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Antonio de Castro Bruni
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | | | - Roberto Xavier de Oliveira
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Milena Dropa
- School of Public Health, Universidade de São Paulo (USP), São Paulo, Brazil
| | | | - Elcio Leal
- Institute of Biological Sciences, Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Carlos Jesus Brandão
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Renan Lourenço Oliveira da Silva
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Beatriz Yukie Iko
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Victor Kenji Matsuoka Kondo
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Ronalda Silva de Araújo
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
| | - Vanessa Barbosa da Silveira
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Tatiane Montes de Andrade
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Danilo Rosa Nunes
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Luiz Mário Ramos Janini
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Juliana Terzi Maricato
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, (UNIFESP), São Paulo, Brazil
| | - Maria Inês Zanoli Sato
- Department of Environmental Analysis, Division of Microbiology and Parasitology, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, CEP 05459-900, Brazil E-mail:
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62
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Holm RH, Nagarkar M, Yeager RA, Talley D, Chaney AC, Rai JP, Mukherjee A, Rai SN, Bhatnagar A, Smith T. Surveillance of RNase P, PMMoV, and CrAssphage in wastewater as indicators of human fecal concentration across urban sewer neighborhoods, Kentucky. FEMS MICROBES 2022; 3:1-12. [PMID: 37228897 PMCID: PMC10117713 DOI: 10.1093/femsmc/xtac003] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/24/2021] [Accepted: 01/25/2022] [Indexed: 09/03/2023] Open
Abstract
Wastewater surveillance has been widely used as a supplemental method to track the community infection levels of severe acute respiratory syndrome coronavirus 2. A gap exists in standardized reporting for fecal indicator concentrations, which can be used to calibrate the primary outcome concentrations from wastewater monitoring for use in epidemiological models. To address this, measurements of fecal indicator concentration among wastewater samples collected from sewers and treatment centers in four counties of Kentucky (N = 650) were examined. Results from the untransformed wastewater data over 4 months of sampling indicated that the fecal indicator concentration of human ribonuclease P (RNase P) ranged from 5.1 × 101 to 1.15 × 106 copies/ml, pepper mild mottle virus (PMMoV) ranged from 7.23 × 103 to 3.53 × 107 copies/ml, and cross-assembly phage (CrAssphage) ranged from 9.69 × 103 to 1.85 × 108 copies/ml. The results showed both regional and temporal variability. If fecal indicators are used as normalization factors, knowing the daily sewer system flow of the sample location may matter more than rainfall. RNase P, while it may be suitable as an internal amplification and sample adequacy control, has less utility than PMMoV and CrAssphage as a fecal indicator in wastewater samples when working at different sizes of catchment area. The choice of fecal indicator will impact the results of surveillance studies using this indicator to represent fecal load. Our results contribute broadly to an applicable standard normalization factor and assist in interpreting wastewater data in epidemiological modeling and monitoring.
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Affiliation(s)
- R H Holm
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - M Nagarkar
- Center for Environmental Solutions and Emergency Response, United States Environmental Protection Agency, Cincinnati, OH 45220, USA
| | - R A Yeager
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
- Department of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray St., Louisville, KY 40202, USA
| | - D Talley
- Louisville/Jefferson County Metropolitan Sewer District, Morris Forman Water Quality Treatment Center, 4522 Algonquin Parkway, Louisville, KY 40211, USA
| | - A C Chaney
- Sanitation District No. 1 of Northern Kentucky, 1045 Eaton Dr., Ft. Wright, Kentucky 41017, USA
| | - J P Rai
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - A Mukherjee
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - S N Rai
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
- Brown Cancer Center, School of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
- Center for Integrative Environmental Health Sciences, 500 S. Preston St., Suite 1319, Louisville, KY 40202, USA
| | - A Bhatnagar
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
| | - T Smith
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
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63
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Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 34818780 DOI: 10.20944/preprints202104.0481.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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64
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Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:149877. [PMID: 34818780 PMCID: PMC8386095 DOI: 10.1016/j.scitotenv.2021.149877] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 05/18/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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Juel MAI, Stark N, Nicolosi B, Lontai J, Lambirth K, Schlueter J, Gibas C, Munir M. Performance evaluation of virus concentration methods for implementing SARS-CoV-2 wastewater based epidemiology emphasizing quick data turnaround. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149656. [PMID: 34418628 PMCID: PMC8363421 DOI: 10.1016/j.scitotenv.2021.149656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 05/12/2023]
Abstract
Wastewater based epidemiology (WBE) has drawn significant attention as an early warning tool to detect and predict the trajectory of COVID-19 cases in a community, in conjunction with public health data. This means of monitoring for outbreaks has been used at municipal wastewater treatment centers to analyze COVID-19 trends in entire communities, as well as by universities and other community living environments to monitor COVID-19 spread in buildings. Sample concentration is crucial, especially when viral abundance in raw wastewater is below the threshold of detection by RT-qPCR analysis. We evaluated the performance of a rapid ultrafiltration-based virus concentration method using InnovaPrep Concentrating Pipette (CP) Select and compared this to the established electronegative membrane filtration (EMF) method. We evaluated sensitivity of SARS-CoV-2 quantification, surrogate virus recovery rate, and sample processing time. Results suggest that the CP Select concentrator is more efficient at concentrating SARS-CoV-2 from wastewater compared to the EMF method. About 25% of samples that tested negative when concentrated with the EMF method produced a positive signal with the CP Select protocol. Increased recovery of the surrogate virus control using the CP Select confirms this observation. We optimized the CP Select protocol by adding AVL lysis buffer and sonication, to increase the recovery of virus. Sonication increased Bovine Coronavirus (BCoV) recovery by 19%, which seems to compensate for viral loss during centrifugation. Filtration time decreases by approximately 30% when using the CP Select protocol, making this an optimal choice for building surveillance applications where quick turnaround time is necessary.
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Affiliation(s)
- Md Ariful Islam Juel
- Department of Civil and Environmental Engineering, 9201 University City Blvd, Charlotte, NC 28223, United States; Department of Leather Engineering, Khulna University of Engineering and Technology, Khulna 9203, Bangladesh
| | - Nicholas Stark
- Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, NC 28223, United States
| | - Bridgette Nicolosi
- Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, NC 28223, United States
| | - Jordan Lontai
- Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, NC 28223, United States; Department of Geography and Earth Sciences, 9201 University City Blvd, Charlotte, NC 28223, United States
| | - Kevin Lambirth
- Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, NC 28223, United States
| | - Jessica Schlueter
- Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, NC 28223, United States; Bioinformatics Research Center, 9201 University City Blvd, Charlotte, NC 28223, United States
| | - Cynthia Gibas
- Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, NC 28223, United States; Bioinformatics Research Center, 9201 University City Blvd, Charlotte, NC 28223, United States
| | - Mariya Munir
- Department of Civil and Environmental Engineering, 9201 University City Blvd, Charlotte, NC 28223, United States; Bioinformatics Research Center, 9201 University City Blvd, Charlotte, NC 28223, United States.
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66
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Ahmed W, Bivins A, Simpson SL, Smith WJM, Metcalfe S, McMinn B, Symonds EM, Korajkic A. Comparative analysis of rapid concentration methods for the recovery of SARS-CoV-2 and quantification of human enteric viruses and a sewage-associated marker gene in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149386. [PMID: 34388890 PMCID: PMC8325557 DOI: 10.1016/j.scitotenv.2021.149386] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 05/18/2023]
Abstract
To support public-health-related disease surveillance and monitoring, it is crucial to concentrate both enveloped and non-enveloped viruses from domestic wastewater. To date, most concentration methods were developed for non-enveloped viruses, and limited studies have directly compared the recovery efficiency of both types of viruses. In this study, the effectiveness of two different concentration methods (Concentrating pipette (CP) method and an adsorption-extraction (AE) method amended with MgCl2) were evaluated for untreated wastewater matrices using three different viruses (SARS-CoV-2 (seeded), human adenovirus 40/41 (HAdV 40/41), and enterovirus (EV)) and a wastewater-associated bacterial marker gene targeting Lachnospiraceae (Lachno3). For SARS-CoV-2, the estimated mean recovery efficiencies were significantly greater by as much as 5.46 times, using the CP method than the AE method amended with MgCl2. SARS-CoV-2 RNA recovery was greater for samples with higher titer seeds regardless of the method, and the estimated mean recovery efficiencies using the CP method were 25.1 ± 11% across ten WWTPs when wastewater samples were seeded with 5 × 104 gene copies (GC) of SARS-CoV-2. Meanwhile, the AE method yielded significantly greater concentrations of indigenous HAdV 40/41 and Lachno3 from wastewater compared to the CP method. Finally, no significant differences in indigenous EV concentrations were identified in comparing the AE and CP methods. These data indicate that the most effective concentration method varies by microbial analyte and that the priorities of the surveillance or monitoring program should be considered when choosing the concentration method.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | | | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Erin M Symonds
- College of Marine Science, University of South Florida, 140 7th Ave South, St. Petersburg, FL 33701, USA
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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67
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Palmer EJ, Maestre JP, Jarma D, Lu A, Willmann E, Kinney KA, Kirisits MJ. Development of a reproducible method for monitoring SARS-CoV-2 in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149405. [PMID: 34365266 PMCID: PMC8328530 DOI: 10.1016/j.scitotenv.2021.149405] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 05/06/2023]
Abstract
Monitoring the genetic signal of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through RNA titers in wastewater has emerged as a promising strategy for tracking community-scale prevalence of coronavirus disease 2019 (COVID-19). Although many studies of SARS-CoV-2 in wastewater have been conducted around the world, a uniform procedure for concentrating the virus in wastewater is lacking. The goal of this study was to comprehensively evaluate how different methods for concentrating the suspended solids in wastewater affect the associated SARS-CoV-2 RNA signal and the time required for processing samples for wastewater-based epidemiology efforts. We additionally consider the effects of sampling location in the wastewater treatment train (i.e., following preliminary or primary treatment), pasteurization, and RNA extraction method. Comparison of the liquid phase to suspended solids obtained via centrifugation or vacuum filtration suggests that the RNA signal of SARS-CoV-2 preferentially occurs in the solids. Therefore, we assert that the recovery of SARS-CoV-2 from wastewater should focus on suspended solids. Our data indicate that the measured SARS-CoV-2 signal is higher among samples taken from the primary clarifier effluent, as opposed to those taken after preliminary treatment. Additionally, we provide evidence that sample pasteurization at 60 °C for 90 min reduces the SARS-CoV-2 signal by approximately 50-55%. Finally, the results indicate that a magnetic bead approach to RNA extraction leads to a higher SARS-CoV-2 signal than does a silica membrane approach.
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Affiliation(s)
- Emma J Palmer
- The University of Texas at Austin, Department of Civil, Architectural, and Environmental Engineering, 301 E. Dean Keeton St., Stop C1786, Austin, TX 78712, United States of America.
| | - Juan P Maestre
- The University of Texas at Austin, Department of Civil, Architectural, and Environmental Engineering, 301 E. Dean Keeton St., Stop C1786, Austin, TX 78712, United States of America.
| | - David Jarma
- The University of Texas at Austin, Department of Civil, Architectural, and Environmental Engineering, 301 E. Dean Keeton St., Stop C1786, Austin, TX 78712, United States of America.
| | - Alisa Lu
- The University of Texas at Austin, Department of Civil, Architectural, and Environmental Engineering, 301 E. Dean Keeton St., Stop C1786, Austin, TX 78712, United States of America.
| | - Elisabeth Willmann
- The University of Texas at Austin, Department of Civil, Architectural, and Environmental Engineering, 301 E. Dean Keeton St., Stop C1786, Austin, TX 78712, United States of America.
| | - Kerry A Kinney
- The University of Texas at Austin, Department of Civil, Architectural, and Environmental Engineering, 301 E. Dean Keeton St., Stop C1786, Austin, TX 78712, United States of America.
| | - Mary Jo Kirisits
- The University of Texas at Austin, Department of Civil, Architectural, and Environmental Engineering, 301 E. Dean Keeton St., Stop C1786, Austin, TX 78712, United States of America.
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68
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Mainardi PH, Bidoia ED. Challenges and emerging perspectives of an international SARS-CoV-2 epidemiological surveillance in wastewater. AN ACAD BRAS CIENC 2021; 93:e20210163. [PMID: 34878048 DOI: 10.1590/0001-3765202120210163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/23/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 is a new type of coronavirus capable to infect humans and cause the severe acute respiratory syndrome COVID-19, a disease that has been causing huge impacts across the Earth. COVID-19 patients, including mild, pre-symptomatic and asymptomatic cases, were often seen to contain infectious fragments of SARS-CoV-2 in feces and urine samples. Therefore, studies to detect the new coronavirus in wastewater, which collect and concentrate human excreta, have been extremely useful as a viral tracking tool in communities. This type of monitoring, in addition to serve as a non-invasive early warning of COVID-19 outbreaks, would provide better predictions about the SARS-CoV-2 spread and strongly contribute to maintenance the global health. Although current methods to detect viruses in wastewater, based on molecular RT-PCR and RT-qPCR techniques, were considered as reliable and provided accurate qualitative and quantitative results, they have been facing considerable challenges concerning the SARS-CoV-2 surveillance. In this review, the methods used to detect the SARS-CoV-2 in wastewater and the challenges to implement an international viral monitoring network were described. The article also addressed the emerging perspectives associated with the SARS-CoV-2 epidemiological surveillance in this environment and the importance of a worldwide collaboration to generate and disseminate the detection results.
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Affiliation(s)
- Pedro H Mainardi
- Universidade Estadual Paulista Júlio de Mesquita Filho /UNESP, Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Av. 24A, 1515, Bela Vista, 13506900 Rio Claro, SP, Brazil
| | - Ederio D Bidoia
- Universidade Estadual Paulista Júlio de Mesquita Filho /UNESP, Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Av. 24A, 1515, Bela Vista, 13506900 Rio Claro, SP, Brazil
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69
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Rubio-Acero R, Beyerl J, Muenchhoff M, Roth MS, Castelletti N, Paunovic I, Radon K, Springer B, Nagel C, Boehm B, Böhmer MM, Graf A, Blum H, Krebs S, Keppler OT, Osterman A, Khan ZN, Hoelscher M, Wieser A. Spatially resolved qualified sewage spot sampling to track SARS-CoV-2 dynamics in Munich - One year of experience. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149031. [PMID: 34346361 PMCID: PMC8294104 DOI: 10.1016/j.scitotenv.2021.149031] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/23/2021] [Accepted: 07/09/2021] [Indexed: 05/03/2023]
Abstract
Wastewater-based epidemiology (WBE) is a tool now increasingly proposed to monitor the SARS-CoV-2 burden in populations without the need for individual mass testing. It is especially interesting in metropolitan areas where spread can be very fast, and proper sewage systems are available for sampling with short flow times and thus little decay of the virus. We started in March 2020 to set up a once-a-week qualified spot sampling protocol in six different locations in Munich carefully chosen to contain primarily wastewater of permanent residential areas, rather than industry or hospitals. We used RT-PCR and sequencing to track the spread of SARS-CoV-2 in the Munich population with temporo-spatial resolution. The study became fully operational in mid-April 2020 and has been tracking SARS-CoV-2 RNA load weekly for one year. Sequencing of the isolated viral RNA was performed to obtain information about the presence and abundance of variants of concern in the Munich area over time. We demonstrate that the evolution of SARS-CoV-2 RNA loads (between <7.5 and 3874/ml) in these different areas within Munich correlates well with official seven day incidence notification data (between 0.0 and 327 per 100,000) obtained from the authorities within the respective region. Wastewater viral loads predicted the dynamic of SARS-CoV-2 local incidence about 3 weeks in advance of data based on respiratory swab analyses. Aligning with multiple different point-mutations characteristic for certain variants of concern, we could demonstrate the gradual increase of variant of concern B.1.1.7 in the Munich population beginning in January 2021, weeks before it became apparent in sequencing results of swabs samples taken from patients living in Munich. Overall, the study highlights the potential of WBE to monitor the SARS-CoV-2 pandemic, including the introduction of variants of concern in a local population.
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Affiliation(s)
- Raquel Rubio-Acero
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany.
| | - Jessica Beyerl
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany.
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, 80336 Munich, Germany; German Center for Infection Research (DZIF), partner site Munich, Germany.
| | | | - Noemi Castelletti
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany.
| | - Ivana Paunovic
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany.
| | - Katja Radon
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, 80336 Munich, Germany; Center for International Health, Ludwig-Maximilians-University, Munich, Germany.
| | - Bernd Springer
- Fire Department, Disaster Control, City of Munich, Germany.
| | | | | | - Merle M Böhmer
- Taskforce Infectiology, Department for Infectious Disease Epidemiology (TFI 2), Bavarian Health and Food Safety Authority, Oberschleissheim, Germany; Institute of Social Medicine and Health Systems Research, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany.
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany.
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany.
| | - Oliver T Keppler
- German Center for Infection Research (DZIF), partner site Munich, Germany; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, 80336 Munich, Germany.
| | - Andreas Osterman
- German Center for Infection Research (DZIF), partner site Munich, Germany; Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU Munich, 80336 Munich, Germany.
| | - Zohaib Nisar Khan
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany.
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany; Center for International Health, Ludwig-Maximilians-University, Munich, Germany; German Center for Infection Research (DZIF), partner site Munich, Germany.
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität (LMU) Munich, 80802 Munich, Germany; German Center for Infection Research (DZIF), partner site Munich, Germany.
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70
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Giraud-Billoud M, Cuervo P, Altamirano JC, Pizarro M, Aranibar JN, Catapano A, Cuello H, Masachessi G, Vega IA. Monitoring of SARS-CoV-2 RNA in wastewater as an epidemiological surveillance tool in Mendoza, Argentina. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148887. [PMID: 34274669 PMCID: PMC8426053 DOI: 10.1016/j.scitotenv.2021.148887] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 05/06/2023]
Abstract
Wastewater-based epidemiology (WBE) is an emerging tool that gives temporal and spatial information on a population's health status. Here, we report the epidemiological dynamics of a population of ~1.2 million residents in the metropolitan region of Mendoza province, Argentina, within the period July 2020 to January 2021. We combined the use of WBE of two wastewater treatment plants with epidemiological surveillance of the corresponding populations. We applied two viral concentration methods (polyethylene glycol precipitation and aluminum-based adsorption-flocculation) and RNA isolation methods in each wastewater sample to increase the possibility of detection and quantification of nucleocapsid markers (N1 and N2) of SARS-CoV-2 by RT-qPCR. Overall, our results allowed us to trace the rise, exponential growth, plateau, and fall of SARS-CoV-2 infections for 26 weeks. Individual analysis for each wastewater treatment plant showed a positive correlation between the viral load of SARS-CoV-2 genetic markers and COVID-19 cases that were diagnosed per week. Our findings indicate that WBE is a useful epidemiological indicator to anticipate the increase in COVID-19 cases and monitor the advance of the pandemic and different waves of infections.
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Affiliation(s)
- Maximiliano Giraud-Billoud
- IHEM, Universidad Nacional de Cuyo, CONICET, Casilla de Correo 33, 5500 Mendoza, Argentina; Universidad Nacional de Cuyo, Facultad de Ciencias Médicas, Instituto de Fisiología, Casilla de Correo 33, 5500 Mendoza, Argentina; Universidad Nacional de Villa Mercedes, Escuela de Ciencias de la Salud-Medicina, Departamento de Ciencias Básicas, 5730 San Luis, Argentina
| | - Paula Cuervo
- Universidad Nacional de Cuyo, Facultad de Ciencias Médicas, Instituto de Fisiología, Casilla de Correo 33, 5500 Mendoza, Argentina
| | - Jorgelina C Altamirano
- Universidad Nacional de Cuyo, Facultad de Ciencias Exactas y Naturales, Casilla de Correo 33, 5500 Mendoza, Argentina; IANIGLA, CONICET, Universidad Nacional de Cuyo, Casilla de Correo 330, Mendoza, Argentina
| | - Marcela Pizarro
- Universidad Nacional de Cuyo, Facultad de Ciencias Médicas, Instituto de Fisiología, Casilla de Correo 33, 5500 Mendoza, Argentina
| | - Julieta N Aranibar
- Universidad Nacional de Cuyo, Facultad de Ciencias Exactas y Naturales, Casilla de Correo 33, 5500 Mendoza, Argentina; IANIGLA, CONICET, Universidad Nacional de Cuyo, Casilla de Correo 330, Mendoza, Argentina
| | | | - Héctor Cuello
- Laboratorio de Virología, Hospital Central de Mendoza, Argentina
| | - Gisela Masachessi
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gómez s/n. Ciudad Universitaria, CP, 5000 Córdoba, Argentina
| | - Israel A Vega
- IHEM, Universidad Nacional de Cuyo, CONICET, Casilla de Correo 33, 5500 Mendoza, Argentina; Universidad Nacional de Cuyo, Facultad de Ciencias Médicas, Instituto de Fisiología, Casilla de Correo 33, 5500 Mendoza, Argentina; Universidad Nacional de Cuyo, Facultad de Ciencias Exactas y Naturales, Casilla de Correo 33, 5500 Mendoza, Argentina.
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71
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Salvo M, Moller A, Alvareda E, Gamazo P, Colina R, Victoria M. Evaluation of low-cost viral concentration methods in wastewaters: Implications for SARS-CoV-2 pandemic surveillances. J Virol Methods 2021; 297:114249. [PMID: 34339765 PMCID: PMC8324412 DOI: 10.1016/j.jviromet.2021.114249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023]
Abstract
In the pandemic of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) many strategies have been performed in order to control viral spread in the population and known the real-time situation about the number of infected persons. In this sense, Wastewater Based Epidemiology (WBE) has been applied as an excellent tool to evaluate the virus circulation in a population. In order to obtain reliable results, three low-cost viral concentration methods were evaluated in this study, polyethylene glycol (PEG) precipitation, skimmed milk flocculation (SM) and Aluminum polychloride flocculation, for Pseudomonas aeruginosa bacteriophage PP7 as a surrogate for non-enveloped viruses and Bovine Coronavirus (BCoV) as a surrogate for enveloped virus, with emphasis for SARS- CoV-2. Our results suggest that PEG precipitation for viral concentration, for both enveloped and non-enveloped virus from wastewater is an appropriate approach since it was more sensitive compared to SM flocculation and Aluminum polychloride flocculation. This methodology can be used for WBE studies in order to follow the epidemiology of the SARS-CoV-2 pandemic, mainly in developing countries where the economic resources are frequently limited.
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Affiliation(s)
- Matías Salvo
- Laboratory of Molecular Virology, CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, Salto CP: 50.000, Uruguay; Water Department, CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, Salto CP: 50.000, Uruguay
| | - Ana Moller
- Laboratory of Molecular Virology, CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, Salto CP: 50.000, Uruguay
| | - Elena Alvareda
- Water Department, CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, Salto CP: 50.000, Uruguay
| | - Pablo Gamazo
- Water Department, CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, Salto CP: 50.000, Uruguay
| | - Rodney Colina
- Laboratory of Molecular Virology, CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, Salto CP: 50.000, Uruguay
| | - Matías Victoria
- Laboratory of Molecular Virology, CENUR Litoral Norte, Universidad de la República, Gral. Rivera 1350, Salto CP: 50.000, Uruguay.
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Chen W, Wang T, Dou Z, Xie X. Self-Driven Pretreatment and Room-Temperature Storage of Water Samples for Virus Detection Using Enhanced Porous Superabsorbent Polymer Beads. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14059-14068. [PMID: 34609845 DOI: 10.1021/acs.est.1c03414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The continuous emergence of infectious viral diseases has become a major threat to public health. To quantify viruses, proper handling of water samples is required to ensure the accuracy and reliability of the testing results. In this study, we develop enhanced porous superabsorbent polymer (PSAP) beads to pretreat and store water samples for virus detection. By applying PSAP beads to collect water samples, the viruses are captured and encapsulated inside the beads while undesired components are excluded. We have successfully demonstrated that the shelf life of the model virus can be effectively extended at room temperature (22 °C) and an elevated temperature (35 °C). Both the infectivity level and genome abundance of the viruses are preserved even in a complex medium such as untreated wastewater. Under the tested conditions, the viral degradation rate constant can be reduced to more than 10 times using the PSAP beads. Therefore, the enhanced PSAP beads provide a low-cost and efficient sample pretreatment and storage method that is feasible and practical for large-scale surveillance of viral pathogens in water samples.
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Affiliation(s)
- Wensi Chen
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ting Wang
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zeou Dou
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Xing Xie
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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73
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Wu J, Wang Z, Lin Y, Zhang L, Chen J, Li P, Liu W, Wang Y, Yao C, Yang K. Technical framework for wastewater-based epidemiology of SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148271. [PMID: 34130001 PMCID: PMC8195746 DOI: 10.1016/j.scitotenv.2021.148271] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/29/2021] [Accepted: 05/30/2021] [Indexed: 05/02/2023]
Abstract
Wastewater-based epidemiology (WBE) is expected to become a powerful tool to monitor the dissemination of SARS-CoV-2 at the community level, which has attracted the attention of scholars all over the world. However, there is not yet a standard protocol to guide its implementation. In this paper, we proposed a comprehensive technical and theoretical framework of relative quantification via qPCR for determining the virus abundance in wastewater and estimating the infection ratio in corresponding communities, which is expected to achieve horizontal and vertical comparability of the data using a human-specific biomarker as the internal reference. Critical factors affecting the virus detectability and the estimation of infection ratio include virus concentration methods, lag-period, per capita virus shedding amount, sewage generation rate, temperature-related decay kinetics of virus/biomarker in wastewater, and hydraulic retention time (HRT), etc. Theoretical simulation shows that the main factors affecting the detectability of virus in sewage are per capita virus shedding amount and sewage generation rate. While the decay of SARS-CoV-2 RNA in sewage is a relatively slow process, which may have limited impact on its detection. Under the ideal condition of high per capita virus shedding amount and low sewage generation rate, it is expected to detect a single infected person within 400,000 people.
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Affiliation(s)
- Jinyong Wu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Zizheng Wang
- West China School of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yufei Lin
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Lihua Zhang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Jing Chen
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Panyu Li
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Wenbin Liu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yabo Wang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Changhong Yao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China.
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74
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Al-Duroobi H, Moghadam SV, Phan DC, Jafarzadeh A, Matta A, Kapoor V. Wastewater surveillance of SARS-CoV-2 corroborates heightened community infection during the initial peak of COVID-19 in Bexar County, Texas. FEMS MICROBES 2021. [DOI: 10.1093/femsmc/xtab015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
ABSTRACT
The purpose of this study was to conduct a preliminary assessment of the levels of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater at the Salitrillo Wastewater Treatment Plant in Texas during the initial peak of coronavirus disease 2019 (COVID-19) outbreak. Raw wastewater influent (24 h composite, time-based 1 L samples, n = 13) was collected weekly during June–August 2020. We measured SARS-CoV-2 RNA in wastewater by reverse transcription droplet digital PCR using the same N1 and N2 primer sets as employed in COVID-19 clinical testing. Virus RNA copies for positive samples (77%) ranged from 1.4 × 102 to 4.1 × 104 copies per liter of wastewater, and exhibited both increasing and decreasing trends, which corresponded well with the COVID-19 weekly infection rate (N1: ρ = 0.558, P = 0.048; N2: ρ = 0.487, P = 0.092). A sharp increase in virus RNA concentrations was observed during July sampling dates, consistent with the highest number of COVID-19 cases reported. This could be attributed to an increase in the spread of COVID-19 infection due to the Fourth of July holiday week gatherings (outdoor gatherings were limited to 100 people during that time). Our data show that wastewater surveillance is an effective tool to determine trends in infectious disease prevalence, and provide complementary information to clinical testing.
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Affiliation(s)
- Haya Al-Duroobi
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Sina V Moghadam
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Duc C Phan
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Arash Jafarzadeh
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Akanksha Matta
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Vikram Kapoor
- Department of Civil and Environmental Engineering, University of Texas at San Antonio, San Antonio, TX 78249, USA
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75
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Rafiee M, Isazadeh S, Mohseni-Bandpei A, Mohebbi SR, Jahangiri-Rad M, Eslami A, Dabiri H, Roostaei K, Tanhaei M, Amereh F. Moore swab performs equal to composite and outperforms grab sampling for SARS-CoV-2 monitoring in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148205. [PMID: 34102442 PMCID: PMC8170911 DOI: 10.1016/j.scitotenv.2021.148205] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) approaches to detect SARS-CoV-2 in municipal wastewater can provide unique information on the incidence or prevalence of COVID-19 in community. However, there are several technical challenges coupled with sewage sampling for SARS-CoV-2, including intermittent shedding of viruses, sampling time, volume, and frequency. Sampling schemes thus may need to be tailored to reach out highly sensitive, accurate, and reliable results. Herein, we compared the accuracy and threshold cycle (Ct) profiles of SARS-CoV-2 in Moore swabs, composite (16-h), and grab samples taken from sewage manholes (n = 17) at the Middle Eastern city of Tehran, Iran, on two occasions (November 2020 and May 2021). Samples were concentrated by polyethylene glycol precipitation and the corresponding Ct values for CDC 'N' and 'ORF1ab' assays were derived by means of real time RT-qPCR. Overall, the Moore swabs performed equal to samples composited over 16 h for qualitative monitoring, and 34/34 (100%) were positive for SARS-CoV-2. The 'N' assay showed the highest detection frequency as compared to 'ORF1ab'. The mean Moore swab Ct profiles were more consistent with 16 h composite sampling as compared with corresponding grab samples, providing hints as to the best sampling protocol to adopt when planning a sewage monitoring campaign particularly under WBE. Furthermore, our analyses on local differences showed somewhat higher virus copy numbers in the southern areas. The experimental design of this study revealed that the Moore swab and composite samples are more sensitive than grab samples, suggesting that the collection of grab samples may be inappropriate for characterizing total number of viral RNA copies in sewage samples. Given the transiently presence of human host-restricted infections such as SARS-CoV-2 and the simplicity and affordability of Moore swab, the method is well suited for disease surveillance in resource poor regions struggling with limited capacity for clinical testing.
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Affiliation(s)
- Mohammad Rafiee
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Siavash Isazadeh
- Environmental Research and Development, American Water Works, Delran, NJ, USA
| | - Anoushiravan Mohseni-Bandpei
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Jahangiri-Rad
- Water Purification Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Akbar Eslami
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Dabiri
- Department of Medical Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Kasra Roostaei
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Tanhaei
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Amereh
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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76
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Xu X, Zheng X, Li S, Lam NS, Wang Y, Chu DKW, Poon LLM, Tun HM, Peiris M, Deng Y, Leung GM, Zhang T. The first case study of wastewater-based epidemiology of COVID-19 in Hong Kong. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148000. [PMID: 34091338 PMCID: PMC8142803 DOI: 10.1016/j.scitotenv.2021.148000] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 05/02/2023]
Abstract
Early detection and surveillance of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) virus are key pre-requisites for the effective control of coronavirus disease (COVID-19). So far, sewage testing has been increasingly employed as an alternative surveillance tool for this disease. However, sampling site characteristics impact the testing results and should be addressed in the early use stage of this emerging tool. In this study, we implemented the sewage testing for SARS-CoV-2 virus across sampling sites with different sewage system characteristics. We first validated a testing method using "positive" samples from a hospital treating COVID-19 patients. This method was used to test 107 sewage samples collected during the third wave of the COVID-19 outbreak in Hong Kong (from June 8 to September 29, 2020), covering sampling sites associated with a COVID-19 hospital, public housing estates, and conventional sewage treatment facilities. The highest viral titer of 1975 copy/mL in sewage was observed in a sample collected from the isolation ward of the COVID-19 hospital. Sewage sampling at individual buildings detected the virus 2 days before the first cases were identified. Sequencing of the detected viral fragment confirmed an identical nucleotide sequence to that of the SARS-CoV-2 isolated from human samples. The virus was also detected in sewage treatment facilities, which serve populations of approximately 40,000 to more than one million people.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Nga Sze Lam
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Daniel K W Chu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Hein Min Tun
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China.
| | - Gabriel M Leung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China.
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77
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Boogaerts T, Jacobs L, De Roeck N, Van den Bogaert S, Aertgeerts B, Lahousse L, van Nuijs ALN, Delputte P. An alternative approach for bioanalytical assay optimization for wastewater-based epidemiology of SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:148043. [PMID: 34323818 PMCID: PMC8152210 DOI: 10.1016/j.scitotenv.2021.148043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 05/02/2023]
Abstract
Wastewater-based epidemiology of SARS-CoV-2 could play a role in monitoring the spread of the virus in the population and controlling possible outbreaks. However, sensitive sample preparation and detection methods are necessary to detect trace levels of SARS-CoV-2 RNA in influent wastewater (IWW). Unlike predecessors, method optimization of a SARS-CoV-2 RNA concentration and detection procedure was performed with IWW samples with high viral SARS-CoV-2 RNA loads. This is of importance since the SARS-CoV-2 genome in IWW might have already been subject to in-sewer degradation into smaller genome fragments or might be present in a different form (e.g. cell debris, …). Centricon Plus-70 (100 kDa) centrifugal filter devices resulted in the lowest and most reproducible Ct-values for SARS-CoV-2 RNA. Lowering the molecular weight cut-off did not improve our limit of detection and quantification (approximately 100 copies/μL for all genes). Quantitative polymerase chain reaction (qPCR) was employed for the amplification of the N1, N2, N3 and E-gene fragments. This is one of the first studies to apply digital polymerase chain reaction (dPCR) for the detection of SARS-CoV-2 RNA in IWW. dPCR showed high variability at low concentration levels (100 copies/μL), indicating that variability in bioanalytical methods for wastewater-based epidemiology of SARS-CoV-2 might be substantial. dPCR results in IWW were in line with the results found with qPCR. On average, the N2-gene fragment showed high in-sample stability in IWW for 10 days of storage at 4 °C. Between-sample variability was substantial due to the low native concentrations in IWW. Additionally, the E-gene fragment proved to be less stable compared to the N2-gene fragment and showed higher variability. Freezing the IWW samples resulted in a 10-fold decay of loads of the N2- and E-gene fragment in IWW.
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Affiliation(s)
- Tim Boogaerts
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
| | - Lotte Jacobs
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Naomi De Roeck
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Siel Van den Bogaert
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Bert Aertgeerts
- Academic Centre for General Practice, KU Leuven, Kapucijnenvoer 7, 3000 Leuven, Belgium
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | | | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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78
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Sanchez-Galan JE, Ureña G, Escovar LF, Fabrega-Duque JR, Coles A, Kurt Z. Challenges to detect SARS-CoV-2 on environmental media, the need and strategies to implement the detection methodologies in wastewaters. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2021; 9:105881. [PMID: 34221893 PMCID: PMC8239206 DOI: 10.1016/j.jece.2021.105881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/15/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Understanding risks, putting in place preventative methods to seamlessly continue daily activities are essential tools to fight a pandemic. All social, commercial and leisure activities have an impact on the environmental media. Therefore, to accurately predict the fate and behavior of viruses in the environment, it is necessary to understand and analyze available detection methods, possible transmission pathways and preventative techniques. The aim of this review is to critically analyze and summarize the research done regarding SARS-COV-2 virus detection, focusing on sampling and laboratory detection methods in environmental media. Special attention will be given to wastewater and sewage sludge. This review has summarized the survival of the virus on surfaces to estimate the risk carried by different environmental media (water, wastewater, air and soil) in order to explain which communities are under higher risk. The critical analysis concludes that the detection of SARS-CoV-2 with current technologies and sampling strategies would reveal the presence of the virus. This information could be used to design systematic sampling points throughout the sewage systems when available, taking into account peak flows and more importantly economic factors on when to sample. Such approaches will provide clues for potential future viral outbreak, saving financial resources by reducing testing necessities for viral detection, hence contributing for more appropriate confinement policies by governments and could be further used to define more precisely post-pandemic or additional waves measures if/ when needed.
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Affiliation(s)
- Javier E Sanchez-Galan
- Facultad de Ingeniería de Sistemas Computacionales (FISC), Universidad Tecnológica de Panamá, Panama
- Grupo de Investigación en Biotecnología, Bioinformática y Biología de Sistemas (GIBBS), Universidad Tecnológica de Panamá, Panama
- Institute of Scientific Research and High Technology Services, Panama City, Panama
| | - Grimaldo Ureña
- Grupo de Investigación en Biotecnología, Bioinformática y Biología de Sistemas (GIBBS), Universidad Tecnológica de Panamá, Panama
- Theoretical Evolutionary Genetics Laboratory, University of Houston, Houston, TX, USA
| | | | - Jose R Fabrega-Duque
- Centro de Investigaciones Hidráulicas e Hidrotécnicas (CIHH), Universidad Tecnologica de Panama, Panama
| | - Alexander Coles
- Centro de Investigaciones Hidráulicas e Hidrotécnicas (CIHH), Universidad Tecnologica de Panama, Panama
| | - Zohre Kurt
- Grupo de Investigación en Biotecnología, Bioinformática y Biología de Sistemas (GIBBS), Universidad Tecnológica de Panamá, Panama
- Urban Risk Center, Florida State University-Panama, Panama
- Institute of Scientific Research and High Technology Services, Panama City, Panama
- Department of Environmental Engineering, Middle East Technical University, Ankara, Turkey
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79
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Lazuka A, Arnal C, Soyeux E, Sampson M, Lepeuple AS, Deleuze Y, Pouradier Duteil S, Lacroix S. COVID-19 wastewater based epidemiology: long-term monitoring of 10 WWTP in France reveals the importance of the sampling context. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 84:1997-2013. [PMID: 34695026 DOI: 10.2166/wst.2021.418] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
SARS-CoV-2 wastewater-based epidemiology (WBE) has been advanced as a relevant indicator of distribution of COVID-19 in communities, supporting classical testing and tracing epidemiological approaches. An extensive sampling campaign, including ten municipal wastewater treatment plants, has been conducted in different cities of France over a 20-week period, encompassing the second peak of COVID-19 outbreak in France. A well-recognised ultrafiltration - RNA extraction - RT-qPCR protocol was used and qualified, showing 5.5 +/- 0.5% recovery yield on heat-inactivated SARS-CoV-2. Importantly the whole, solid and liquid, fraction of wastewater was used for virus concentration in this study. Campaign results showed medium- to strong- correlation between SARS-CoV-2 WBE data and COVID-19 prevalence. To go further, statistical relationships between WWTP inlet flow rate and rainfall were studied and taken into account for each WWTP in order to calculate contextualized SARS-CoV-2 loads. This metric presented improved correlation strengths with COVID-19 prevalence for WWTP particularly submitted and sensitive to rain. Such findings highlighted that SARS-CoV-2 WBE data ultimately require to be contextualized for relevant interpretation.
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Affiliation(s)
- A Lazuka
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - C Arnal
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - E Soyeux
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - M Sampson
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - A-S Lepeuple
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - Y Deleuze
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
| | - S Pouradier Duteil
- Veolia Eau France, 30 rue Madeleine Vionnet, 93300, Aubervilliers, France
| | - S Lacroix
- Veolia, Scientific & Technical Expertise Departement, Chemin de la Digue, 78600 Maisons-Laffitte, France E-mail:
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80
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Kabdaşlı I, Tünay O. Concentration techniques tailored for the detection of SARS-CoV-2 genetic material in domestic wastewater and treatment plant sludge: A review. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2021; 9:106296. [PMID: 34485054 PMCID: PMC8405238 DOI: 10.1016/j.jece.2021.106296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 05/06/2023]
Abstract
Upon the outbreak of COVID-19 pandemic, detection and quantification of SARS-CoV-2 genetic material in domestic wastewater have led to an increase in the efforts to define and implement the wastewater-based epidemiology (WBE). This application provides valuable information to define local contamination monitoring, emergence of COVID-19 and its variants and many other aspects to cope with and control the pandemic. WBE surveillance, however, requires several consecutive steps such as sampling, pretreatment and concentration of samples, and detection and quantification of SARS-CoV-2 genetic material in wastewater. In this review paper, the literature regarding to all these applications reviewed considering their advantages, disadvantages as well as their applicability. A specific emphasis was placed on the last step, detection and quantification since it covers the most critical procedure for concentrating the virus before measurement. Evaluation of the existing data indicating ultrafiltration, polyethylene glycol (PEG) precipitation and electronegative membrane filtration (ENMF) were the most promising techniques for concentration. The ongoing studies are proposed to be continued within the context of standard methods. Future research needs are delineated and suggestions are made for details.
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Affiliation(s)
- Işık Kabdaşlı
- İstanbul Technical University, Civil Engineering Faculty, Environmental Engineering Department, Ayazağa Campus, Sarıyer, İstanbul 34469, Republic of Turkey
| | - Olcay Tünay
- İstanbul Technical University, Civil Engineering Faculty, Environmental Engineering Department, Ayazağa Campus, Sarıyer, İstanbul 34469, Republic of Turkey
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81
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Rouchka EC, Chariker JH, Saurabh K, Waigel S, Zacharias W, Zhang M, Talley D, Santisteban I, Puccio M, Moyer S, Holm RH, Yeager RA, Sokoloski KJ, Fuqua J, Bhatnagar A, Smith T. The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale. Pathogens 2021; 10:1271. [PMID: 34684220 PMCID: PMC8541652 DOI: 10.3390/pathogens10101271] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/03/2021] [Accepted: 09/28/2021] [Indexed: 01/08/2023] Open
Abstract
Throughout the course of the ongoing SARS-CoV-2 pandemic there has been a need for approaches that enable rapid monitoring of public health using an unbiased and minimally invasive means. A major way this has been accomplished is through the regular assessment of wastewater samples by qRT-PCR to detect the prevalence of viral nucleic acid with respect to time and location. Further expansion of SARS-CoV-2 wastewater monitoring efforts to include the detection of variants of interest/concern through next-generation sequencing has enhanced the understanding of the SARS-CoV-2 outbreak. In this report, we detail the results of a collaborative effort between public health and metropolitan wastewater management authorities and the University of Louisville to monitor the SARS-CoV-2 pandemic through the monitoring of aggregate wastewater samples over a period of 28 weeks. Through the use of next-generation sequencing approaches the polymorphism signatures of Variants of Concern/Interest were evaluated to determine the likelihood of their prevalence within the community on the basis of their relative dominance within sequence datasets. Our data indicate that wastewater monitoring of water quality treatment centers and smaller neighborhood-scale catchment areas is a viable means by which the prevalence and genetic variation of SARS-CoV-2 within a metropolitan community of approximately one million individuals may be monitored, as our efforts detected the introduction and emergence of variants of concern in the city of Louisville. Importantly, these efforts confirm that regional emergence and spread of variants of interest/concern may be detected as readily in aggregate wastewater samples as compared to the individual wastewater sheds. Furthermore, the information gained from these efforts enabled targeted public health efforts including increased outreach to at-risk communities and the deployment of mobile or community-focused vaccination campaigns.
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Affiliation(s)
- Eric C. Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville, 323 E. Chestnut St., Louisville, KY 40202, USA;
- KY INBRE Bioinformatics Core, University of Louisville, 522 E. Gray St., Louisville, KY 40202, USA;
| | - Julia H. Chariker
- KY INBRE Bioinformatics Core, University of Louisville, 522 E. Gray St., Louisville, KY 40202, USA;
| | - Kumar Saurabh
- Brown Cancer Center, University of Louisville, 530 S. Jackson St., Louisville, KY 40202, USA;
| | - Sabine Waigel
- Department of Medicine, University of Louisville, 530 S. Jackson St., Louisville, KY 40402, USA; (S.W.); (W.Z.)
| | - Wolfgang Zacharias
- Department of Medicine, University of Louisville, 530 S. Jackson St., Louisville, KY 40402, USA; (S.W.); (W.Z.)
| | - Mei Zhang
- Department of Neuroscience, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA;
| | - Daymond Talley
- Louisville/Jefferson County Metropolitan Sewer District, Morris Forman Water Quality Treatment Center, 4522 Algonquin Parkway, Louisville, KY 40211, USA;
| | - Ian Santisteban
- Department of Pharmacology and Toxicology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA;
- Center for Predictive Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Madeline Puccio
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA; (M.P.); (R.H.H.); (R.A.Y.); (A.B.); (T.S.)
| | - Sarah Moyer
- Department of Health Management and System Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray St., Louisville, KY 40202, USA;
- Department of Public Health and Wellness, Louisville Metro Government, 400 E. Gray St., Louisville, KY 40202, USA
| | - Rochelle H. Holm
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA; (M.P.); (R.H.H.); (R.A.Y.); (A.B.); (T.S.)
| | - Ray A. Yeager
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA; (M.P.); (R.H.H.); (R.A.Y.); (A.B.); (T.S.)
- Department of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray St., Louisville, KY 40202, USA
| | - Kevin J. Sokoloski
- Center for Predictive Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
- Department of Microbiology and Immunology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Joshua Fuqua
- Department of Pharmacology and Toxicology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA;
- Center for Predictive Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Aruni Bhatnagar
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA; (M.P.); (R.H.H.); (R.A.Y.); (A.B.); (T.S.)
| | - Ted Smith
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA; (M.P.); (R.H.H.); (R.A.Y.); (A.B.); (T.S.)
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82
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Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, Lee WL, McElroy KA, Rhode SF, Matus M, Wuertz S, Thompson J, Alm EJ. Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020. WATER RESEARCH 2021; 202:117400. [PMID: 34274898 PMCID: PMC8249441 DOI: 10.1016/j.watres.2021.117400] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/11/2021] [Accepted: 06/28/2021] [Indexed: 05/18/2023]
Abstract
Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. Here we describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states, covering 13% of the U.S. population from February 18 to June 2, 2020. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with overall viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases. Wastewater surveillance had a high detection rate (>80%) of SARS-CoV-2 when the daily incidence exceeded 13 per 100,000 people. Detection rates were positively associated with wastewater treatment plant catchment size. To our knowledge, this work represents the largest-scale wastewater-based SARS-CoV-2 monitoring campaign to date, encompassing a wide diversity of wastewater treatment facilities and geographic locations. Our findings demonstrate that a national wastewater-based approach to disease surveillance may be feasible and effective.
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Affiliation(s)
- Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jianbo Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Katya Moniz
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Federica Armas
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Mary Bushman
- Harvard T.H. Chan School of Public Health, Harvard University, USA
| | - Peter R Chai
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, USA; The Fenway Institute, Fenway Health, Boston, MA, USA
| | | | - Timothy B Erickson
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, USA; The Koch Institute for Integrated Cancer Research, Massachusetts Institute of Technology, USA; Harvard Humanitarian Initiative, Harvard University
| | | | | | - Xiaoqiong Gu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - William P Hanage
- Harvard T.H. Chan School of Public Health, Harvard University, USA
| | | | - Wei Lin Lee
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | | | - Steven F Rhode
- Massachusetts Water Resources Authority, Boston, MA, USA
| | | | - Stefan Wuertz
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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83
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Chik AHS, Glier MB, Servos M, Mangat CS, Pang XL, Qiu Y, D'Aoust PM, Burnet JB, Delatolla R, Dorner S, Geng Q, Giesy JP, McKay RM, Mulvey MR, Prystajecky N, Srikanthan N, Xie Y, Conant B, Hrudey SE. Comparison of approaches to quantify SARS-CoV-2 in wastewater using RT-qPCR: Results and implications from a collaborative inter-laboratory study in Canada. J Environ Sci (China) 2021; 107:218-229. [PMID: 34412784 PMCID: PMC7929783 DOI: 10.1016/j.jes.2021.01.029] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 05/20/2023]
Abstract
Detection of SARS-CoV-2 RNA in wastewater is a promising tool for informing public health decisions during the COVID-19 pandemic. However, approaches for its analysis by use of reverse transcription quantitative polymerase chain reaction (RT-qPCR) are still far from standardized globally. To characterize inter- and intra-laboratory variability among results when using various methods deployed across Canada, aliquots from a real wastewater sample were spiked with surrogates of SARS-CoV-2 (gamma-radiation inactivated SARS-CoV-2 and human coronavirus strain 229E [HCoV-229E]) at low and high levels then provided "blind" to eight laboratories. Concentration estimates reported by individual laboratories were consistently within a 1.0-log10 range for aliquots of the same spiked condition. All laboratories distinguished between low- and high-spikes for both surrogates. As expected, greater variability was observed in the results amongst laboratories than within individual laboratories, but SARS-CoV-2 RNA concentration estimates for each spiked condition remained mostly within 1.0-log10 ranges. The no-spike wastewater aliquots provided yielded non-detects or trace levels (<20 gene copies/mL) of SARS-CoV-2 RNA. Detections appear linked to methods that included or focused on the solids fraction of the wastewater matrix and might represent in-situ SARS-CoV-2 to the wastewater sample. HCoV-229E RNA was not detected in the no-spike aliquots. Overall, all methods yielded comparable results at the conditions tested. Partitioning behavior of SARS-CoV-2 and spiked surrogates in wastewater should be considered to evaluate method effectiveness. A consistent method and laboratory to explore wastewater SARS-CoV-2 temporal trends for a given system, with appropriate quality control protocols and documented in adequate detail should succeed.
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Affiliation(s)
- Alex H S Chik
- Consultant to Canadian Water Network Inc., Kitchener, Canada; Presently at Ontario Clean Water Agency, Mississauga, Canada
| | - Melissa B Glier
- Environmental Microbiology, BC Centre for Disease Control, Vancouver, Canada
| | - Mark Servos
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Chand S Mangat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Xiao-Li Pang
- Public Health Laboratory, Alberta Precision Laboratory, Edmonton, Canada; Department of Laboratory Medicine & Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2G3, Canada
| | - Yuanyuan Qiu
- Department of Laboratory Medicine & Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2G3, Canada
| | | | - Jean-Baptiste Burnet
- Département des génies civil, géologique et des mines, Polytechnique Montréal, Montréal, Canada
| | | | - Sarah Dorner
- Département des génies civil, géologique et des mines, Polytechnique Montréal, Montréal, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Canada
| | - John P Giesy
- Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, Canada
| | - Robert Mike McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Natalie Prystajecky
- Environmental Microbiology, BC Centre for Disease Control, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | | | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, Canada
| | | | - Steve E Hrudey
- Department of Laboratory Medicine & Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2G3, Canada.
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84
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Gibas C, Lambirth K, Mittal N, Juel MAI, Barua VB, Roppolo Brazell L, Hinton K, Lontai J, Stark N, Young I, Quach C, Russ M, Kauer J, Nicolosi B, Chen D, Akella S, Tang W, Schlueter J, Munir M. Implementing building-level SARS-CoV-2 wastewater surveillance on a university campus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 782:146749. [PMID: 33838367 DOI: 10.1101/2020.12.31.20248843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/20/2021] [Accepted: 03/21/2021] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic has been a source of ongoing challenges and presents an increased risk of illness in group environments, including jails, long-term care facilities, schools, and residential college campuses. Early reports that the SARS-CoV-2 virus was detectable in wastewater in advance of confirmed cases sparked widespread interest in wastewater-based epidemiology (WBE) as a tool for mitigation of COVID-19 outbreaks. One hypothesis was that wastewater surveillance might provide a cost-effective alternative to other more expensive approaches such as pooled and random testing of groups. In this paper, we report the outcomes of a wastewater surveillance pilot program at the University of North Carolina at Charlotte, a large urban university with a substantial population of students living in on-campus dormitories. Surveillance was conducted at the building level on a thrice-weekly schedule throughout the university's fall residential semester. In multiple cases, wastewater surveillance enabled the identification of asymptomatic COVID-19 cases that were not detected by other components of the campus monitoring program, which also included in-house contact tracing, symptomatic testing, scheduled testing of student athletes, and daily symptom reporting. In the context of all cluster events reported to the University community during the fall semester, wastewater-based testing events resulted in the identification of smaller clusters than were reported in other types of cluster events. Wastewater surveillance was able to detect single asymptomatic individuals in dorms with resident populations of 150-200. While the strategy described was developed for COVID-19, it is likely to be applicable to mitigation of future pandemics in universities and other group-living environments.
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Affiliation(s)
- Cynthia Gibas
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America; Bioinformatics Research Center, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America.
| | - Kevin Lambirth
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America.
| | - Neha Mittal
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Md Ariful Islam Juel
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Visva Bharati Barua
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Lauren Roppolo Brazell
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Keshawn Hinton
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Jordan Lontai
- Department of Geography and Earth Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Nicholas Stark
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Isaiah Young
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Cristine Quach
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Morgan Russ
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Jacob Kauer
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Bridgette Nicolosi
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Don Chen
- Department of Engineering Technology and Construction Management, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Srinivas Akella
- Department of Computer Science, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Wenwu Tang
- Department of Geography and Earth Sciences, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America; Center for Applied Geographic Information Systems, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Jessica Schlueter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America; Bioinformatics Research Center, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
| | - Mariya Munir
- Department of Civil and Environmental Engineering, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States of America
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85
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Mousazadeh M, Ashoori R, Paital B, Kabdaşlı I, Frontistis Z, Hashemi M, Sandoval MA, Sherchan S, Das K, Emamjomeh MM. Wastewater Based Epidemiology Perspective as a Faster Protocol for Detecting Coronavirus RNA in Human Populations: A Review with Specific Reference to SARS-CoV-2 Virus. Pathogens 2021; 10:1008. [PMID: 34451472 PMCID: PMC8401392 DOI: 10.3390/pathogens10081008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/21/2022] Open
Abstract
Wastewater-based epidemiology (WBE) has a long history of identifying a variety of viruses from poliovirus to coronaviruses, including novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The presence and detection of SARS-CoV-2 in human feces and its passage into the water bodies are significant public health challenges. Hence, the hot issue of WBE of SARS-CoV-2 in the coronavirus respiratory disease (COVID-19) pandemic is a matter of utmost importance (e.g., SARS-CoV-1). The present review discusses the background, state of the art, actual status, and prospects of WBE, as well as the detection and quantification protocols of SARS-CoV-2 in wastewater. The SARS-CoV-2 detection studies have been performed in different water matrixes such as influent and effluent of wastewater treatment plants, suburban pumping stations, hospital wastewater, and sewer networks around the globe except for Antarctica. The findings revealed that all WBE studies were in accordance with clinical and epidemiological data, which correlates the presence of SARS-CoV-2 ribonucleic acid (RNA) with the number of new daily positive cases officially reported. This last was confirmed via Reverse Transcriptase-quantitative Polymerase Chain Reaction (RT-qPCR) testing which unfortunately is not suitable for real-time surveillance. In addition, WBE concept may act as a faster protocol to alert the public health authorities to take administrative orders (possible re-emerging infections) due to the impracticality of testing all citizens in a short time with limited diagnostic facilities. A comprehensive and integrated review covering all steps starting from sampling to molecular detection of SARS-CoV-2 in wastewater has been made to guide for the development well-defined and reliable protocols.
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Affiliation(s)
- Milad Mousazadeh
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran;
- Department of Environmental Health Engineering, School of Health, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Razieh Ashoori
- Department of Environmental Health Engineering, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran;
| | - Biswaranjan Paital
- Redox Regulation Laboratory, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar 751003, India;
| | - Işık Kabdaşlı
- Environmental Engineering Department, Civil Engineering Faculty, Ayazağa Campus, İstanbul Technical University, İstanbul 34469, Turkey;
| | - Zacharias Frontistis
- Department of Chemical Engineering, University of Western Macedonia, 50132 Kozani, Greece;
| | - Marjan Hashemi
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran;
| | - Miguel A. Sandoval
- Laboratorio de Electroquímica Medio Ambiental LEQMA, Departamento de Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile USACH, Casilla 40, Correo 33, Santiago 9170022, Chile;
- Departamento de Ingeniería Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Samendra Sherchan
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 7011, USA;
| | - Kabita Das
- Department of Philosophy, Utkal University, Bhubaneswar 751004, India;
| | - Mohammad Mahdi Emamjomeh
- Social Determinants of Health Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
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86
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Amereh F, Negahban-Azar M, Isazadeh S, Dabiri H, Masihi N, Jahangiri-Rad M, Rafiee M. Sewage Systems Surveillance for SARS-CoV-2: Identification of Knowledge Gaps, Emerging Threats, and Future Research Needs. Pathogens 2021. [PMID: 34451410 DOI: 10.3390/pathogens10080946.pmid:34451410;pmcid:pmc8402176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
The etiological agent for novel coronavirus (COVID-19, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), not only affects the human respiratory system, but also the gastrointestinal tract resulting in gastrointestinal manifestations. The high rate of asymptomatic infected individuals has challenged the estimation of infection spread based on patients' surveillance, and thus alternative approaches such as wastewater-based epidemiology (WBE) have been proposed. Accordingly, the number of publications on this topic has increased substantially. The present systematic review thus aimed at providing state-of-the-knowledge on the occurrence and existing methods for sampling procedures, detection/quantification of SARS-CoV-2 in sewage samples, as well as anticipating challenges and providing future research direction to improve the current scientific knowledge. Articles were collected from three scientific databases. Only studies reporting measurements of virus in stool, urine, and wastewater samples were included. Results showed that improving the scientific community's understanding in these avenues is essential if we are to develop appropriate policy and management tools to address this pandemic pointing particularly towards WBE as a new paradigm in public health. It was also evident that standardized protocols are needed to ensure reproducibility and comparability of outcomes. Areas that require the most improvements are sampling procedures, concentration/enrichment, detection, and quantification of virus in wastewater, as well as positive controls. Results also showed that selecting the most accurate population estimation method for WBE studies is still a challenge. While the number of people infected in an area could be approximately estimated based on quantities of virus found in wastewater, these estimates should be cross-checked by other sources of information to draw a more comprehensive conclusion. Finally, wastewater surveillance can be useful as an early warning tool, a management tool, and/or a way for investigating vaccination efficacy and spread of new variants.
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Affiliation(s)
- Fatemeh Amereh
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran
- Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran
| | - Masoud Negahban-Azar
- Department of Environmental Science and Technology, University of Maryland, College Park, MD 20740, USA
| | - Siavash Isazadeh
- Environmental Service, Suez Water North America, Paramus, NJ 07652, USA
| | - Hossein Dabiri
- Department of Medical Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran
| | - Najmeh Masihi
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran
| | - Mahsa Jahangiri-Rad
- Water Purification Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran 19168, Iran
| | - Mohammad Rafiee
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran
- Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran
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87
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Amereh F, Negahban-Azar M, Isazadeh S, Dabiri H, Masihi N, Jahangiri-rad M, Rafiee M. Sewage Systems Surveillance for SARS-CoV-2: Identification of Knowledge Gaps, Emerging Threats, and Future Research Needs. Pathogens 2021; 10:946. [PMID: 34451410 PMCID: PMC8402176 DOI: 10.3390/pathogens10080946] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/04/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023] Open
Abstract
The etiological agent for novel coronavirus (COVID-19, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), not only affects the human respiratory system, but also the gastrointestinal tract resulting in gastrointestinal manifestations. The high rate of asymptomatic infected individuals has challenged the estimation of infection spread based on patients' surveillance, and thus alternative approaches such as wastewater-based epidemiology (WBE) have been proposed. Accordingly, the number of publications on this topic has increased substantially. The present systematic review thus aimed at providing state-of-the-knowledge on the occurrence and existing methods for sampling procedures, detection/quantification of SARS-CoV-2 in sewage samples, as well as anticipating challenges and providing future research direction to improve the current scientific knowledge. Articles were collected from three scientific databases. Only studies reporting measurements of virus in stool, urine, and wastewater samples were included. Results showed that improving the scientific community's understanding in these avenues is essential if we are to develop appropriate policy and management tools to address this pandemic pointing particularly towards WBE as a new paradigm in public health. It was also evident that standardized protocols are needed to ensure reproducibility and comparability of outcomes. Areas that require the most improvements are sampling procedures, concentration/enrichment, detection, and quantification of virus in wastewater, as well as positive controls. Results also showed that selecting the most accurate population estimation method for WBE studies is still a challenge. While the number of people infected in an area could be approximately estimated based on quantities of virus found in wastewater, these estimates should be cross-checked by other sources of information to draw a more comprehensive conclusion. Finally, wastewater surveillance can be useful as an early warning tool, a management tool, and/or a way for investigating vaccination efficacy and spread of new variants.
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Affiliation(s)
- Fatemeh Amereh
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran; (F.A.); (N.M.)
- Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran
| | - Masoud Negahban-Azar
- Department of Environmental Science and Technology, University of Maryland, College Park, MD 20740, USA
| | - Siavash Isazadeh
- Environmental Service, Suez Water North America, Paramus, NJ 07652, USA;
| | - Hossein Dabiri
- Department of Medical Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran;
| | - Najmeh Masihi
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran; (F.A.); (N.M.)
| | - Mahsa Jahangiri-rad
- Water Purification Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran 19168, Iran;
| | - Mohammad Rafiee
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran; (F.A.); (N.M.)
- Department of Environmental Health Engineering, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran 35511, Iran
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88
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Li X, Zhang S, Shi J, Luby SP, Jiang G. Uncertainties in estimating SARS-CoV-2 prevalence by wastewater-based epidemiology. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 415:129039. [PMID: 33642938 PMCID: PMC7896122 DOI: 10.1016/j.cej.2021.129039] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/03/2021] [Accepted: 02/15/2021] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) is a promising approach for estimating population-wide COVID-19 prevalence through detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. However, various methodological challenges associated with WBE would affect the accuracy of prevalence estimation. To date, the overall uncertainty of WBE and the impact of each step on the prevalence estimation are largely unknown. This study divided the WBE approach into five steps (i.e., virus shedding; in-sewer transportation; sampling and storage; analysis of SARS-CoV-2 RNA concentration in wastewater; back-estimation) and further summarized and quantified the uncertainties associated with each step through a systematic review. Although the shedding of SARS-CoV-2 RNA varied greatly between COVID-19 positive patients, with more than 10 infected persons in the catchment area, the uncertainty caused by the excretion rate became limited for the prevalence estimation. Using a high-frequency flow-proportional sampling and estimating the prevalence through actual water usage data significantly reduced the overall uncertainties to around 20-40% (relative standard deviation, RSD). And under such a scenario, the analytical uncertainty of SARS-CoV-2 RNA in wastewater was the dominant factor. This highlights the importance of using surrogate viruses as internal or external standards during the wastewater analysis, and the need for further improvement on analytical approaches to minimize the analytical uncertainty. This study supports the application of WBE as a complementary surveillance strategy for monitoring COVID-19 prevalence and provides methodological improvements and suggestions to enhance the reliability for future studies.
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Affiliation(s)
- Xuan Li
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Shuxin Zhang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Jiahua Shi
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
| | - Stephen P Luby
- Woods Institute for the Environment, Stanford University, United States
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
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89
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McMinn BR, Korajkic A, Kelleher J, Herrmann MP, Pemberton AC, Ahmed W, Villegas EN, Oshima K. Development of a large volume concentration method for recovery of coronavirus from wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 774:145727. [PMID: 33607441 PMCID: PMC7870434 DOI: 10.1016/j.scitotenv.2021.145727] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/26/2021] [Accepted: 02/04/2021] [Indexed: 04/15/2023]
Abstract
Levels of severe acute respiratory coronavirus type 2 (SARS CoV 2) RNA in wastewater could act as an effective means to monitor coronavirus disease 2019 (COVID-19) within communities. However, current methods used to detect SARS CoV 2 RNA in wastewater are limited in their ability to process sufficient volumes of source material, inhibiting our ability to assess viral load. Typically, viruses are concentrated from large liquid volumes using two stage concentration, primary and secondary. Here, we evaluated a dead-end hollow fiber ultrafilter (D-HFUF) for primary concentration, followed by the CP Select™ for secondary concentration from 2 L volumes of primary treated wastewater. Various amendments to each concentration procedure were investigated to optimally recover seeded OC43 (betacoronavirus) from wastewater. During primary concentration, the D-HFUF recovered 69 ± 18% (n = 29) of spiked OC43 from 2 L of wastewater. For secondary concentration, the CP Select™ system using the Wastewater Application settings was capable of processing 100 mL volumes of primary filter eluates in <25 min. A hand-driven syringe elution proved to be significantly superior (p = 0.0299) to the CP Select™ elution for recovering OC43 from filter eluates, 48 ± 2% compared to 31 ± 3%, respectively. For the complete method (primary and secondary concentration combined), the D-HFUF and CP select/syringe elution achieved overall 22 ± 4% recovery of spiked OC43 through (n = 8) replicate filters. Given the lack of available standardized methodology confounded by the inherent limitations of relying on viral RNA for wastewater surveillance of SARS CoV 2, it is important to acknowledge these challenges when interpreting this data to estimate community infection rates. However, the development of methods that can substantially increase sample volumes will likely allow for reporting of quantifiable viral data for wastewater surveillance, equipping public health officials with information necessary to better estimate community infection rates.
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Affiliation(s)
- Brian R McMinn
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States.
| | - Asja Korajkic
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Julie Kelleher
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Michael P Herrmann
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Adin C Pemberton
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Qld 4102, Australia
| | - Eric N Villegas
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
| | - Kevin Oshima
- Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268, United States
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90
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Boogaerts T, Jacobs L, De Roeck N, Van den Bogaert S, Aertgeerts B, Lahousse L, van Nuijs ALN, Delputte P. An alternative approach for bioanalytical assay optimization for wastewater-based epidemiology of SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:148043. [PMID: 34323818 DOI: 10.1101/2021.02.12.21251626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 05/18/2023]
Abstract
Wastewater-based epidemiology of SARS-CoV-2 could play a role in monitoring the spread of the virus in the population and controlling possible outbreaks. However, sensitive sample preparation and detection methods are necessary to detect trace levels of SARS-CoV-2 RNA in influent wastewater (IWW). Unlike predecessors, method optimization of a SARS-CoV-2 RNA concentration and detection procedure was performed with IWW samples with high viral SARS-CoV-2 RNA loads. This is of importance since the SARS-CoV-2 genome in IWW might have already been subject to in-sewer degradation into smaller genome fragments or might be present in a different form (e.g. cell debris, …). Centricon Plus-70 (100 kDa) centrifugal filter devices resulted in the lowest and most reproducible Ct-values for SARS-CoV-2 RNA. Lowering the molecular weight cut-off did not improve our limit of detection and quantification (approximately 100 copies/μL for all genes). Quantitative polymerase chain reaction (qPCR) was employed for the amplification of the N1, N2, N3 and E-gene fragments. This is one of the first studies to apply digital polymerase chain reaction (dPCR) for the detection of SARS-CoV-2 RNA in IWW. dPCR showed high variability at low concentration levels (100 copies/μL), indicating that variability in bioanalytical methods for wastewater-based epidemiology of SARS-CoV-2 might be substantial. dPCR results in IWW were in line with the results found with qPCR. On average, the N2-gene fragment showed high in-sample stability in IWW for 10 days of storage at 4 °C. Between-sample variability was substantial due to the low native concentrations in IWW. Additionally, the E-gene fragment proved to be less stable compared to the N2-gene fragment and showed higher variability. Freezing the IWW samples resulted in a 10-fold decay of loads of the N2- and E-gene fragment in IWW.
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Affiliation(s)
- Tim Boogaerts
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
| | - Lotte Jacobs
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Naomi De Roeck
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Siel Van den Bogaert
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Bert Aertgeerts
- Academic Centre for General Practice, KU Leuven, Kapucijnenvoer 7, 3000 Leuven, Belgium
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | | | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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91
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D'Aoust PM, Graber TE, Mercier E, Montpetit D, Alexandrov I, Neault N, Baig AT, Mayne J, Zhang X, Alain T, Servos MR, Srikanthan N, MacKenzie M, Figeys D, Manuel D, Jüni P, MacKenzie AE, Delatolla R. Catching a resurgence: Increase in SARS-CoV-2 viral RNA identified in wastewater 48 h before COVID-19 clinical tests and 96 h before hospitalizations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021. [PMID: 33508669 DOI: 10.1016/j.scitotenv.2021.145319l] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Curtailing the Spring 2020 COVID-19 surge required sweeping and stringent interventions by governments across the world. Wastewater-based COVID-19 epidemiology programs have been initiated in many countries to provide public health agencies with a complementary disease tracking metric and non-discriminating surveillance tool. However, their efficacy in prospectively capturing resurgences following a period of low prevalence is unclear. In this study, the SARS-CoV-2 viral signal was measured in primary clarified sludge harvested every two days at the City of Ottawa's water resource recovery facility during the summer of 2020, when clinical testing recorded daily percent positivity below 1%. In late July, increases of >400% in normalized SARS-CoV-2 RNA signal in wastewater were identified 48 h prior to reported >300% increases in positive cases that were retrospectively attributed to community-acquired infections. During this resurgence period, SARS-CoV-2 RNA signal in wastewater preceded the reported >160% increase in community hospitalizations by approximately 96 h. This study supports wastewater-based COVID-19 surveillance of populations in augmenting the efficacy of diagnostic testing, which can suffer from sampling biases or timely reporting as in the case of hospitalization census.
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Affiliation(s)
- Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Elisabeth Mercier
- Department of Chemical Engineering, University of Ottawa, K1N 6N5, Canada
| | - Danika Montpetit
- Department of Chemical Engineering, University of Ottawa, K1N 6N5, Canada
| | - Ilya Alexandrov
- ActivSignal LLC., 27 Strathmore Rd., Natick, MA 01760, United States
| | - Nafisa Neault
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Aiman Tariq Baig
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Janice Mayne
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Xu Zhang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo N2L 3G1, Canada
| | | | - Malcolm MacKenzie
- ActivSignal LLC., 27 Strathmore Rd., Natick, MA 01760, United States
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada; Canadian Institute for Advanced Research, Toronto M5G 1M1, Canada
| | - Douglas Manuel
- Department of Family Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Peter Jüni
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto M5T 3M6, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada.
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92
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D'Aoust PM, Graber TE, Mercier E, Montpetit D, Alexandrov I, Neault N, Baig AT, Mayne J, Zhang X, Alain T, Servos MR, Srikanthan N, MacKenzie M, Figeys D, Manuel D, Jüni P, MacKenzie AE, Delatolla R. Catching a resurgence: Increase in SARS-CoV-2 viral RNA identified in wastewater 48 h before COVID-19 clinical tests and 96 h before hospitalizations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:145319. [PMID: 33508669 PMCID: PMC7826013 DOI: 10.1016/j.scitotenv.2021.145319] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 04/14/2023]
Abstract
Curtailing the Spring 2020 COVID-19 surge required sweeping and stringent interventions by governments across the world. Wastewater-based COVID-19 epidemiology programs have been initiated in many countries to provide public health agencies with a complementary disease tracking metric and non-discriminating surveillance tool. However, their efficacy in prospectively capturing resurgences following a period of low prevalence is unclear. In this study, the SARS-CoV-2 viral signal was measured in primary clarified sludge harvested every two days at the City of Ottawa's water resource recovery facility during the summer of 2020, when clinical testing recorded daily percent positivity below 1%. In late July, increases of >400% in normalized SARS-CoV-2 RNA signal in wastewater were identified 48 h prior to reported >300% increases in positive cases that were retrospectively attributed to community-acquired infections. During this resurgence period, SARS-CoV-2 RNA signal in wastewater preceded the reported >160% increase in community hospitalizations by approximately 96 h. This study supports wastewater-based COVID-19 surveillance of populations in augmenting the efficacy of diagnostic testing, which can suffer from sampling biases or timely reporting as in the case of hospitalization census.
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Affiliation(s)
- Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Elisabeth Mercier
- Department of Chemical Engineering, University of Ottawa, K1N 6N5, Canada
| | - Danika Montpetit
- Department of Chemical Engineering, University of Ottawa, K1N 6N5, Canada
| | - Ilya Alexandrov
- ActivSignal LLC., 27 Strathmore Rd., Natick, MA 01760, United States
| | - Nafisa Neault
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Aiman Tariq Baig
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Janice Mayne
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Xu Zhang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo N2L 3G1, Canada
| | | | - Malcolm MacKenzie
- ActivSignal LLC., 27 Strathmore Rd., Natick, MA 01760, United States
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada; Canadian Institute for Advanced Research, Toronto M5G 1M1, Canada
| | - Douglas Manuel
- Department of Family Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Peter Jüni
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto M5T 3M6, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada.
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93
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Wilder ML, Middleton F, Larsen DA, Du Q, Fenty A, Zeng T, Insaf T, Kilaru P, Collins M, Kmush B, Green HC. Co-quantification of crAssphage increases confidence in wastewater-based epidemiology for SARS-CoV-2 in low prevalence areas. WATER RESEARCH X 2021; 11:100100. [PMID: 33842875 PMCID: PMC8021452 DOI: 10.1016/j.wroa.2021.100100] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/16/2021] [Accepted: 04/01/2021] [Indexed: 05/17/2023]
Abstract
Wastewater surveillance of SARS-CoV-2 RNA is increasingly being incorporated into public health efforts to respond to the COVID-19 pandemic. In order to obtain the maximum benefit from these efforts, approaches to wastewater monitoring need to be rapid, sensitive, and relatable to relevant epidemiological parameters. In this study, we present an ultracentrifugation-based method for the concentration of SARS-CoV-2 wastewater RNA and use crAssphage, a bacteriophage specific to the human gut, to help account for RNA loss during transit in the wastewater system and sample processing. With these methods, we were able to detect, and sometimes quantify, SARS-CoV-2 RNA from 20 mL wastewater samples within as little as 4.5 hours. Using known concentrations of bovine coronavirus RNA and deactivated SARS-CoV-2, we estimate recovery rates of approximately 7-12% of viral RNA using our method. Results from 24 sewersheds across Upstate New York during the spring and summer of 2020 suggested that stronger signals of SARS-CoV-2 RNA from wastewater may be indicative of greater COVID-19 incidence in the represented service area approximately one week in advance. SARS-CoV-2 wastewater RNA was quantifiable in some service areas with daily positives tests of less than 1 per 10,000 people or when weekly positive test rates within a sewershed were as low as 1.7%. crAssphage DNA concentrations were significantly lower during periods of high flow in almost all areas studied. After accounting for flow rate and population served, crAssphage levels per capita were estimated to be about 1.35 × 1011 and 2.42 × 108 genome copies per day for DNA and RNA, respectively. A negative relationship between per capita crAssphage RNA and service area size was also observed likely reflecting degradation of RNA over long transit times. Our results reinforce the potential for wastewater surveillance to be used as a tool to supplement understanding of infectious disease transmission obtained by traditional testing and highlight the potential for crAssphage co-detection to improve interpretations of wastewater surveillance data.
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Affiliation(s)
- Maxwell L. Wilder
- Department of Environmental and Forest Biology, SUNY-ESF, Syracuse, NY 13210
| | - Frank Middleton
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY 13210
| | - David A. Larsen
- Department of Public Health, Syracuse University, Syracuse, NY 13244
| | - Qian Du
- Quadrant Biosciences, Syracuse, NY 13210
| | - Ariana Fenty
- Department of Environmental and Forest Biology, SUNY-ESF, Syracuse, NY 13210
| | - Teng Zeng
- Department of Civil & Environmental Engineering, Syracuse University, Syracuse, NY 13244
| | - Tabassum Insaf
- Bureau of Environmental and Occupational Epidemiology, New York State Department of Health, Albany, NY 12337
- Department of Epidemiology and Biostatistics, University at Albany, Rensselaer, NY 12144
| | - Pruthvi Kilaru
- Department of Public Health, Syracuse University, Syracuse, NY 13244
| | - Mary Collins
- Department of Environmental Studies, SUNY-ESF, Syracuse, NY 13210
| | - Brittany Kmush
- Department of Public Health, Syracuse University, Syracuse, NY 13244
| | - Hyatt C. Green
- Department of Environmental and Forest Biology, SUNY-ESF, Syracuse, NY 13210
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94
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Bhattacharya P, Kumar M, Islam MT, Haque R, Chakraborty S, Ahmad A, Niazi NK, Cetecioglu Z, Nilsson D, Ijumulana J, van der Voorn T, Jakariya M, Hossain M, Ahmed F, Rahman M, Akter N, Johnston D, Ahmed KM. Prevalence of SARS-CoV-2 in Communities Through Wastewater Surveillance-a Potential Approach for Estimation of Disease Burden. CURRENT POLLUTION REPORTS 2021; 7:160-166. [PMID: 33842197 PMCID: PMC8021931 DOI: 10.1007/s40726-021-00178-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/18/2021] [Indexed: 05/17/2023]
Abstract
The episodic outbreak of COVID-19 due to SARS-CoV-2 is severely affecting the economy, and the global count of infected patients is increasing. The actual number of patients had been underestimated due to limited facilities for testing as well as asymptomatic nature of the expression of COVID-19 on individual basis. Tragically, for emerging economies with high population density, the situation has been more complex due to insufficient testing facilities for diagnosis of the disease. However, the recent reports about persistent shedding of viral RNA of SARS-CoV-2 in the human feces have created a possibility to track the prevalence and trends of the disease in communities, known as wastewater-based epidemiology (WBE). In this article, we highlight the current limitations and future prospects for WBE to manage pandemics.
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Affiliation(s)
- Prosun Bhattacharya
- Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-11428 Stockholm, Sweden
- KWR Watercycle Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, The Netherlands
| | - Manish Kumar
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Ahmedabad, Gujarat 382 355 India
| | - Md. Tahmidul Islam
- Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-11428 Stockholm, Sweden
- WaterAid Bangladesh, House 97/B, Road 25, Block A, Banani, Dhaka, 1213 Bangladesh
| | - Rehnuma Haque
- Environmental Interventions Unit, Infectious Disease Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212 Bangladesh
| | - Sudip Chakraborty
- Department of DIMES, University of Calabria, Via P. Bucci, Cubo 42/a, 87036 Rende, Italy
| | - Arslan Ahmad
- Department of Environmental Technology, Wageningen University and Research (WUR), Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands
| | - Nabeel Khan Niazi
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, 38040 Pakistan
- School of Civil Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 Australia
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, Teknikringen 42, Stockholm, SE-10044 Sweden
| | - David Nilsson
- WaterCenter@KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-11428 Stockholm, Sweden
| | - Julian Ijumulana
- Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-11428 Stockholm, Sweden
| | - Tom van der Voorn
- University of Osnabrück, Institute of Environmental Systems Research, Barbarastr. 12, 49069 Osnabrück, Germany
| | - Md. Jakariya
- Department of Environmental Science and Management, North South University, Bashundhara, Dhaka, 1229 Bangladesh
| | - Maqsud Hossain
- Department of Biochemistry and Microbiology, NSU Genome Research Institute (NGRI), North South University, Bashundhara, Dhaka, 1229 Bangladesh
| | - Firoz Ahmed
- Department of Microbiology, Noakhali University of Science and Technology, Noakhali, Bangladesh
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Disease Division, icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka, 1212 Bangladesh
| | - Nargis Akter
- Water Sanitation and Hygiene Section, United Nations Children’s Fund, BSL Office Complex, 1 Minto Road, Dhaka, 1000 Bangladesh
| | - Dara Johnston
- Water Sanitation and Hygiene Section, United Nations Children’s Fund, BSL Office Complex, 1 Minto Road, Dhaka, 1000 Bangladesh
| | - Kazi Matin Ahmed
- Department of Geology, University of Dhaka, Dhaka, 1000 Bangladesh
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95
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Keshaviah A, Hu XC, Henry M. Developing a Flexible National Wastewater Surveillance System for COVID-19 and Beyond. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:45002. [PMID: 33877858 PMCID: PMC8057681 DOI: 10.1289/ehp8572] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/04/2021] [Accepted: 03/26/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Wastewater testing offers a cost-effective strategy for measuring population disease prevalence and health behaviors. For COVID-19, wastewater surveillance addresses testing gaps and provides an early warning for outbreaks. As U.S. federal agencies build a National Wastewater Surveillance System around the pandemic, thinking through ways to develop flexible frameworks for wastewater sampling, testing, and reporting can avoid unnecessary system overhauls for future infectious disease, chronic disease, and drug epidemics. OBJECTIVES We discuss ways to transform a historically academic exercise into a tool for epidemic response. We generalize lessons learned by a global network of wastewater researchers around validation and implementation for COVID-19 and opioids while also drawing on our experience with wastewater-based epidemiology in the United States. DISCUSSION Sustainable wastewater surveillance requires coordination between health and safety officials, utilities, labs, and researchers. Adapting sampling frequency, type, and location to threat level, community vulnerability, biomarker properties, and decisions that wastewater data will inform can increase the practical value of the data. Marketplace instabilities, coupled with a fragmented testing landscape due to specialization, may require officials to engage multiple labs to test for known and unknown threats. Government funding can stabilize the market, balancing commercial pressures with public good, and incentivize data sharing. When reporting results, standardizing metrics and contextualizing wastewater data with health resource data can provide insights into a community's vulnerability and identify strategies to prevent health care systems from being overwhelmed. If wastewater data will inform policy decisions for an entire community, comparing characteristics of the wastewater treatment plant's service population to those of the larger community can help determine whether the wastewater data are generalizable. Ethical protocols may be needed to protect privacy and avoid stigmatization. With data-driven approaches to sample collection, analysis, and interpretation, officials can use wastewater surveillance for adaptive resource allocation, pandemic management, and program evaluation. https://doi.org/10.1289/EHP8572.
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96
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Philo SE, Keim EK, Swanstrom R, Ong AQW, Burnor EA, Kossik AL, Harrison JC, Demeke BA, Zhou NA, Beck NK, Shirai JH, Meschke JS. A comparison of SARS-CoV-2 wastewater concentration methods for environmental surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 760:144215. [PMID: 33340739 PMCID: PMC7832770 DOI: 10.1016/j.scitotenv.2020.144215] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 05/08/2023]
Abstract
Wastewater1 surveillance of SARS-CoV-2 may be a useful supplement to clinical surveillance as it is shed in feces, there are many asymptomatic cases, and diagnostic testing can have capacity limitations and extended time to results. Although numerous studies have utilized wastewater surveillance for SARS-CoV-2, the methods used were developed and/or standardized for other pathogens. This study evaluates multiple methods for concentration and recovery of SARS-CoV-2 and seeded human coronavirus OC43 from municipal primary wastewater and/or sludge from the Greater Seattle Area (March-July 2020). Methods evaluated include the bag-mediated filtration system (BMFS), with and without Vertrel™ extraction, skimmed milk flocculation, with and without Vertrel™ extraction, polyethylene glycol (PEG) precipitation, ultrafiltration, and sludge extraction. Total RNA was extracted from wastewater concentrates and analyzed for SARS-CoV-2 and OC43 with RT-qPCR. Skimmed milk flocculation without Vertrel™ extraction performed consistently over time and between treatment plants in Seattle-area wastewater with the lowest average OC43 Cq value and smallest variability (24.3; 95% CI: 23.8-24.9), most frequent SARS-CoV-2 detection (48.8% of sampling events), and highest average OC43 percent recovery (9.1%; 95% CI: 6.2-11.9%). Skimmed milk flocculation is also beneficial because it is feasible in low-resource settings. While the BMFS had the highest average volume assayed of 11.9 mL (95% CI: 10.7-13.1 mL), the average OC43 percent recovery was low (0.7%; 95% CI: 0.4-1.0%). Ultrafiltration and PEG precipitation had low average OC43 percent recoveries of 1.0% (95% CI: 0.5-1.6%) and 3.2% (95% CI: 1.3-5.1%), respectively. The slopes and efficiency for the SARS-CoV-2 standard curves were not consistent over time, confirming the need to include a standard curve each run rather than using a single curve for multiple plates. Results suggest that the concentration and detection methods used must be validated for the specific water matrix using a recovery control to assess performance over time.
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Affiliation(s)
- Sarah E Philo
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Erika K Keim
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Rachael Swanstrom
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Angelo Q W Ong
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Elisabeth A Burnor
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Alexandra L Kossik
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Joanna C Harrison
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Bethel A Demeke
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Nicolette A Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Nicola K Beck
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Jeffry H Shirai
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - J Scott Meschke
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA.
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97
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Pérez-Cataluña A, Cuevas-Ferrando E, Randazzo W, Falcó I, Allende A, Sánchez G. Comparing analytical methods to detect SARS-CoV-2 in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143870. [PMID: 33338788 PMCID: PMC7722604 DOI: 10.1016/j.scitotenv.2020.143870] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 05/09/2023]
Abstract
Wastewater based epidemiology (WBE) has emerged as a reliable strategy to assess the coronavirus disease 2019 (COVID-19) pandemic. Recent publications suggest that SARS-CoV-2 detection in wastewater is technically feasible; however, many different protocols are available and most of the methods applied have not been properly validated. To this end, different procedures to concentrate and extract inactivated SARS-CoV-2 and surrogates were initially evaluated. Urban wastewater seeded with gamma-irradiated SARS-CoV-2, porcine epidemic diarrhea virus (PEDV), and mengovirus (MgV) was used to test the concentration efficiency of an aluminum-based adsorption-precipitation method and a polyethylene glycol (PEG) precipitation protocol. Moreover, two different RNA extraction methods were compared in this study: a commercial manual spin column centrifugation kit and an automated protocol based on magnetic silica beads. Overall, the evaluated concentration methods did not impact the recovery of gamma-irradiated SARS-CoV-2 nor MgV, while extraction methods showed significant differences for PEDV. Mean recovery rates of 42.9 ± 9.5%, 27.5 ± 14.3% and 9.0 ± 2.2% were obtained for gamma-irradiated SARS-CoV-2, PEDV and MgV, respectively. Limits of detection (LoD95%) for five genomic SARS-CoV-2 targets (N1, N2, gene E, IP2 and IP4) ranged from 1.56 log genome equivalents (ge)/mL (N1) to 2.22 log ge/mL (IP4) when automated system was used; while values ranging between 2.08 (N1) and 2.34 (E) log ge/mL were observed when using column-based extraction method. Different targets were also evaluated in naturally contaminated wastewater samples with 91.2%, 85.3%, 70.6%, 79.4% and 73.5% positivity, for N1, N2, E, IP2 and IP4, respectively. Our benchmarked comparison study suggests that the aluminum precipitation method coupled with the automated nucleic extraction represents a method of acceptable sensitivity to provide readily results of interest for SARS-CoV-2 WBE surveillance.
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Affiliation(s)
- Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain; Department of Microbiology and Ecology, University of Valencia, Av. Dr. Moliner, 50, Burjassot, 46100, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Ana Allende
- Research Group on Quality and Safety of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100 Murcia, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain.
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98
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Donia A, Hassan SU, Zhang X, Al-Madboly L, Bokhari H. COVID-19 Crisis Creates Opportunity towards Global Monitoring & Surveillance. Pathogens 2021; 10:256. [PMID: 33668358 PMCID: PMC7996165 DOI: 10.3390/pathogens10030256] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/13/2021] [Accepted: 02/22/2021] [Indexed: 01/07/2023] Open
Abstract
The spectrum of emerging new diseases as well as re-emerging old diseases is broadening as infectious agents evolve, adapt, and spread at enormous speeds in response to changing ecosystems. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recent phenomenon and may take a while to understand its transmission routes from less traveled territories, ranging from fomite exposure routes to wastewater transmission. The critical challenge is how to negotiate with such catastrophic pandemics in high-income countries (HICs ~20% of the global population) and low-and middle-income countries (LMICs ~ 80% of the global population) with a total global population size of approximately eight billion, where practical mass testing and tracing is only a remote possibility, particularly in low-and middle-income countries (LMICs). Keeping in mind the population distribution disparities of high-income countries (HICs) and LMICs and urbanisation trends over recent years, traditional wastewater-based surveillance such as that used to combat polio may help in addressing this challenge. The COVID-19 era differs from any previous pandemics or global health challenges in the sense that there is a great deal of curiosity within the global community to find out everything about this virus, ranging from diagnostics, potential vaccines/therapeutics, and possible routes of transmission. In this regard, the fact that the gut is the common niche for both poliovirus and SARS-CoV-2, and due to the shedding of the virus through faecal material into sewerage systems, the need for long-term wastewater surveillance and developing early warning systems for better preparedness at local and global levels is increasingly apparent. This paper aims to provide an insight into the ongoing COVID-19 crisis, how it can be managed, and what measures are required to deal with a current global international public health concern. Additionally, it shed light on the importance of using wastewater surveillance strategy as an early warning practical tool suitable for massive passive screening, as well as the urgent need for microfluidic technology as a rapid and cost-effective approach tracking SARS-CoV-2 in wastewater.
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Affiliation(s)
- Ahmed Donia
- Biosciences Department, Faculty of Science, Comsats University Islamabad, Islamabad 45550, Pakistan;
| | - Sammer-ul Hassan
- Mechanical Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK;
| | - Xunli Zhang
- Mechanical Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, UK;
| | - Lamiaa Al-Madboly
- Pharmaceutical Microbiology Department, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt;
| | - Habib Bokhari
- Biosciences Department, Faculty of Science, Comsats University Islamabad, Islamabad 45550, Pakistan;
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99
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Murtas R, Decarli A, Russo AG. Trend of pneumonia diagnosis in emergency departments as a COVID-19 surveillance system: a time series study. BMJ Open 2021; 11:e044388. [PMID: 33558358 PMCID: PMC7871231 DOI: 10.1136/bmjopen-2020-044388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVE In Italy, the first diagnosis of COVID-19 was confirmed on 20 February 2020 in the Lombardy region. Given the rapid spread of the infection in the population, it was suggested that in Europe, and specifically in Italy, the virus had already been present in the last months of 2019. In this paper, we aim to evaluate the hypothesis on the early presence of the virus in Italy by analysing data on trends of access to emergency departments (EDs) of subjects with a diagnosis of pneumonia during the 2015-2020 period. DESIGN Time series cohort study. SETTING We collected data on visits due to pneumonia between 1 October 2015 and 31 May 2020 in all EDs of the Agency for Health Protection of Milan (ATS of Milan). Trend in the winter of 2019-2020 was compared with those in the previous 4 years in order to identify unexpected signals potentially associated with the occurrence of the pandemic. Aggregated data were analysed using a Poisson regression model adjusted for seasonality and influenza outbreaks. PRIMARY OUTCOME MEASURES : Daily pneumonia-related visits in EDs. RESULTS : In the studied period, we observed 105 651 pneumonia-related ED visits. Compared with the expected, a lower occurrence was observed in January 2020, while an excess of pneumonia visits started in the province of Lodi on 21 February 2020, and almost 10 days later was observed in the remaining territory of the ATS of Milan. Overall, the peak in excess was found on 17 March 2020 (369 excess visits compared with previous years, 95% CI 353 to 383) and ended in May 2020, the administrative end of the Italian lockdown. CONCLUSIONS : An early warning system based on routinely collected administrative data could be a feasible and low-cost strategy to monitor the actual situation of the virus spread both at local and national levels.
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Affiliation(s)
- Rossella Murtas
- Epidemiology Unit, Agency for the Protection of Health of the Metropolitan Area of Milan, Milano, Lombardia, Italy
| | - Adriano Decarli
- Epidemiology Unit, Agency for the Protection of Health of the Metropolitan Area of Milan, Milano, Lombardia, Italy
| | - Antonio Giampiero Russo
- Epidemiology Unit, Agency for the Protection of Health of the Metropolitan Area of Milan, Milano, Lombardia, Italy
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