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Williams RC, Perry WB, Lambert-Slosarska K, Futcher B, Pellett C, Richardson-O'Neill I, Paterson S, Grimsley JMS, Wade MJ, Weightman AJ, Farkas K, Jones DL. Examining the stability of viral RNA and DNA in wastewater: Effects of storage time, temperature, and freeze-thaw cycles. WATER RESEARCH 2024; 259:121879. [PMID: 38865915 DOI: 10.1016/j.watres.2024.121879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024]
Abstract
Wastewater-based epidemiology (WBE) has been demonstrably successful as a relatively unbiased tool for monitoring levels of SARS-CoV-2 virus circulating in communities during the COVID-19 pandemic. Accumulated biobanks of wastewater samples allow retrospective exploration of spatial and temporal trends for public health indicators such as chemicals, viruses, antimicrobial resistance genes, and the possible emergence of novel human or zoonotic pathogens. We investigated virus resilience to time, temperature, and freeze-thaw cycles, plus the optimal storage conditions to maintain the stability of genetic material (RNA/DNA) of viral +ssRNA (Envelope - E, Nucleocapsid - N and Spike protein - S genes of SARS-CoV-2), dsRNA (Phi6 phage) and circular dsDNA (crAssphage) in wastewater. Samples consisted of (i) processed and extracted wastewater samples, (ii) processed and extracted distilled water samples, and (iii) raw, unprocessed wastewater samples. Samples were stored at -80 °C, -20 °C, 4 °C, or 20 °C for 10 days, going through up to 10 freeze-thaw cycles (once per day). Sample stability was measured using reverse transcription quantitative PCR, quantitative PCR, automated electrophoresis, and short-read whole genome sequencing. Exploring different areas of the SARS-CoV-2 genome demonstrated that the S gene in processed and extracted samples showed greater sensitivity to freeze-thaw cycles than the E or N genes. Investigating surrogate and normalisation viruses showed that Phi6 remains a stable comparison for SARS-CoV-2 in a laboratory setting and crAssphage was relatively resilient to temperature variation. Recovery of SARS-CoV-2 in raw unprocessed samples was significantly greater when stored at 4 °C, which was supported by the sequencing data for all viruses - both time and freeze-thaw cycles negatively impacted sequencing metrics. Historical extracts stored at -80 °C that were re-quantified 12, 14 and 16 months after original quantification showed no major changes. This study highlights the importance of the fast processing and extraction of wastewater samples, following which viruses are relatively robust to storage at a range of temperatures.
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Affiliation(s)
- Rachel C Williams
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
| | - William B Perry
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | | | - Ben Futcher
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK; Department of Oncology, Medical Sciences Division, University of Oxford, Old Road Campus Research Building, Headington, Oxford, OX3 7DQ, UK
| | - Cameron Pellett
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | | | - Steve Paterson
- Centre for Genomic Research, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jasmine M S Grimsley
- UK Health Security Agency, Data Analytics & Surveillance Group, 10 South Colonnade, Canary Wharf, London, E14 4PU, UK; The London Data Company, London, EC2N 2AT, UK
| | - Matthew J Wade
- UK Health Security Agency, Data Analytics & Surveillance Group, 10 South Colonnade, Canary Wharf, London, E14 4PU, UK
| | - Andrew J Weightman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Kata Farkas
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Davey L Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
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Morecchiato F, Coppi M, Niccolai C, Antonelli A, Di Gloria L, Calà P, Mancuso F, Ramazzotti M, Lotti T, Lubello C, Rossolini GM. Evaluation of different molecular systems for detection and quantification of SARS-CoV-2 RNA from wastewater samples. J Virol Methods 2024; 328:114956. [PMID: 38796134 DOI: 10.1016/j.jviromet.2024.114956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
Wastewater-based epidemiology has proved to be a suitable approach for tracking the spread of epidemic agents including SARS-CoV-2 RNA. Different protocols have been developed for quantitative detection of SARS-CoV-2 RNA from wastewater samples, but little is known on their performance. In this study we compared three protocols based on Reverse Transcription Real Time-PCR (RT-PCR) and one based on Droplet Digital PCR (ddPCR) for SARS-CoV-2 RNA detection from 35 wastewater samples. Overall, SARS-CoV-2 RNA was detected by at least one method in 85.7 % of samples, while 51.4 %, 22.8 % and 8.6 % resulted positive with two, three or all four methods, respectively. Protocols based on commercial RT-PCR assays and on Droplet Digital PCR showed an overall higher sensitivity vs. an in-house assay. The use of more than one system, targeting different genes, could be helpful to increase detection sensitivity.
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Affiliation(s)
- Fabio Morecchiato
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Claudia Niccolai
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Leandro Di Gloria
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50, Firenze (FI) 50134, Italy
| | - Piergiuseppe Calà
- Tuscany Region, Department of Prevention Local Health Authority Tuscany Center, Via S. Salvi, 12, Firenze (FI) 50135, Italy
| | - Fabrizio Mancuso
- Ingegnerie Toscane - Area R&D, Via Bellatalla, 1, Pisa (PI) 56121, Italy
| | - Matteo Ramazzotti
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50, Firenze (FI) 50134, Italy
| | - Tommaso Lotti
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3, Firenze (FI) 50139, Italy
| | - Claudio Lubello
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3, Firenze (FI) 50139, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy.
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Farkas K, Kevill JL, Adwan L, Garcia-Delgado A, Dzay R, Grimsley JMS, Lambert-Slosarska K, Wade MJ, Williams RC, Martin J, Drakesmith M, Song J, McClure V, Jones DL. Near-source passive sampling for monitoring viral outbreaks within a university residential setting. Epidemiol Infect 2024; 152:e31. [PMID: 38329110 PMCID: PMC10894896 DOI: 10.1017/s0950268824000190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has proven to be a powerful tool for the population-level monitoring of pathogens, particularly severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For assessment, several wastewater sampling regimes and methods of viral concentration have been investigated, mainly targeting SARS-CoV-2. However, the use of passive samplers in near-source environments for a range of viruses in wastewater is still under-investigated. To address this, near-source passive samples were taken at four locations targeting student hall of residence. These were chosen as an exemplar due to their high population density and perceived risk of disease transmission. Viruses investigated were SARS-CoV-2 and its variants of concern (VOCs), influenza viruses, and enteroviruses. Sampling was conducted either in the morning, where passive samplers were in place overnight (17 h) and during the day, with exposure of 7 h. We demonstrated the usefulness of near-source passive sampling for the detection of VOCs using quantitative polymerase chain reaction (qPCR) and next-generation sequencing (NGS). Furthermore, several outbreaks of influenza A and sporadic outbreaks of enteroviruses (some associated with enterovirus D68 and coxsackieviruses) were identified among the resident student population, providing evidence of the usefulness of near-source, in-sewer sampling for monitoring the health of high population density communities.
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Affiliation(s)
- Kata Farkas
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | - Jessica L. Kevill
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | - Latifah Adwan
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | | | - Rande Dzay
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | - Jasmine M. S. Grimsley
- Data Analytics & Surveillance Group, UK Health Security Agency, London, UK
- The London Data Company, London, UK
| | | | - Matthew J. Wade
- Data Analytics & Surveillance Group, UK Health Security Agency, London, UK
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, UK
| | - Rachel C. Williams
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
| | - Javier Martin
- Division of Vaccines, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Mark Drakesmith
- Communicable Disease Surveillance Centre, Public Health Wales, Cardiff, UK
| | - Jiao Song
- Communicable Disease Surveillance Centre, Public Health Wales, Cardiff, UK
| | - Victoria McClure
- Communicable Disease Surveillance Centre, Public Health Wales, Cardiff, UK
| | - Davey L. Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, UK
- Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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