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Girón-Guzmán I, Cuevas-Ferrando E, Barranquero R, Díaz-Reolid A, Puchades-Colera P, Falcó I, Pérez-Cataluña A, Sánchez G. Urban wastewater-based epidemiology for multi-viral pathogen surveillance in the Valencian region, Spain. WATER RESEARCH 2024; 255:121463. [PMID: 38537489 DOI: 10.1016/j.watres.2024.121463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 04/24/2024]
Abstract
Wastewater-based epidemiology (WBE) has lately arised as a promising tool for monitoring and tracking viral pathogens in communities. In this study, we analysed WBE's role as a multi-pathogen surveillance strategy to detect the presence of several viral illness causative agents. Thus, an epidemiological study was conducted from October 2021 to February 2023 to estimate the weekly levels of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Respiratory Syncytial virus (RSV), and Influenza A virus (IAV) in influent wastewater samples (n = 69). In parallel, a one-year study (October 2021 to October 2022) was performed to assess the presence of pathogenic human enteric viruses. Besides, monitoring of proposed viral fecal contamination indicators crAssphage and Pepper mild mottle virus (PMMoV) was also assessed, along with plaque counting of somatic coliphages. Genetic material of rotavirus (RV), human astrovirus (HAStV), and norovirus genogroup I (GI) and GII was found in almost all samples, while hepatitis A and E viruses (HAV and HEV) only tested positive in 3.77 % and 22.64 % of the samples, respectively. No seasonal patterns were overall found for enteric viruses, although RVs had a peak prevalence in the winter months. All samples tested positive for SARS-CoV-2 RNA, with a mean concentration of 5.43 log genome copies per liter (log GC/L). The tracking of the circulating SARS-CoV-2 variants of concern (VOCs) was performed by both duplex RT-qPCR and next generation sequencing (NGS). Both techniques reliably showed how the dominant VOC transitioned from Delta to Omicron during two weeks in Spain in December 2021. RSV and IAV viruses peaked in winter months with mean concentrations 6.40 and 4.10 log GC/L, respectively. Moreover, the three selected respiratory viruses strongly correlated with reported clinical data when normalised by wastewater physico-chemical parameters and presented weaker correlations when normalising sewage concentration levels with crAssphage or somatic coliphages titers. Finally, predictive models were generated for each respiratory virus, confirming high reliability on WBE data as an early-warning system and communities illness monitoring system. Overall, this study presents WBE as an optimal tool for multi-pathogen tracking reflecting viral circulation and diseases trends within a selected area, its value as a multi-pathogen early-warning tool stands out due to its public health interest.
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Affiliation(s)
- Inés Girón-Guzmán
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Enric Cuevas-Ferrando
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain.
| | - Regino Barranquero
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Azahara Díaz-Reolid
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Pablo Puchades-Colera
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Irene Falcó
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain; Department of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Alba Pérez-Cataluña
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Gloria Sánchez
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain.
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2
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Perry WB, Chrispim MC, Barbosa MRF, de Souza Lauretto M, Razzolini MTP, Nardocci AC, Jones O, Jones DL, Weightman A, Sato MIZ, Montagner C, Durance I. Cross-continental comparative experiences of wastewater surveillance and a vision for the 21st century. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170842. [PMID: 38340868 DOI: 10.1016/j.scitotenv.2024.170842] [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: 07/21/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
The COVID-19 pandemic has brought the epidemiological value of monitoring wastewater into sharp focus. The challenges of implementing and optimising wastewater monitoring vary significantly from one region to another, often due to the array of different wastewater systems around the globe, as well as the availability of resources to undertake the required analyses (e.g. laboratory infrastructure and expertise). Here we reflect on the local and shared challenges of implementing a SARS-CoV-2 monitoring programme in two geographically and socio-economically distinct regions, São Paulo state (Brazil) and Wales (UK), focusing on design, laboratory methods and data analysis, and identifying potential guiding principles for wastewater surveillance fit for the 21st century. Our results highlight the historical nature of region-specific challenges to the implementation of wastewater surveillance, including previous experience of using wastewater surveillance, stakeholders involved, and nature of wastewater infrastructure. Building on those challenges, we then highlight what an ideal programme would look like if restrictions such as resource were not a constraint. Finally, we demonstrate the value of bringing multidisciplinary skills and international networks together for effective wastewater surveillance.
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Affiliation(s)
| | - Mariana Cardoso Chrispim
- Environmental and Biosciences Department, School of Business, Innovation and Sustainability, Halmstad University, Kristian IV:s väg 3, 30118 Halmstad, Sweden
| | - Mikaela Renata Funada Barbosa
- Environmental Analysis Department, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil; NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Marcelo de Souza Lauretto
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Arts, Sciences and Humanities, University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo CEP 03828-000, Brazil
| | - Maria Tereza Pepe Razzolini
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Public Health, University of Sao Paulo, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Adelaide Cassia Nardocci
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Public Health, University of Sao Paulo, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Owen Jones
- School of Mathematics, Cardiff University, Cardiff CF24 4AG, UK
| | - Davey L Jones
- Environment Centre Wales, Bangor University, Bangor LL57 2UW, UK; Food Futures Institute, Murdoch University, Murdoch WA 6105, Australia
| | | | - Maria Inês Zanoli Sato
- Environmental Analysis Department, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil; NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Cassiana Montagner
- Environmental Chemistry Laboratory, Institute of Chemistry, University of Campinas, Campinas, São Paulo 13083970, Brazil
| | - Isabelle Durance
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.
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3
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Mullins N, Alashraf AR, McDermott K, Brown RS, Payne SJ. Polyethylenimine mediated recovery of SARS-CoV-2 and total viral RNA: Impact of aqueous conditions on behaviour and recovery. WATER RESEARCH 2024; 253:121207. [PMID: 38401469 DOI: 10.1016/j.watres.2024.121207] [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: 07/03/2023] [Revised: 10/28/2023] [Accepted: 01/26/2024] [Indexed: 02/26/2024]
Abstract
Wastewater-based epidemiology (WBE) is an emerging, practical surveillance tool for monitoring community levels of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, SC2). However, a paucity of data exists regarding SARS-CoV-2 and viral biomarker behaviour in aqueous and wastewater environments. Therefore, there is a pressing need to develop efficient and robust methods that both improve method sensitivity and reduce time and cost. We present a novel method for SARS-CoV-2, Human Coronavirus 229E (229E), and Pepper Mild Mottle Virus (PMMoV) recovery utilizing surface charge-based attraction via the branched cationic polymer, polyethylenimine (PEI). Initially, dose-optimization experiments demonstrated that low concentrations of PEI (0.001% w/v) proved most effective at flocculating suspended viruses and viral material, including additional unbound SC2 viral fragments and/or RNA from raw wastewater. A design-of-experiments (DOE) approach was used to optimize virus and/or viral material aggregation behaviour and recovery across varying aqueous conditions, revealing pH as a major influence on recoverability in this system, combinatorially due to both a reduction in viral material surface charge and increased protonation of PEI-bound amine groups. Overall, this method has shown great promise in significantly improving quantitative viral recovery, providing a straightforward and effective augmentation to standard centrifugation techniques.
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Affiliation(s)
- Nathan Mullins
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; McMaster University, Department of Chemical Engineering, Hamilton, Ontario, L8S 4L7, Canada
| | - Abdul Rahman Alashraf
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada
| | | | - R Stephen Brown
- Queen's University, Department of Chemistry and School of Environmental Studies, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada.
| | - Sarah Jane Payne
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada.
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4
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Toribio-Avedillo D, Gómez-Gómez C, Sala-Comorera L, Galofré B, Muniesa M. Adapted methods for monitoring influenza virus and respiratory syncytial virus in sludge and wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170636. [PMID: 38331285 DOI: 10.1016/j.scitotenv.2024.170636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Wastewater-based surveillance constitutes a valuable methodology for the continuous monitoring of viral circulation, with the capacity to function as an early warning system. It holds particular significance in scenarios where respiratory viruses exhibit overlapping clinical presentations, as occurs with SARS-CoV-2, influenza virus (IV), and respiratory syncytial virus (RSV), and allows seasonal virus outbreaks to be distinguished from COVID-19 peaks. Furthermore, sewage sludge, given it harbors concentrated human waste from a large population, serves as a substantial reservoir for pathogen detection. To effectively integrate wastewater-based epidemiology into infectious disease surveillance, the detection methods employed in wastewater samples must be adapted to the distinct characteristics of sludge matrices. In this study, we adapted and applied protocols for the detection of IV and RSV in sewage sludge, comparing their performance with the results obtained in wastewater. To assess the efficiency of these protocols, sludge and wastewater samples were spiked with IV and RSV RNA, either free or incorporated in lentiviral particles. Samples were concentrated using the aluminum hydroxide adsorption-precipitation method before viral RNA extraction. Absolute virus quantification was carried out by RT-qPCR, including an internal control to monitor potential inhibitory factors. Recovery efficiencies for both free IV and RSV RNA were 60 % in sludge, and 75 % and 71 % respectively in wastewater, whereas the values for IV and RSV RNA in lentiviral particles were 16 % and 10 % in sludge and 21 % and 17 % in wastewater respectively. Additionally, the protocol enabled the quantification of naturally occurring IV and RSV in wastewater and sludge samples collected from two wastewater treatment plants during the winter months, thus affirming the efficacy of the employed methodologies.
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Affiliation(s)
- Daniel Toribio-Avedillo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain
| | - Clara Gómez-Gómez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain
| | - Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643 Annex, Floor 0, E-08028 Barcelona, Spain.
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5
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Rivadulla M, Lois M, Elena AX, Balboa S, Suarez S, Berendonk TU, Romalde JL, Garrido JM, Omil F. Occurrence and fate of CECs (OMPs, ARGs and pathogens) during decentralised treatment of black water and grey water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:169863. [PMID: 38190906 DOI: 10.1016/j.scitotenv.2023.169863] [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: 08/31/2023] [Revised: 12/13/2023] [Accepted: 12/31/2023] [Indexed: 01/10/2024]
Abstract
Decentralised wastewater treatment is becoming a suitable strategy to reduce cost and environmental impact. In this research, the performance of two technologies treating black water (BW) and grey water (GW) fractions of urban sewage is carried out in a decentralised treatment of the wastewater produced in three office buildings. An Anaerobic Membrane Bioreactor (AnMBR) treating BW and a Hybrid preanoxic Membrane Bioreactor (H-MBR) containing small plastic carrier elements, treating GW were operated at pilot scale. Their potential on reducing the release of contaminants of emerging concern (CECs) such as Organic Micropollutants (OMPs), Antibiotic Resistance Genes (ARGs) and pathogens was studied. After 226 d of operation, a stable operation was achieved in both systems: the AnMBR removed 92.4 ± 2.5 % of influent COD, and H-MBR removed 89.7 ± 3.5 %. Regarding OMPs, the profile of compounds differed between BW and GW, being BW the matrix with more compounds detected at higher concentrations (up to μg L-1). For example, in the case of ibuprofen the concentrations in BW were 23.63 ± 3.97 μg L-1, 3 orders of magnitude higher than those detected in GW. The most abundant ARGs were sulfonamide resistant genes (sul1) and integron class 1 (intl1) in both BW and GW. Pathogenic bacteria counts were reduced between 1 and 3 log units in the AnMBR. Bacterial loads in GW were much lower than in BW, being no bacterial re-growth observed for the GW effluents after treatment in the H-MBR. None of the selected enteric viruses was detected in GW treatment line.
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Affiliation(s)
- M Rivadulla
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain.
| | - M Lois
- CRETUS, Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - A X Elena
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | - S Balboa
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - S Suarez
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - T U Berendonk
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | - J L Romalde
- CRETUS, Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - J M Garrido
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - F Omil
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
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6
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Akter J, Smith WJM, Gebrewold M, Kim I, Simpson SL, Bivins A, Ahmed W. Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167964. [PMID: 37865239 DOI: 10.1016/j.scitotenv.2023.167964] [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: 09/22/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARS-CoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 × 102 GC/reaction, with greater analytical sensitivity at 2 × 101 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 × 103 GC/reaction. For SARS-CoV-2 seeded wastewater samples, the US CDC N1 assay exhibited greater analytical sensitivity than the US CDC N2, E_Sarbeco, and RT-LAMP assays. Out of 30 wastewater samples, RT-qPCR detected endogenous SARS-CoV-2 RNA in 29 samples, while RT-LAMP identified 27 positive samples, with 20 displaying consistent amplifications in all three RT-LAMP technical replicates. Agreement analysis revealed a strong concordance between RT-LAMP and the US CDC N1 and E_Sarbeco RT-qPCR assays (κ = 0.474) but lower agreement with the US CDC N2 RT-qPCR assay (κ = 0.359). Quantification of SARS-CoV-2 RNA in positive samples revealed a strong correlation between the US CDC N1 and E_Sarbeco assays, while the US CDC N1 and US CDC N2 assays exhibited weak correlation. Logistic regression analysis indicated that RT-LAMP results correlated with RNA quantified by the US CDC N1 and E_Sarbeco assays, with 95 % limits of detection of 3.99 and 3.47 log10 GC/15 mL, respectively. In conclusion, despite lower sensitivity compared to RT-qPCR assays, RT-LAMP may offer advantages for wastewater surveillance, such as rapid results (estimated as twice as fast), and simplicity, making it a valuable tool in the shifting landscape of COVID-19 wastewater surveillance. Furthermore, LAMP positive wastewater samples might be prioritized for SARS-CoV-2 sequencing due to reduced analytical sensitivity. These findings support the use of RT-LAMP as a specific and efficient method for screening wastewater samples for SARS-CoV-2, particularly in resource-limited settings.
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Affiliation(s)
- Jesmin Akter
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea; CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Metasebia Gebrewold
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Ilho Kim
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea
| | | | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
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7
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Baz Lomba JA, Pires J, Myrmel M, Arnø JK, Madslien EH, Langlete P, Amato E, Hyllestad S. Effectiveness of environmental surveillance of SARS-CoV-2 as an early-warning system: Update of a systematic review during the second year of the pandemic. JOURNAL OF WATER AND HEALTH 2024; 22:197-234. [PMID: 38295081 PMCID: wh_2023_279 DOI: 10.2166/wh.2023.279] [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
The aim of this updated systematic review was to offer an overview of the effectiveness of environmental surveillance (ES) of SARS-CoV-2 as a potential early-warning system (EWS) for COVID-19 and new variants of concerns (VOCs) during the second year of the pandemic. An updated literature search was conducted to evaluate the added value of ES of SARS-CoV-2 for public health decisions. The search for studies published between June 2021 and July 2022 resulted in 1,588 publications, identifying 331 articles for full-text screening. A total of 151 publications met our inclusion criteria for the assessment of the effectiveness of ES as an EWS and early detection of SARS-CoV-2 variants. We identified a further 30 publications among the grey literature. ES confirms its usefulness as an EWS for detecting new waves of SARS-CoV-2 infection with an average lead time of 1-2 weeks for most of the publication. ES could function as an EWS for new VOCs in areas with no registered cases or limited clinical capacity. Challenges in data harmonization and variant detection require standardized approaches and innovations for improved public health decision-making. ES confirms its potential to support public health decision-making and resource allocation in future outbreaks.
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Affiliation(s)
- Jose Antonio Baz Lomba
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway E-mail:
| | - João Pires
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway; ECDC fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jorunn Karterud Arnø
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Elisabeth Henie Madslien
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Petter Langlete
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Ettore Amato
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Susanne Hyllestad
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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8
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Garcia-Pedemonte D, Carcereny A, Gregori J, Quer J, Garcia-Cehic D, Guerrero L, Ceretó-Massagué A, Abid I, Bosch A, Costafreda MI, Pintó RM, Guix S. Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater. Int J Mol Sci 2023; 24:17184. [PMID: 38139015 PMCID: PMC10743471 DOI: 10.3390/ijms242417184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Shortly after the beginning of the SARS-CoV-2 pandemic, many countries implemented sewage sentinel systems to monitor the circulation of the virus in the population. A fundamental part of these surveillance programs is the variant tracking through sequencing approaches to monitor and identify new variants or mutations that may be of importance. Two of the main sequencing platforms are Illumina and Oxford Nanopore Technologies. Here, we compare the performance of MiSeq (Illumina) and MinION (Oxford Nanopore Technologies), as well as two different data processing pipelines, to determine the effect they may have on the results. MiSeq showed higher sequencing coverage, lower error rate, and better capacity to detect and accurately estimate variant abundances than MinION R9.4.1 flow cell data. The use of different variant callers (LoFreq and iVar) and approaches to calculate the variant proportions had a remarkable impact on the results generated from wastewater samples. Freyja, coupled with iVar, may be more sensitive and accurate than LoFreq, especially with MinION data, but it comes at the cost of having a higher error rate. The analysis of MinION R10.4.1 flow cell data using Freyja combined with iVar narrows the gap with MiSeq performance in terms of read quality, accuracy, sensitivity, and number of detected mutations. Although MiSeq should still be considered as the standard method for SARS-CoV-2 variant tracking, MinION's versatility and rapid turnaround time may represent a clear advantage during the ongoing pandemic.
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Affiliation(s)
- David Garcia-Pedemonte
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Albert Carcereny
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases—Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Campus, 08035 Barcelona, Spain; (J.G.); (J.Q.); (D.G.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases—Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Campus, 08035 Barcelona, Spain; (J.G.); (J.Q.); (D.G.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Diseases—Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Campus, 08035 Barcelona, Spain; (J.G.); (J.Q.); (D.G.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Laura Guerrero
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain;
| | - Adrià Ceretó-Massagué
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain;
| | - Islem Abid
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Center of Excellence in Biotechnology Research, College of Applied Science, King Saud University, Riyadh 11495, Saudi Arabia
| | - Albert Bosch
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Maria Isabel Costafreda
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Rosa M. Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, 08028 Barcelona, Spain; (D.G.-P.); (A.C.); (I.A.); (A.B.); (M.I.C.)
- Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
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9
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Brunner FS, Payne A, Cairns E, Airey G, Gregory R, Pickwell ND, Wilson M, Carlile M, Holmes N, Hill V, Child H, Tomlinson J, Ahmed S, Denise H, Rowe W, Frazer J, Aerle RV, Evens N, Porter J, Templeton K, Jeffries AR, Loose M, Paterson S. Utility of wastewater genomic surveillance compared to clinical surveillance to track the spread of the SARS-CoV-2 Omicron variant across England. WATER RESEARCH 2023; 247:120804. [PMID: 37925861 DOI: 10.1016/j.watres.2023.120804] [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: 08/25/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
The world has moved into a new stage of managing the SARS-CoV-2 pandemic with minimal restrictions and reduced testing in the population, leading to reduced genomic surveillance of virus variants in individuals. Wastewater-based epidemiology (WBE) can provide an alternative means of tracking virus variants in the population but decision-makers require confidence that it can be applied to a national scale and is comparable to individual testing data. We analysed 19,911 samples from 524 wastewater sites across England at least twice a week between November 2021 and February 2022, capturing sewage from >70% of the English population. We used amplicon-based sequencing and the phylogeny based de-mixing tool Freyja to estimate SARS-CoV-2 variant frequencies and compared these to the variant dynamics observed in individual testing data from clinical and community settings. We show that wastewater data can reconstruct the spread of the Omicron variant across England since November 2021 in close detail and aligns closely with epidemiological estimates from individual testing data. We also show the temporal and spatial spread of Omicron within London. Our wastewater data further reliably track the transition between Omicron subvariants BA1 and BA2 in February 2022 at regional and national levels. Our demonstration that WBE can track the fast-paced dynamics of SARS-CoV-2 variant frequencies at a national scale and closely match individual testing data in time shows that WBE can reliably fill the monitoring gap left by reduced individual testing in a more affordable way.
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Affiliation(s)
- Franziska S Brunner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - Alexander Payne
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Edward Cairns
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - George Airey
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - Richard Gregory
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - Natalie D Pickwell
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Myles Wilson
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Matthew Carlile
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Nadine Holmes
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Harry Child
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Jasmine Tomlinson
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Suhel Ahmed
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Hubert Denise
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK
| | - William Rowe
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK
| | - Jacob Frazer
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas, Barrack Road, Weymouth, DT 8UB, UK
| | - Nicholas Evens
- Monitoring Laboratories, National Monitoring, Environment Agency EX6 8FD, UK
| | - Jonathan Porter
- Monitoring Laboratories, National Monitoring, Environment Agency EX6 8FD, UK
| | - Kate Templeton
- NHS Lothian, Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Aaron R Jeffries
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Matt Loose
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK.
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10
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Hasing ME, Lee BE, Gao T, Li Q, Qiu Y, Ellehoj E, Graber TE, Fuzzen M, Servos M, Landgraff C, Delatolla R, Tipples G, Zelyas N, Hinshaw D, Maal-Bared R, Sikora C, Parkins M, Hubert CRJ, Frankowski K, Hrudey SE, Pang XL. Wastewater surveillance monitoring of SARS-CoV-2 variants of concern and dynamics of transmission and community burden of COVID-19. Emerg Microbes Infect 2023; 12:2233638. [PMID: 37409382 PMCID: PMC10408568 DOI: 10.1080/22221751.2023.2233638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/04/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Wastewater-based surveillance is a valuable approach for monitoring COVID-19 at community level. Monitoring SARS-CoV-2 variants of concern (VOC) in wastewater has become increasingly relevant when clinical testing capacity and case-based surveillance are limited. In this study, we ascertained the turnover of six VOC in Alberta wastewater from May 2020 to May 2022. Wastewater samples from nine wastewater treatment plants across Alberta were analysed using VOC-specific RT-qPCR assays. The performance of the RT-qPCR assays in identifying VOC in wastewater was evaluated against next generation sequencing. The relative abundance of each VOC in wastewater was compared to positivity rate in COVID-19 testing. VOC-specific RT-qPCR assays performed comparatively well against next generation sequencing; concordance rates ranged from 89% to 98% for detection of Alpha, Beta, Gamma, Omicron BA.1 and Omicron BA.2, with a slightly lower rate of 85% for Delta (p < 0.01). Elevated relative abundance of Alpha, Delta, Omicron BA.1 and BA.2 were each associated with increased COVID-19 positivity rate. Alpha, Delta and Omicron BA.2 reached 90% relative abundance in wastewater within 80, 111 and 62 days after their initial detection, respectively. Omicron BA.1 increased more rapidly, reaching a 90% relative abundance in wastewater after 35 days. Our results from VOC surveillance in wastewater correspond with clinical observations that Omicron is the VOC with highest disease burden over the shortest period in Alberta to date. The findings suggest that changes in relative abundance of a VOC in wastewater can be used as a supplementary indicator to track and perhaps predict COVID-19 burden in a population.
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Affiliation(s)
- Maria E. Hasing
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Bonita E. Lee
- Department of Paediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Tiejun Gao
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Qiaozhi Li
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Erik Ellehoj
- Ellehoj Redmond Consulting, Edmonton, Alberta, Canada
| | - Tyson E. Graber
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mark Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Graham Tipples
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Nathan Zelyas
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Deena Hinshaw
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Christopher Sikora
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaoli L. Pang
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
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11
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Mallah N, Pardo-Seco J, Ares-Gómez S, López-Pérez LR, González-Pérez JM, Rosón B, Otero-Barrós MT, Durán-Parrondo C, Nartallo-Penas V, Mirás-Carballal S, Rodríguez-Tenreiro-Sánchez C, Rivero-Calle I, Gómez-Carballa A, Salas A, Martinón-Torres F. COVID-19 vaccine effectiveness in children by age groups. A population-based study in Galicia, Spain. Pediatr Allergy Immunol 2023; 34:e14037. [PMID: 37877845 DOI: 10.1111/pai.14037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/25/2023] [Accepted: 09/30/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Studies on vaccine effectiveness (VE) against COVID-19 in the pediatric population are outgoing. We aimed to quantify VE against SARS-CoV-2 in two pediatric age groups, 5-11 and 12-17-year-old, while considering vaccine type, SARS-CoV-2 variant, and duration of protection. METHODS A population-based test-negative control study was undertaken in Galicia, Spain. Children 5-11-year-old received the Comirnaty® (Pfizer, US) vaccine, while those aged 12-17-year-old received the Comirnaty® (Pfizer, US) or SpikeVax® (ModernaTX, Inc) vaccine. Participants were categorized into unvaccinated (0 doses or one dose with <14 days since vaccination), partially vaccinated (only one dose with ≥14 days, or two doses with <14 days after the second dose administration), and fully vaccinated (two doses with ≥14 days after the second injection). Adjusted odds ratios (OR) and their 95% confidence intervals (CI) were estimated using multiple logistic regression models. VE was calculated as (1-OR) * 100. Stratified and sensitivity analyses were performed. RESULTS In the fully vaccinated 5-11-year-old children, VE against the Omicron variant was 44.1% (95% CI: 38.2%-49.4%). In the fully vaccinated 12-17-year-old individuals, VE was 83.4% (95% CI: 81.2%-85.3%) against Delta and 74.8% (95% CI: 58.5%-84.9%) against Omicron. Comirnaty® and SpikeVax® vaccines showed a similar magnitude of VE against Delta [Comirnaty® VE: 81.9% (95% CI: 79.3%-84.1%) and SpikeVax® VE: 85.3% (95% CI: 81.9%-88.1%)]. Comirnaty® (Pfizer, US; VE: 79.7%; 95% CI: 50.7%-92.4%) showed a slightly higher magnitude of protection against Omicron than SpikeVax® (ModernaTX, Inc), yet with an overlapping CI (VE: 74.3%; 95% CI: 56.6%-84.9%). VE was maintained in all age subgroups in both pediatric populations, but it declined over time. CONCLUSIONS In Galicia, mRNA VE was moderate against SARS-CoV-2 infections in the 5-11-year-old populations, but high in older children. VE declined over time, suggesting a potential need for booster dose schedules.
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Affiliation(s)
- Narmeen Mallah
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia, Spain
- WHO Collaborating Centre for Vaccine Safety, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Preventive Medicine, University of Santiago de Compostela (USC), Santiago de Compostela, Galicia, Spain
| | - Jacobo Pardo-Seco
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia, Spain
- WHO Collaborating Centre for Vaccine Safety, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Sonia Ares-Gómez
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia, Spain
- WHO Collaborating Centre for Vaccine Safety, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis-Ricardo López-Pérez
- Subdirección de Sistemas y Tecnologías de la Información, Servizo Galego de Saude, Santiago de Compostela, Galicia, Spain
| | - Juan-Manuel González-Pérez
- Subdirección de Sistemas y Tecnologías de la Información, Servizo Galego de Saude, Santiago de Compostela, Galicia, Spain
| | - Benigno Rosón
- Subdirección de Sistemas y Tecnologías de la Información, Servizo Galego de Saude, Santiago de Compostela, Galicia, Spain
| | - María-Teresa Otero-Barrós
- Dirección Xeral de Saude Pública, Consellería de Sanidade, Xunta de Galicia, Santiago de Compostela, Galicia, Spain
| | - Carmen Durán-Parrondo
- Dirección Xeral de Saude Pública, Consellería de Sanidade, Xunta de Galicia, Santiago de Compostela, Galicia, Spain
| | - Victoria Nartallo-Penas
- Dirección Xeral de Saude Pública, Consellería de Sanidade, Xunta de Galicia, Santiago de Compostela, Galicia, Spain
| | - Susana Mirás-Carballal
- Dirección Xeral de Saude Pública, Consellería de Sanidade, Xunta de Galicia, Santiago de Compostela, Galicia, Spain
| | - Carmen Rodríguez-Tenreiro-Sánchez
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia, Spain
- WHO Collaborating Centre for Vaccine Safety, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia, Spain
- WHO Collaborating Centre for Vaccine Safety, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario and University of Santiago de Compostela (USC), Santiago de Compostela, Galicia, Spain
| | - Alberto Gómez-Carballa
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia, Spain
- WHO Collaborating Centre for Vaccine Safety, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio Salas
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia, Spain
- WHO Collaborating Centre for Vaccine Safety, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Unidade de Xenética, Facultade de Medicina, Instituto de Ciencias Forenses, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Galicia, Spain
- GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago, Servizo Galego de Saúde, Santiago de Compostela, Galicia, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia, Spain
- WHO Collaborating Centre for Vaccine Safety, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario and University of Santiago de Compostela (USC), Santiago de Compostela, Galicia, Spain
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12
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Mattei M, Pintó RM, Guix S, Bosch A, Arenas A. Analysis of SARS-CoV-2 in wastewater for prevalence estimation and investigating clinical diagnostic test biases. WATER RESEARCH 2023; 242:120223. [PMID: 37354838 PMCID: PMC10265495 DOI: 10.1016/j.watres.2023.120223] [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: 03/10/2023] [Revised: 05/10/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Here we analyze SARS-CoV-2 genome copies in Catalonia's wastewater during the Omicron peak and develop a mathematical model to estimate the number of infections and the temporal relationship between reported and unreported cases. 1-liter samples from 16 wastewater treatment plants were collected and used in a compartmental epidemiological model. The average correlation between genome copies and reported cases was 0.85, with an average delay of 8.8 days. The model estimated that 53% of the population was infected, compared to the 19% reported cases. The under-reporting was highest in November and December 2021. The maximum genome copies shed in feces by an infected individual was estimated to range from 1.4×108 gc/g to 4.4×108 gc/g. Our framework demonstrates the potential of wastewater data as a leading indicator for daily new infections, particularly in contexts with low detection rates. It also serves as a complementary tool for prevalence estimation and offers a general approach for integrating wastewater data into compartmental models.
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Affiliation(s)
- Mattia Mattei
- Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, 43007 Tarragona, Spain.
| | - Rosa M Pintó
- Enteric Virus Laboratory, School of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, School of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, School of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Alex Arenas
- Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, 43007 Tarragona, Spain; Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, 99354, USA.
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13
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Fuzzen M, Harper NBJ, Dhiyebi HA, Srikanthan N, Hayat S, Bragg LM, Peterson SW, Yang I, Sun JX, Edwards EA, Giesy JP, Mangat CS, Graber TE, Delatolla R, Servos MR. An improved method for determining frequency of multiple variants of SARS-CoV-2 in wastewater using qPCR assays. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163292. [PMID: 37030387 PMCID: PMC10079313 DOI: 10.1016/j.scitotenv.2023.163292] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 06/01/2023]
Abstract
Wastewater-based surveillance has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Variants of Concern (VOCs) have been detected in wastewater by use of reverse transcription polymerase chain reaction (RT-PCR) or whole genome sequencing (WGS). Rapid, reliable RT-PCR assays continue to be needed to determine the relative frequencies of VOCs and sub-lineages in wastewater-based surveillance programs. The presence of multiple mutations in a single region of the N-gene allowed for the design of a single amplicon, multiple probe assay, that can distinguish among several VOCs in wastewater RNA extracts. This approach which multiplexes probes designed to target mutations associated with specific VOC's along with an intra-amplicon universal probe (non-mutated region) was validated in singleplex and multiplex. The prevalence of each mutation (i.e. VOC) is estimated by comparing the abundance of the targeted mutation with a non-mutated and highly conserved region within the same amplicon. This is advantageous for the accurate and rapid estimation of variant frequencies in wastewater. The N200 assay was applied to monitor frequencies of VOCs in wastewater extracts from several communities in Ontario, Canada in near real time from November 28, 2021 to January 4, 2022. This includes the period of the rapid replacement of the Delta variant with the introduction of the Omicron variant in these Ontario communities in early December 2021. The frequency estimates using this assay were highly reflective of clinical WGS estimates for the same communities. This style of qPCR assay, which simultaneously measures signal from a non-mutated comparator probe and multiple mutation-specific probes contained within a single qPCR amplicon, can be applied to future assay development for rapid and accurate estimations of variant frequencies.
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Affiliation(s)
- Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
| | | | - Hadi A Dhiyebi
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Nivetha Srikanthan
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Samina Hayat
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Leslie M Bragg
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Shelley W Peterson
- One-Health Division, Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3M4, Canada
| | - Ivy Yang
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - J X Sun
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Elizabeth A Edwards
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - John P Giesy
- Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
| | - Chand S Mangat
- One-Health Division, Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3M4, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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14
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Férez JA, Cuevas-Ferrando E, Ayala-San Nicolás M, Simón Andreu PJ, López R, Truchado P, Sánchez G, Allende A. Wastewater-Based Epidemiology to Describe the Evolution of SARS-CoV-2 in the South-East of Spain, and Application of Phylogenetic Analysis and a Machine Learning Approach. Viruses 2023; 15:1499. [PMID: 37515186 PMCID: PMC10386001 DOI: 10.3390/v15071499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The COVID-19 pandemic has posed a significant global threat, leading to several initiatives for its control and management. One such initiative involves wastewater-based epidemiology, which has gained attention for its potential to provide early warning of virus outbreaks and real-time information on its spread. In this study, wastewater samples from two wastewater treatment plants (WWTPs) located in the southeast of Spain (region of Murcia), namely Murcia, and Cartagena, were analyzed using RT-qPCR and high-throughput sequencing techniques to describe the evolution of SARS-CoV-2 in the South-East of Spain. Additionally, phylogenetic analysis and machine learning approaches were applied to develop a pre-screening tool for the identification of differences among the variant composition of different wastewater samples. The results confirmed that the levels of SARS-CoV-2 in these wastewater samples changed concerning the number of SARS-CoV-2 cases detected in the population, and variant occurrences were in line with clinical reported data. The sequence analyses helped to describe how the different SARS-CoV-2 variants have been replaced over time. Additionally, the phylogenetic analysis showed that samples obtained at close sampling times exhibited a higher similarity than those obtained more distantly in time. A second analysis using a machine learning approach based on the mutations found in the SARS-CoV-2 spike protein was also conducted. Hierarchical clustering (HC) was used as an efficient unsupervised approach for data analysis. Results indicated that samples obtained in October 2022 in Murcia and Cartagena were significantly different, which corresponded well with the different virus variants circulating in the two locations. The proposed methods in this study are adequate for comparing consensus sequence types of the SARS-CoV-2 sequences as a preliminary evaluation of potential changes in the variants that are circulating in a given population at a specific time point.
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Affiliation(s)
- Jose A Férez
- Research Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, 30100 Murcia, Spain
| | - Enric Cuevas-Ferrando
- Environmental Virology and Food Safety Lab (VISAFELab), Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980 Valencia, Spain
| | - María Ayala-San Nicolás
- Research Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, 30100 Murcia, Spain
| | - Pedro J Simón Andreu
- Entidad Regional de Saneamiento y Depuración de Murcia (ESAMUR), Avda. Juan Carlos I, s/n. Ed. Torre Jemeca, 30009 Murcia, Spain
| | - Román López
- Entidad Regional de Saneamiento y Depuración de Murcia (ESAMUR), Avda. Juan Carlos I, s/n. Ed. Torre Jemeca, 30009 Murcia, Spain
| | - Pilar Truchado
- Research Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, 30100 Murcia, Spain
| | - Gloria Sánchez
- Environmental Virology and Food Safety Lab (VISAFELab), Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980 Valencia, Spain
| | - Ana Allende
- Research Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, 30100 Murcia, Spain
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15
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Lanzarini NM, Mannarino CF, Ribeiro AVC, Prado T, Vahia LS, Siqueira MM, Resende PC, Quintaes BR, Miagostovich MP. SARS-CoV-2 surveillance-based on municipal solid waste leachate in Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:67368-67377. [PMID: 37101215 PMCID: PMC10132925 DOI: 10.1007/s11356-023-27019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Municipal solid waste leachate-based epidemiology is an alternative viral tracking tool that applies fresh truck leachate as an early warning of public health emergencies. This study aimed to investigate the potential of SARS-CoV-2 surveillance based on solid waste fresh truck leachate. Twenty truck leachate samples were ultracentrifugated, nucleic acid extracted, and real-time RT-qPCR SARS-CoV-2 N1/N2 applied. Viral isolation, variant of concern (N1/N2) inference, and whole genome sequencing were also performed. SARS-CoV-2 was detected on 40% (8/20) of samples, with a concentration from 2.89 to 6.96 RNA Log10 100 mL-1. The attempt to isolate SARS-CoV-2 and recover the whole genome was not successful; however, positive samples were characterized as possible pre-variant of concern (pre-VOC), VOC Alpha (B.1.1.7) and variant of interest Zeta (P.2). This approach revealed an alternative tool to infer SARS-CoV-2 in the environment and may help the management of local surveillance, health, and social policies.
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Affiliation(s)
- Natália Maria Lanzarini
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil.
| | - Camille Ferreira Mannarino
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - André Vinicius Costa Ribeiro
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Leonardo Saboia Vahia
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | | | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
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16
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Girón-Guzmán I, Díaz-Reolid A, Cuevas-Ferrando E, Falcó I, Cano-Jiménez P, Comas I, Pérez-Cataluña A, Sánchez G. Evaluation of two different concentration methods for surveillance of human viruses in sewage and their effects on SARS-CoV-2 sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160914. [PMID: 36526211 PMCID: PMC9744676 DOI: 10.1016/j.scitotenv.2022.160914] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 05/05/2023]
Abstract
During the current COVID-19 pandemic, wastewater-based epidemiology (WBE) emerged as a reliable strategy both as a surveillance method and a way to provide an overview of the SARS-CoV-2 variants circulating among the population. Our objective was to compare two different concentration methods, a well-established aluminum-based procedure (AP) and the commercially available Maxwell® RSC Enviro Wastewater TNA Kit (TNA) for human enteric virus, viral indicators and SARS-CoV-2 surveillance. Additionally, both concentration methods were analyzed for their impact on viral infectivity, and nucleic acids obtained from each method were also evaluated by massive sequencing for SARS-CoV-2. The percentage of SARS-CoV-2 positive samples using the AP method accounted to 100 %, 83.3 %, and 33.3 % depending on the target region while 100 % positivity for these same three target regions was reported using the TNA procedure. The concentrations of norovirus GI, norovirus GII and HEV using the TNA method were significantly greater than for the AP method while no differences were reported for rotavirus, astrovirus, crAssphage and PMMoV. Furthermore, TNA kit in combination with the Artic v4 primer scheme yields the best SARS-CoV-2 sequencing results. Regarding impact on infectivity, the concentration method used by the TNA kit showed near-complete lysis of viruses. Our results suggest that although the performance of the TNA kit was higher than that of the aluminum procedure, both methods are suitable for the analysis of enveloped and non-enveloped viruses in wastewater by molecular methods.
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Affiliation(s)
- Inés Girón-Guzmán
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Azahara Díaz-Reolid
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
| | - Pablo Cano-Jiménez
- Instituto de Biomedicina de Valencia (IBV-CSIC), C/ Jaume Roig, 11, Valencia 46010, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), C/ Jaume Roig, 11, Valencia 46010, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain.
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna 46980, Valencia, Spain
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17
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Girón-Guzmán I, Díaz-Reolid A, Truchado P, Carcereny A, García-Pedemonte D, Hernáez B, Bosch A, Pintó RM, Guix S, Allende A, Alcamí A, Pérez-Cataluña A, Sánchez G. Spanish wastewater reveals the current spread of Monkeypox virus. WATER RESEARCH 2023; 231:119621. [PMID: 36693290 PMCID: PMC9845017 DOI: 10.1016/j.watres.2023.119621] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/01/2022] [Accepted: 01/15/2023] [Indexed: 05/09/2023]
Abstract
Besides nasopharyngeal swabs, monkeypox virus (MPXV) DNA has been detected in a variety of samples such as saliva, semen, urine and fecal samples. Using the environmental surveillance network previously developed in Spain for the routine wastewater surveillance of SARS-CoV-2 (VATar COVID-19), we have analyzed the presence of MPXV DNA in wastewater from different areas of Spain. Samples (n = 312) from 24 different wastewater treatment plants were obtained between May 9 (week 19 of 2022) and August 4 (week 31 of 2022). Following concentration of viral particles by a validated aluminum adsorption-precipitation method, a qPCR procedure allowed us to detect MPXV DNA in 56 wastewater samples collected from May 16 to August 4, 2022, with values ranging between 2.2 × 103 to 8.7 × 104 genome copies (gc)/L. This study shows that MPXV DNA can be reproducibly detected by qPCR in longitudinal samples collected from different Spanish wastewater treatment plants. According to data from the National Epidemiological Surveillance Network (RENAVE) in Spain a total of 6,119 cases have been confirmed as of August 19, 2022. However, and based on the wastewater data, the reported clinical cases seem to be underestimated and asymptomatic infections may be more frequent than expected.
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Affiliation(s)
- Inés Girón-Guzmán
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain
| | - Azahara Díaz-Reolid
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain
| | - Pilar Truchado
- Department of Food Science and Technology, CEBAS-CSIC, Research Group on Quality and Safety of Fruits and Vegetables, Campus Universitario de Espinardo, 25, Murcia 30100, Spain
| | - Albert Carcereny
- Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, Spain
| | - David García-Pedemonte
- Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, Spain
| | - Bruno Hernáez
- Molecular Biology Center Severo Ochoa, CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, Spain
| | - Rosa María Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology, and Statistics, Section of Microbiology, Virology, and Biotechnology, School of Biology, University of Barcelona, Barcelona, Spain
| | - Ana Allende
- Department of Food Science and Technology, CEBAS-CSIC, Research Group on Quality and Safety of Fruits and Vegetables, Campus Universitario de Espinardo, 25, Murcia 30100, Spain
| | - Antonio Alcamí
- Molecular Biology Center Severo Ochoa, CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Alba Pérez-Cataluña
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain.
| | - Gloria Sánchez
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Avda. Catedrático Agustín Escardino 7, Valencia, Paterna 46980, Spain.
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18
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Zheng X, Wang M, Deng Y, Xu X, Lin D, Zhang Y, Li S, Ding J, Shi X, Yau CI, Poon LLM, Zhang T. A rapid, high-throughput, and sensitive PEG-precipitation method for SARS-CoV-2 wastewater surveillance. WATER RESEARCH 2023; 230:119560. [PMID: 36623382 PMCID: PMC9803703 DOI: 10.1016/j.watres.2022.119560] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
The effective application of wastewater surveillance is dependent on testing capacity and sensitivity to obtain high spatial resolution testing results for a timely targeted public health response. To achieve this purpose, the development of rapid, high-throughput, and sensitive virus concentration methods is urgently needed. Various protocols have been developed and implemented in wastewater surveillance networks so far, however, most of them lack the ability to scale up testing capacity or cannot achieve sufficient sensitivity for detecting SARS-CoV-2 RNA at low prevalence. In the present study, using positive raw wastewater in Hong Kong, a PEG precipitation-based three-step centrifugation method was developed, including low-speed centrifugation for large particles removal and the recovery of viral nucleic acid, and medium-speed centrifugation for the concentration of viral nucleic acid. This method could process over 100 samples by two persons per day to reach the process limit of detection (PLoD) of 3286 copies/L wastewater. Additionally, it was found that the testing capacity could be further increased by decreasing incubation and centrifugation time without significantly influencing the method sensitivity. The entire procedure uses ubiquitous reagents and instruments found in most laboratories to obtain robust testing results. This high-throughput, cost-effective, and sensitive tool will promote the establishment of nearly real-time wastewater surveillance networks for valuable public health information.
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Affiliation(s)
- Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Mengying Wang
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Danxi Lin
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yulin Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chung In Yau
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR, China.
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19
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Farkas K, Pellett C, Williams R, Alex-Sanders N, Bassano I, Brown MR, Denise H, Grimsley JMS, Kevill JL, Khalifa MS, Pântea I, Story R, Wade MJ, Woodhall N, Jones DL. Rapid Assessment of SARS-CoV-2 Variant-Associated Mutations in Wastewater Using Real-Time RT-PCR. Microbiol Spectr 2023; 11:e0317722. [PMID: 36629447 PMCID: PMC9927140 DOI: 10.1128/spectrum.03177-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/11/2022] [Indexed: 01/12/2023] Open
Abstract
Within months of the COVID-19 pandemic being declared on March 20, 2020, novel, more infectious variants of SARS-CoV-2 began to be detected in geospatially distinct regions of the world. With international travel being a lead cause of spread of the disease, the importance of rapidly identifying variants entering a country is critical. In this study, we utilized wastewater-based epidemiology (WBE) to monitor the presence of variants in wastewater generated in managed COVID-19 quarantine facilities for international air passengers entering the United Kingdom. Specifically, we developed multiplex reverse transcription quantitative PCR (RT-qPCR) assays for the identification of defining mutations associated with Beta (K417N), Gamma (K417T), Delta (156/157DEL), and Kappa (E154K) variants which were globally prevalent at the time of sampling (April to July 2021). The assays sporadically detected mutations associated with the Beta, Gamma, and Kappa variants in 0.7%, 2.3%, and 0.4% of all samples, respectively. The Delta variant was identified in 13.3% of samples, with peak detection rates and concentrations observed in May 2021 (24%), concurrent with its emergence in the United Kingdom. The RT-qPCR results correlated well with those from sequencing, suggesting that PCR-based detection is a good predictor for variant presence; although, inadequate probe binding may lead to false positive or negative results. Our findings suggest that WBE coupled with RT-qPCR may be used as a rapid, initial assessment to identify emerging variants at international borders and mass quarantining facilities. IMPORTANCE With the global spread of COVID-19, it is essential to identify emerging variants which may be more harmful or able to escape vaccines rapidly. To date, the gold standard to assess variants circulating in communities has been the sequencing of the S gene or the whole genome of SARS-CoV-2; however, that approach is time-consuming and expensive. In this study, we developed two duplex RT-qPCR assays to detect and quantify defining mutations associated with the Beta, Gamma, Delta, and Kappa variants. The assays were validated using RNA extracts derived from wastewater samples taken at quarantine facilities. The results showed good correlation with the results of sequencing and demonstrated the emergence of the Delta variant in the United Kingdom in May 2021. The assays developed here enable the assessment of variant-specific mutations within 2 h after the RNA extract was generated which is essential for outbreak rapid response.
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Affiliation(s)
- Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, United Kingdom
| | - Cameron Pellett
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Rachel Williams
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Natasha Alex-Sanders
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Irene Bassano
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Mathew R. Brown
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Hubert Denise
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
| | - Jasmine M. S. Grimsley
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- The London Data Company, London, United Kingdom
| | - Jessica L. Kevill
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Mohammad S. Khalifa
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University, London, United Kingdom
| | - Igor Pântea
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Rich Story
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- Servita Professional Services (UK) Ltd., London, United Kingdom
| | - Matthew J. Wade
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Nick Woodhall
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Davey L. Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
- Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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20
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Ahmed F, Tscharke B, O'Brien JW, Hall WD, Cabot PJ, Sowa PM, Samanipour S, Thomas KV. National Wastewater Reconnaissance of Analgesic Consumption in Australia. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1712-1720. [PMID: 36637365 DOI: 10.1021/acs.est.2c06691] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
A wastewater-based epidemiology (WBE) method is presented to estimate analgesic consumption and assess the burden of treated pain in Australian communities. Wastewater influent samples from 60 communities, representing ∼52% of Australia's population, were analyzed to quantify the concentration of analgesics used to treat pain and converted to estimates of the amount of drug consumed per day per 1000 inhabitants using pharmacokinetics and WBE data. Consumption was standardized to the defined daily dose per day per 1000 people. The population burden of pain treatment was classified as mild to moderate pain (for non-opioid analgesics) and strong to severe pain (for opioid analgesics). The mean per capita weighted total DDD of non-opioid analgesics was 0.029 DDD/day/person, and that of opioid-based analgesics was 0.037 DDD/day/person across Australia. A greater burden of pain (mild to moderate or strong to severe pain index) was observed at regional and remote sites. The correlation analysis of pain indices with different socioeconomic descriptors revealed that pain affects populations from high to low socioeconomic groups. Australians spent an estimated US $3.5 (AU $5) per day on analgesics. Our findings suggest that WBE could be an effective surveillance tool for estimating the consumption of analgesics at a population scale and assessing the total treated pain burden in communities.
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Affiliation(s)
- Fahad Ahmed
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane, Queensland4102, Australia
| | - Benjamin Tscharke
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane, Queensland4102, Australia
| | - Jake W O'Brien
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane, Queensland4102, Australia
| | - Wayne D Hall
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane, Queensland4102, Australia
- Centre for Youth Substance Abuse Research, The University of Queensland, Herston, Brisbane, Queensland4029, Australia
| | - Peter J Cabot
- School of Pharmacy, The University of Queensland, Brisbane, Queensland4102, Australia
| | - P Marcin Sowa
- Centre for the Business and Economics of Health, The University of Queensland, Brisbane, Queensland4067, Australia
| | - Saer Samanipour
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane, Queensland4102, Australia
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam1090, The Netherlands
| | - Kevin V Thomas
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane, Queensland4102, Australia
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21
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Bonanno Ferraro G, Veneri C, Mancini P, Iaconelli M, Suffredini E, Bonadonna L, Lucentini L, Bowo-Ngandji A, Kengne-Nde C, Mbaga DS, Mahamat G, Tazokong HR, Ebogo-Belobo JT, Njouom R, Kenmoe S, La Rosa G. A State-of-the-Art Scoping Review on SARS-CoV-2 in Sewage Focusing on the Potential of Wastewater Surveillance for the Monitoring of the COVID-19 Pandemic. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:315-354. [PMID: 34727334 PMCID: PMC8561373 DOI: 10.1007/s12560-021-09498-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/21/2021] [Indexed: 05/07/2023]
Abstract
The outbreak of coronavirus infectious disease-2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has rapidly spread throughout the world. Several studies have shown that detecting SARS-CoV-2 in untreated wastewater can be a useful tool to identify new outbreaks, establish outbreak trends, and assess the prevalence of infections. On 06 May 2021, over a year into the pandemic, we conducted a scoping review aiming to summarize research data on SARS-CoV-2 in sewage. Papers dealing with raw sewage collected at wastewater treatment plants, sewer networks, septic tanks, and sludge treatment facilities were included in this review. We also reviewed studies on sewage collected in community settings such as private or municipal hospitals, healthcare facilities, nursing homes, dormitories, campuses, airports, aircraft, and cruise ships. The literature search was conducted using the electronic databases PubMed, EMBASE, and Web Science Core Collection. This comprehensive research yielded 1090 results, 66 of which met the inclusion criteria and are discussed in this review. Studies from 26 countries worldwide have investigated the occurrence of SARS-CoV-2 in sewage of different origin. The percentage of positive samples in sewage ranged from 11.6 to 100%, with viral concentrations ranging from ˂LOD to 4.6 × 108 genome copies/L. This review outlines the evidence currently available on wastewater surveillance: (i) as an early warning system capable of predicting COVID-19 outbreaks days or weeks before clinical cases; (ii) as a tool capable of establishing trends in current outbreaks; (iii) estimating the prevalence of infections; and (iv) studying SARS-CoV-2 genetic diversity. In conclusion, as a cost-effective, rapid, and reliable source of information on the spread of SARS-CoV-2 and its variants in the population, wastewater surveillance can enhance genomic and epidemiological surveillance with independent and complementary data to inform public health decision-making during the ongoing pandemic.
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Affiliation(s)
- G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - P Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Bonadonna
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Lucentini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - A Bowo-Ngandji
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - C Kengne-Nde
- Research Monitoring and Planning Unit, National Aids Control Committee, Douala, Cameroon
| | - D S Mbaga
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - G Mahamat
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - H R Tazokong
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - J T Ebogo-Belobo
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - R Njouom
- Virology Department, Centre Pasteur of Cameroon, Yaounde, Cameroon
| | - S Kenmoe
- Virology Department, Centre Pasteur of Cameroon, Yaounde, Cameroon
| | - G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy.
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22
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Quasispecies Fitness Partition to Characterize the Molecular Status of a Viral Population. Negative Effect of Early Ribavirin Discontinuation in a Chronically Infected HEV Patient. Int J Mol Sci 2022; 23:ijms232314654. [PMID: 36498981 PMCID: PMC9739305 DOI: 10.3390/ijms232314654] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
The changes occurring in viral quasispecies populations during infection have been monitored using diversity indices, nucleotide diversity, and several other indices to summarize the quasispecies structure in a single value. In this study, we present a method to partition quasispecies haplotypes into four fractions according to their fitness: the master haplotype, rare haplotypes at two levels (those present at <0.1%, and those at 0.1−1%), and a fourth fraction that we term emerging haplotypes, present at frequencies >1%, but less than that of the master haplotype. We propose that by determining the changes occurring in the volume of the four quasispecies fitness fractions together with those of the Hill number profile we will be able to visualize and analyze the molecular changes in the composition of a quasispecies with time. To develop this concept, we used three data sets: a technical clone of the complete SARS-CoV-2 spike gene, a subset of data previously used in a study of rare haplotypes, and data from a clinical follow-up study of a patient chronically infected with HEV and treated with ribavirin. The viral response to ribavirin mutagenic treatment was selection of a rich set of synonymous haplotypes. The mutation spectrum was very complex at the nucleotide level, but at the protein (phenotypic/functional) level the pattern differed, showing a highly prevalent master phenotype. We discuss the putative implications of this observation in relation to mutagenic antiviral treatment.
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23
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Xie Y, Challis JK, Oloye FF, Asadi M, Cantin J, Brinkmann M, McPhedran KN, Hogan N, Sadowski M, Jones PD, Landgraff C, Mangat C, Servos MR, Giesy JP. RNA in Municipal Wastewater Reveals Magnitudes of COVID-19 Outbreaks across Four Waves Driven by SARS-CoV-2 Variants of Concern. ACS ES&T WATER 2022; 2:1852-1862. [PMID: 37552734 PMCID: PMC8887651 DOI: 10.1021/acsestwater.1c00349] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 05/07/2023]
Abstract
There are no standardized protocols for quantifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater to date, especially for population normalization. Here, a pipeline was developed, applied, and assessed to quantify SARS-CoV-2 and key variants of concern (VOCs) RNA in wastewater at Saskatoon, Canada. Normalization approaches using recovery ratio and extraction efficiency, wastewater parameters, or population indicators were assessed by comparing to daily numbers of new cases. Viral load was positively correlated with daily new cases reported in the sewershed. Wastewater surveillance (WS) had a lead time of approximately 7 days, which indicated surges in the number of new cases. WS revealed the variant α and δ driving the third and fourth wave, respectively. The adjustment with the recovery ratio and extraction efficiency improved the correlation between viral load and daily new cases. Normalization of viral concentration to concentrations of the artificial sweetener acesulfame K improved the trend of viral load during the Christmas and New Year holidays when populations were dynamic and variable. Acesulfame K performed better than pepper mild mottle virus, creatinine, and ammonia for population normalization. Hence, quality controls to characterize recovery ratios and extraction efficiencies and population normalization with acesulfame are promising for precise WS programs supporting decision-making in public health.
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Affiliation(s)
- Yuwei Xie
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Jonathan K. Challis
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Femi F. Oloye
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental
Engineering, College of Engineering, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5A9,
Canada
| | - Jenna Cantin
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Markus Brinkmann
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- School of Environment and Sustainability,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- Global Institute for Water Security,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5,
Canada
| | - Kerry N. McPhedran
- Department of Civil, Geological and Environmental
Engineering, College of Engineering, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5A9,
Canada
- Global Institute for Water Security,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5,
Canada
| | - Natacha Hogan
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- College of Agriculture and Bioresources, Department of
Animal and Poultry Sciences, University of Saskatchewan,
Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department,
City of Saskatoon, Saskatoon, Saskatchewan S7M 1X5,
Canada
| | - Paul D. Jones
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- School of Environment and Sustainability,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology
Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
R3E 3R2, Canada
- Food Science Department, University of
Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Chand Mangat
- Antimicrobial Resistance and Nosocomial Infections,
National Microbiology Laboratory, Public Health Agency of
Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Mark R. Servos
- Department of Biology, University of
Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - John P. Giesy
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- Department of Veterinary Biomedical Sciences,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4,
Canada
- Department of Environmental Sciences,
Baylor University, Waco, Texas 76706, United
States
- Department of Zoology and Center for Integrative
Toxicology, Michigan State University, East Lansing, Michigan
48824, United States
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24
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Tamáš M, Potocarova A, Konecna B, Klucar Ľ, Mackulak T. Wastewater Sequencing-An Innovative Method for Variant Monitoring of SARS-CoV-2 in Populations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:9749. [PMID: 35955106 PMCID: PMC9367975 DOI: 10.3390/ijerph19159749] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 05/14/2023]
Abstract
The SARS-CoV-2 outbreak has already affected more than 555 million people, and 6.3 million people have died. Due to its high infectivity, it is crucial to track SARS-CoV-2 outbreaks early to prevent the spread of infection. Wastewater monitoring appears to be a powerful and effective tool for managing epidemiological situations. Due to emerging mutations of SARS-CoV-2, there is a need to monitor mutations in order to control the pandemic. Since the sequencing of randomly chosen individuals is time-consuming and expensive, sequencing of wastewater plays an important role in revealing the dynamics of infection in a population. The sampling method used is a crucial factor and significantly impacts the results. Wastewater can be collected as a grab sample or as a 24 h composite sample. Another essential factor is the sample volume, as is the method of transport used. This review discusses different pretreatment procedures and RNA extraction, which may be performed using various methods, such as column-based extraction, TRIzol, or magnetic extraction. Each of the methods has its advantages and disadvantages, which are described accordingly. RT-qPCR is a procedure that confirms the presence of SARS-CoV-2 genes before sequencing. This review provides an overview of currently used methods for preparing wastewater samples, from sampling to sequencing.
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Affiliation(s)
- Michal Tamáš
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 81372 Bratislava, Slovakia
| | - Alena Potocarova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Barbora Konecna
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Ľubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia
| | - Tomas Mackulak
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
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Wu F, Lee WL, Chen H, Gu X, Chandra F, Armas F, Xiao A, Leifels M, Rhode SF, Wuertz S, Thompson J, Alm EJ. Making waves: Wastewater surveillance of SARS-CoV-2 in an endemic future. WATER RESEARCH 2022; 219:118535. [PMID: 35605390 PMCID: PMC9062764 DOI: 10.1016/j.watres.2022.118535] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 05/28/2023]
Abstract
Wastewater-based surveillance (WBS) has been widely used as a public health tool to monitor the emergence and spread of SARS-CoV-2 infections in populations during the COVID-19 pandemic. Coincident with the global vaccination efforts, the world is also enduring new waves of SARS-CoV-2 variants. Reinfections and vaccine breakthroughs suggest an endemic future where SARS-CoV-2 continues to persist in the general population. In this treatise, we aim to explore the future roles of wastewater surveillance. Practically, WBS serves as a relatively affordable and non-invasive tool for mass surveillance of SARS-CoV-2 infection while minimizing privacy concerns, attributes that make it extremely suited for its long-term usage. In an endemic future, the utility of WBS will include 1) monitoring the trend of viral loads of targets in wastewater for quantitative estimate of changes in disease incidence; 2) sampling upstream for pinpointing infections in neighborhoods and at the building level; 3) integrating wastewater and clinical surveillance for cost-efficient population surveillance; and 4) genome sequencing wastewater samples to track circulating and emerging variants in the population. We further discuss the challenges and future developments of WBS to reduce inconsistencies in wastewater data worldwide, improve its epidemiological inference, and advance viral tracking and discovery as a preparation for the next viral pandemic.
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Affiliation(s)
- Fuqing Wu
- Center for Infectious Disease, Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA.
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | | | - Stefan Wuertz
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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26
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Jiang C, Liu S, Zhang T, Liu Q, Alvarez PJJ, Chen W. Current Methods and Prospects for Analysis and Characterization of Nanomaterials in the Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:7426-7447. [PMID: 35584364 DOI: 10.1021/acs.est.1c08011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Analysis and characterization of naturally occurring and engineered nanomaterials in the environment are critical for understanding their environmental behaviors and defining real exposure scenarios for environmental risk assessment. However, this is challenging primarily due to the low concentration, structural heterogeneity, and dynamic transformation of nanomaterials in complex environmental matrices. In this critical review, we first summarize sample pretreatment methods developed for separation and preconcentration of nanomaterials from environmental samples, including natural waters, wastewater, soils, sediments, and biological media. Then, we review the state-of-the-art microscopic, spectroscopic, mass spectrometric, electrochemical, and size-fractionation methods for determination of mass and number abundance, as well as the morphological, compositional, and structural properties of nanomaterials, with discussion on their advantages and limitations. Despite recent advances in detecting and characterizing nanomaterials in the environment, challenges remain to improve the analytical sensitivity and resolution and to expand the method applications. It is important to develop methods for simultaneous determination of multifaceted nanomaterial properties for in situ analysis and characterization of nanomaterials under dynamic environmental conditions and for detection of nanoscale contaminants of emerging concern (e.g., nanoplastics and biological nanoparticles), which will greatly facilitate the standardization of nanomaterial analysis and characterization methods for environmental samples.
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Affiliation(s)
- Chuanjia Jiang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, 38 Tongyan Rd., Tianjin 300350, China
| | - Songlin Liu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, 38 Tongyan Rd., Tianjin 300350, China
| | - Tong Zhang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, 38 Tongyan Rd., Tianjin 300350, China
| | - Qian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Wei Chen
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, 38 Tongyan Rd., Tianjin 300350, China
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27
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Liang Y, Zou L, Lin H, Li B, Zhao J, Wang H, Sun J, Chen J, Mo Y, Yang X, Deng X, Tang S. Detection of Major SARS-CoV-2 Variants of Concern in Clinical Samples via CRISPR-Cas12a-Mediated Mutation-Specific Assay. ACS Synth Biol 2022; 11:1811-1823. [PMID: 35481381 DOI: 10.1021/acssynbio.1c00643] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Objectives: Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose a great threat and burden to global public health. Here, we evaluated a clustered regularly interspaced short palindromic repeat-associated enzyme 12a (CRISPR-Cas12a)-based method for detecting major SARS-CoV-2 variants of concern (VOCs) in SARS-CoV-2 positive clinical samples. Methods: Allele-specific CRISPR RNAs (crRNAs) targeting the signature mutations in the spike protein of SARS-CoV-2 are designed. A total of 59 SARS-CoV-2 positive oropharyngeal swab specimens were used to evaluate the performance of the CRISPR-Cas12a-mediated assay to identify major SARS-CoV-2 VOCs. Results: Compared with Sanger sequencing, the eight allele-specific crRNAs analyzed can specifically identify the corresponding mutations with a positive predictive value of 83.3-100% and a negative predictive value of 85.7-100%. Our CRISPR-Cas12a-mediated assay distinguished wild-type and four major VOCs (Alpha, Beta, Delta, and Omicron) of SARS-CoV-2 with a sensitivity of 93.8-100.0% and a specificity of 100.0%. The two methods showed a concordance of 98.3% (58/59) with a κ value of 0.956-1.000, while seven (11.9%) samples were found to be positive for extra mutations by the CRISPR-based assay. Furthermore, neither virus titers nor the sequences adjacent to the signature mutations were associated with the variation of fluorescence intensity detected or the false-positive reaction observed when testing clinical samples. In addition, there was no cross-reaction observed when detecting 33 SARS-CoV-2 negative clinical samples infected with common respiratory pathogens. Conclusions: The CRISPR-Cas12a-based genotyping assay is highly sensitive and specific when detecting both the SARS-CoV-2 wild-type strain and major VOCs. It is a simple and rapid assay that can monitor and track the circulating SARS-CoV-2 variants and the dynamics of the coronavirus disease 2019 (COVID-19) pandemic and can be easily implemented in resource-limited settings.
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Affiliation(s)
- Yuanhao Liang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Lirong Zou
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Hongqing Lin
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Baisheng Li
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Jianhui Zhao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Haiying Wang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Jiufeng Sun
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Jingdiao Chen
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Yanling Mo
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Xingfen Yang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Xiaoling Deng
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou 511430, China
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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28
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Carcereny A, Garcia-Pedemonte D, Martínez-Velázquez A, Quer J, Garcia-Cehic D, Gregori J, Antón A, Andrés C, Pumarola T, Chacón-Villanueva C, Borrego CM, Bosch A, Guix S, Pintó RM. Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. ENVIRONMENTAL RESEARCH 2022; 208:112720. [PMID: 35074352 PMCID: PMC8782736 DOI: 10.1016/j.envres.2022.112720] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/02/2022] [Accepted: 01/08/2022] [Indexed: 05/25/2023]
Abstract
Wastewater based epidemiology (WBE) offers an overview of the SARS-CoV-2 variants circulating among the population thereby serving as a proper surveillance method. The variant of concern (VOC) Alpha was first identified in September 2020 in the United Kingdom, and rapidly became dominant across Europe. Our objective was to elucidate the Alpha VOC outcompetition rate and identify mutations in the spike glycoprotein (S) gene, indicative of the circulation of the Alpha VOC and/or other variants in the population through wastewater analysis. In the period covered by this study (November 2020-April 2021), forteen wastewater treatment plants (WWTPs) were weekly sampled. The total number of SARS-CoV-2 genome copies per L (GC/L) was determined with a Real-Time qPCR, targeting the N gene. Surveillance of the Alpha VOC circulation was ascertained using a duplex RT-qPCR, targeting and discriminating the S gene. Our results showed that in a period of 6 weeks the Alpha VOC was present in all the studied WWTPs, and became dominant in 11 weeks on average. The outcompetition rates of the Alpha VOC were estimated, and their relationship with different parameters statistically analyzed. The rapid spread of the Alpha VOC was influenced by its initial input and by the previous circulation of SARS-COV-2 in the population. This latter point could be explained by its higher transmissibility, particularly advantadgeous when a certain degree of herd immunity exists. Moreover, the presence of signature mutations of SARS-COV-2 variants were established by deep-sequencing of the complete S gene. The circulation of the Alpha VOC in the area under study was confirmed, and additionally two combinations of mutations in the S glycoprotein (T73A and D253N, and S477N and A522S) that could affect antibody binding were identified.
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Affiliation(s)
- Albert Carcereny
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain
| | - David Garcia-Pedemonte
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain
| | - Adán Martínez-Velázquez
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Andrés Antón
- Microbiology Department, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain
| | - Cristina Andrés
- Microbiology Department, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain
| | - Tomàs Pumarola
- Microbiology Department, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain
| | | | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain.
| | - Susana Guix
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain.
| | - Rosa M Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain.
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29
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Jiang AZ, Nian F, Chen H, McBean EA. Passive Samplers, an Important Tool for Continuous Monitoring of the COVID-19 Pandemic. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:32326-32334. [PMID: 35137317 PMCID: PMC9072756 DOI: 10.1007/s11356-022-19073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/02/2022] [Indexed: 05/05/2023]
Abstract
The global pandemic caused by COVID-19 has resulted in major costs around the world, costs with dimensions in every aspect, from peoples' daily living to the global economy. As the pandemic progresses, the virus evolves, and more vaccines become available, and the 'battle against the virus' continues. As part of the battle, Wastewater-Based Epidemiology (WBE) technologies are being widely deployed in essential roles for SARS-CoV-2 detection and monitoring. While focusing on demonstrating the advantages of passive samplers as a tool in WBE, this review provides a holistic view of the current WBE applications in monitoring SARS-CoV-2 with the integration of the most up-to-date data. A novel scenario example based on a recent Nanjing (China) outbreak in July 2021 is used to illustrate the potential benefits of using passive samplers to monitor COVID-19 and to facilitate effective control of future major outbreaks. The presented contents and how the application of passive samplers indicates that this technology can be beneficial at different levels, varying from building to community to regional. Countries and regions that have the pandemic well under control or have low positive case occurrences have the potential to significantly benefit from deploying passive samplers as a measure to identify and suppress outbreaks.
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Affiliation(s)
- Albert Z. Jiang
- School of Engineering, University of Guelph, 50 Stone Rd. E, Guelph, N1G 2W1 Canada
| | - Fulin Nian
- Department of Digestive, Shanghai Pudong Hospital, Fudan University Affiliated Pudong Medical Center, 2800 Gongwei Road, Shanghai, 201399 China
| | - Han Chen
- College of Environmental Science and Engineering/Sino-Canada Joint R&D Centre for Water and Environmental Safety, Nankai University, Tianjin, 300071 China
| | - Edward A. McBean
- School of Engineering, University of Guelph, 50 Stone Rd. E, Guelph, N1G 2W1 Canada
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Oh C, Sashittal P, Zhou A, Wang L, El-Kebir M, Nguyen TH. Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Appl Environ Microbiol 2022; 88:e0228921. [PMID: 35285246 PMCID: PMC9004361 DOI: 10.1128/aem.02289-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Monitoring the prevalence of SARS-CoV-2 variants is necessary to make informed public health decisions during the COVID-19 pandemic. PCR assays have received global attention, facilitating a rapid understanding of variant dynamics because they are more accessible and scalable than genome sequencing. However, as PCR assays target only a few mutations, their accuracy could be reduced when these mutations are not exclusive to the target variants. Here we introduce PRIMES, an algorithm that evaluates the sensitivity and specificity of SARS-CoV-2 variant-specific PCR assays across different geographical regions by incorporating sequences deposited in the GISAID database. Using PRIMES, we determined that the accuracy of several PCR assays decreased when applied beyond the geographic scope of the study in which the assays were developed. Subsequently, we used this tool to design Alpha and Delta variant-specific PCR assays for samples from Illinois, USA. In silico analysis using PRIMES determined the sensitivity/specificity to be 0.99/0.99 for the Alpha variant-specific PCR assay and 0.98/1.00 for the Delta variant-specific PCR assay in Illinois, respectively. We applied these two variant-specific PCR assays to six local sewage samples and determined the dominant SARS-CoV-2 variant of either the wild type, the Alpha variant, or the Delta variant. Using next-generation sequencing (NGS) of the spike (S) gene amplicons of the Delta variant-dominant samples, we found six mutations exclusive to the Delta variant (S:T19R, S:Δ156/157, S:L452R, S:T478K, S:P681R, and S:D950N). The consistency between the variant-specific PCR assays and the NGS results supports the applicability of PRIMES. IMPORTANCE Monitoring the introduction and prevalence of variants of concern (VOCs) and variants of interest (VOIs) in a community can help the local authorities make informed public health decisions. PCR assays can be designed to keep track of SARS-CoV-2 variants by measuring unique mutation markers that are exclusive to the target variants. However, the mutation markers may not be exclusive to the target variants because of regional and temporal differences in variant dynamics. We introduce PRIMES, an algorithm that enables the design of reliable PCR assays for variant detection. Because PCR is more accessible, scalable, and robust for sewage samples than sequencing technology, our findings will contribute to improving global SARS-CoV-2 variant surveillance.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Palash Sashittal
- Department of Computer Science, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Mohammed El-Kebir
- Department of Computer Science, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
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Rodríguez Rasero FJ, Moya Ruano LA, Rasero Del Real P, Cuberos Gómez L, Lorusso N. Associations between SARS-CoV-2 RNA concentrations in wastewater and COVID-19 rates in days after sampling in small urban areas of Seville: A time series study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150573. [PMID: 34582878 PMCID: PMC8464400 DOI: 10.1016/j.scitotenv.2021.150573] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 05/03/2023]
Abstract
Wastewater surveillance systems for SARS-CoV-2 can be used to support public health decisions, complementary to clinical surveillance. We examined the lead-lag associations between SARS-CoV-2 RNA copies in wastewater and COVID-19 rates in relatively small urban areas of Seville, adjusting for internal mobility, temperature, and wastewater-related variables. The association COVID-19 rates-RNA copies were statistically significant from three to 27 days after sampling. Temperature is a confounding factor for both viral RNA counts and mobility. The model that best fitted data used cases six days after sampling. A logarithmic unit increase in viral RNA count in wastewater was associated with a 26.9% increase in COVID-19 rate per 100,000 inhabitants (95% CI: 13.1-42.4%), within the urban area, six days later. Surveillance system for SARS-CoV-2 in wastewater has great potential for public health. Knowing the specific association between SARS-CoV-2 RNA copies in wastewater and COVID-19 daily rates may help to improve its performance.
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Affiliation(s)
| | - Luis A Moya Ruano
- Regional Ministry of Health and Families of Andalusia, Avenida de la Innovación s/n, 41020 Seville, Spain.
| | - Pablo Rasero Del Real
- Metropolitan Water Supply and Sanitation Company of Seville (EMASESA) Escuelas Pías, 1 41003 Seville, Spain.
| | - Lucila Cuberos Gómez
- Metropolitan Water Supply and Sanitation Company of Seville (EMASESA) Escuelas Pías, 1 41003 Seville, Spain.
| | - Nicola Lorusso
- Regional Ministry of Health and Families of Andalusia, Avenida de la Innovación s/n, 41020 Seville, Spain.
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Itarte M, Bofill-Mas S, Martínez-Puchol S, Torrell H, Ceretó A, Carrasco M, Forés E, Canela N, Girones R, Rusiñol M. Looking for a needle in a haystack. SARS-CoV-2 variant characterization in sewage. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2021; 24:100308. [PMID: 34849439 PMCID: PMC8621506 DOI: 10.1016/j.coesh.2021.100308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
SARS-CoV-2 variants are emerging worldwide, and monitoring them is key in providing early warnings. Here, we summarize the different analytical approaches currently used to study the dissemination of SARS-CoV-2 variants in wastewater and discuss their advantages and disadvantages. We also provide preliminary results of two sensitive and cost-effective approaches: variant-specific reverse transcription-nested PCR assays and a nonvariant-specific amplicon deep sequencing strategy that targets three key regions of the viral spike protein. Next-generation sequencing approaches enable the simultaneous detection of signature mutations of different variants of concern in a single assay and may be the best option to explore the real picture at a particular time. Targeted PCR approaches focused on specific signature mutations will need continuous updating but are sensitive and cost-effective.
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Affiliation(s)
- Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Helena Torrell
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Reus, Spain
| | - Adrià Ceretó
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Reus, Spain
| | - Marina Carrasco
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Eva Forés
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Reus, Spain
| | - Rosina Girones
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Catalonia, Spain
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