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Sarekoski A, Lipponen A, Hokajärvi AM, Räisänen K, Tiwari A, Paspaliari D, Lehto KM, Oikarinen S, Heikinheimo A, Pitkänen T. Simultaneous biomass concentration and subsequent quantitation of multiple infectious disease agents and antimicrobial resistance genes from community wastewater. ENVIRONMENT INTERNATIONAL 2024; 191:108973. [PMID: 39182255 DOI: 10.1016/j.envint.2024.108973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/01/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
Wastewater-based surveillance (WBS) of infectious disease agents is increasingly seen as a reliable source of population health data. To date, wastewater-based surveillance efforts have largely focused on individual pathogens. However, given that wastewater contains a broad range of pathogens circulating in the population, a more comprehensive approach could enhance its usability. We focused on the simultaneous detection of SARS-CoV-2, sapovirus, Campylobacter jejuni, Campylobacter coli, Salmonella spp., pathogenic Escherichia coli, Cryptosporidium spp., Giardia spp. and antimicrobial resistance genes (ARGs) of clinical relevance. To achieve this goal, biomass concentration and nucleic acid extraction methods were optimized, and samples were analyzed by using a set of (RT)-qPCR and (HT)-qPCR methods. We determined the prevalence and the spatial and temporal trends of the targeted pathogens and collected novel information on ARGs in Finnish wastewater. In addition, the use of different wastewater concentrates, namely the ultrafiltered concentrate of the supernatant and the centrifuged pellet, and the effect of freezing and thawing wastewater prior to sample processing were investigated with the indicator microbe crAssphage. Freeze-thawing of wastewater decreased the gene copy count of crAssphage in comparison to analyzing fresh samples (p < 0.001). Campylobacters were most abundant in two of the four studied summer months (30 % detection rate) and in wastewaters from regions with intensive animal farming. Salmonella, however, was detected in 40 % of the samples without any clear seasonal trends, and the highest gene copy numbers were recorded from the largest wastewater treatment plants. Beta-lactamase resistance genes that have commonly been detected in bacteria isolated from humans in Finland, namely blaCTX-M, blaOXA48, blaNDM, and blaKPC, were also frequently detected in wastewaters (100, 98, 98, and 70 % detection rates, respectively). These results confirm the reliability of using wastewater in public health surveillance and demonstrate the possibility to simultaneously perform WBS of multiple pathogens.
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Affiliation(s)
- Anniina Sarekoski
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, Agnes Sjöbergin katu 2, Helsinki FI-00014, Finland.
| | - Anssi Lipponen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland.
| | - Anna-Maria Hokajärvi
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland.
| | - Kati Räisänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Mannerheimintie 166, Helsinki FI-00271, Finland.
| | - Ananda Tiwari
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland.
| | - Dafni Paspaliari
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Mannerheimintie 166, Helsinki FI-00271, Finland.
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland.
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland.
| | - Annamari Heikinheimo
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, Agnes Sjöbergin katu 2, Helsinki FI-00014, Finland; Finnish Food Authority, Alvar Aallon katu 5, FI-60100 Seinäjoki, Finland.
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, Neulaniementie 4, Kuopio FI-70701, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, Agnes Sjöbergin katu 2, Helsinki FI-00014, Finland.
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2
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Bayati M, Hsieh HY, Hsu SY, Qasim S, Li C, Belenchia A, Klutts J, Zemmer SA, Sibley K, Reynolds M, Semkiw E, Johnson HY, Lyddon T, Wieberg CG, Wenzel J, Johnson MC, Lin CH. The different adsorption-degradation behaviors of SARS-CoV-2 by bioactive chemicals in wastewater: The suppression kinetics and their implications for wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 938:173609. [PMID: 38815826 DOI: 10.1016/j.scitotenv.2024.173609] [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: 12/04/2023] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Wastewater-Based Epidemiology (WBE) is widely used to monitor the progression of SARS-CoV-2 pandemic. While there is a clear correlation between the number of COVID patients in a sewershed and the viral load in the wastewater, there is notable variability across different treatment plants. In particular, some facilities consistently exhibit higher viral content per diagnosed patient, implying a potential underestimation of the number of COVID patients, while others show a low viral load per diagnosed case, indicating potential attenuation of genetic material from the sewershed. In this study, we investigated the impact of nonylphenol ethoxylate (NPHE), linear alkylbenzene sulfonic acid (LABS), bisoctyl dimethyl ammonium chloride (BDAC), and didecyldimethylammonium chloride (DDAC), the surfactants that have been commonly used as detergents, emulsifiers, wetting agents on the stability of SARS-CoV-2 in wastewater. The results showed multiple and dynamic mechanisms, including degradation and desorption, can occur simultaneously during the interaction between SARS-CoV-2 and different chemicals depending on the physicochemical properties of each chemical. Through the elucidation of the dynamic interactions, the findings from this study could help the state health organizations and scientific community to optimize the SARS-CoV-2 wastewater-based epidemiology strategies.
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Affiliation(s)
- Mohamed Bayati
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA; Environmental Engineering Department, Tikrit University, Tikrit, Iraq
| | - Hsin-Yeh Hsieh
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Shu-Yu Hsu
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA; Center for Agroforestry, University of Missouri, Columbia, MO 65201, USA
| | - Sally Qasim
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Chenhui Li
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Anthony Belenchia
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Jessica Klutts
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65201, USA
| | - Sally A Zemmer
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO, USA
| | - Kristen Sibley
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO, USA
| | - Melissa Reynolds
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Elizabeth Semkiw
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Hwei-Yiing Johnson
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Terri Lyddon
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65201, USA
| | - Chris G Wieberg
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO, USA
| | - Jeff Wenzel
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65201, USA
| | - Chung-Ho Lin
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA; Center for Agroforestry, University of Missouri, Columbia, MO 65201, USA.
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3
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Liu Y, Sapoval N, Gallego-García P, Tomás L, Posada D, Treangen TJ, Stadler LB. Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater. Nat Commun 2024; 15:4545. [PMID: 38806450 PMCID: PMC11133379 DOI: 10.1038/s41467-024-48334-w] [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: 11/15/2023] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
Wastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants of concerns and can be used to screen for novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that are rare, or entirely missing, in existing SARS-CoV-2 databases. While previous approaches have focused on specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and investigating their potential origin. We present Crykey, a tool for rapidly identifying rare linked-read mutations across the genome of SARS-CoV-2. We evaluated the utility of Crykey on over 3,000 wastewater and over 22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations in wastewater that represent potential circulating cryptic lineages, serving as a new computational tool for wastewater surveillance of SARS-CoV-2.
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Affiliation(s)
- Yunxi Liu
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Pilar Gallego-García
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Laura Tomás
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - David Posada
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310, Vigo, Spain
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, 77005, USA.
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA.
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4
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Zhang M, Roldan-Hernandez L, Boehm A. Persistence of human respiratory viral RNA in wastewater-settled solids. Appl Environ Microbiol 2024; 90:e0227223. [PMID: 38501669 PMCID: PMC11022535 DOI: 10.1128/aem.02272-23] [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: 12/16/2023] [Accepted: 03/01/2024] [Indexed: 03/20/2024] Open
Abstract
Wastewater-based epidemiology has emerged as a valuable tool for monitoring respiratory viral diseases within communities by analyzing concentrations of viral nucleic-acids in wastewater. However, little is known about the fate of respiratory virus nucleic-acids in wastewater. Two important fate processes that may modulate their concentrations in wastewater as they move from household drains to the point of collection include sorption or partitioning to wastewater solids and degradation. This study investigated the decay kinetics of genomic nucleic-acids of seven human respiratory viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus (RSV), human coronavirus (HCoV)-OC43, HCoV-229E, HCoV-NL63, human rhinovirus (HRV), and influenza A virus (IAV), as well as pepper mild mottle virus (PMMoV) in wastewater solids. Viruses (except for PMMoV) were spiked into wastewater solids and their concentrations were followed for 50 days at three different temperatures (4°C, 22°C, and 37°C). Viral genomic RNA decayed following first-order kinetics with decay rate constants k from 0 to 0.219 per day. Decay rate constants k were not different from 0 for all targets in solids incubated at 4°C; k values were largest at 37°C and at this temperature, k values were similar across nucleic-acid targets. Regardless of temperature, there was limited viral RNA decay, with an estimated 0% to 20% reduction, over the typical residence times of sewage in the piped systems between input and collection point (<1 day). The k values reported herein can be used directly in fate and transport models to inform the interpretation of measurements made during wastewater surveillance.IMPORTANCEUnderstanding whether or not the RNA targets quantified for wastewater-based epidemiology (WBE) efforts decay during transport between drains and the point of sample collection is critical for data interpretation. Here we show limited decay of viral RNA targets typically measured for respiratory disease WBE.
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Affiliation(s)
- Mengyang Zhang
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
| | - Laura Roldan-Hernandez
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
| | - Alexandria Boehm
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
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Keck JW, Adatorwovor R, Liversedge M, Mijotavich B, Olsson C, Strike WD, Amirsoleimani A, Noble A, Torabi S, Rockward A, Banadaki MD, Smith T, Lacy P, Berry SM. Wastewater Surveillance for Identifying SARS-CoV-2 Infections in Long-Term Care Facilities, Kentucky, USA, 2021-2022. Emerg Infect Dis 2024; 30:530-538. [PMID: 38407144 PMCID: PMC10902530 DOI: 10.3201/eid3003.230888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Persons living in long-term care facilities (LTCFs) were disproportionately affected by COVID-19. We used wastewater surveillance to detect SARS-CoV-2 infection in this setting by collecting and testing 24-hour composite wastewater samples 2-4 times weekly at 6 LTCFs in Kentucky, USA, during March 2021-February 2022. The LTCFs routinely tested staff and symptomatic and exposed residents for SARS-CoV-2 using rapid antigen tests. Of 780 wastewater samples analyzed, 22% (n = 173) had detectable SARS-CoV-2 RNA. The LTCFs reported 161 positive (of 16,905) SARS-CoV-2 clinical tests. The wastewater SARS-CoV-2 signal showed variable correlation with clinical test data; we observed the strongest correlations in the LTCFs with the most positive clinical tests (n = 45 and n = 58). Wastewater surveillance was 48% sensitive and 80% specific in identifying SARS-CoV-2 infections found on clinical testing, which was limited by frequency, coverage, and rapid antigen test performance.
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Affiliation(s)
| | - Reuben Adatorwovor
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | | | - Blazan Mijotavich
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | - Cullen Olsson
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | - William D. Strike
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | - Atena Amirsoleimani
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | - Ann Noble
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | - Soroosh Torabi
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | - Alexus Rockward
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | - Mohammad Dehghan Banadaki
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | - Ted Smith
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | - Parker Lacy
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
| | - Scott M. Berry
- University of Kentucky, Lexington, Kentucky, USA (J.W. Keck, R. Adatorwovor, M. Liversedge, C. Olsson, W.D. Strike, A. Amirsoleimani, A. Noble, S. Torabi, A. Rockward, M. Dehghan Banadaki, S.M. Berry)
- University of Louisville, Louisville, Kentucky, USA (T. Smith)
- Trilogy Health Services, LLC, Louisville (P. Lacy)
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Abreu MADF, Lopes BC, Assemany PP, Souza ADR, Siniscalchi LAB. COVID-19 cases, vaccination, and SARS-CoV-2 in wastewater: insights from a Brazilian municipality. JOURNAL OF WATER AND HEALTH 2024; 22:268-277. [PMID: 38421621 PMCID: wh_2024_159 DOI: 10.2166/wh.2024.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Vaccines combatting COVID-19 demonstrate the ability to protect against disease and hospitalization, and reduce the likelihood of death caused by SARS-CoV-2. In addition, monitoring viral loads in sewage emerges as another crucial strategy in the epidemiological context, enabling early and collective detection of outbreaks. The study aimed to monitor the viral concentration of SARS-CoV-2 in untreated sewage in a Brazilian municipality. Also, it attempted to correlate these measurements with the number of clinical cases and deaths resulting from COVID-19 between July 2021 and July 2022. SARS-CoV-2 viral RNA was quantified by RT-qPCR. Pearson's correlation was performed to analyze the variables' relationship using the number of cases, deaths, vaccinated individuals, and viral concentration of SARS-CoV-2. The results revealed a significant negative correlation (p < 0.05) between the number of vaccinated individuals and the viral concentration of SARS-CoV-2, suggesting that after vaccination, the RNA viral load concentration was reduced in the sample population by the circulating concentration of wastewater. Consequently, wastewater monitoring, in addition to functioning as an early warning system for the circulation of SARS-CoV-2 and other pathogens, can offer a novel perspective that enhances decision-making, strengthens vaccination campaigns, and contributes to authorities establishing systematic networks for monitoring SARS-CoV-2.
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Affiliation(s)
- Mariana Aparecida de Freitas Abreu
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil; Applied Microbiology Laboratory at the Environmental Engineering Department of UFLA, Federal University of Lavras (UFLA), Lavras, Brazil E-mail:
| | - Bruna Coelho Lopes
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Paula Peixoto Assemany
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil; Applied Microbiology Laboratory at the Environmental Engineering Department of UFLA, Federal University of Lavras (UFLA), Lavras, Brazil
| | - Aline Dos Reis Souza
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil
| | - Luciene Alves Batista Siniscalchi
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil; Applied Microbiology Laboratory at the Environmental Engineering Department of UFLA, Federal University of Lavras (UFLA), Lavras, Brazil
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7
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Jobling K, Quintela-Baluja M, Hassard F, Adamou P, Blackburn A, Research Team T, McIntyre-Nolan S, O'Mara O, Romalde JL, Di Cesare M, Graham DW. Comparison of gene targets and sampling regimes for SARS-CoV-2 quantification for wastewater epidemiology in UK prisons. JOURNAL OF WATER AND HEALTH 2024; 22:64-76. [PMID: 38295073 PMCID: wh_2023_093 DOI: 10.2166/wh.2023.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Prisons are high-risk settings for infectious disease transmission, due to their enclosed and semi-enclosed environments. The proximity between prisoners and staff, and the diversity of prisons reduces the effectiveness of non-pharmaceutical interventions, such as social distancing. Therefore, alternative health monitoring methods, such as wastewater-based epidemiology (WBE), are needed to track pathogens, including SARS-CoV-2. This pilot study assessed WBE to quantify SARS-CoV-2 prevalence in prison wastewater to determine its utility within a health protection system for residents. The study analysed 266 samples from six prisons in England over a 12-week period for nucleoprotein 1 (N1 gene) and envelope protein (E gene) using quantitative reverse transcriptase-polymerase chain reaction. Both gene assays successfully detected SARS-CoV-2 fragments in wastewater samples, with both genes significantly correlating with COVID-19 case numbers across the prisons (p < 0.01). However, in 25% of the SARS-positive samples, only one gene target was detected, suggesting that both genes be used to reduce false-negative results. No significant differences were observed between 14- and 2-h composite samples, although 2-h samples showed greater signal variance. Population normalisation did not improve correlations between the N1 and E genes and COVID-19 case data. Overall, WBE shows considerable promise for health protection in prison settings.
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Affiliation(s)
- Kelly Jobling
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; The authors contributed equally to the manuscript. E-mail:
| | - Marcos Quintela-Baluja
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; The authors contributed equally to the manuscript
| | - Francis Hassard
- Cranfield Water Science Institute, Cranfield University, Cranfield MK43 0AL, UK
| | - Panagiota Adamou
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Adrian Blackburn
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | | | | | - Jesus L Romalde
- CRETUS, Departamento de Microbiología y Parasitología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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8
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Liu AB, Lee D, Jalihal AP, Hanage WP, Springer M. Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics. Nat Commun 2023; 14:8479. [PMID: 38123536 PMCID: PMC10733317 DOI: 10.1038/s41467-023-44199-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Researchers and policymakers have proposed systems to detect novel pathogens earlier than existing surveillance systems by monitoring samples from hospital patients, wastewater, and air travel, in order to mitigate future pandemics. How much benefit would such systems offer? We developed, empirically validated, and mathematically characterized a quantitative model that simulates disease spread and detection time for any given disease and detection system. We find that hospital monitoring could have detected COVID-19 in Wuhan 0.4 weeks earlier than it was actually discovered, at 2,300 cases (standard error: 76 cases) compared to 3,400 (standard error: 161 cases). Wastewater monitoring would not have accelerated COVID-19 detection in Wuhan, but provides benefit in smaller catchments and for asymptomatic or long-incubation diseases like polio or HIV/AIDS. Air travel monitoring does not accelerate outbreak detection in most scenarios we evaluated. In sum, early detection systems can substantially mitigate some future pandemics, but would not have changed the course of COVID-19.
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Affiliation(s)
- Andrew Bo Liu
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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Liu Y, Sapoval N, Gallego-García P, Tomás L, Posada D, Treangen TJ, Stadler LB. Crykey: Rapid Identification of SARS-CoV-2 Cryptic Mutations in Wastewater. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.16.23291524. [PMID: 37986916 PMCID: PMC10659477 DOI: 10.1101/2023.06.16.23291524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
We present Crykey, a computational tool for rapidly identifying cryptic mutations of SARS-CoV-2. Specifically, we identify co-occurring single nucleotide mutations on the same sequencing read, called linked-read mutations, that are rare or entirely missing in existing databases, and have the potential to represent novel cryptic lineages found in wastewater. While previous approaches exist for identifying cryptic linked-read mutations from specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and for tens of thousands of samples and with increased scrutiny, given their potential to represent either artifacts or hidden SARS-CoV-2 lineages. Crykey fills this gap by identifying rare linked-read mutations that pass stringent computational filters to limit the potential for artifacts. We evaluate the utility of Crykey on >3,000 wastewater and >22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over a three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations representing potential cryptic lineages in wastewater.
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Affiliation(s)
- Yunxi Liu
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Pilar Gallego-García
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
| | - Laura Tomás
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Lauren B. Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA
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Thapar I, Langan LM, Davis H, Norman RS, Bojes HK, Brooks BW. Influence of storage conditions and multiple freeze-thaw cycles on N1 SARS-CoV-2, PMMoV, and BCoV signal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165098. [PMID: 37392884 PMCID: PMC10307669 DOI: 10.1016/j.scitotenv.2023.165098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
Wastewater-based epidemiology/wastewater-based surveillance (WBE/WBS) continues to serve as an effective means of monitoring various diseases, including COVID-19 and the emergence of SARS-CoV-2 variants, at the population level. As the use of WBE expands, storage conditions of wastewater samples will play a critical role in ensuring the accuracy and reproducibility of results. In this study, the impacts of water concentration buffer (WCB), storage temperature, and freeze-thaw cycles on the detection of SARS-CoV-2 and other WBE-related gene targets were examined. Freeze-thawing of concentrated samples did not significantly affect (p > 0.05) crossing/cycle threshold (Ct) value for any of the gene targets studied (SARS-CoV-2 N1, PMMoV, and BCoV). However, use of WCB during concentration resulted in a significant (p < 0.05) decrease in Ct for all targets, and storage at -80 °C (in contrast to -20 °C) appeared preferable for wastewater storage signal stability based on decreased Ct values, although this was only significantly different (p < 0.05) for the BCoV target. Interestingly, when Ct values were converted to gene copies per influent sample, no significant differences (p > 0.05) were observed in any of the targets examined. Stability of RNA targets in concentrated wastewater against freeze-thaw degradation supports archiving of concentrated samples for use in retrospective examination of COVID-19 trends and tracing SARS-CoV-2 variants and potentially other viruses, and provides a starting point for establishing a consistent procedure for specimen collection and storage for the WBE/WBS community.
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Affiliation(s)
- Isha Thapar
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA
| | - Laura M Langan
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA.
| | - Haley Davis
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US-1, Fort Pierce, FL 34946, USA
| | - R Sean Norman
- Department of Environmental Health Sciences, Arnold School of Public Health, South Carolina, 921 Assembly St., Columbia, SC 29208, USA
| | - Heidi K Bojes
- Environmental Epidemiology and Disease Registries Section, Texas Department of State Health Services, Austin, TX 78756, USA
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA; Institute of Biomedical Studies, Baylor University, One Bear Place #97224, Waco, TX 76798, USA
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11
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Breadner PR, Dhiyebi HA, Fattahi A, Srikanthan N, Hayat S, Aucoin MG, Boegel SJ, Bragg LM, Craig PM, Xie Y, Giesy JP, Servos MR. A comparative analysis of the partitioning behaviour of SARS-CoV-2 RNA in liquid and solid fractions of wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165095. [PMID: 37355124 PMCID: PMC10287177 DOI: 10.1016/j.scitotenv.2023.165095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
As fragments of SARS-CoV-2 RNA can be quantified and measured temporally in wastewater, surveillance of concentrations of SARS-CoV-2 in wastewater has become a vital resource for tracking the spread of COVID-19 in and among communities. However, the absence of standardized methods has affected the interpretation of data for public health efforts. In particular, analyzing either the liquid or solid fraction has implications for the interpretation of how viral RNA is quantified. Characterizing how SARS-CoV-2 or its RNA fragments partition in wastewater is a central part of understanding fate and behaviour in wastewater. In this study, partitioning of SARS-CoV-2 was investigated by use of centrifugation with varied durations of spin and centrifugal force, polyethylene glycol (PEG) precipitation followed by centrifugation, and ultrafiltration of wastewater. Partitioning of the endogenous pepper mild mottled virus (PMMoV), used to normalize the SARS-CoV-2 signal for fecal load in trend analysis, was also examined. Additionally, two surrogates for coronavirus, human coronavirus 229E and murine hepatitis virus, were analyzed as process controls. Even though SARS-CoV-2 has an affinity for solids, the total RNA copies of SARS-CoV-2 per wastewater sample, after centrifugation (12,000 g, 1.5 h, no brake), were partitioned evenly between the liquid and solid fractions. Centrifugation at greater speeds for longer durations resulted in a shift in partitioning for all viruses toward the solid fraction except for PMMoV, which remained mostly in the liquid fraction. The surrogates more closely reflected the partitioning of SARS-CoV-2 under high centrifugation speed and duration while PMMoV did not. Interestingly, ultrafiltration devices were inconsistent in estimating RNA copies in wastewater, which can influence the interpretation of partitioning. Developing a better understanding of the fate of SARS-CoV-2 in wastewater and creating a foundation of best practices is the key to supporting the current pandemic response and preparing for future potential infectious diseases.
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Affiliation(s)
- Patrick R Breadner
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Hadi A Dhiyebi
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Azar Fattahi
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Nivetha Srikanthan
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Samina Hayat
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Marc G Aucoin
- Department of Chemical Engineering, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Scott J Boegel
- Department of Chemical Engineering, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Leslie M Bragg
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Paul M Craig
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada
| | - Yuwei Xie
- Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; Toxicology Centre, University of Saskatchewan, 44 Campus Dr, Saskatoon, Saskatchewan S7N 5B3, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, 44 Campus Dr, Saskatoon, Saskatchewan S7N 5B3, Canada; Department of Environmental Science, Baylor University, One Bear Place, Waco, TX 76798, USA
| | - Mark R Servos
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, Ontario N2L 3G1, Canada.
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12
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Liu AB, Lee D, Jalihal AP, Hanage WP, Springer M. Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.08.23291050. [PMID: 37398047 PMCID: PMC10312821 DOI: 10.1101/2023.06.08.23291050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Researchers and policymakers have proposed systems to detect novel pathogens earlier than existing surveillance systems by monitoring samples from hospital patients, wastewater, and air travel, in order to mitigate future pandemics. How much benefit would such systems offer? We developed, empirically validated, and mathematically characterized a quantitative model that simulates disease spread and detection time for any given disease and detection system. We find that hospital monitoring could have detected COVID-19 in Wuhan 0.4 weeks earlier than it was actually discovered, at 2,300 cases (standard error: 76 cases) compared to 3,400 (standard error: 161 cases). Wastewater monitoring would not have accelerated COVID-19 detection in Wuhan, but provides benefit in smaller catchments and for asymptomatic or long-incubation diseases like polio or HIV/AIDS. Monitoring of air travel provides little benefit in most scenarios we evaluated. In sum, early detection systems can substantially mitigate some future pandemics, but would not have changed the course of COVID-19.
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Affiliation(s)
- Andrew Bo Liu
- Department of Systems Biology, Harvard Medical School; Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | | | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health; Boston, MA, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School; Boston, MA, USA
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13
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Zhu K, Hill C, Muirhead A, Basu M, Brown J, Brinton MA, Hayat MJ, Venegas-Vargas C, Reis MG, Casanovas-Massana A, Meschke JS, Ko AI, Costa F, Stauber CE. Zika virus RNA persistence and recovery in water and wastewater: An approach for Zika virus surveillance in resource-constrained settings. WATER RESEARCH 2023; 241:120116. [PMID: 37270953 PMCID: PMC10330535 DOI: 10.1016/j.watres.2023.120116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
During the 2015-2016 Zika virus (ZIKV) epidemic in the Americas, serological cross-reactivity with other flaviviruses and relatively high costs of nucleic acid testing in the region hindered the capacity for widespread diagnostic testing. In such cases where individual testing is not feasible, wastewater monitoring approaches may offer a means of community-level public health surveillance. To inform such approaches, we characterized the persistence and recovery of ZIKV RNA in experiments where we spiked cultured ZIKV into surface water, wastewater, and a combination of both to examine the potential for detection in open sewers serving communities most affected by the ZIKV outbreak, such as those in Salvador, Bahia, Brazil. We used reverse transcription droplet digital PCR to quantify ZIKV RNA. In our persistence experiments, we found that the persistence of ZIKV RNA decreased with increasing temperature, significantly decreased in surface water versus wastewater, and significantly decreased when the initial concentration of virus was lowered by one order of magnitude. In our recovery experiments, we found higher percent recovery of ZIKV RNA in pellets versus supernatants from the same sample, higher recoveries in pellets using skimmed milk flocculation, lower recoveries of ZIKV RNA in surface water versus wastewater, and lower recoveries from a freeze thaw. We also analyzed samples collected from Salvador, Brazil during the ZIKV outbreak (2015-2016) that consisted of archived samples obtained from open sewers or environmental waters thought to be contaminated by sewage. Although we did not detect any ZIKV RNA in the archived Brazil samples, results from these persistence and recovery experiments serve to inform future wastewater monitoring efforts in open sewers, an understudied and important application of wastewater monitoring.
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Affiliation(s)
- Kevin Zhu
- Department of Civil and Environmental Engineering, College of Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cailee Hill
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA 30303, USA
| | - Aaron Muirhead
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA 30303, USA
| | - Mausumi Basu
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 303034, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Margo A Brinton
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA 303034, USA
| | - Matthew J Hayat
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA 30303, USA
| | - Cristina Venegas-Vargas
- Department of Large Animal Clinical Sciences, College Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Mitermayer G Reis
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Rua Waldemar Falcão, 121, Salvador Bahia, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06511, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06511, USA
| | - J Scott Meschke
- Department of Environmental and Occupational Health, School of Public Health, University of Washington, Seattle, WA, USA
| | - Albert I Ko
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Rua Waldemar Falcão, 121, Salvador Bahia, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06511, USA
| | - Federico Costa
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Rua Waldemar Falcão, 121, Salvador Bahia, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06511, USA; Institute of Collective Health, Federal University of Bahia, Canela, Salvador 40110-040, Brazil
| | - Christine E Stauber
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA 30303, USA.
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14
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Atoui A, Cordevant C, Chesnot T, Gassilloud B. SARS-CoV-2 in the environment: Contamination routes, detection methods, persistence and removal in wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163453. [PMID: 37059142 PMCID: PMC10091716 DOI: 10.1016/j.scitotenv.2023.163453] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/01/2023]
Abstract
The present study reviewed the occurrence of SARS-CoV-2 RNA and the evaluation of virus infectivity in feces and environmental matrices. The detection of SARS-CoV-2 RNA in feces and wastewater samples, reported in several studies, has generated interest and concern regarding the possible fecal-oral route of SARS-CoV-2 transmission. To date, the presence of viable SARS-CoV-2 in feces of COVID-19 infected people is not clearly confirmed although its isolation from feces of six different patients. Further, there is no documented evidence on the infectivity of SARS-CoV-2 in wastewater, sludge and environmental water samples, although the viral genome has been detected in these matrices. Decay data revealed that SARS-CoV-2 RNA persisted longer than infectious particle in all aquatic environment, indicating that genome quantification of SARS-CoV-2 does not imply the presence of infective viral particles. In addition, this review also outlined the fate of SARS-CoV-2 RNA during the different steps in the wastewater treatment plant and focusing on the virus elimination along the sludge treatment line. Studies showed complete removal of SARS-CoV-2 during the tertiary treatment. Moreover, thermophilic sludge treatments present high efficiency in SARS-CoV-2 inactivation. Further studies are required to provide more evidence with respect to the inactivation behavior of infectious SARS-CoV-2 in different environmental matrices and to examine factors affecting SARS-CoV-2 persistence.
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Affiliation(s)
- Ali Atoui
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France.
| | - Christophe Cordevant
- ANSES, Strategy and Programs Department, Research and Reference Division, Maisons-Alfort F-94 700, France
| | - Thierry Chesnot
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France
| | - Benoît Gassilloud
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France
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15
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Torabi S, Amirsoleimani A, Dehghan Banadaki M, Strike WD, Rockward A, Noble A, Liversedge M, Keck JW, Berry SM. Stabilization of SARS-CoV-2 RNA in wastewater via rapid RNA extraction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:162992. [PMID: 36948314 PMCID: PMC10028336 DOI: 10.1016/j.scitotenv.2023.162992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/21/2022] [Accepted: 03/17/2023] [Indexed: 05/13/2023]
Abstract
Wastewater-based Epidemiology (WBE) has contributed to surveillance of SARS-CoV-2 in communities across the world. Both symptomatic and asymptomatic patients with COVID-19 can shed the virus through the gastrointestinal tract, enabling the quantification of the virus in stool and ultimately in wastewater (WW). Unfortunately, instability of SARS-CoV-2 RNA in wastewater limits the utility of WBE programs, particularly in remote/rural regions where reliable cold storage and/or rapid shipping may be unavailable. This study examined whether rapid SARS-CoV-2 RNA extraction on the day of sample collection could minimize degradation. Importantly, the extraction technology used in these experiments, termed exclusion-based sample preparation (ESP), is lightweight, portable, and electricity-free, making it suitable for implementation in remote settings. We demonstrated that immediate RNA extraction followed by ambient storage significantly increased the RNA half-life compared to raw wastewater samples stored at both 4 °C or ambient temperature. Given that RNA degradation negatively impacts both the sensitivity and precision of WBE measurements, efforts must be made to mitigate degradation in order to maximize the potential impact of WBE on public health.
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Affiliation(s)
- Soroosh Torabi
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States of America
| | - Atena Amirsoleimani
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States of America
| | - Mohammad Dehghan Banadaki
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States of America
| | - William Dalton Strike
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States of America
| | - Alexus Rockward
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States of America
| | - Ann Noble
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States of America
| | - Matthew Liversedge
- Department of Family and Community Medicine, College of Medicine, University of Kentucky, United States of America
| | - James W Keck
- Department of Family and Community Medicine, College of Medicine, University of Kentucky, United States of America
| | - Scott M Berry
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States of America; Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States of America.
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16
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Asadi M, Oloye FF, Xie Y, Cantin J, Challis JK, McPhedran KN, Yusuf W, Champredon D, Xia P, De Lange C, El-Baroudy S, Servos MR, Jones PD, Giesy JP, Brinkmann M. A wastewater-based risk index for SARS-CoV-2 infections among three cities on the Canadian Prairie. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162800. [PMID: 36914129 PMCID: PMC10008033 DOI: 10.1016/j.scitotenv.2023.162800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/01/2023]
Abstract
Wastewater surveillance (WWS) is useful to better understand the spreading of coronavirus disease 2019 (COVID-19) in communities, which can help design and implement suitable mitigation measures. The main objective of this study was to develop the Wastewater Viral Load Risk Index (WWVLRI) for three Saskatchewan cities to offer a simple metric to interpret WWS. The index was developed by considering relationships between reproduction number, clinical data, daily per capita concentrations of virus particles in wastewater, and weekly viral load change rate. Trends of daily per capita concentrations of SARS-CoV-2 in wastewater for Saskatoon, Prince Albert, and North Battleford were similar during the pandemic, suggesting that per capita viral load can be useful to quantitatively compare wastewater signals among cities and develop an effective and comprehensible WWVLRI. The effective reproduction number (Rt) and the daily per capita efficiency adjusted viral load thresholds of 85 × 106 and 200 × 106 N2 gene counts (gc)/population day (pd) were determined. These values with rates of change were used to categorize the potential for COVID-19 outbreaks and subsequent declines. The weekly average was considered 'low risk' when the per capita viral load was 85 × 106 N2 gc/pd. A 'medium risk' occurs when the per capita copies were between 85 × 106 and 200 × 106 N2 gc/pd. with a rate of change <100 %. The start of an outbreak is indicated by a 'medium-high' risk classification when the week-over-week rate of change was >100 %, and the absolute magnitude of concentrations of viral particles was >85 × 106 N2 gc/pd. Lastly, a 'high risk' occurs when the viral load exceeds 200 × 106 N2 gc/pd. This methodology provides a valuable resource for decision-makers and health authorities, specifically given the limitation of COVID-19 surveillance based on clinical data.
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Affiliation(s)
- Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Warsame Yusuf
- Public Health Risk Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - David Champredon
- Public Health Risk Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Pu Xia
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Chantel De Lange
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Seba El-Baroudy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Integrative Biology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada.
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17
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van Boven M, Hetebrij WA, Swart A, Nagelkerke E, van der Beek RF, Stouten S, Hoogeveen RT, Miura F, Kloosterman A, van der Drift AMR, Welling A, Lodder WJ, de Roda Husman AM. Patterns of SARS-CoV-2 circulation revealed by a nationwide sewage surveillance programme, the Netherlands, August 2020 to February 2022. Euro Surveill 2023; 28:2200700. [PMID: 37347416 PMCID: PMC10288829 DOI: 10.2807/1560-7917.es.2023.28.25.2200700] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/16/2023] [Indexed: 06/23/2023] Open
Abstract
BackgroundSurveillance of SARS-CoV-2 in wastewater offers a near real-time tool to track circulation of SARS-CoV-2 at a local scale. However, individual measurements of SARS-CoV-2 in sewage are noisy, inherently variable and can be left-censored.AimWe aimed to infer latent virus loads in a comprehensive sewage surveillance programme that includes all sewage treatment plants (STPs) in the Netherlands and covers 99.6% of the Dutch population.MethodsWe applied a multilevel Bayesian penalised spline model to estimate time- and STP-specific virus loads based on water flow-adjusted SARS-CoV-2 qRT-PCR data for one to four sewage samples per week for each of the more than 300 STPs.ResultsThe model captured the epidemic upsurges and downturns in the Netherlands, despite substantial day-to-day variation in the measurements. Estimated STP virus loads varied by more than two orders of magnitude, from ca 1012 virus particles per 100,000 persons per day in the epidemic trough in August 2020 to almost 1015 per 100,000 in many STPs in January 2022. The timing of epidemics at the local level was slightly shifted between STPs and municipalities, which resulted in less pronounced peaks and troughs at the national level.ConclusionAlthough substantial day-to-day variation is observed in virus load measurements, wastewater-based surveillance of SARS-CoV-2 that is performed at high sampling frequency can track long-term progression of an epidemic at a local scale in near real time.
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Affiliation(s)
- Michiel van Boven
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Wouter A Hetebrij
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Arno Swart
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Erwin Nagelkerke
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Rudolf Fhj van der Beek
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sjors Stouten
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Rudolf T Hoogeveen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Fuminari Miura
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Center for Marine Environmental Studies (CMES), Ehime University, Ehime, Japan
| | - Astrid Kloosterman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Centre for Environmental Safety and Security, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Anne-Merel R van der Drift
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Anne Welling
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Willemijn J Lodder
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ana Maria de Roda Husman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Institute for Risk Assessment Science (IRAS), Utrecht University, Utrecht, the Netherlands
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18
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Gonçalves-Brito AS, Magaldi M, Farias BO, Nascimento APA, Flores C, Montenegro KS, Lopes-Carvalho M, Gimenez A, Costa VSC, Assunção VC, Quidorne CS, Bianco K, Clementino MM. Environmental genomic surveillance of SARS-CoV-2 in wastewater in Rio de Janeiro, Brazil. JOURNAL OF WATER AND HEALTH 2023; 21:653-662. [PMID: 37254912 PMCID: wh_2023_034 DOI: 10.2166/wh.2023.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Wastewater-based epidemiology can be a complementary approach for monitoring SARS-CoV-2 prevalence, diversity, and geographic distribution. It is a complementary approach regarding its prevalence and diversity, and geographic distribution. The study aimed to evaluate the genetic diversity of SARS-CoV-2 in two wastewater treatment plants (WWTPs) in Rio de Janeiro, Brazil. Samples were collected over a period of January to December 2021 and were concentrated with PEG8000 and the presence of SARS-CoV-2 was detected using E and N1 genes. Partial sequencing of the SARS-CoV-2 genomes resulted in the identification of variants of concern and variants of interest throughout the collection period. It was possible to identify the Mu, Delta, Gamma and Omicron variants in WWTP1; on the contrary, no variants were observed in WWTP2. To the best of our knowledge, we detected the variant Mu (B.1.621) containing characteristic mutations (S:E484K, S:N501Y) from WWTP, for the first time, in Brazil. Another Mu variant detected from clinical surveillance was announced one month after our finding. The detection of SARS-CoV-2 in wastewater can serve as a tool to monitor the prevalence and epidemiology in each community, helping to understand the spread of the virus among the population.
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Affiliation(s)
- Andressa S Gonçalves-Brito
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail: ; Fiocruz Genomic Network, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Mariana Magaldi
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail: ; Fiocruz Genomic Network, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Beatriz Oliveira Farias
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail: ; Fiocruz Genomic Network, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil
| | - Ana Paula Alves Nascimento
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail:
| | - Claudia Flores
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail:
| | - Kaylanne S Montenegro
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail:
| | - Maiara Lopes-Carvalho
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail:
| | - Aline Gimenez
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail:
| | - Vinícius Souza Carvalho Costa
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail:
| | - Vinícius Carneiro Assunção
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail:
| | - Camila Silva Quidorne
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail:
| | - Kayo Bianco
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail: ; Fiocruz Genomic Network, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil; COVID-19 Monitoring Network in Wastewater, São Paulo, Brazil
| | - Maysa M Clementino
- National Institute of Quality Control in Health - INCQS, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil E-mail: ; Fiocruz Genomic Network, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ 4365, Brazil; COVID-19 Monitoring Network in Wastewater, São Paulo, Brazil
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19
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Tavazzi S, Cacciatori C, Comero S, Fatta-Kassinos D, Karaolia P, Iakovides IC, Loutsiou P, Gutierrez-Aguirre I, Lengar Z, Bajde I, Tenson T, Kisand V, Laas P, Panksep K, Tammert H, Mariani G, Skejo H, Gawlik BM. Short-term stability of wastewater samples for storage and shipment in the context of the EU Sewage Sentinel System for SARS-CoV-2. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:109623. [PMID: 36890876 PMCID: PMC9979635 DOI: 10.1016/j.jece.2023.109623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
In the context of an EU-wide surveillance system for SARS-CoV-2 in wastewater, recommended by the European Commission, this study aims to provide scientific support to the adequacy of transport and storage conditions of samples both in terms of duration and samples temperature. Three laboratories in Slovenia, Cyprus and Estonia investigated the short-term, one-week, isochronous stability of wastewater samples by RT-qPCR based detection of SARS-CoV-2 genes. The results were tested for statistical significance to determine uncertainty of quantification and shelf-life, at testing temperatures of + 20 °C and - 20 °C, relative to reference at + 4 °C. Samples were collected from three urban wastewater treatment plant influents and analysed respectively for SARS-CoV-2 genes N1, N2 (Laboratory 1), N2, E (Laboratory 2) and N3 (Laboratory 3), with various analytical methods. For a period of 7/8 days at + 20 °C, decreasing trends of measured concentrations were observed for all genes resulting in instability according to the statistical analysis, while at - 20 °C the trend of variation was stable only for N1, N2 (Laboratory 1) and N3 (Laboratory 3). Trends for gene E concentrations at - 20 °C (Laboratory 2) could not be tested statistically for stability because of lack of data. Over a period of just 3 days at + 20 °C, the variation was statistically non-significant indicating stability for genes N1, E and N3 for laboratories 1, 2 and 3, respectively. Nonetheless, the outcome of the study presents evidence to support the choice of the selected temperature at which samples shall be preserved during storage before analysis or transport to the laboratory. The conditions (+4 °C, ∼ few days) chosen for EU wastewater surveillance are in accordance with these results, highlighting the importance of stability testing of environmental samples to determine the short-term analytical uncertainty.
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Affiliation(s)
- S Tavazzi
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - C Cacciatori
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - S Comero
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - D Fatta-Kassinos
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - P Karaolia
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - I C Iakovides
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
- Department of Civil and Environmental Engineering, School of Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - P Loutsiou
- Nireas-International Water Research Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | | | - Z Lengar
- National Institute of Biology, Vecna Pot 111, SI-1000 Ljubljana, Slovenia
| | - I Bajde
- National Institute of Biology, Vecna Pot 111, SI-1000 Ljubljana, Slovenia
| | - T Tenson
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - V Kisand
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - P Laas
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - K Panksep
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - H Tammert
- Institute of Technology, University of Tartu, Nooruse 1, E-50411 Tartu, Estonia
| | - G Mariani
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - H Skejo
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
| | - B M Gawlik
- Ocean and Water Unit, Joint Research Centre, European Commission, via E. Fermi 2749, T.P. 120, I-21027 Ispra, Italy
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20
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Abstract
Millions of Norway rats (Rattus norvegicus) inhabit New York City (NYC), presenting the potential for transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to rats. We evaluated SARS-CoV-2 exposure among 79 rats captured from NYC during the fall of 2021. Our results showed that 13 of the 79 rats (16.5%) tested IgG- or IgM-positive, and partial SARS-CoV-2 genomes were recovered from all 4 rats that were qRT-PCR (reverse transcription-quantitative PCR)-positive. Genomic analyses suggest these viruses were associated with genetic lineage B, which was predominant in NYC in the spring of 2020 during the early pandemic period. To further investigate rat susceptibility to SARS-CoV-2 variants, we conducted a virus challenge study and showed that Alpha, Delta, and Omicron variants can cause infections in wild-type Sprague Dawley (SD) rats, including high replication levels in the upper and lower respiratory tracts and induction of both innate and adaptive immune responses. Additionally, the Delta variant resulted in the highest infectivity. In summary, our results indicate that rats are susceptible to infection with Alpha, Delta, and Omicron variants, and wild Norway rats in the NYC municipal sewer systems have been exposed to SARS-CoV-2. Our findings highlight the need for further monitoring of SARS-CoV-2 in urban rat populations and for evaluating the potential risk of secondary zoonotic transmission from these rat populations back to humans. IMPORTANCE The host tropism expansion of SARS-CoV-2 raises concern for the potential risk of reverse-zoonotic transmission of emerging variants into rodent species, including wild rat species. In this study, we present both genetic and serological evidence for SARS-CoV-2 exposure to the New York City wild rat population, and these viruses may be linked to the viruses that were circulating during the early stages of the pandemic. We also demonstrated that rats are susceptible to additional variants (i.e., Alpha, Delta, and Omicron) that have been predominant in humans and that susceptibility to infection varies by variant. Our findings highlight the reverse zoonosis of SARS-CoV-2 to urban rats and the need for further monitoring of SARS-CoV-2 in rat populations for potential secondary zoonotic transmission to humans.
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21
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Davis A, Keely SP, Brinkman NE, Bohrer Z, Ai Y, Mou X, Chattopadhyay S, Hershey O, Senko J, Hull N, Lytmer E, Quintero A, Lee J. Evaluation of intra- and inter-lab variability in quantifying SARS-CoV-2 in a state-wide wastewater monitoring network. ENVIRONMENTAL SCIENCE : WATER RESEARCH & TECHNOLOGY 2023; 9:1053-1068. [PMID: 37701755 PMCID: PMC10494892 DOI: 10.1039/d2ew00737a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
In December 2019, SARS-CoV-2, the virus that causes coronavirus disease 2019, was first reported and subsequently triggered a global pandemic. Wastewater monitoring, a strategy for quantifying viral gene concentrations from wastewater influents within a community, has served as an early warning and management tool for the spread of SARS-CoV-2 in a community. Ohio built a collaborative statewide wastewater monitoring network that is supported by eight labs (university, government, and commercial laboratories) with unique sample processing workflows. Consequently, we sought to characterize the variability in wastewater monitoring results for network labs. Across seven trials between October 2020 and November 2021, eight participating labs successfully quantified two SARS-CoV-2 RNA targets and human fecal indicator virus targets in wastewater sample aliquots with reproducible results, although recovery efficiencies of spiked surrogates ranged from 3 to 75%. When SARS-CoV-2 gene fragment concentrations were adjusted for recovery efficiency and flow, the proportion of variance between laboratories was minimized, serving as the best model to account for between-lab variance. Another adjustment factor (alone and in different combinations with the above factors) considered to account for sample and measurement variability includes fecal marker normalization. Genetic quantification variability can be attributed to many factors, including the methods, individual samples, and water quality parameters. In addition, statistically significant correlations were observed between SARS-CoV-2 RNA and COVID-19 case numbers, supporting the notion that wastewater surveillance continues to serve as an effective monitoring tool. This study serves as a real-time example of multi-laboratory collaboration for public health preparedness for infectious diseases.
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Affiliation(s)
- Angela Davis
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, 1841 Neil Avenue, Columbus, OH 43210, USA
| | - Scott P Keely
- United States Environmental Protection Agency, Office of Research and Development, USA
| | - Nichole E Brinkman
- United States Environmental Protection Agency, Office of Research and Development, USA
| | | | - Yuehan Ai
- Department of Food Science & Technology, The Ohio State University, USA
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, USA
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, Department of Biology and Department of Geosciences, University of Toledo, USA
| | - Olivia Hershey
- Department of Geosciences and Biology, University of Akron, USA
| | - John Senko
- Department of Geosciences and Biology, University of Akron, USA
| | - Natalie Hull
- Department of Civil, Environmental and Geodetic Engineering and Sustainability Institute, The Ohio State University, USA
| | - Eva Lytmer
- Department of Biological Sciences, Bowling Green State University, USA
| | | | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, 1841 Neil Avenue, Columbus, OH 43210, USA
- Department of Food Science & Technology, The Ohio State University, USA
- Infectious Diseases Institute, The Ohio State University, USA
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22
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Henriques TB, Cassini ST, de Pinho Keller R. Contribution of wastewater-based epidemiology to SARS-CoV-2 screening in Brazil and the United States. JOURNAL OF WATER AND HEALTH 2023; 21:343-353. [PMID: 37338314 PMCID: wh_2023_260 DOI: 10.2166/wh.2023.260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Wastewater-based epidemiology (WBE) is a valuable tool for investigating the existence, prevalence, and spread of pathogens, such as SARS-CoV-2, in a given population. WBE, proposed as part of the SARS-CoV-2 surveillance strategy for monitoring virus circulation, may complement clinical data and contribute to reducing the spread of the disease through early detection. In developing countries such as Brazil, where clinical data are scarce, information obtained from wastewater monitoring can be crucial for designing public health interventions. In the United States, the country with the largest number of confirmed SARS-CoV-2 cases worldwide, WBE programs have begun to be carried out to investigate correlations with coronavirus disease 2019 (COVID-19) clinical data and support health agencies in decision-making to prevent the spread of the disease. This systematic review aimed to assess the contribution of WBE to SARS-CoV-2 screening in Brazil and the United States and compare studies conducted in a developed and developing country. Studies in Brazil and the United States showed WBE to be an important epidemiological surveillance strategy in the context of the COVID-19 pandemic. WBE approaches are useful for early detection of COVID-19 outbreaks, estimation of clinical cases, and assessment of the effectiveness of vaccination program.
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Affiliation(s)
- Taciane Barbosa Henriques
- Sanitation Laboratory, Department of Environmental Engineering, Federal University of Espírito Santo, Vitória, Espirito Santo, Brazil E-mail:
| | - Servio Túlio Cassini
- Sanitation Laboratory, Department of Environmental Engineering, Federal University of Espírito Santo, Vitória, Espirito Santo, Brazil E-mail:
| | - Regina de Pinho Keller
- Sanitation Laboratory, Department of Environmental Engineering, Federal University of Espírito Santo, Vitória, Espirito Santo, Brazil E-mail:
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23
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SARS-CoV-2 exposure in Norway rats ( Rattus norvegicus) from New York City. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.11.18.517156. [PMID: 36451891 PMCID: PMC9709794 DOI: 10.1101/2022.11.18.517156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Millions of Norway rats (Rattus norvegicus) inhabit New York City (NYC), presenting the potential for transmission of SARS-CoV-2 from humans to rats and other wildlife. We evaluated SARS-CoV-2 exposure among 79 rats captured from NYC during the fall of 2021. Results showed that 13 of 79 rats (16.5%) tested IgG or IgM positive, and partial genomes of SARS-CoV-2 were recovered from four rats that were qRT-PCR positive. Using a virus challenge study, we also showed that Alpha, Delta, and Omicron variants can cause robust infections in wild-type Sprague Dawley (SD) rats, including high level replications in the upper and lower respiratory tracts and induction of both innate and adaptive immune responses. Additionally, the Delta variant resulted in the highest infectivity. In summary, our results indicated that rats are susceptible to infection with Alpha, Delta, and Omicron variants, and rats in the NYC municipal sewer systems have been exposed to SARS-CoV-2. Our findings highlight the potential risk of secondary zoonotic transmission from urban rats and the need for further monitoring of SARS-CoV-2 in those populations.
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24
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Maksimovic Carvalho Ferreira O, Lengar Ž, Kogej Z, Bačnik K, Bajde I, Milavec M, Županič A, Mehle N, Kutnjak D, Ravnikar M, Gutierrez-Aguirre I. Evaluation of Methods and Processes for Robust Monitoring of SARS-CoV-2 in Wastewater. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:384-400. [PMID: 35999429 PMCID: PMC9398038 DOI: 10.1007/s12560-022-09533-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/01/2022] [Indexed: 05/15/2023]
Abstract
The SARS-CoV-2 pandemic has accelerated the development of virus concentration and molecular-based virus detection methods, monitoring systems and overall approach to epidemiology. Early into the pandemic, wastewater-based epidemiology started to be employed as a tool for tracking the virus transmission dynamics in a given area. The complexity of wastewater coupled with a lack of standardized methods led us to evaluate each step of the analysis individually and see which approach gave the most robust results for SARS-CoV-2 monitoring in wastewater. In this article, we present a step-by-step, retrospective view on the method development and implementation for the case of a pilot monitoring performed in Slovenia. We specifically address points regarding the thermal stability of the samples during storage, screening for the appropriate sample concentration and RNA extraction procedures and real-time PCR assay selection. Here, we show that the temperature and duration of the storage of the wastewater sample can have a varying impact on the detection depending on the structural form in which the SARS-CoV-2 target is present. We found that concentration and RNA extraction using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using semi-automated kit from Promega give the most optimal results out of the seven methods tested. Lastly, we confirm the use of N1 and N2 assays developed by the CDC (USA) as the best performing assays among four tested in combination with Fast Virus 1-mastermix. Data show a realistic overall process for method implementation as well as provide valuable information in regards to how different approaches in the analysis compare to one another under the specific conditions present in Slovenia during a pilot monitoring running from the beginning of the pandemic.
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Affiliation(s)
- Olivera Maksimovic Carvalho Ferreira
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
- International Postgraduate School Jožef Stefan, Jamova cesta 39, 1000, Ljubljana, Slovenia.
| | - Živa Lengar
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Zala Kogej
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
- International Postgraduate School Jožef Stefan, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Katarina Bačnik
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Irena Bajde
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Mojca Milavec
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Anže Županič
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Dvorec Lanthieri, Glavni trg 8, 5271, Vipava, Slovenia
| | - Denis Kutnjak
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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25
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Strike W, Amirsoleimani A, Olaleye A, Noble A, Lewis K, Faulkner L, Backus S, Lindeman S, Eterovich K, Fraley M, Banadaki MD, Torabi S, Rockward A, Zeitlow E, Liversedge M, Keck J, Berry S. Development and Validation of a Simplified Method for Analysis of SARS-CoV-2 RNA in University Dormitories. ACS ES&T WATER 2022; 2:1984-1991. [PMID: 37552725 PMCID: PMC9115885 DOI: 10.1021/acsestwater.2c00044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 05/26/2023]
Abstract
Over the course of the COVID-19 pandemic, wastewater surveillance has become a useful tool for describing SARS-CoV-2 prevalence in populations of varying size, from individual facilities (e.g., university residence halls, nursing homes, prisons) to entire municipalities. Wastewater analysis for SARS-CoV-2 RNA requires specialized equipment, expensive consumables, and expert staff, limiting its feasibility and scalability. Further, the extremely labile nature of viral RNA complicates sample transportation, especially in regions with limited access to reliable cold chains. Here, we present a new method for wastewater analysis, termed exclusion-based sample preparation (ESP), that substantially simplifies workflow (at least 70% decrease in time; 40% decrease in consumable usage compared with traditional techniques) by targeting the labor-intensive processing steps of RNA purification and concentration. To optimize and validate this method, we analyzed wastewater samples from residence halls at the University of Kentucky, of which 34% (44/129) contained detectible SARS-CoV-2 RNA. Although concurrent clinical testing was not comprehensive, student infections were identified in the 7 days following a positive wastewater detection in 68% of samples. This pilot study among university residence halls validated the performance and utility of the ESP method, laying the foundation for future studies in regions of the world where wastewater testing is not currently feasible.
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Affiliation(s)
- William Strike
- Departments of Biomedical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Atena Amirsoleimani
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Abisola Olaleye
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Ann Noble
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Kevin Lewis
- Environmental Quality Management, University of Kentucky, 355 Cooper Drive, Lexington, KY 40508
| | - Lee Faulkner
- Environmental Quality Management, University of Kentucky, 355 Cooper Drive, Lexington, KY 40508
| | - Spencer Backus
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Sierra Lindeman
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Katrina Eterovich
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Melicity Fraley
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Mohammad Dehghan Banadaki
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Soroosh Torabi
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Alexus Rockward
- Departments of Biomedical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Eli Zeitlow
- Department of Mechanical Engineering, University of Wisconsin-Platteville, 1 University Plaza, Platteville, WI 53818
| | - Matthew Liversedge
- Family and Community Medicine, University of Kentucky 2195 Harrodsburg Rd, Ste 125, Lexington, KY 40504
| | - James Keck
- Family and Community Medicine, University of Kentucky 2195 Harrodsburg Rd, Ste 125, Lexington, KY 40504
| | - Scott Berry
- Departments of Biomedical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
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26
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Roldan-Hernandez L, Graham KE, Duong D, Boehm AB. Persistence of Endogenous SARS-CoV-2 and Pepper Mild Mottle Virus RNA in Wastewater-Settled Solids. ACS ES&T WATER 2022; 2:1944-1952. [PMID: 36380769 PMCID: PMC8938836 DOI: 10.1021/acsestwater.2c00003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Limited information is available on the decay rate of endogenous SARS-CoV-2 and pepper mild mottle virus (PMMoV) RNA in wastewater and primary settled solids, potentially limiting an understanding of how transit or holding times within wastewater infrastructure might impact RNA measurements and their relationship to community COVID-19 infections. In this study, primary settled solids samples were collected from two wastewater treatment plants in the San Francisco Bay Area. Samples were thoroughly mixed, aliquoted into subsamples, and stored at 4, 22, and 37 °C for 10 days. The concentrations of SARS-CoV-2 (N1 and N2 targets) and PMMoV RNA were measured using an RT-ddPCR. Limited decay (<1 log10 reduction) was observed in the detection of viral RNA targets at all temperature conditions, suggesting that SARS-CoV-2 and PMMoV RNA can be highly persistent in solids. First-order decay rate constants ranged from 0.011 to 0.098 day-1 for SARS-CoV-2 RNA and from 0.010 to 0.091 day-1 for PMMoV RNA depending on the temperature conditions. A slower decay was observed for SARS-CoV-2 RNA in primary settled solids compared to previously reported decay in wastewater influent. Further research is needed to understand if solid content and wastewater characteristics might influence the persistence of viral RNA targets.
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Affiliation(s)
- Laura Roldan-Hernandez
- Department
of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford 94305, California, United States
| | - Katherine E. Graham
- Department
of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford 94305, California, United States
| | - Dorothea Duong
- Verily
Life Sciences, San Francisco, California 94080, United States
| | - Alexandria B. Boehm
- Department
of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford 94305, California, United States
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27
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Guérin-Rechdaoui S, Bize A, Levesque-Ninio C, Janvier A, Lacroix C, Le Brizoual F, Barbier J, Amsaleg CR, Azimi S, Rocher V. Fate of SARS-CoV-2 coronavirus in wastewater treatment sludge during storage and thermophilic anaerobic digestion. ENVIRONMENTAL RESEARCH 2022; 214:114057. [PMID: 35995225 PMCID: PMC9391084 DOI: 10.1016/j.envres.2022.114057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/31/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Since the COVID-19 outbreak has started in late 2019, SARS-CoV-2 has been widely detected in human stools and in urban wastewater. No infectious SARS-CoV-2 particles have been detected in raw wastewater until now, but it has been reported occasionally in human stools. This has raised questions on the fate of SARS-CoV-2 during wastewater treatment and notably in its end-product, wastewater treatment sludge, which is classically valorized by land spreading for agricultural amendment. In the present work, we focused on SARS-CoV-2 stability in wastewater treatment sludge, either during storage (4 °C, room temperature) or thermophilic anaerobic digestion (50 °C). Anaerobic digestion is one of the possible processes for sludge valorization. Experiments were conducted in laboratory pilots; SARS-CoV-2 detection was based on RT-quantitative PCR or RT-digital droplet PCR. In addition to SARS-CoV-2, Bovine Coronavirus (BCoV) particles were used as surrogate virus. The RNA from SARS-CoV-2 particles, inactivated or not, was close to the detection limit but stable in wastewater treatment sludge, over the whole duration of the assays at 4 °C (55 days) and at ambient temperature (∼20 °C, 25 days). By contrast, the RNA levels of BCoV and inactivated SARS-CoV-2 particles decreased rapidly during the thermophilic anaerobic digestion of wastewater treatment sludge lasting for 5 days, with final levels that were close to the detection limit. Although the particles' infectivity was not assessed, these results suggest that thermophilic anaerobic digestion is a suitable process for sludge sanitation, consistent with previous knowledge on other coronaviruses.
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Affiliation(s)
| | - Ariane Bize
- Université Paris-Saclay, INRAE, PROSE, Antony, 92160, France
| | - Camille Levesque-Ninio
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Alice Janvier
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Carlyne Lacroix
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
| | - Florence Le Brizoual
- LABOCEA, Fougères. BioAgroPolis, 10 Rue Claude Bourgelat CS 30616 - Javené, Fougères Cedex, 35306, France
| | - Jérôme Barbier
- ID Solutions, Development Department, Grabels, 34790, France
| | | | - Sam Azimi
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
| | - Vincent Rocher
- SIAAP, Innovation Department, 82 Avenue Kléber, Colombes, 92700, France
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28
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Hsu SY, Bayati M, Li C, Hsieh HY, Belenchia A, Klutts J, Zemmer SA, Reynolds M, Semkiw E, Johnson HY, Foley T, Wieberg CG, Wenzel J, Johnson MC, Lin CH. Biomarkers selection for population normalization in SARS-CoV-2 wastewater-based epidemiology. WATER RESEARCH 2022; 223:118985. [PMID: 36030667 PMCID: PMC9376872 DOI: 10.1016/j.watres.2022.118985] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/15/2022] [Accepted: 08/13/2022] [Indexed: 05/29/2023]
Abstract
Wastewater-based epidemiology (WBE) has been one of the most cost-effective approaches to track the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) levels in the communities since the coronavirus disease 2019 (COVID-19) outbreak in 2020. Normalizing SARS-CoV-2 concentrations by the population biomarkers in wastewater is critical for interpreting the viral loads, comparing the epidemiological trends among the sewersheds, and identifying the vulnerable communities. In this study, five population biomarkers, pepper mild mottle virus (PMMoV), creatinine (CRE), 5-hydroxyindoleacetic acid (5-HIAA), caffeine (CAF) and its metabolite paraxanthine (PARA) were investigated and validated for their utility in normalizing the SARS-CoV-2 loads through two normalizing approaches using the data from 64 wastewater treatment plants (WWTPs) in Missouri. Their utility in assessing the real-time population contributing to the wastewater was also evaluated. The best performing candidate was further tested for its capacity for improving correlation between normalized SARS-CoV-2 loads and the clinical cases reported in the City of Columbia, Missouri, a university town with a constantly fluctuating population. Our results showed that, except CRE, the direct and indirect normalization approaches using biomarkers allow accounting for the changes in wastewater dilution and differences in relative human waste input over time regardless flow volume and population of the given WWTP. Among selected biomarkers, PARA is the most reliable population biomarker in determining the SARS-CoV-2 load per capita due to its high accuracy, low variability, and high temporal consistency to reflect the change in population dynamics and dilution in wastewater. It also demonstrated its excellent utility for real-time assessment of the population contributing to the wastewater. In addition, the viral loads normalized by the PARA-estimated population significantly improved the correlation (rho=0.5878, p < 0.05) between SARS-CoV-2 load per capita and case numbers per capita. This chemical biomarker complements the current normalization scheme recommended by CDC and helps us understand the size, distribution, and dynamics of local populations for forecasting the prevalence of SARS-CoV2 within each sewershed.
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Affiliation(s)
- Shu-Yu Hsu
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA; Center for Agroforestry, University of Missouri, Columbia, MO 65201, USA
| | - Mohamed Bayati
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Chenhui Li
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Hsin-Yeh Hsieh
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Anthony Belenchia
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Jessica Klutts
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO, USA
| | - Sally A Zemmer
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO, USA
| | - Melissa Reynolds
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Elizabeth Semkiw
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Hwei-Yiing Johnson
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Trevor Foley
- Missouri Department of Corrections, Jefferson City, MO, USA
| | - Chris G Wieberg
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO, USA
| | - Jeff Wenzel
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65201, USA
| | - Chung-Ho Lin
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA; Center for Agroforestry, University of Missouri, Columbia, MO 65201, USA.
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29
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Bayati M, Hsieh HY, Hsu SY, Li C, Rogers E, Belenchia A, Zemmer SA, Blanc T, LePage C, Klutts J, Reynolds M, Semkiw E, Johnson HY, Foley T, Wieberg CG, Wenzel J, Lyddon T, LePique M, Rushford C, Salcedo B, Young K, Graham M, Suarez R, Ford A, Lei Z, Sumner L, Mooney BP, Wei X, Greenlief CM, Johnson MC, Lin CH. Identification and quantification of bioactive compounds suppressing SARS-CoV-2 signals in wastewater-based epidemiology surveillance. WATER RESEARCH 2022; 221:118824. [PMID: 35830746 PMCID: PMC9253601 DOI: 10.1016/j.watres.2022.118824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 05/21/2023]
Abstract
Recent SARS-CoV-2 wastewater-based epidemiology (WBE) surveillance have documented a positive correlation between the number of COVID-19 patients in a sewershed and the level of viral genetic material in the wastewater. Efforts have been made to use the wastewater SARS-CoV-2 viral load to predict the infected population within each sewershed using a multivariable regression approach. However, reported clear and sustained variability in SARS-CoV-2 viral load among treatment facilities receiving industrial wastewater have made clinical prediction challenging. Several classes of molecules released by regional industries and manufacturing facilities, particularly the food processing industry, can significantly suppress the SARS-CoV-2 signals in wastewater by breaking down the lipid-bilayer of the membranes. Therefore, a systematic ranking process in conjugation with metabolomic analysis was developed to identify the wastewater treatment facilities exhibiting SARS-CoV-2 suppression and identify and quantify the chemicals suppressing the SARS-COV-2 signals. By ranking the viral load per diagnosed case among the sewersheds, we successfully identified the wastewater treatment facilities in Missouri, USA that exhibit SARS-CoV-2 suppression (significantly lower than 5 × 1011 gene copies/reported case) and determined their suppression rates. Through both untargeted global chemical profiling and targeted analysis of wastewater samples, 40 compounds were identified as candidates of SARS-CoV-2 signal suppressors. Among these compounds, 14 had higher concentrations in wastewater treatment facilities that exhibited SARS-CoV-2 signal suppression compared to the unsuppressed control facilities. Stepwise regression analyses indicated that 4-nonylphenol, palmitelaidic acid, sodium oleate, and polyethylene glycol dioleate are positively correlated with SARS-CoV-2 signal suppression rates. Suppression activities were further confirmed by incubation studies, and the suppression kinetics for each bioactive compound were determined. According to the results of these experiments, bioactive molecules in wastewater can significantly reduce the stability of SARS-CoV-2 genetic marker signals. Based on the concentrations of these chemical suppressors, a correction factor could be developed to achieve more reliable and unbiased surveillance results for wastewater treatment facilities that receive wastewater from similar industries.
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Affiliation(s)
- Mohamed Bayati
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Hsin-Yeh Hsieh
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Shu-Yu Hsu
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA; Center for Agroforestry, University of Missouri, Columbia, MO 65211, USA
| | - Chenhui Li
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Elizabeth Rogers
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA; Center for Agroforestry, University of Missouri, Columbia, MO 65211, USA
| | - Anthony Belenchia
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO 65109, USA
| | - Sally A Zemmer
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65101, USA
| | - Todd Blanc
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65101, USA
| | - Cindy LePage
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65101, USA
| | - Jessica Klutts
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65101, USA
| | - Melissa Reynolds
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO 65109, USA
| | - Elizabeth Semkiw
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO 65109, USA
| | - Hwei-Yiing Johnson
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO 65109, USA
| | - Trevor Foley
- Missouri Department of Corrections, Jefferson City, MO 65109, USA
| | - Chris G Wieberg
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65101, USA
| | - Jeff Wenzel
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO 65109, USA
| | - Terri Lyddon
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Mary LePique
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Clayton Rushford
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Braxton Salcedo
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Kara Young
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Madalyn Graham
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Reinier Suarez
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Anarose Ford
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Zhentian Lei
- Metabolomics Center, Department of Biochemistry, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Lloyd Sumner
- Metabolomics Center, Department of Biochemistry, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Brian P Mooney
- Charles W. Gehrke Proteomics Center, Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Xing Wei
- Charles W. Gehrke Proteomics Center, Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - C Michael Greenlief
- Charles W. Gehrke Proteomics Center, Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Chung-Ho Lin
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA; Center for Agroforestry, University of Missouri, Columbia, MO 65211, USA.
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30
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Wolfe M, Hughes B, Duong D, Chan-Herur V, Wigginton KR, White BJ, Boehm AB. Detection of SARS-CoV-2 Variants Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in Wastewater Settled Solids Using Mutation-Specific Assays Is Associated with Regional Detection of Variants in Clinical Samples. Appl Environ Microbiol 2022; 88:e0004522. [PMID: 35380449 DOI: 10.1101/2022.01.17.22269439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Changes in the circulation of SARS-CoV-2 variants of concern (VOCs) may require changes in the public health response to the COVID-19 pandemic, as they have the potential to evade vaccines and pharmaceutical interventions and may be more transmissive than other SARS-CoV-2 variants. As such, it is essential to track and prevent their spread in susceptible communities. We developed digital reverse transcription (RT)-PCR assays for mutations characteristic of VOCs and used them to quantify those mutations in samples of wastewater settled solids collected from a publicly owned treatment works (POTW) during different phases of the COVID-19 pandemic. Wastewater concentrations of single mutations characteristic of each VOC, normalized by the concentration of a conserved SARS-CoV-2 N gene, correlate with regional estimates of the proportion of clinical infections caused by each VOC. These results suggest that targeted RT-PCR assays can be used to detect variants circulating in communities and inform the public health response to the pandemic. IMPORTANCE Wastewater represents a pooled biological sample of the contributing community and thus a resource for assessing community health. Here, we show that emergence, spread, and disappearance of SARS-CoV-2 infections caused by variants of concern are reflected in the presence of variant genomic RNA in wastewater settled solids. This work highlights an important public health use case for wastewater.
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Affiliation(s)
- Marlene Wolfe
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | | | - Dorothea Duong
- Verily Life Sciences, South San Francisco, California, USA
| | | | - Krista R Wigginton
- Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Bradley J White
- Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandria B Boehm
- Civil and Environmental Engineering, Stanford Universitygrid.168010.e, Stanford, California, USA
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31
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Detection of SARS-CoV-2 Variants Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in Wastewater Settled Solids Using Mutation-Specific Assays Is Associated with Regional Detection of Variants in Clinical Samples. Appl Environ Microbiol 2022; 88:e0004522. [PMID: 35380449 PMCID: PMC9040616 DOI: 10.1128/aem.00045-22] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Changes in the circulation of SARS-CoV-2 variants of concern (VOCs) may require changes in the public health response to the COVID-19 pandemic, as they have the potential to evade vaccines and pharmaceutical interventions and may be more transmissive than other SARS-CoV-2 variants. As such, it is essential to track and prevent their spread in susceptible communities. We developed digital reverse transcription (RT)-PCR assays for mutations characteristic of VOCs and used them to quantify those mutations in samples of wastewater settled solids collected from a publicly owned treatment works (POTW) during different phases of the COVID-19 pandemic. Wastewater concentrations of single mutations characteristic of each VOC, normalized by the concentration of a conserved SARS-CoV-2 N gene, correlate with regional estimates of the proportion of clinical infections caused by each VOC. These results suggest that targeted RT-PCR assays can be used to detect variants circulating in communities and inform the public health response to the pandemic. IMPORTANCE Wastewater represents a pooled biological sample of the contributing community and thus a resource for assessing community health. Here, we show that emergence, spread, and disappearance of SARS-CoV-2 infections caused by variants of concern are reflected in the presence of variant genomic RNA in wastewater settled solids. This work highlights an important public health use case for wastewater.
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32
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Sakarovitch C, Schlosser O, Courtois S, Proust-Lima C, Couallier J, Pétrau A, Litrico X, Loret JF. Monitoring of SARS-CoV-2 in wastewater: what normalisation for improved understanding of epidemic trends? JOURNAL OF WATER AND HEALTH 2022; 20:712-726. [PMID: 35482387 DOI: 10.2166/wh.2022.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2 RNA quantification in wastewater has emerged as a relevant additional means to monitor the COVID-19 pandemic. However, the concentration can be affected by black water dilution factors or movements of the sewer shed population, leading to misinterpretation of measurement results. The aim of this study was to evaluate the performance of different indicators to accurately interpret SARS-CoV-2 in wastewater. Weekly/bi-weekly measurements from three cities in France were analysed from February to September 2021. The concentrations of SARS-CoV-2 gene copies were normalised to the faecal-contributing population using simple sewage component indicators. To reduce the measurement error, a composite index was created to combine simultaneously the information carried by the simple indicators. The results showed that the regularity (mean absolute difference between observation and the smoothed curve) of the simple indicators substantially varied across sampling points. The composite index consistently showed better regularity compared to the other indicators and was associated to the lowest variation in correlation coefficient across sampling points. These findings suggest the recommendation for the use of a composite index in wastewater-based epidemiology to compensate for variability in measurement results.
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Affiliation(s)
| | | | - Sophie Courtois
- SUEZ, CIRSEE, 38 rue du Président Wilson, 78230 Le Pecq, France
| | - Cécile Proust-Lima
- Université de Bordeaux, INSERM, Bordeaux Population Health Center, UMR1219, F-33000 Bordeaux, France
| | - Joanne Couallier
- SUEZ, LYRE, 15 av Léonard de Vinci, 33600 Pessac, France E-mail:
| | - Agnès Pétrau
- SUEZ Rivages Pro Tech, Technopôle Izarbel, 2 Allée Théodore Monod, 64210 Bidart, France
| | - Xavier Litrico
- SUEZ, CB21, 16 Place de l'Iris, 92040 Paris La Défense, France
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33
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Hsu SY, Bayati MB, Li C, Hsieh HY, Belenchia A, Klutts J, Zemmer SA, Reynolds M, Semkiw E, Johnson HY, Foley T, Wieberg CG, Wenzel J, Johnson MC, Lin CH. Biomarkers Selection for Population Normalization in SARS-CoV-2 Wastewater-based Epidemiology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.03.14.22272359. [PMID: 35313587 PMCID: PMC8936110 DOI: 10.1101/2022.03.14.22272359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Wastewater-based epidemiology (WBE) has been one of the most cost-effective approaches to track the SARS-CoV-2 levels in the communities since the COVID-19 outbreak in 2020. Normalizing SARS-CoV-2 concentrations by the population biomarkers in wastewater can be critical for interpreting the viral loads, comparing the epidemiological trends among the sewersheds, and identifying the vulnerable communities. In this study, five population biomarkers, pepper mild mottle virus (pMMoV), creatinine (CRE), 5-hydroxyindoleacetic acid (5-HIAA), caffeine (CAF) and its metabolite paraxanthine (PARA) were investigated for their utility in normalizing the SARS-CoV-2 loads through developed direct and indirect approaches. Their utility in assessing the real-time population contributing to the wastewater was also evaluated. The best performed candidate was further tested for its capacity for improving correlation between normalized SARS-CoV-2 loads and the clinical cases reported in the City of Columbia, Missouri, a university town with a constantly fluctuated population. Our results showed that, except CRE, the direct and indirect normalization approaches using biomarkers allow accounting for the changes in wastewater dilution and differences in relative human waste input over time regardless flow volume and population at any given WWTP. Among selected biomarkers, PARA is the most reliable population biomarker in determining the SARS-CoV-2 load per capita due to its high accuracy, low variability, and high temporal consistency to reflect the change in population dynamics and dilution in wastewater. It also demonstrated its excellent utility for real-time assessment of the population contributing to the wastewater. In addition, the viral loads normalized by the PARA-estimated population significantly improved the correlation ( rho =0.5878, p <0.05) between SARS-CoV-2 load per capita and case numbers per capita. This chemical biomarker offers an excellent alternative to the currently CDC-recommended pMMoV genetic biomarker to help us understand the size, distribution, and dynamics of local populations for forecasting the prevalence of SARS-CoV2 within each sewershed. HIGHLIGHT bullet points The paraxanthine (PARA), the metabolite of the caffeine, is a more reliable population biomarker in SARS-CoV-2 wastewater-based epidemiology studies than the currently recommended pMMoV genetic marker.SARS-CoV-2 load per capita could be directly normalized using the regression functions derived from correlation between paraxanthine and population without flowrate and population data.Normalizing SARS-CoV-2 levels with the chemical marker PARA significantly improved the correlation between viral loads per capita and case numbers per capita.The chemical marker PARA demonstrated its excellent utility for real-time assessment of the population contributing to the wastewater.
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Affiliation(s)
- Shu-Yu Hsu
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
- Center for Agroforestry, University of Missouri, Columbia, MO 65201, USA
| | - Mohamed B Bayati
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Chenhui Li
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Hsin-Yeh Hsieh
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Anthony Belenchia
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Jessica Klutts
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO, USA
| | - Sally A Zemmer
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO, USA
| | - Melissa Reynolds
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Elizabeth Semkiw
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Hwei-Yiing Johnson
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Trevor Foley
- Missouri Department of Corrections, Jefferson City, MO, USA
| | - Chris G Wieberg
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO, USA
| | - Jeff Wenzel
- Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center, Columbia, MO 65201, USA
| | - Chung-Ho Lin
- School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
- Center for Agroforestry, University of Missouri, Columbia, MO 65201, USA
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34
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Smyth DS, Trujillo M, Gregory DA, Cheung K, Gao A, Graham M, Guan Y, Guldenpfennig C, Hoxie I, Kannoly S, Kubota N, Lyddon TD, Markman M, Rushford C, San KM, Sompanya G, Spagnolo F, Suarez R, Teixeiro E, Daniels M, Johnson MC, Dennehy JJ. Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Nat Commun 2022; 13:635. [PMID: 35115523 PMCID: PMC8813986 DOI: 10.1038/s41467-022-28246-3] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/10/2022] [Indexed: 11/21/2022] Open
Abstract
Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we deep sequence most of the receptor binding domain coding sequence of the S protein of SARS-CoV-2 isolated from the New York City wastewater. Here we report detecting increasing frequencies of novel cryptic SARS-CoV-2 lineages not recognized in GISAID's EpiCoV database. These lineages contain mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern. Some of these mutations expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. Finally, pseudoviruses containing the spike amino acid sequence of these lineages were resistant to different classes of receptor binding domain neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these lineages, including the possibility that these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir.
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Affiliation(s)
- Davida S Smyth
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX, 78224, USA
| | - Monica Trujillo
- Department of Biological Sciences and Geology, Queensborough Community College of The City University of New York, Queens, NY, 11364, USA
| | - Devon A Gregory
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Kristen Cheung
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Anna Gao
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Maddie Graham
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Yue Guan
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Caitlyn Guldenpfennig
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Irene Hoxie
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Sherin Kannoly
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Nanami Kubota
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Terri D Lyddon
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Michelle Markman
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Clayton Rushford
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Kaung Myat San
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Geena Sompanya
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX, 78224, USA
| | - Fabrizio Spagnolo
- Department of Biological & Environmental Sciences, Long Island University-Post, Greenvale, New York, 11548, USA
| | - Reinier Suarez
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Emma Teixeiro
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Mark Daniels
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
| | - John J Dennehy
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA.
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