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Champredon D, Papst I, Yusuf W. ern: An [Formula: see text] package to estimate the effective reproduction number using clinical and wastewater surveillance data. PLoS One 2024; 19:e0305550. [PMID: 38905266 PMCID: PMC11192340 DOI: 10.1371/journal.pone.0305550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/31/2024] [Indexed: 06/23/2024] Open
Abstract
The effective reproduction number, [Formula: see text], is an important epidemiological metric used to assess the state of an epidemic, as well as the effectiveness of public health interventions undertaken in response. When [Formula: see text] is above one, it indicates that new infections are increasing, and thus the epidemic is growing, while an [Formula: see text] is below one indicates that new infections are decreasing, and so the epidemic is under control. There are several established software packages that are readily available to statistically estimate [Formula: see text] using clinical surveillance data. However, there are comparatively few accessible tools for estimating [Formula: see text] from pathogen wastewater concentration, a surveillance data stream that cemented its utility during the COVID-19 pandemic. We present the [Formula: see text] package ern that aims to perform the estimation of the effective reproduction number from real-world wastewater or aggregated clinical surveillance data in a user-friendly way.
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Affiliation(s)
- David Champredon
- Public Health Risk Sciences Division, Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
| | - Irena Papst
- Public Health Risk Sciences Division, Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
| | - Warsame Yusuf
- Public Health Risk Sciences Division, Public Health Agency of Canada, National Microbiology Laboratory, Guelph, Ontario, Canada
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2
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Ngqwala B, Msolo L, Ebomah KE, Nontongana N, Okoh AI. Distribution of SARS-CoV-2 Genomes in Wastewaters and the Associated Potential Infection Risk for Plant Workers in Typical Urban and Peri-Urban Communities of the Buffalo City Region, South Africa. Viruses 2024; 16:871. [PMID: 38932163 PMCID: PMC11209190 DOI: 10.3390/v16060871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater has been reported in several studies and similar research can be used as a proxy for an early warning of potential Coronavirus disease 2019 (COVID-19) outbreaks. This study focused on profiling the incidence of SARS-CoV-2 genomes in wastewater samples obtained from facilities located in the Buffalo City Municipality. Raw samples were collected weekly using the grab technique for a period of 48 weeks. Ribonucleic acids were extracted from the samples, using the QIAGEN Powersoil Total RNA Extraction kit, and extracted RNA samples were further profiled for the presence of SARS-CoV-2 genomes using Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) technique. Furthermore, various environmental matrices were utilized to estimate the potential health risk to plant operators associated with exposure to SARS-CoV-2 viral particles using the quantitative microbiological risk assessment (QMRA) model. Our findings revealed the prevalence of SARS-CoV-2 genomes with concentrations that ranged from 0.22 × 103 to 17.60 × 103 genome copies per milliliter (GC/mL). Different exposure scenarios were employed for the QMRA model, and the findings indicate a probability of infection (P(i)) ranging from 0.93% to 37.81% across the study sites. Similarly, the P(i) was highly significant (p < 0.001) for the 20 mL volumetric intake as compared to other volumetric intake scenarios, and high P(i) was also observed in spring, autumn, and winter for all WWTPs. The P(i) was significantly different (p < 0.05) with respect to the different seasons and with respect to different volume scenarios.
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Affiliation(s)
- Balisa Ngqwala
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (L.M.); (K.E.E.); (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
| | - Luyanda Msolo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (L.M.); (K.E.E.); (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
| | - Kingsley Ehi Ebomah
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (L.M.); (K.E.E.); (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
| | - Nolonwabo Nontongana
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (L.M.); (K.E.E.); (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa; (L.M.); (K.E.E.); (N.N.); (A.I.O.)
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
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Chen C, Kaur G, Adiga A, Espinoza B, Venkatramanan S, Warren A, Lewis B, Crow J, Singh R, Lorentz A, Toney D, Marathe M. Wastewater-based Epidemiology for COVID-19 Surveillance: A Survey. ARXIV 2024:arXiv:2403.15291v1. [PMID: 38562450 PMCID: PMC10984000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The pandemic of COVID-19 has imposed tremendous pressure on public health systems and social economic ecosystems over the past years. To alleviate its social impact, it is important to proactively track the prevalence of COVID-19 within communities. The traditional way to estimate the disease prevalence is to estimate from reported clinical test data or surveys. However, the coverage of clinical tests is often limited and the tests can be labor-intensive, requires reliable and timely results, and consistent diagnostic and reporting criteria. Recent studies revealed that patients who are diagnosed with COVID-19 often undergo fecal shedding of SARS-CoV-2 virus into wastewater, which makes wastewater-based epidemiology (WBE) for COVID-19 surveillance a promising approach to complement traditional clinical testing. In this paper, we survey the existing literature regarding WBE for COVID-19 surveillance and summarize the current advances in the area. Specifically, we have covered the key aspects of wastewater sampling, sample testing, and presented a comprehensive and organized summary of wastewater data analytical methods. Finally, we provide the open challenges on current wastewater-based COVID-19 surveillance studies, aiming to encourage new ideas to advance the development of effective wastewater-based surveillance systems for general infectious diseases.
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Affiliation(s)
- Chen Chen
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Gursharn Kaur
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Aniruddha Adiga
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Baltazar Espinoza
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Srinivasan Venkatramanan
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Andrew Warren
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Bryan Lewis
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Justin Crow
- Virginia Department of Health, Richmond, 23219, United States
| | - Rekha Singh
- Virginia Department of Health, Richmond, 23219, United States
| | - Alexandra Lorentz
- Division of Consolidated Laboratory Services, Department of General Services, Richmond, 23219, United States
| | - Denise Toney
- Division of Consolidated Laboratory Services, Department of General Services, Richmond, 23219, United States
| | - Madhav Marathe
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
- Department of Computer Science, University of Virginia, Charlottesville, 22904, United States
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4
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Kanchan S, Ogden E, Kesheri M, Skinner A, Miliken E, Lyman D, Armstrong J, Sciglitano L, Hampikian G. COVID-19 hospitalizations and deaths predicted by SARS-CoV-2 levels in Boise, Idaho wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167742. [PMID: 37852488 DOI: 10.1016/j.scitotenv.2023.167742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/22/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023]
Abstract
The viral load of COVID-19 in untreated wastewater from Idaho's capital city Boise, ID (Ada County) has been used to predict changes in hospital admissions (statewide in Idaho) and deaths (Ada County) using distributed fixed lag modeling and artificial neural networks (ANN). The wastewater viral counts were used to determine the lag time between peaks in wastewater viral counts and COVID-19 hospitalizations as well as deaths (14 and 23 days, respectively). Quantitative measurement of SARS-CoV-2 viral RNA counts in the untreated wastewater was determined three times a week using RT-qPCR over a span of 13 months. To mitigate the effects of PCR inhibitors in wastewater, a series of dilution tests were conducted, and the 1/4 dilution was used to generate the most successful model. Wastewater SARS-CoV-2 viral RNA counts and hospitalization from June 7, 2021 to December 29, 2021 were used as training data to predict hospitalizations; and wastewater SARS-CoV-2 viral RNA counts and deaths from June 7, 2021 to December 20, 2021 were used as training data to predict deaths. These training data were used to make predictive ANN models for future hospitalizations and deaths. To the best of our knowledge, this is the first report of prediction of deaths from COVID-19 based on wastewater SARS-CoV-2 viral RNA counts using machine learning-based multilayered ANN. The applied modeling demonstrates that wastewater surveillance data can be combined with hospitalizations and death data to generate machine learning-based ANN models that predict future COVID-19 hospital admissions and deaths, providing an early warning for medical response teams and healthcare policymakers.
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Affiliation(s)
- Swarna Kanchan
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America; Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, 25701, United States of America
| | - Ernie Ogden
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Minu Kesheri
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America; Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, 25701, United States of America
| | - Alexis Skinner
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Erin Miliken
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Devyn Lyman
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Jacob Armstrong
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Lawrence Sciglitano
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Greg Hampikian
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America.
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Pellegrinelli L, Galli C, Seiti A, Primache V, Hirvonen A, Schiarea S, Salmoiraghi G, Castiglioni S, Ammoni E, Cereda D, Binda S, Pariani E. Wastewater-based epidemiology revealed in advance the increase of enterovirus circulation during the Covid-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166539. [PMID: 37625729 DOI: 10.1016/j.scitotenv.2023.166539] [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: 04/29/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Wastewater-based epidemiology (WBE) was conducted to track Enteroviruses (EVs) circulation in the Milan metropolitan area (Northern Italy) during Covid-19 pandemic (March 2020-December 2022). 202 composite 24-hour wastewater samples (WWSs) were collected weekly from March 24, 2020, to December 29, 2022 at the inlet of two wastewater treatment plants (WWTP) in Milan (1.5 million inhabitants). EV-RNA was quantified and molecular characterization of non-polio EVs (NPEV) was performed by Sanger sequence analysis. Data from WWS were matched with virological data collected in the framework of Influenza-Like Illness (ILI) surveillance in the same place and time. EV-RNA was identified in 88.2 % of WWSs. The peak in EVs circulation was observed in late August 2020 (upon conclusion of the first national lockdown), in late August 2021, and in mid-April 2022. EV-RNA concentration in WWS (normalized as copies/d/1000 people) at peak of circulation presented a yearly increase (2020: 2.47 × 1010; 2021: 6.81 × 1010; 2022: 2.14 × 1011). This trend overlapped with trend in EV-positivity rate in ILI cases, expanded from 21.7 % in 2021 to 55.6 % in 2022. EV trends in WWS preceded clinical sample detections in 2021 and 2022 by eight and five weeks, respectively, acting as an early warning of outbreak. Although sequencing of EV-positive WWSs revealed the presence of multiple EV strains, typing remained inconclusive. Molecular characterization of EVs in clinical samples revealed the co-circulation of several genotypes: EV-A accounted for 60 % of EVs, EV-B for 16.7 %, EV-D68 for 23.3 %. EVs were circulating in Milan metropolitan area between March 2020 and December 2022. The epidemiological trends unfolded the progressive accumulation of EV transmission in the population after removal of Covid-19 restrictions. The increased circulation of EVs in 2021-2022 was identified at least 35 days in advance compared to the analysis of clinical data. The inconclusive results of Sanger sequencing lookout for improvement and innovative molecular approaches to deepen track EVs.
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Affiliation(s)
- Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Arlinda Seiti
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Valeria Primache
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Aurora Hirvonen
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Silvia Schiarea
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giulia Salmoiraghi
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Sara Castiglioni
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Emanuela Ammoni
- Directorate General for Health, Lombardy Region, Milan, Italy
| | - Danilo Cereda
- Directorate General for Health, Lombardy Region, Milan, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
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6
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Wang H, Churqui MP, Tunovic T, Enache L, Johansson A, Lindh M, Lagging M, Nyström K, Norder H. Measures against COVID-19 affected the spread of human enteric viruses in a Swedish community, as found when monitoring wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165012. [PMID: 37353026 PMCID: PMC10284612 DOI: 10.1016/j.scitotenv.2023.165012] [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: 02/28/2023] [Revised: 05/25/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023]
Abstract
The quantification of viral genomes in wastewater reflects the prevalence of viral infections within the community. Knowledge of how the spread of common enteric viruses in the community was affected by the Swedish COVID-19 interventions is limited. To investigate this, the weekly wastewater samples collected for monitoring SARS-CoV-2 throughout the COVID-19 pandemic at the Rya sewage treatment plant in Gothenburg were also analyzed for adenovirus, norovirus GII, astrovirus, and rotavirus. The amount of each viral genome was quantified by real-time-qPCR and compared with the quantity of these viral genomes in wastewater from 2017. The results showed that the winter seasonality of norovirus GII and rotavirus in wastewater observed in 2017 was interrupted shortly after the introduction of the COVID-19 interventions, and they remained at low level throughout the pandemic. The circulation pattern of astrovirus and adenovirus was less affected. When the COVID-19 restrictions were lifted in 2022, a dramatic increase was observed in the amount of norovirus GII, rotavirus, and adenovirus genomes in wastewater. The changes in abundance and seasonality of some viruses identified through wastewater monitoring were consistent with changes in the number of patients diagnosed with these viruses. These findings suggest that moderate intervention to prevent COVID-19 significantly reduced the spread of some enteric viruses in the community. The results show that wastewater monitoring is a valuable tool for detecting the spread and outbreaks of viral infections that may cause gastroenteritis also when people do not seek medical help, such as during the COVID-19 pandemic.
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Affiliation(s)
- Hao Wang
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, Gothenburg, Sweden.
| | - Marianela Patzi Churqui
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Timur Tunovic
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Magnus Lindh
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, Gothenburg, Sweden
| | - Martin Lagging
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, Gothenburg, Sweden
| | - Kristina Nyström
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, Gothenburg, Sweden
| | - Heléne Norder
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, Gothenburg, Sweden
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Lombardi A, Voli A, Mancusi A, Girardi S, Proroga YTR, Pierri B, Olivares R, Cossentino L, Suffredini E, La Rosa G, Fusco G, Pizzolante A, Porta A, Campiglia P, Torre I, Pennino F, Tosco A. SARS-CoV-2 RNA in Wastewater and Bivalve Mollusk Samples of Campania, Southern Italy. Viruses 2023; 15:1777. [PMID: 37632119 PMCID: PMC10459311 DOI: 10.3390/v15081777] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
SARS-CoV-2 can be detected in the feces of infected people, consequently in wastewater, and in bivalve mollusks, that are able to accumulate viruses due to their ability to filter large amounts of water. This study aimed to monitor SARS-CoV-2 RNA presence in 168 raw wastewater samples collected from six wastewater treatment plants (WWTPs) and 57 mollusk samples obtained from eight harvesting sites in Campania, Italy. The monitoring period spanned from October 2021 to April 2022, and the results were compared and correlated with the epidemiological situation. In sewage, the ORF1b region of SARS-CoV-2 was detected using RT-qPCR, while in mollusks, three targets-RdRp, ORF1b, and E-were identified via RT-dPCR. Results showed a 92.3% rate of positive wastewater samples with increased genomic copies (g.c.)/(day*inhabitant) in December-January and March-April 2022. In the entire observation period, 54.4% of mollusks tested positive for at least one SARS-CoV-2 target, and the rate of positive samples showed a trend similar to that of the wastewater samples. The lower SARS-CoV-2 positivity rate in bivalve mollusks compared to sewages is a direct consequence of the seawater dilution effect. Our data confirm that both sample types can be used as sentinels to detect SARS-CoV-2 in the environment and suggest their potential use in obtaining complementary information on SARS-CoV-2.
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Affiliation(s)
- Annalisa Lombardi
- Department of Public Health, University “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy; (A.L.)
| | - Antonia Voli
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
| | - Andrea Mancusi
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Santa Girardi
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Yolande Thérèse Rose Proroga
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Biancamaria Pierri
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Renato Olivares
- Campania Regional Environmental Protection Agency (ARPAC), Via Vicinale Santa Maria del Pianto, 80143 Naples, Italy; (R.O.); (L.C.)
| | - Luigi Cossentino
- Campania Regional Environmental Protection Agency (ARPAC), Via Vicinale Santa Maria del Pianto, 80143 Naples, Italy; (R.O.); (L.C.)
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Giovanna Fusco
- Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.F.); (A.P.)
| | - Antonio Pizzolante
- Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.F.); (A.P.)
| | - Amalia Porta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
| | - Ida Torre
- Department of Public Health, University “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy; (A.L.)
| | - Francesca Pennino
- Department of Public Health, University “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy; (A.L.)
| | - Alessandra Tosco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
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8
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Ciannella S, González-Fernández C, Gomez-Pastora J. Recent progress on wastewater-based epidemiology for COVID-19 surveillance: A systematic review of analytical procedures and epidemiological modeling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:162953. [PMID: 36948304 PMCID: PMC10028212 DOI: 10.1016/j.scitotenv.2023.162953] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 05/13/2023]
Abstract
On March 11, 2020, the World Health Organization declared the coronavirus disease 2019 (COVID-19), whose causative agent is the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a pandemic. This virus is predominantly transmitted via respiratory droplets and shed via sputum, saliva, urine, and stool. Wastewater-based epidemiology (WBE) has been able to monitor the circulation of viral pathogens in the population. This tool demands both in-lab and computational work to be meaningful for, among other purposes, the prediction of outbreaks. In this context, we present a systematic review that organizes and discusses laboratory procedures for SARS-CoV-2 RNA quantification from a wastewater matrix, along with modeling techniques applied to the development of WBE for COVID-19 surveillance. The goal of this review is to present the current panorama of WBE operational aspects as well as to identify current challenges related to it. Our review was conducted in a reproducible manner by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic reviews. We identified a lack of standardization in wastewater analytical procedures. Regardless, the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) approach was the most reported technique employed to detect and quantify viral RNA in wastewater samples. As a more convenient sample matrix, we suggest the solid portion of wastewater to be considered in future investigations due to its higher viral load compared to the liquid fraction. Regarding the epidemiological modeling, the data-driven approach was consistently used for the prediction of variables associated with outbreaks. Future efforts should also be directed toward the development of rapid, more economical, portable, and accurate detection devices.
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Affiliation(s)
- Stefano Ciannella
- Department of Chemical Engineering, Texas Tech University, Lubbock 79409, TX, USA.
| | - Cristina González-Fernández
- Department of Chemical Engineering, Texas Tech University, Lubbock 79409, TX, USA; Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Avda. Los Castros, s/n, 39005 Santander, Spain.
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9
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Yang K, Guo J, Møhlenberg M, Zhou H. SARS-CoV-2 surveillance in medical and industrial wastewater-a global perspective: a narrative review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:63323-63334. [PMID: 36988799 PMCID: PMC10049894 DOI: 10.1007/s11356-023-26571-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/16/2023] [Indexed: 05/11/2023]
Abstract
The novel coronavirus SARS-CoV-2 has spread at an unprecedented rate since late 2019, leading to the global COVID-19 pandemic. During the pandemic, being able to detect SARS-CoV-2 in human populations with high coverage quickly is a huge challenge. As SARS-CoV-2 is excreted in human excreta and thus exposed to the aqueous environment through sewers, the goal is to develop an ideal, non-invasive, cost-effective epidemiological method for detecting SARS-CoV-2. Wastewater surveillance has gained widespread interest and is increasingly being investigated as an effective early warning tool for monitoring the spread and evolution of the virus. This review emphasizes important findings on SARS-CoV-2 wastewater-based epidemiology (WBE) in different continents and techniques used to detect SARS-CoV-2 in wastewater during the period 2020-2022. The results show that WBE is a valuable population-level method for monitoring SARS-CoV-2 and is a valuable early warning alert. It can assist policymakers in formulating relevant policies to avoid the negative impacts of early or delayed action. Such strategy can also help avoid unnecessary wastage of medical resources, rationalize vaccine distribution, assist early detection, and contain large-scale outbreaks.
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Affiliation(s)
- Kaiwen Yang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Liutai Road 1166, Wenjiang, Chengdu, 610000, China
| | - Jinlin Guo
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Liutai Road 1166, Wenjiang, Chengdu, 610000, China
| | - Michelle Møhlenberg
- Department of Biomedicine, Høegh-Guldbergs Gade 10, Building 1115, DK-8000, Aarhus C, Denmark
| | - Hao Zhou
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Liutai Road 1166, Wenjiang, Chengdu, 610000, China.
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10
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Gagliano E, Biondi D, Roccaro P. Wastewater-based epidemiology approach: The learning lessons from COVID-19 pandemic and the development of novel guidelines for future pandemics. CHEMOSPHERE 2023; 313:137361. [PMID: 36427570 PMCID: PMC9678975 DOI: 10.1016/j.chemosphere.2022.137361] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) provides a comprehensive real-time framework of population attitude and health status. This approach is attracting the interest of medical community and health authorities to monitor the prevalence of a virus (such as the severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) among a community. Indeed, WBE is currently fine-tuning as environmental surveillance tool for coronavirus disease 2019 (COVID-19) pandemic. After a bibliometric analysis conducted to discover the research trends in WBE field, this work aimed to side-by-side compare the conventional method based on clinical testing with WBE approach. Furthermore, novel guidelines were developed to apply the WBE approach to a pandemic. The growing interest on WBE approach for COVID-19 pandemic is demonstrated by looking at the sharp increase in scientific papers published in the last years and at the ongoing studies on viral quantification methods and analytical procedures. The side-by-side comparison highlighted the ability of WBE to identify the hot-spot areas faster than the conventional approach, reducing the costs (e.g., rational use of available resources) and the gatherings at medical centers. Contrary to clinical testing, WBE has the surveillance capacity for preventing the virus resurgence, including asymptomatic contribution, and ensuring the preservation of medical staff health by avoiding the exposure to the virus infection during clinical testing. As extensively reported, the time in collecting epidemiological data is crucial for establishing the prevention and mitigation measures that are essential for curbing a pandemic. The developed guidelines can help to build a WBE system useful to control any future pandemic.
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Affiliation(s)
- Erica Gagliano
- Department of Civil Engineering and Architecture, University of Catania, Catania, Italy; Department of Civil, Chemical and Environmental Engineering, University of Genoa, Genoa, Italy
| | - Deborah Biondi
- Department of Civil Engineering and Architecture, University of Catania, Catania, Italy
| | - Paolo Roccaro
- Department of Civil Engineering and Architecture, University of Catania, Catania, Italy.
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11
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Amendola A, Canuti M, Bianchi S, Kumar S, Fappani C, Gori M, Colzani D, Kosakovsky Pond SL, Miura S, Baggieri M, Marchi A, Borghi E, Zuccotti G, Raviglione MC, Magurano F, Tanzi E. Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy. ENVIRONMENTAL RESEARCH 2022; 215:113979. [PMID: 36029839 PMCID: PMC9404229 DOI: 10.1016/j.envres.2022.113979] [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: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 05/12/2023]
Abstract
As a reference laboratory for measles and rubella surveillance in Lombardy, we evaluated the association between SARS-CoV-2 infection and measles-like syndromes, providing preliminary evidence for undetected early circulation of SARS-CoV-2. Overall, 435 samples from 156 cases were investigated. RNA from oropharyngeal swabs (N = 148) and urine (N = 141) was screened with four hemi-nested PCRs and molecular evidence for SARS-CoV-2 infection was found in 13 subjects. Two of the positive patients were from the pandemic period (2/12, 16.7%, March 2020-March 2021) and 11 were from the pre-pandemic period (11/44, 25%, August 2019-February 2020). Sera (N = 146) were tested for anti-SARS-CoV-2 IgG, IgM, and IgA antibodies. Five of the RNA-positive individuals also had detectable anti-SARS-CoV-2 antibodies. No strong evidence of infection was found in samples collected between August 2018 and July 2019 from 100 patients. The earliest sample with evidence of SARS-CoV-2 RNA was from September 12, 2019, and the positive patient was also positive for anti-SARS-CoV-2 antibodies (IgG and IgM). Mutations typical of B.1 strains previously reported to have emerged in January 2020 (C3037T, C14408T, and A23403G), were identified in samples collected as early as October 2019 in Lombardy. One of these mutations (C14408T) was also identified among sequences downloaded from public databases that were obtained by others from samples collected in Brazil in November 2019. We conclude that a SARS-CoV-2 progenitor capable of producing a measles-like syndrome may have emerged in late June-late July 2019 and that viruses with mutations characterizing B.1 strain may have been spreading globally before the first Wuhan outbreak. Our findings should be complemented by high-throughput sequencing to obtain additional sequence information. We highlight the importance of retrospective surveillance studies in understanding the early dynamics of COVID-19 spread and we encourage other groups to perform retrospective investigations to seek confirmatory proofs of early SARS-CoV-2 circulation.
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Affiliation(s)
- Antonella Amendola
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Marta Canuti
- Department of Health Sciences, University of Milan, 20142, Milan, Italy.
| | - Silvia Bianchi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, 19122, Philadelphia, USA; Department of Biology, Temple University, 19122, Philadelphia, USA; Center for Excellence in Genome Medicine and Research, King Abdulaziz University, 22252, Jeddah, Saudi Arabia.
| | - Clara Fappani
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Maria Gori
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Daniela Colzani
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, 19122, Philadelphia, USA; Department of Biology, Temple University, 19122, Philadelphia, USA.
| | - Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Temple University, 19122, Philadelphia, USA; Department of Biology, Temple University, 19122, Philadelphia, USA.
| | - Melissa Baggieri
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Antonella Marchi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Elisa Borghi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
| | - Gianvincenzo Zuccotti
- Department of Paediatrics, Children Hospital V. Buzzi, University of Milan, 20154, Milan, Italy; Romeo and Enrica Invernizzi Pediatric Research Center, University of Milan, 20154, Milan, Italy.
| | - Mario C Raviglione
- Centre for Multidisciplinary Research in Health Science, University of Milan, 20122, Milan, Italy.
| | - Fabio Magurano
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161, Rome, Italy.
| | - Elisabetta Tanzi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, 20133, Milan, Italy.
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12
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Wastewater Surveillance Captured an Increase in Adenovirus Circulation in Milan (Italy) during the First Quarter of 2022. Viruses 2022; 14:v14112351. [PMID: 36366449 PMCID: PMC9697775 DOI: 10.3390/v14112351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/11/2022] [Accepted: 10/22/2022] [Indexed: 02/01/2023] Open
Abstract
The quantification and molecular characterization of the AdV genome in urban wastewater samples (WWSs) collected weekly at a wastewater treatment plant (WWTP) in Milan from 1 January 2021 (week 2021-01) to 1 May 2022 (week 2022-17) were performed. The concentration of the AdV genome was graphically compared with the AdV positive rate observed in the respiratory/gastrointestinal specimens from individuals hospitalized with acute respiratory/gastrointestinal infections collected from one of the major hospitals in Milan in the same time series. An increase in the AdV circulation in WWSs was seen from November 2021, peaking in March 2022 and overlapped with an increase in the AdV positive rate in respiratory/fecal samples from individuals hospitalized with acute respiratory/gastrointestinal infections. The molecular characterization of the hexon hypervariable region of loop 1 of AdV revealed the presence of the species F type 41 in WWSs collected from February 2022 to April 2022. The wastewater surveillance of AdV can provide crucial epidemiological characteristics regarding AdV, particularly where no clinical surveillance is ongoing. The increase in the AdV circulation in Milan both in WWSs and clinical samples temporally overlapped with the outbreak of severe acute pediatric hepatitis observed in Europe and needs to be better investigated.
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13
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Fahrenfeld NL, Morales Medina WR, D'Elia S, Deshpande AS, Ehasz G. Year-long wastewater monitoring for SARS-CoV-2 signals in combined and separate sanitary sewers. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2022; 94:e10768. [PMID: 35918060 PMCID: PMC9350404 DOI: 10.1002/wer.10768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/07/2022] [Accepted: 07/01/2022] [Indexed: 05/14/2023]
Abstract
COVID-19 wastewater-based epidemiology has been performed in catchments of various sizes and sewer types with many short-term studies available and multi-seasonal studies emerging. The objective of this study was to compare weekly observations of SARS-CoV-2 genes in municipal wastewater across multiple seasons for different systems as a factor of sewer type (combined, separate sanitary) and system size. Sampling occurred following the first wave of SARS-CoV-2 cases in the study region (June 2020) and continued through the third wave (May 2021), the period during which clinical testing was widely available and different variants dominated clinical cases. The strongest correlations were observed between wastewater N1 concentrations and the cumulative clinical cases reported in the 2 weeks prior to wastewater sampling, followed by the week prior, new cases, and the week after wastewater sampling. Sewer type and size did not necessarily explain the strength of the correlations, indicating that other non-sewer factors may be impacting the observations. In-system sampling results for the largest system sampled are presented for 1 month. Removing wet weather days from the data sets improved even the flow-normalized correlations for the systems, potentially indicating that interpreting results during wet weather events may be more complicated than simply accounting for dilution. PRACTITIONER POINTS: SARS-CoV-2 in wastewater correlated best with total clinical cases reported in 2 weeks before wastewater sampling at the utility level. Study performed when clinical testing was widespread during the year after the first COVID-19 wave in the region. Sewer type and size did not necessarily explain correlation strength between clinical cases and wastewater-based epidemiology results. Removing wet weather days improved correlations for 3/4 utilities studied, including both separate sanitary and combined sewers.
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Affiliation(s)
- Nicole L. Fahrenfeld
- Department of Civil and Environmental EngineeringRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - William R. Morales Medina
- Department of Microbiology and Molecular GeneticsRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Present address:
American WaterDelranNew JerseyUSA
| | - Stephanie D'Elia
- Department of Biochemistry and MicrobiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Aishwarya S. Deshpande
- Department of Biochemistry and MicrobiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Genevieve Ehasz
- Department of Civil and Environmental EngineeringRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
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14
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Shaheen MNF, Elmahdy EM, Shahein YE. The first detection of SARS-CoV-2 RNA in urban wastewater in Giza, Egypt. JOURNAL OF WATER AND HEALTH 2022; 20:1212-1222. [PMID: 36044190 DOI: 10.2166/wh.2022.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The new coronavirus (SARS-CoV-2) is a respiratory virus causing coronavirus disease (COVID-19). Individuals with COVID-19 can shed the viral genome in their feces, even if they do not have symptoms, and the virus can be detected in wastewater. The current study provides the first surveillance of SARS-CoV-2 RNA genome in the wastewater in Egypt. To study this aim, untreated influent (n = 48) and treated effluent (n = 48) samples were collected between January and December 2021 from the wastewater treatment plant in Giza. The viral RNA genome was determined by reverse transcription-polymerase chain reaction (RT-PCR) (S, E, and N target regions) and real-time quantitative reverse transcription-PCR (RT-qPCR) (N1 and N2 target regions). The RT-PCR assay failed to detect SARS-CoV-2 RNA in all samples analyzed, whereas RT-qPCR succeeded in the detection of N gene of SARS-CoV-2 in 62.5% of untreated influent samples. The RT-qPCR Ct values of those samples tested positive ranged from 19.9 to 30.1 with a mean of 23. The treated effluent samples were negative for viral RNA detected by both RT-PCR and RT-qPCR, indicating the efficiency of the sewage treatment plant in degrading SARS-CoV-2. Our preliminary findings provide evidence for the value of wastewater epidemiology approach for the surveillance of SARS-CoV-2 in the population to assist in the responses of public health to COVID-19 outbreak.
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Affiliation(s)
- Mohamed N F Shaheen
- Environmental Virology Laboratory, Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, Dokki 12622, Giza, Egypt E-mail: ,
| | - Elmahdy M Elmahdy
- Environmental Virology Laboratory, Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, Dokki 12622, Giza, Egypt E-mail: ,
| | - Yasser E Shahein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, 12622 Dokki, Cairo, Egypt
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15
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Fahrenfeld NL, Morales Medina WR, D'Elia S, Deshpande AS, Ehasz G. Year-long wastewater monitoring for SARS-CoV-2 signals in combined and separate sanitary sewers. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2022; 94:e10768. [PMID: 35918060 DOI: 10.1021/acsestwater.1c00345] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/07/2022] [Accepted: 07/01/2022] [Indexed: 05/27/2023]
Abstract
COVID-19 wastewater-based epidemiology has been performed in catchments of various sizes and sewer types with many short-term studies available and multi-seasonal studies emerging. The objective of this study was to compare weekly observations of SARS-CoV-2 genes in municipal wastewater across multiple seasons for different systems as a factor of sewer type (combined, separate sanitary) and system size. Sampling occurred following the first wave of SARS-CoV-2 cases in the study region (June 2020) and continued through the third wave (May 2021), the period during which clinical testing was widely available and different variants dominated clinical cases. The strongest correlations were observed between wastewater N1 concentrations and the cumulative clinical cases reported in the 2 weeks prior to wastewater sampling, followed by the week prior, new cases, and the week after wastewater sampling. Sewer type and size did not necessarily explain the strength of the correlations, indicating that other non-sewer factors may be impacting the observations. In-system sampling results for the largest system sampled are presented for 1 month. Removing wet weather days from the data sets improved even the flow-normalized correlations for the systems, potentially indicating that interpreting results during wet weather events may be more complicated than simply accounting for dilution. PRACTITIONER POINTS: SARS-CoV-2 in wastewater correlated best with total clinical cases reported in 2 weeks before wastewater sampling at the utility level. Study performed when clinical testing was widespread during the year after the first COVID-19 wave in the region. Sewer type and size did not necessarily explain correlation strength between clinical cases and wastewater-based epidemiology results. Removing wet weather days improved correlations for 3/4 utilities studied, including both separate sanitary and combined sewers.
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Affiliation(s)
- Nicole L Fahrenfeld
- Department of Civil and Environmental Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - William R Morales Medina
- Department of Microbiology and Molecular Genetics, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Stephanie D'Elia
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Aishwarya S Deshpande
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Genevieve Ehasz
- Department of Civil and Environmental Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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16
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Cappelli F, Longoni O, Rigato J, Rusconi M, Sala A, Fochi I, Palumbo MT, Polesello S, Roscioli C, Salerno F, Stefani F, Bettinetti R, Valsecchi S. Suspect screening of wastewaters to trace anti-COVID-19 drugs: Potential adverse effects on aquatic environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153756. [PMID: 35151733 PMCID: PMC8830926 DOI: 10.1016/j.scitotenv.2022.153756] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 05/06/2023]
Abstract
During the first period of the SARS-CoV-2 pandemic, the lack of specific therapeutic treatments led to the provisional use of a number of drugs, with a continuous review of health protocols when new scientific evidence emerged. The management of this emergency sanitary situation could not take care of the possible indirect adverse effects on the environment, such as the release of a large amount of pharmaceuticals from wastewater treatment plants. The massive use of drugs, which were never used so widely until then, implied new risks for the aquatic environment. In this study, a suspect screening approach using Liquid Chromatography-High Resolution Mass Spectrometry techniques, allowed us to survey the presence of pharmaceuticals used for COVID-19 treatment in three WWTPs of Lombardy region, where the first European cluster of SARS-CoV-2 cases was detected. Starting from a list of sixty-three suspect compounds used against COVID-19 (including some metabolites and transformation products), six compounds were fully identified and monitored together with other target analytes, mainly pharmaceuticals of common use. A monthly monitoring campaign was conducted in a WWTP from April to December 2020 and the temporal trends of some anti-COVID-19 drugs were positively correlated with those of COVID-19 cases and deaths. The comparison of the average emission loads among the three WWTPs evidenced that the highest loads of hydroxychloroquine, azithromycin and ciprofloxacin were measured in the WWTP which received the sewages from a hospital specializing in the treatment of COVID-19 patients. The monitoring of the receiving water bodies evidenced the presence of eight compounds of high ecological concern, whose risk was assessed in terms of toxicity and the possibility of inducing antibiotic and viral resistance. The results clearly showed that the enhanced, but not completely justified, use of ciprofloxacin and azithromycin represented a risk for antibiotic resistance in the aquatic ecosystems.
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Affiliation(s)
- Francesca Cappelli
- Water Research Institute-National Research Council (IRSA-CNR), 20861 Brugherio, MB, Italy; University of Insubria, Department of Human Science of the Innovation for the Territory, 22100 Como, CO, Italy.
| | | | | | | | | | - Igor Fochi
- Thermo Fisher Scientific s.p.a., 20090 Rodano, MI, Italy
| | - Maria Teresa Palumbo
- Water Research Institute-National Research Council (IRSA-CNR), 20861 Brugherio, MB, Italy
| | - Stefano Polesello
- Water Research Institute-National Research Council (IRSA-CNR), 20861 Brugherio, MB, Italy
| | - Claudio Roscioli
- Water Research Institute-National Research Council (IRSA-CNR), 20861 Brugherio, MB, Italy
| | - Franco Salerno
- Water Research Institute-National Research Council (IRSA-CNR), 20861 Brugherio, MB, Italy
| | - Fabrizio Stefani
- Water Research Institute-National Research Council (IRSA-CNR), 20861 Brugherio, MB, Italy
| | - Roberta Bettinetti
- University of Insubria, Department of Human Science of the Innovation for the Territory, 22100 Como, CO, Italy
| | - Sara Valsecchi
- Water Research Institute-National Research Council (IRSA-CNR), 20861 Brugherio, MB, Italy
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17
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Evaluation of Pre-Analytical and Analytical Methods for Detecting SARS-CoV-2 in Municipal Wastewater Samples in Northern Italy. WATER 2022. [DOI: 10.3390/w14050833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
(1) Background: The surveillance of SARS-CoV-2 RNA in urban wastewaters allows one to monitor the presence of the virus in a population, including asymptomatic and symptomatic individuals, capturing the real circulation of this pathogen. The aim of this study was to evaluate the performance of different pre-analytical and analytical methods for identifying the presence of SARS-CoV-2 in untreated municipal wastewaters samples by conducting an inter-laboratory proficiency test. (2) Methods: three methods of concentration, namely, (A) Dextran and PEG-6000 two-phase separation, (B) PEG-8000 precipitation without a chloroform purification step and (C) PEG-8000 precipitation with a chloroform purification step were combined with three different protocols of RNA extraction by using commercial kits and were tested by using two primers/probe sets in three different master mixes. (3) Results: PEG-8000 precipitation without chloroform treatment showed the best performance in the SARS-CoV-2 recovery; no major differences were observed among the protocol of RNA extraction and the one-step real-time RT-PCR master mix kits. The highest analytic sensitivity was observed by using primers/probe sets targeting the N1/N3 fragments of SARS-CoV-2. (4) Conclusions: PEG-8000 precipitation in combination with real-time RT-PCR targeting the N gene (two fragments) was the best performing workflow for the detection of SARS-CoV-2 RNA in municipal wastewaters.
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18
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Canuti M, Bianchi S, Kolbl O, Pond SLK, Kumar S, Gori M, Fappani C, Colzani D, Borghi E, Zuccotti G, Raviglione MC, Tanzi E, Amendola A. Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence? BMJ Glob Health 2022; 7:e008386. [PMID: 35296465 PMCID: PMC8927931 DOI: 10.1136/bmjgh-2021-008386] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/19/2022] [Indexed: 01/22/2023] Open
Abstract
Two years after the start of the COVID-19 pandemic, key questions about the emergence of its aetiological agent (SARS-CoV-2) remain a matter of considerable debate. Identifying when SARS-CoV-2 began spreading among people is one of those questions. Although the current canonically accepted timeline hypothesises viral emergence in Wuhan, China, in November or December 2019, a growing body of diverse studies provides evidence that the virus may have been spreading worldwide weeks, or even months, prior to that time. However, the hypothesis of earlier SARS-CoV-2 circulation is often dismissed with prejudicial scepticism and experimental studies pointing to early origins are frequently and speculatively attributed to false-positive tests. In this paper, we critically review current evidence that SARS-CoV-2 had been circulating prior to December of 2019, and emphasise how, despite some scientific limitations, this hypothesis should no longer be ignored and considered sufficient to warrant further larger-scale studies to determine its veracity.
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Affiliation(s)
- Marta Canuti
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Bianchi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Otto Kolbl
- Faculty of Arts, University of Lausanne, Lausanne, Switzerland
| | - Sergei L Kosakovsky Pond
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Sudhir Kumar
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maria Gori
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Clara Fappani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Daniela Colzani
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Elisa Borghi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Gianvincenzo Zuccotti
- Department of Pediatrics, Ospedale dei Bambini, Università degli Studi di Milano, Milan, Italy
- Romeo and Enrica Invernizzi Pediatric Research Center, Università degli Studi di Milano, Milan, Italy
| | - Mario C Raviglione
- Centre for Multidisciplinary Research in Health Science, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Tanzi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
| | - Antonella Amendola
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
- Coordinated Research Center "EpiSoMI", Università degli Studi di Milano, Milan, Italy
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