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Rashid SA, Rajendiran S, Nazakat R, Mohammad Sham N, Khairul Hasni NA, Anasir MI, Kamel KA, Muhamad Robat R. A scoping review of global SARS-CoV-2 wastewater-based epidemiology in light of COVID-19 pandemic. Heliyon 2024; 10:e30600. [PMID: 38765075 PMCID: PMC11098849 DOI: 10.1016/j.heliyon.2024.e30600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Recently, wastewater-based epidemiology (WBE) research has experienced a strong impetus during the Coronavirus disease 2019 (COVID-19) pandemic. However, a few technical issues related to surveillance strategies, such as standardized procedures ranging from sampling to testing protocols, need to be resolved in preparation for future infectious disease outbreaks. This review highlights the study characteristics, potential use of WBE and overview of methods, as well as methods utilized to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including its variant in wastewater. A literature search was performed electronically in PubMed and Scopus according to PRISMA guidelines for relevant peer-reviewed articles published between January 2020 and March 2022. The search identified 588 articles, out of which 221 fulfilled the necessary criteria and are discussed in this review. Most global WBE studies were conducted in North America (n = 75, 34 %), followed by Europe (n = 68, 30.8 %), and Asia (n = 43, 19.5 %). The review also showed that most of the application of WBE observed were to correlate SARS-CoV-2 ribonucleic acid (RNA) trends in sewage with epidemiological data (n = 90, 40.7 %). The techniques that were often used globally for sample collection, concentration, preferred matrix recovery control and various sample types were also discussed. Overall, this review provided a framework for researchers specializing in WBE to apply strategic approaches to their research questions in achieving better functional insights. In addition, areas that needed more in-depth analysis, data collection, and ideas for new initiatives were identified.
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Affiliation(s)
- Siti Aishah Rashid
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Sakshaleni Rajendiran
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Raheel Nazakat
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Noraishah Mohammad Sham
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Nurul Amalina Khairul Hasni
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Mohd Ishtiaq Anasir
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Khayri Azizi Kamel
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health (NIH), Ministry of Health, Shah Alam, Selangor, Malaysia
| | - Rosnawati Muhamad Robat
- Occupational & Environmental Health Unit, Public Health Division, Selangor State Health Department, Ministry of Health Malaysia, Malaysia
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Parkins MD, Lee BE, Acosta N, Bautista M, Hubert CRJ, Hrudey SE, Frankowski K, Pang XL. Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond. Clin Microbiol Rev 2024; 37:e0010322. [PMID: 38095438 PMCID: PMC10938902 DOI: 10.1128/cmr.00103-22] [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] [Indexed: 03/16/2024] Open
Abstract
Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.
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Affiliation(s)
- Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O’Brien Institute of Public Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole Acosta
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maria Bautista
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Provincial Health Laboratory, Alberta Health Services, Calgary, Alberta, Canada
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Van Poelvoorde LAE, Gobbo A, Nauwelaerts SJD, Verhaegen B, Lesenfants M, Janssens R, Hutse V, Fraiture MA, De Keersmaecker S, Herman P, Van Hoorde K, Roosens N. Development of a reverse transcriptase digital droplet polymerase chain reaction-based approach for SARS-CoV-2 variant surveillance in wastewater. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e10999. [PMID: 38414298 DOI: 10.1002/wer.10999] [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: 11/27/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/29/2024]
Abstract
An urgent need for effective surveillance strategies arose due to the global emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although vaccines and antivirals are available, concerns persist about the evolution of new variants with potentially increased infectivity, transmissibility, and immune evasion. Therefore, variant monitoring is crucial for public health decision-making. Wastewater-based surveillance has proven to be an effective tool to monitor SARS-CoV-2 variants within populations. Specific SARS-CoV-2 variants are detected and quantified in wastewater in this study using a reverse transcriptase digital droplet polymerase chain reaction (RT-ddPCR) approach. The 11 designed assays were first validated in silico using a substantial dataset of high-quality SARS-CoV-2 genomes to ensure comprehensive variant coverage. The assessment of the sensitivity and specificity with reference material showed the capability of the developed assays to reliably identify target mutations while minimizing false positives and false negatives. The applicability of the assays was evaluated using wastewater samples from a wastewater treatment plant in Ghent, Belgium. The quantification of the specific mutations linked to the variants of concern present in these samples was calculated using these assays based on the detection of single mutations, which confirms their use for real-world variant surveillance. In conclusion, this study provides an adaptable protocol to monitor SARS-CoV-2 variants in wastewater with high sensitivity and specificity. Its potential for broader application in other viral surveillance contexts highlights its added value for rapid response to emerging infectious diseases. PRACTITIONER POINTS: Robust RT-ddPCR methodology for specific SARS-CoV-2 variants of concern detection in wastewater. Rigorous validation that demonstrates high sensitivity and specificity. Demonstration of real-world applicability using wastewater samples. Valuable tool for rapid response to emerging infectious diseases.
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Affiliation(s)
| | - Andrea Gobbo
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Marie Lesenfants
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Raphael Janssens
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Veronik Hutse
- Epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | | | | | | | | | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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4
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Thakali O, Mercier É, Eid W, Wellman M, Brasset-Gorny J, Overton AK, Knapp JJ, Manuel D, Charles TC, Goodridge L, Arts EJ, Poon AFY, Brown RS, Graber TE, Delatolla R, DeGroot CT. Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation. Sci Rep 2024; 14:3728. [PMID: 38355869 PMCID: PMC10866965 DOI: 10.1038/s41598-024-54319-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/11/2024] [Indexed: 02/16/2024] Open
Abstract
Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity of RT-qPCR has been achieved, in part, by monitoring two or more genomic loci of SARS-CoV-2. In Ontario, Canada, the provincial Wastewater Surveillance Initiative reports the average copies of the CDC N1 and N2 loci normalized to the fecal biomarker pepper mild mottle virus. In November 2021, the emergence of the Omicron variant of concern, harboring a C28311T mutation within the CDC N1 probe region, challenged the accuracy of the consensus between the RT-qPCR measurements of the N1 and N2 loci of SARS-CoV-2. In this study, we developed and applied a novel real-time dual loci quality assurance and control framework based on the relative difference between the loci measurements to the City of Ottawa dataset to identify a loss of sensitivity of the N1 assay in the period from July 10, 2022 to January 31, 2023. Further analysis via sequencing and allele-specific RT-qPCR revealed a high proportion of mutations C28312T and A28330G during the study period, both in the City of Ottawa and across the province. It is hypothesized that nucleotide mutations in the probe region, especially A28330G, led to inefficient annealing, resulting in reduction in sensitivity and accuracy of the N1 assay. This study highlights the importance of implementing quality assurance and control criteria to continually evaluate, in near real-time, the accuracy of the signal produced in wastewater surveillance applications that rely on detection of pathogens whose genomes undergo high rates of mutation.
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Affiliation(s)
- Ocean Thakali
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Martin Wellman
- The Ottawa Hospital Research Institute, 1053 Carling Ave, Ottawa, ON, K1Y 4E9, Canada
| | - Julia Brasset-Gorny
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Alyssa K Overton
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Jennifer J Knapp
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Douglas Manuel
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
- Department of Family Medicine, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON, K1N 6N5, Canada
- School of Epidemiology and Public Health, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON, K1N 6N5, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Lawrence Goodridge
- Department of Food Science, Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Art F Y Poon
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - R Stephen Brown
- School of Environmental Studies and Department of Chemistry, Queen's University, Kingston, ON, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher T DeGroot
- Department of Mechanical and Materials Engineering, Western University, London, ON, N6A 5B9, Canada.
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Champredon D, Becker D, Peterson SW, Mejia E, Hizon N, Schertzer A, Djebli M, Oloye FF, Xie Y, Asadi M, Cantin J, Pu X, Osunla CA, Brinkmann M, McPhedran KN, Servos MR, Giesy JP, Mangat C. Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data. BMC Infect Dis 2024; 24:139. [PMID: 38287244 PMCID: PMC10823614 DOI: 10.1186/s12879-024-08997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND The spread of SARS-CoV-2 has been studied at unprecedented levels worldwide. In jurisdictions where molecular analysis was performed on large scales, the emergence and competition of numerous SARS-CoV-2lineages have been observed in near real-time. Lineage identification, traditionally performed from clinical samples, can also be determined by sampling wastewater from sewersheds serving populations of interest. Variants of concern (VOCs) and SARS-CoV-2 lineages associated with increased transmissibility and/or severity are of particular interest. METHOD Here, we consider clinical and wastewater data sources to assess the emergence and spread of VOCs in Canada retrospectively. RESULTS We show that, overall, wastewater-based VOC identification provides similar insights to the surveillance based on clinical samples. Based on clinical data, we observed synchrony in VOC introduction as well as similar emergence speeds across most Canadian provinces despite the large geographical size of the country and differences in provincial public health measures. CONCLUSION In particular, it took approximately four months for VOC Alpha and Delta to contribute to half of the incidence. In contrast, VOC Omicron achieved the same contribution in less than one month. This study provides significant benchmarks to enhance planning for future VOCs, and to some extent for future pandemics caused by other pathogens, by quantifying the rate of SARS-CoV-2 VOCs invasion in Canada.
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Affiliation(s)
- David Champredon
- Public Health Agency of Canada, National Microbiology Laboratory, Public Health Risk Sciences Division, Guelph, ON, Canada.
| | - Devan Becker
- Public Health Agency of Canada, National Microbiology Laboratory, Public Health Risk Sciences Division, Guelph, ON, Canada
| | - Shelley W Peterson
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
| | - Edgard Mejia
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
| | - Nikho Hizon
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
| | - Andrea Schertzer
- Public Health Agency of Canada, Centre for Immunization and Respiratory Infectious Diseases, Ottawa, ON, Canada
| | - Mohamed Djebli
- Public Health Agency of Canada, Centre for Immunization and Respiratory Infectious Diseases, Ottawa, ON, Canada
| | - Femi F Oloye
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Chemistry, Division of Physical and Computational Sciences, University of Pittsburgh at Bradford, Bradford, United States.
| | - Yuwei Xie
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Xia Pu
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Charles A Osunla
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Markus Brinkmann
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
- Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - John P Giesy
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Environmental Sciences, Baylor University, Waco, TX, USA.
- Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Chand Mangat
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
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6
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Sun J, Yang MI, Peng J, Khan I, Lopez JJ, Chan R, Edwards EA, Peng H. Underestimation of SARS-CoV-2 in wastewater due to single or double mutations in the N1 qPCR probe binding region. WATER RESEARCH X 2024; 22:100221. [PMID: 38590726 PMCID: PMC11000202 DOI: 10.1016/j.wroa.2024.100221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
Wastewater surveillance using RT-qPCR has now been widely adopted to track circulating levels of SARS-CoV-2 virus in many sewersheds. The CDC qPCR assays targeting two regions (N1 and N2) within the N gene are commonly used, but a discrepancy between the two biomarkers has been noticed by independent studies using these methods since late 2021. The reason is presumed to be due to mutations in regions targeted by the N1 qPCR probe. In this study, we systematically investigated and unequivocally confirmed that the underlying reason for this discrepancy was mutations in the N1 probe target, and that a single mutation could cause a significant drop in signal. We first confirmed the proportion of related mutations in wastewater samples (Jan 2021-Dec 2022) using nested PCR and LC-MS. Based on relative proportions of N1 alleles, we separated the wastewater data into four time periods corresponding to different variant waves: Period I (Alpha and Delta waves with 0 mutation), Period II (BA.1/BA.2 waves with a single mutation found in all Omicron strains), Period III (BA.5.2* wave with two mutations), and Period IV (BQ.1* wave with two mutations). Significantly lower N1 copies relative to N2 copies in samples from Periods II-IV compared to those from Period I was observed in wastewater. To further pinpoint the extent to which each mutation impacted N1 quantification, we compared the qPCR response among different synthetic oligomers with corresponding mutations. This study highlighted the impact of even just one or two mutations on qPCR-based wastewater surveillance of SARS-CoV-2.
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Affiliation(s)
- Jianxian Sun
- Department of Chemistry, University of Toronto, 80 St George Street, Toronto, ON, M5S 3H6, Canada
| | - Minqing Ivy Yang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, 80 St George Street, Toronto, ON, M5S 3H6, Canada
| | - Ismail Khan
- Department of Chemistry, University of Toronto, 80 St George Street, Toronto, ON, M5S 3H6, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Jhoselyn Jaramillo Lopez
- Department of Chemistry, University of Toronto, 80 St George Street, Toronto, ON, M5S 3H6, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Ronny Chan
- Department of Chemistry, University of Toronto, 80 St George Street, Toronto, ON, M5S 3H6, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Hui Peng
- Department of Chemistry, University of Toronto, 80 St George Street, Toronto, ON, M5S 3H6, Canada
- School of the Environment, University of Toronto, 80 St George Street, Toronto, ON, M5S 3H6, Canada
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7
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Xu X, Deng Y, Ding J, Shi X, Zheng X, Wang D, Yang Y, Liu L, Wang C, Li S, Gu H, Poon LLM, Zhang T. Refining detection methods for emerging SARS-CoV-2 mutants in wastewater: A case study on the Omicron variants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166215. [PMID: 37591380 DOI: 10.1016/j.scitotenv.2023.166215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
COVID-19 is an ongoing public health threat worldwide driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Wastewater surveillance has emerged as a complementary tool to clinical surveillance to control the COVID-19 pandemic. With the emergence of new variants of SARS-CoV-2, accumulated mutations that occurred in the SARS-CoV-2 genome raise new challenges for RT-qPCR diagnosis used in wastewater surveillance. There is a pressing need to develop refined methods for modifying primer/probes to better detect these emerging variants in wastewater. Here, we exemplified this process by focusing on the Omicron variants, for which we have developed and validated a modified detection method. We first modified the primers/probe mismatches of three assays commonly used in wastewater surveillance according to in silico analysis results for the mutations of 882 sequences collected during the fifth-wave outbreak in Hong Kong, and then evaluated them alongside the seven original assays. The results showed that five of seven original assays had better sensitivity for detecting Omicron variants, with the limits of detection (LoDs) ranging from 1.53 to 2.76 copies/μL. UCDC-N1 and Charité-E sets had poor performances, having LoDs higher than 10 copies/μL and false-positive/false-negative results in wastewater testing, probably due to the mismatch and demonstrating the need for modification of primer/probe sequences. The modified assays exhibited higher sensitivity and specificity, along with better reproducibility in detecting 81 wastewater samples. In addition, the sequencing results of six wastewater samples by Illumina also validated the presence of mismatches in the primer/probe binding sites of the three assays. This study highlights the importance of re-configuration of the primer-probe sets and refinements for the sequences to ensure the diagnostic effectiveness of RT-qPCR detection.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Haogao Gu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Leo L M Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Sassoon Road, Hong Kong, China; HKU-Pasteur Research Pole, The University of Hong Kong, Sassoon Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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8
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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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9
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Niedre-Otomere B, Kampenusa I, Trofimova J, Bodrenko J, Vangravs R, Skenders G, Nikisins S, Savicka O. Multiplexed RT-qPCR Coupled with Whole-Genome Sequencing to Monitor a SARS-CoV-2 Omicron Variant of Concern in a Hospital Laboratory Setting in Latvia. Diagnostics (Basel) 2023; 13:3467. [PMID: 37998603 PMCID: PMC10670528 DOI: 10.3390/diagnostics13223467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023] Open
Abstract
At the end of 2021, the SARS-CoV-2 Omicron variant of concern (VOC) displaced the previously dominant Delta VOC and enhanced diagnostic and therapeutic challenges worldwide. Respiratory specimens submitted to the Riga East University Hospital Laboratory Service by the central and regional hospitals of Latvia from January to March 2022 that were positive for SARS-CoV-2 RNA were tested by commercial multiplexed RT-qPCR targeting three of the Omicron VOC signature mutations: ΔH69/V70, E484A, and N501Y. Of the specimens tested and analyzed in parallel by whole-genome sequencing (WGS), 964 passed the internal quality criteria (genome coverage ≥90%, read depth ≥400×) and the Nextstrain's quality threshold for "good". We validated the detection accuracy of RT-qPCR for each target individually by using WGS as a control. The results were concordant with both approaches for 938 specimens, with the correct classification rate exceeding 96% for each target (CI 95%); however, the presumptive WHO label was misassigned for 21 specimens. The RT-qPCR genotyping provided an acceptable means to pre-monitor the prevalence of the two presumptive Omicron VOC sublineages, BA.1 and BA.2.
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10
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Lee J, Acosta N, Waddell BJ, Du K, Xiang K, Van Doorn J, Low K, Bautista MA, McCalder J, Dai X, Lu X, Chekouo T, Pradhan P, Sedaghat N, Papparis C, Buchner Beaudet A, Chen J, Chan L, Vivas L, Westlund P, Bhatnagar S, Stefani S, Visser G, Cabaj J, Bertazzon S, Sarabi S, Achari G, Clark RG, Hrudey SE, Lee BE, Pang X, Webster B, Ghali WA, Buret AG, Williamson T, Southern DA, Meddings J, Frankowski K, Hubert CRJ, Parkins MD. Campus node-based wastewater surveillance enables COVID-19 case localization and confirms lower SARS-CoV-2 burden relative to the surrounding community. WATER RESEARCH 2023; 244:120469. [PMID: 37634459 DOI: 10.1016/j.watres.2023.120469] [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: 03/18/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023]
Abstract
Wastewater-based surveillance (WBS) has been established as a powerful tool that can guide health policy at multiple levels of government. However, this approach has not been well assessed at more granular scales, including large work sites such as University campuses. Between August 2021 and April 2022, we explored the occurrence of SARS-CoV-2 RNA in wastewater using qPCR assays from multiple complimentary sewer catchments and residential buildings spanning the University of Calgary's campus and how this compared to levels from the municipal wastewater treatment plant servicing the campus. Real-time contact tracing data was used to evaluate an association between wastewater SARS-CoV-2 burden and clinically confirmed cases and to assess the potential of WBS as a tool for disease monitoring across worksites. Concentrations of wastewater SARS-CoV-2 N1 and N2 RNA varied significantly across six sampling sites - regardless of several normalization strategies - with certain catchments consistently demonstrating values 1-2 orders higher than the others. Relative to clinical cases identified in specific sewersheds, WBS provided one-week leading indicator. Additionally, our comprehensive monitoring strategy enabled an estimation of the total burden of SARS-CoV-2 for the campus per capita, which was significantly lower than the surrounding community (p≤0.001). Allele-specific qPCR assays confirmed that variants across campus were representative of the community at large, and at no time did emerging variants first debut on campus. This study demonstrates how WBS can be efficiently applied to locate hotspots of disease activity at a very granular scale, and predict disease burden across large, complex worksites.
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Affiliation(s)
- Jangwoo Lee
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Barbara J Waddell
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Kristine Du
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Kevin Xiang
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Jennifer Van Doorn
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Kashtin Low
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Maria A Bautista
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Janine McCalder
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Xiaotian Dai
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada
| | - Xuewen Lu
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada
| | - Thierry Chekouo
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada; Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, USA
| | - Puja Pradhan
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Navid Sedaghat
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Chloe Papparis
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Alexander Buchner Beaudet
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Jianwei Chen
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Leslie Chan
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Laura Vivas
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | | | - Srijak Bhatnagar
- Department of Biological Sciences, University of Calgary, Calgary, Canada; Faculty of Science and Technology, Athabasca University, Athabasca, Alberta, Canada
| | - September Stefani
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Gail Visser
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada
| | - Jason Cabaj
- Department of Community Health Sciences, University of Calgary, Calgary, Canada; Department of Medicine, University of Calgary and Alberta Health Services, Calgary, Canada; Provincial Population & Public Health, Alberta Health Services, Calgary, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, Canada
| | | | - Shahrzad Sarabi
- Department of Geography, University of Calgary, Calgary, Canada
| | - Gopal Achari
- Department of Civil Engineering, University of Calgary, Calgary, Canada
| | - Rhonda G Clark
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Steve E Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Analytical and Environmental Toxicology, University of Alberta, Edmonton, Alberta, Canada
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada; Women & Children's Health Research Institute, Li Ka Shing Institute of Virology, Edmonton, Alberta, Canada
| | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Alberta Precision Laboratories, Public Health Laboratory, Alberta Health Services, Edmonton, Alberta, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - Brendan Webster
- Occupational Health Staff Wellness, University of Calgary, Calgary, Canada
| | - William Amin Ghali
- Department of Community Health Sciences, University of Calgary, Calgary, Canada; Department of Medicine, University of Calgary and Alberta Health Services, Calgary, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, Canada; Centre for Health Informatics, University of Calgary, Calgary, Canada
| | - Andre Gerald Buret
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Tyler Williamson
- Department of Community Health Sciences, University of Calgary, Calgary, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, Canada; Centre for Health Informatics, University of Calgary, Calgary, Canada
| | - Danielle A Southern
- Department of Community Health Sciences, University of Calgary, Calgary, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, Canada; Centre for Health Informatics, University of Calgary, Calgary, Canada
| | - Jon Meddings
- Department of Medicine, University of Calgary and Alberta Health Services, Calgary, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta T2N 2V5, Canada; Department of Medicine, University of Calgary and Alberta Health Services, Calgary, Canada; O'Brien Institute for Public Health, University of Calgary, Calgary, Canada.
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11
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Sheng T, Chen H, Lei Y, Zhang B, Zhu H. An indirect competitive assay-based method for the sensitive determination of tetracycline residue using a real-time fluorescence-based quantitative polymerase chain reaction. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4892-4899. [PMID: 37718682 DOI: 10.1039/d3ay01072d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Tetracycline (TC) is an effective antibiotic used to treat humans and livestock, but its inappropriate use imposes toxic effects, including pollution, on environmental ecology and food. Currently, sensitive, accurate, and cost-effective methods that can detect lower concentrations of TC residues in environmental and food samples are needed. In this study, a novel indirect competitive assay-based aptamer method was developed for detecting TC residues through signal amplification by real-time fluorescence-based quantitative polymerase chain reaction. The response surface methodology was introduced to optimize the optimal concentrations (influencing factors) of the three types of single-stranded DNA in the competitive assay process. The optimal conditions for the three types of ssDNA were 112 nM for the specific aptamer of TC (Apt40), 115 nM for the signal DNA, and 83 nM for the DNA catcher. As expected, under optimal conditions, the Ct value was linearly related to the logarithm of TC concentration. The calibration curve equation was Ct = -0.34516 log[TC] + 9.9345 (R2 = 0.998) in the range of 10-3-103 ng mL-1, and the limit of detection was 7.02 × 10-5 ng mL-1. The new method was effectively applied to detect TC residues in wastewater, honey, and milk samples. It achieved an average recovery rate of 101.19% with a small variation of 5.16%. The validation was carried out using an enzyme-linked immunosorbent assay. This approach demonstrates high sensitivity and selectivity, making it well suited for detecting leftover antibiotics in food when using suitable aptamers.
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Affiliation(s)
- Tianying Sheng
- School of Environmental Engineering, Henan University of Technology, Zhengzhou 450001, PR China.
| | - Hanyu Chen
- School of Environmental Engineering, Henan University of Technology, Zhengzhou 450001, PR China.
| | - Yingying Lei
- School of Environmental Engineering, Henan University of Technology, Zhengzhou 450001, PR China.
| | - Baozhong Zhang
- School of Environmental Engineering, Henan University of Technology, Zhengzhou 450001, PR China.
| | - Huina Zhu
- School of Environmental Engineering, Henan University of Technology, Zhengzhou 450001, PR China.
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12
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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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13
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Koets L, van Leeuwen K, Derlagen M, van Wijk J, Keijzer N, Feenstra JDM, Gandhi M, Sorel O, van de Laar TJW, Koppelman MHGM. Efficient SARS-CoV-2 Surveillance during the Pandemic-Endemic Transition Using PCR-Based Genotyping Assays. Microbiol Spectr 2023; 11:e0345022. [PMID: 37154727 PMCID: PMC10269661 DOI: 10.1128/spectrum.03450-22] [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: 08/29/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOC) pose an increased risk to public health due to higher transmissibility and/or immune escape. In this study, we assessed the performance of a custom TaqMan SARS-CoV-2 mutation panel consisting of 10 selected real-time PCR (RT-PCR) genotyping assays compared to whole-genome sequencing (WGS) for identification of 5 VOC circulating in The Netherlands. SARS-CoV-2 positive samples (N = 664), collected during routine PCR screening (15 ≤ CT ≤ 32) between May-July 2021 and December 2021-January 2022, were selected and analyzed using the RT-PCR genotyping assays. VOC lineage was determined based on the detected mutation profile. In parallel, all samples underwent WGS with the Ion AmpliSeq SARS-CoV-2 research panel. Among 664 SARS-CoV-2 positive samples, the RT-PCR genotyping assays classified 31.2% as Alpha (N = 207); 48.9% as Delta (N = 325); 19.4% as Omicron (N = 129), 0.3% as Beta (N = 2), and 1 sample as a non-VOC. Matching results were obtained using WGS in 100% of the samples. RT-PCR genotyping assays enable accurate detection of SARS-CoV-2 VOC. Furthermore, they are easily implementable, and the costs and turnaround time are significantly reduced compared to WGS. For this reason, a higher proportion of SARS-CoV-2 positive cases in the VOC surveillance testing can be included, while reserving valuable WGS resources for identification of new variants. Therefore, RT-PCR genotyping assays would be a powerful method to include in SARS-CoV-2 surveillance testing. IMPORTANCE The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genome changes constantly. It is estimated that there are thousands of variants of SARS-CoV-2 by now. Some of those variants, variants of concern (VOC), pose an increased risk to public health due to higher transmissibility and/or immune escape. Pathogen surveillance helps researchers, epidemiologists, and public health officials to monitor the evolution of infectious diseases agents, alert on the spread of pathogens, and develop counter measures like vaccines. The technique used for the pathogen surveillance is called sequence analysis which makes it possible to examine the building blocks of SARS-CoV-2. In this study, a new PCR method based on the detection of specific changes of those building blocks is presented. This method enables a fast, accurate and cheap determination of different SARS-CoV-2 VOC. Therefore, it would be a powerful method to include in SARS-CoV-2 surveillance testing.
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Affiliation(s)
- Lianne Koets
- Sanquin Research and Lab Services, National Screening Laboratory of Sanquin, Amsterdam, The Netherlands
| | - Karin van Leeuwen
- Sanquin Diagnostics, Department of Phagocytes Diagnostics, Amsterdam, The Netherlands
| | - Maaike Derlagen
- Sanquin Diagnostics, Department of Immune Cytology, Amsterdam, The Netherlands
| | - Jalenka van Wijk
- Sanquin Diagnostics, Department of Immune Cytology, Amsterdam, The Netherlands
| | - Nadia Keijzer
- Sanquin Diagnostics, Department of Immune Cytology, Amsterdam, The Netherlands
| | | | - Manoj Gandhi
- Thermo Fisher Scientific, South San Francisco, California, USA
| | - Oceane Sorel
- Thermo Fisher Scientific, South San Francisco, California, USA
| | - Thijs J. W. van de Laar
- Sanquin Research, Department of Blood-Borne Infections, Amsterdam, The Netherlands
- Onze Lieve Vrouwe Gasthuis, Laboratory of Medical Microbiology, Amsterdam, The Netherlands
| | - Marco H. G. M. Koppelman
- Sanquin Research and Lab Services, National Screening Laboratory of Sanquin, Amsterdam, The Netherlands
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14
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Trigo-Tasende N, Vallejo JA, Rumbo-Feal S, Conde-Pérez K, Vaamonde M, López-Oriona Á, Barbeito I, Nasser-Ali M, Reif R, Rodiño-Janeiro BK, Fernández-Álvarez E, Iglesias-Corrás I, Freire B, Tarrío-Saavedra J, Tomás L, Gallego-García P, Posada D, Bou G, López-de-Ullibarri I, Cao R, Ladra S, Poza M. Wastewater early warning system for SARS-CoV-2 outbreaks and variants in a Coruña, Spain. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27877-3. [PMID: 37286834 DOI: 10.1007/s11356-023-27877-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
Wastewater-based epidemiology has been widely used as a cost-effective method for tracking the COVID-19 pandemic at the community level. Here we describe COVIDBENS, a wastewater surveillance program running from June 2020 to March 2022 in the wastewater treatment plant of Bens in A Coruña (Spain). The main goal of this work was to provide an effective early warning tool based in wastewater epidemiology to help in decision-making at both the social and public health levels. RT-qPCR procedures and Illumina sequencing were used to weekly monitor the viral load and to detect SARS-CoV-2 mutations in wastewater, respectively. In addition, own statistical models were applied to estimate the real number of infected people and the frequency of each emerging variant circulating in the community, which considerable improved the surveillance strategy. Our analysis detected 6 viral load waves in A Coruña with concentrations between 103 and 106 SARS-CoV-2 RNA copies/L. Our system was able to anticipate community outbreaks during the pandemic with 8-36 days in advance with respect to clinical reports and, to detect the emergence of new SARS-CoV-2 variants in A Coruña such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529 and BA.2) in wastewater with 42, 30, and 27 days, respectively, before the health system did. Data generated here helped local authorities and health managers to give a faster and more efficient response to the pandemic situation, and also allowed important industrial companies to adapt their production to each situation. The wastewater-based epidemiology program developed in our metropolitan area of A Coruña (Spain) during the SARS-CoV-2 pandemic served as a powerful early warning system combining statistical models with mutations and viral load monitoring in wastewater over time.
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Affiliation(s)
- Noelia Trigo-Tasende
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Juan A Vallejo
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Soraya Rumbo-Feal
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Kelly Conde-Pérez
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Manuel Vaamonde
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Ángel López-Oriona
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Inés Barbeito
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Mohammed Nasser-Ali
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Rubén Reif
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), University of Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
| | - Bruno K Rodiño-Janeiro
- BFlow, University of Santiago de Compostela (USC) and Health Research Institute of Santiago de Compostela (IDIS), Campus Vida, 15706, Santiago de Compostela, A Coruña, Spain
| | - Elisa Fernández-Álvarez
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Iago Iglesias-Corrás
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Borja Freire
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Javier Tarrío-Saavedra
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Laura Tomás
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
| | - Pilar Gallego-García
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
| | - David Posada
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310, Vigo, Spain
| | - Germán Bou
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain
| | - Ignacio López-de-Ullibarri
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Ricardo Cao
- Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruña (UDC), Campus de Elviña, 15071 , A Coruña, Spain
| | - Susana Ladra
- University of A Coruña (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory, Campus de Elviña, 15071, A Coruña, Spain
| | - Margarita Poza
- University of A Coruña (UDC) - Microbiome and Health group (meiGAbiome), Institute of Biomedical Research (INIBIC) - University Hospital of A Coruña (CHUAC) - Interdisciplinary Center for Chemistry and Biology (CICA) - Spanish Network for Infectious Diseases (CIBERINFEC-ISCIII), Campus da Zapateira, 15008, A Coruña, Spain.
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15
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Peterson S, Daigle J, Dueck C, Nagasawa A, Mulvey M, Mangat CS. Real-time quantitative reverse transcription polymerase chain reaction detection of SARS-CoV-2 Delta variant in Canadian wastewater. CANADA COMMUNICABLE DISEASE REPORT = RELEVE DES MALADIES TRANSMISSIBLES AU CANADA 2023; 49:213-220. [PMID: 38414535 PMCID: PMC10898651 DOI: 10.14745/ccdr.v49i05a07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern are associated with increased infectivity, severity, and mortality of coronavirus disease 2019 (COVID-19) and have been increasingly detected in clinical and wastewater surveillance in Canada and internationally. In this study, we present a real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay for detection of the N gene D377Y mutation associated with the SARS-CoV-2 Delta variant in wastewater. Methods Wastewater samples (n=980) were collected from six cities and 17 rural communities across Canada from July to November 2021 and screened for the D377Y mutation. Results The Delta variant was detected in all major Canadian cities and northern remote regions, and half of the southern rural communities. The sensitivity and specificity of this assay were sufficient for detection and quantitation of the Delta variant in wastewater to aid in rapid population-level screening and surveillance. Conclusion This study demonstrates a novel cost-effective RT-qPCR assay for tracking the spread of the SARS-CoV-2 Delta variant. This rapid assay can be easily integrated into current wastewater surveillance programs to aid in population-level variant tracking.
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Affiliation(s)
- Shelley Peterson
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Jade Daigle
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Codey Dueck
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Audra Nagasawa
- Centre for Population Health Data, Statistics Canada, Ottawa, ON
| | - Michael Mulvey
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB
| | - Chand S Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
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16
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Prado T, Rey-Benito G, Miagostovich MP, Sato MIZ, Rajal VB, Filho CRM, Pereira AD, Barbosa MRF, Mannarino CF, da Silva AS. Wastewater-based epidemiology for preventing outbreaks and epidemics in Latin America - Lessons from the past and a look to the future. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161210. [PMID: 36581294 DOI: 10.1016/j.scitotenv.2022.161210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Wastewater-based epidemiology (WBE) is an approach with the potential to complement clinical surveillance systems. Using WBE, it is possible to carry out an early warning of a possible outbreak, monitor spatial and temporal trends of infectious diseases, produce real-time results and generate representative epidemiological information in a territory, especially in areas of social vulnerability. Despite the historical uses of this approach, particularly in the Global Polio Eradication Initiative, and for other pathogens, it was during the COVID-19 pandemic that occurred an exponential increase in environmental surveillance programs for SARS-CoV-2 in wastewater, with many experiences and developments in the field of public health using data for decision making and prioritizing actions to control the pandemic. In Latin America, WBE was applied in heterogeneous contexts and with emphasis on populations that present many socio-environmental inequalities, a condition shared by all Latin American countries. This manuscript addresses the concepts and applications of WBE in public health actions, as well as different experiences in Latin American countries, and discusses a model to implement this surveillance system at the local or national level. We emphasize the need to implement this sentinel surveillance system in countries that want to detect the early entry and spread of new pathogens and monitor outbreaks or epidemics of infectious agents in their territories as a complement of public health surveillance systems.
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Affiliation(s)
- Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil.
| | - Gloria Rey-Benito
- Pan American Health Organization (PAHO/WHO), 525 23rd St NW, Washington, DC 20037, United States of America.
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Maria Inês Zanoli Sato
- Department of Environmental Analysis, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil
| | - Veronica Beatriz Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Facultad de Ingeniería, UNSa, Av. Bolivia 5150, Salta 4400, Argentina; Singapore Centre for Environmental Life Science Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Cesar Rossas Mota Filho
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Alyne Duarte Pereira
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Mikaela Renata Funada Barbosa
- Department of Environmental Analysis, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil
| | - Camille Ferreira Mannarino
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, CEP 21040-360, Brazil
| | - Agnes Soares da Silva
- Pan American Health Organization (PAHO/WHO), 525 23rd St NW, Washington, DC 20037, United States of America.
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17
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Van Poelvoorde LAE, Picalausa C, Gobbo A, Verhaegen B, Lesenfants M, Herman P, Van Hoorde K, Roosens NHC. Development of a Droplet Digital PCR to Monitor SARS-CoV-2 Omicron Variant BA.2 in Wastewater Samples. Microorganisms 2023; 11:microorganisms11030729. [PMID: 36985302 PMCID: PMC10059707 DOI: 10.3390/microorganisms11030729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Wastewater-based surveillance can be used as a complementary method to other SARS-CoV-2 surveillance systems. It allows the emergence and spread of infections and SARS-CoV-2 variants to be monitored in time and place. This study presents an RT-ddPCR method that targets the T19I amino acid mutation in the spike protein of the SARS-CoV-2 genomes, which is specific to the BA.2 variant (omicron). The T19I assay was evaluated both in silico and in vitro for its inclusivity, sensitivity, and specificity. Moreover, wastewater samples were used as a proof of concept to monitor and quantify the emergence of the BA.2 variant from January until May 2022 in the Brussels-Capital Region which covers a population of more than 1.2 million inhabitants. The in silico analysis showed that more than 99% of the BA.2 genomes could be characterized using the T19I assay. Subsequently, the sensitivity and specificity of the T19I assay were successfully experimentally evaluated. Thanks to our specific method design, the positive signal from the mutant probe and wild-type probe of the T19I assay was measured and the proportion of genomes with the T19I mutation, characteristic of the BA.2 mutant, compared to the entire SARS-CoV-2 population was calculated. The applicability of the proposed RT-ddPCR method was evaluated to monitor and quantify the emergence of the BA.2 variant over time. To validate this assay as a proof of concept, the measurement of the proportion of a specific circulating variant with genomes containing the T19I mutation in comparison to the total viral population was carried out in wastewater samples from wastewater treatment plants in the Brussels-Capital Region in the winter and spring of 2022. This emergence and proportional increase in BA.2 genomes correspond to what was observed in the surveillance using respiratory samples; however, the emergence was observed slightly earlier, which suggests that wastewater sampling could be an early warning system and could be an interesting alternative to extensive human testing.
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Affiliation(s)
| | - Corinne Picalausa
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Andrea Gobbo
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | | | - Marie Lesenfants
- Epidemiology of Infectious Diseases, Sciensano, 1050 Brussels, Belgium
| | | | | | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
- Correspondence:
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18
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Combined Use of RT-qPCR and NGS for Identification and Surveillance of SARS-CoV-2 Variants of Concern in Residual Clinical Laboratory Samples in Miami-Dade County, Florida. Viruses 2023; 15:v15030593. [PMID: 36992302 PMCID: PMC10059866 DOI: 10.3390/v15030593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Over the course of the COVID-19 pandemic, SARS-CoV-2 variants of concern (VOCs) with increased transmissibility and immune escape capabilities, such as Delta and Omicron, have triggered waves of new COVID-19 infections worldwide, and Omicron subvariants continue to represent a global health concern. Tracking the prevalence and dynamics of VOCs has clinical and epidemiological significance and is essential for modeling the progression and evolution of the COVID-19 pandemic. Next generation sequencing (NGS) is recognized as the gold standard for genomic characterization of SARS-CoV-2 variants, but it is labor and cost intensive and not amenable to rapid lineage identification. Here we describe a two-pronged approach for rapid, cost-effective surveillance of SARS-CoV-2 VOCs by combining reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) and periodic NGS with the ARTIC sequencing method. Variant surveillance by RT-qPCR included the commercially available TaqPath COVID-19 Combo Kit to track S-gene target failure (SGTF) associated with the spike protein deletion H69-V70, as well as two internally designed and validated RT-qPCR assays targeting two N-terminal-domain (NTD) spike gene deletions, NTD156-7 and NTD25-7. The NTD156-7 RT-qPCR assay facilitated tracking of the Delta variant, while the NTD25-7 RT-qPCR assay was used for tracking Omicron variants, including the BA.2, BA.4, and BA.5 lineages. In silico validation of the NTD156-7 and NTD25-7 primers and probes compared with publicly available SARS-CoV-2 genome databases showed low variability in regions corresponding to oligonucleotide binding sites. Similarly, in vitro validation with NGS-confirmed samples showed excellent correlation. RT-qPCR assays allow for near-real-time monitoring of circulating and emerging variants allowing for ongoing surveillance of variant dynamics in a local population. By performing periodic sequencing of variant surveillance by RT-qPCR methods, we were able to provide ongoing validation of the results obtained by RT-qPCR screening. Rapid SARS-CoV-2 variant identification and surveillance by this combined approach served to inform clinical decisions in a timely manner and permitted better utilization of sequencing resources.
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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: 5] [Impact Index Per Article: 5.0] [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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Acosta N, Bautista MA, Waddell BJ, Du K, McCalder J, Pradhan P, Sedaghat N, Papparis C, Beaudet AB, Chen J, Van Doorn J, Xiang K, Chan L, Vivas L, Low K, Lu X, Lee J, Westlund P, Chekouo T, Dai X, Cabaj J, Bhatnagar S, Ruecker N, Achari G, Clark RG, Pearce C, Harrison JJ, Meddings J, Leal J, Ellison J, Missaghi B, Kanji JN, Larios O, Rennert‐May E, Kim J, Hrudey SE, Lee BE, Pang X, Frankowski K, Conly J, Hubert CRJ, Parkins MD. Surveillance for SARS-CoV-2 and its variants in wastewater of tertiary care hospitals correlates with increasing case burden and outbreaks. J Med Virol 2023; 95:e28442. [PMID: 36579780 PMCID: PMC9880705 DOI: 10.1002/jmv.28442] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022]
Abstract
Wastewater-based SARS-CoV-2 surveillance enables unbiased and comprehensive monitoring of defined sewersheds. We performed real-time monitoring of hospital wastewater that differentiated Delta and Omicron variants within total SARS-CoV-2-RNA, enabling correlation to COVID-19 cases from three tertiary-care facilities with >2100 inpatient beds in Calgary, Canada. RNA was extracted from hospital wastewater between August/2021 and January/2022, and SARS-CoV-2 quantified using RT-qPCR. Assays targeting R203M and R203K/G204R established the proportional abundance of Delta and Omicron, respectively. Total and variant-specific SARS-CoV-2 in wastewater was compared to data for variant specific COVID-19 hospitalizations, hospital-acquired infections, and outbreaks. Ninety-six percent (188/196) of wastewater samples were SARS-CoV-2 positive. Total SARS-CoV-2 RNA levels in wastewater increased in tandem with total prevalent cases (Delta plus Omicron). Variant-specific assessments showed this increase to be mainly driven by Omicron. Hospital-acquired cases of COVID-19 were associated with large spikes in wastewater SARS-CoV-2 and levels were significantly increased during outbreaks relative to nonoutbreak periods for total SARS-CoV2, Delta and Omicron. SARS-CoV-2 in hospital wastewater was significantly higher during the Omicron-wave irrespective of outbreaks. Wastewater-based monitoring of SARS-CoV-2 and its variants represents a novel tool for passive COVID-19 infection surveillance, case identification, containment, and potentially to mitigate viral spread in hospitals.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | | | - Barbara J. Waddell
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Kristine Du
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Janine McCalder
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Puja Pradhan
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Navid Sedaghat
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Chloe Papparis
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | | | - Jianwei Chen
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | | | - Kevin Xiang
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Leslie Chan
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Laura Vivas
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Kashtin Low
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Xuewen Lu
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
| | - Jangwoo Lee
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | | | - Thierry Chekouo
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada,Division of Biostatistics, School of Public HealthUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Xiaotian Dai
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
| | - Jason Cabaj
- Department of Community Health SciencesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Provincial Population & Public HealthAlberta Health ServicesCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
| | - Srijak Bhatnagar
- Faculty of Science and TechnologyAthabasca UniversityAthabascaAlbertaCanada
| | | | - Gopal Achari
- Department of Civil EngineeringUniversity of CalgaryCalgaryCanada
| | - Rhonda G. Clark
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Craig Pearce
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Joe J. Harrison
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Jon Meddings
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Jenine Leal
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Community Health SciencesUniversity of CalgaryCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Jennifer Ellison
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Bayan Missaghi
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Jamil N. Kanji
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada,Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada,Department of Pathology and Laboratory MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Oscar Larios
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada,Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada
| | - Elissa Rennert‐May
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Community Health SciencesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Joseph Kim
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada,Department of Analytical and Environmental ToxicologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Bonita E. Lee
- Department of PediatricsUniversity of AlbertaEdmontonAlbertaCanada,Women & Children's Health Research InstituteEdmontonAlbertaCanada,Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Xiaoli Pang
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada,Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada,Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin Frankowski
- Advancing Canadian Water AssetsUniversity of CalgaryCalgaryCanada
| | - John Conly
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Department of Pathology and Laboratory MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | | | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
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21
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D'Aoust PM, Tian X, Towhid ST, Xiao A, Mercier E, Hegazy N, Jia JJ, Wan S, Kabir MP, Fang W, Fuzzen M, Hasing M, Yang MI, Sun J, Plaza-Diaz J, Zhang Z, Cowan A, Eid W, Stephenson S, Servos MR, Wade MJ, MacKenzie AE, Peng H, Edwards EA, Pang XL, Alm EJ, Graber TE, Delatolla R. Wastewater to clinical case (WC) ratio of COVID-19 identifies insufficient clinical testing, onset of new variants of concern and population immunity in urban communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158547. [PMID: 36067855 PMCID: PMC9444156 DOI: 10.1016/j.scitotenv.2022.158547] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/10/2022] [Accepted: 09/01/2022] [Indexed: 05/14/2023]
Abstract
Clinical testing has been the cornerstone of public health monitoring and infection control efforts in communities throughout the COVID-19 pandemic. With the anticipated reduction of clinical testing as the disease moves into an endemic state, SARS-CoV-2 wastewater surveillance (WWS) will have greater value as an important diagnostic tool. An in-depth analysis and understanding of the metrics derived from WWS is required to interpret and utilize WWS-acquired data effectively (McClary-Gutierrez et al., 2021; O'Keeffe, 2021). In this study, the SARS-CoV-2 wastewater signal to clinical cases (WC) ratio was investigated across seven cities in Canada over periods ranging from 8 to 21 months. This work demonstrates that significant increases in the WC ratio occurred when clinical testing eligibility was modified to appointment-only testing, identifying a period of insufficient clinical testing (resulting in a reduction to testing access and a reduction in the number of daily tests) in these communities, despite increases in the wastewater signal. Furthermore, the WC ratio decreased significantly in 6 of the 7 studied locations, serving as a potential signal of the emergence of the Alpha variant of concern (VOC) in a relatively non-immunized community (40-60 % allelic proportion), while a more muted decrease in the WC ratio signaled the emergence of the Delta VOC in a relatively well-immunized community (40-60 % allelic proportion). Finally, a significant decrease in the WC ratio signaled the emergence of the Omicron VOC, likely because of the variant's greater effectiveness at evading immunity, leading to a significant number of new reported clinical cases, even when community immunity was high. The WC ratio, used as an additional monitoring metric, could complement clinical case counts and wastewater signals as individual metrics in its potential ability to identify important epidemiological occurrences, adding value to WWS as a diagnostic technology during the COVID-19 pandemic and likely for future pandemics.
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Affiliation(s)
- Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Xin Tian
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | | | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Elisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Nada Hegazy
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Shen Wan
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Md Pervez Kabir
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Wanting Fang
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Maria Hasing
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Minqing Ivy Yang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Jianxian Sun
- Department of Chemistry, University of Toronto, Toronto, Canada
| | - Julio Plaza-Diaz
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Zhihao Zhang
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Aaron Cowan
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Sean Stephenson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - Matthew J Wade
- Data, Analytics and Surveillance Group, UK Health Security Agency, London, United Kingdom
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Hui Peng
- Department of Chemistry, University of Toronto, Toronto, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Canada.
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22
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Malla B, Thakali O, Shrestha S, Segawa T, Kitajima M, Haramoto E. Application of a high-throughput quantitative PCR system for simultaneous monitoring of SARS-CoV-2 variants and other pathogenic viruses in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158659. [PMID: 36096223 PMCID: PMC9461275 DOI: 10.1016/j.scitotenv.2022.158659] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 05/11/2023]
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuously emerging, highlighting the importance of regular surveillance of SARS-CoV-2 and other epidemiologically significant pathogenic viruses in the current context. Reverse transcription-quantitative PCR (RT-qPCR) is expensive, time-consuming, labor-intensive, requires a large reagent volume, and only tests a few targets in a single run. High-throughput qPCR (HT-qPCR) utilizing the Biomark HD system (Fluidigm) can be used as an alternative. This study applied an HT-qPCR to simultaneously detect SARS-CoV-2, SARS-CoV-2 nucleotide substituted RNA, and other pathogenic viruses in wastewater. Wastewater samples were collected from the coronavirus disease 2019 (COVID-19) quarantine facility between October 2020 and February 2021 (n = 4) and from the combined and separated sewer lines of a wastewater treatment plant (WWTP) in Yokkaichi, Mie Prefecture, Japan, between March and August 2021 (n = 23 each). The samples were analyzed by HT-qPCR using five SARS-CoV-2, nine SARS-CoV-2 spike gene nucleotide substitution-specific, five pathogenic viruses, and three process control assays. All samples from the quarantine facility tested positive for SARS-CoV-2 and the nucleotide substitutions N501Y and S69-70 del (Alpha variant) were detected in the December 2020 sample, coinciding with the first clinical case in Japan. Only three WWTP samples were positive when tested with a single SARS-CoV-2 assay, whereas more than eight samples were positive when tested with all assays, indicating that using multiple assays increases the likelihood of detection. The nucleotide substitution L452R (Delta variant) was detected in the WWTP samples of Mie Prefecture in April 2021, but the detection of Delta variant from patients had not been reported until May 2021. Aichi virus 1 and norovirus GII were prevalent in WWTP samples. This study demonstrated that HT-qPCR may be the most time- and cost-efficient method for tracking COVID-19 and broadly monitoring community health.
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Affiliation(s)
- Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Ocean Thakali
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan; Institute for the Advanced Study of Sustainability, United Nations University, 5-53-70 Jingumae, Shibuya-ku, Tokyo 150-8925, Japan
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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23
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Hoar C, McClary-Gutierrez J, Wolfe MK, Bivins A, Bibby K, Silverman AI, McLellan SL. Looking Forward: The Role of Academic Researchers in Building Sustainable Wastewater Surveillance Programs. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:125002. [PMID: 36580023 PMCID: PMC9799055 DOI: 10.1289/ehp11519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND In just over 2 years, tracking the COVID-19 pandemic through wastewater surveillance advanced from early reports of successful SARS-CoV-2 RNA detection in untreated wastewater to implementation of programs in at least 60 countries. Early wastewater monitoring efforts primarily originated in research laboratories and are now transitioning into more formal surveillance programs run in commercial and public health laboratories. A major challenge in this progression has been to simultaneously optimize methods and build scientific consensus while implementing surveillance programs, particularly during the rapidly changing landscape of the pandemic. Translating wastewater surveillance results for effective use by public health agencies also remains a key objective for the field. OBJECTIVES We examined the evolution of wastewater surveillance to identify model collaborations and effective partnerships that have created rapid and sustained success. We propose needed areas of research and key roles academic researchers can play in the framework of wastewater surveillance to aid in the transition from early monitoring efforts to more formalized programs within the public health system. DISCUSSION Although wastewater surveillance has rapidly developed as a useful public health tool for tracking COVID-19, there remain technical challenges and open scientific questions that academic researchers are equipped to address. This includes validating methodology and backfilling important knowledge gaps, such as fate and transport of surveillance targets and epidemiological links to wastewater concentrations. Our experience in initiating and implementing wastewater surveillance programs in the United States has allowed us to reflect on key barriers and draw useful lessons on how to promote synergy between different areas of expertise. As wastewater surveillance programs are formalized, the working relationships developed between academic researchers, commercial and public health laboratories, and data users should promote knowledge co-development. We believe active involvement of academic researchers will contribute to building robust surveillance programs that will ultimately provide new insights into population health. https://doi.org/10.1289/EHP11519.
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Affiliation(s)
- Catherine Hoar
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, New York, USA
| | - Jill McClary-Gutierrez
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marlene K. Wolfe
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Indiana, USA
| | - Andrea I. Silverman
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, New York, USA
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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24
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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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25
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Jiang W, Ji W, Zhang Y, Xie Y, Chen S, Jin Y, Duan G. An Update on Detection Technologies for SARS-CoV-2 Variants of Concern. Viruses 2022; 14:v14112324. [PMID: 36366421 PMCID: PMC9693800 DOI: 10.3390/v14112324] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/15/2022] [Accepted: 10/20/2022] [Indexed: 01/18/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is responsible for the global epidemic of Coronavirus Disease 2019 (COVID-19), with a significant impact on the global economy and human safety. Reverse transcription-quantitative polymerase chain reaction (RT-PCR) is the gold standard for detecting SARS-CoV-2, but because the virus's genome is prone to mutations, the effectiveness of vaccines and the sensitivity of detection methods are declining. Variants of concern (VOCs) include Alpha, Beta, Gamma, Delta, and Omicron, which are able to evade recognition by host immune mechanisms leading to increased transmissibility, morbidity, and mortality of COVID-19. A range of research has been reported on detection techniques for VOCs, which is beneficial to prevent the rapid spread of the epidemic, improve the effectiveness of public health and social measures, and reduce the harm to human health and safety. However, a meaningful translation of this that reduces the burden of disease, and delivers a clear and cohesive message to guide daily clinical practice, remains preliminary. Herein, we summarize the capabilities of various nucleic acid and protein-based detection methods developed for VOCs in identifying and differentiating current VOCs and compare the advantages and disadvantages of each method, providing a basis for the rapid detection of VOCs strains and their future variants and the adoption of corresponding preventive and control measures.
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Affiliation(s)
- Wenjie Jiang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Wangquan Ji
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yu Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yaqi Xie
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
- Henan Key Laboratory of Molecular Medicine, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (S.C.); (Y.J.); (G.D.); Tel.: +86-13523408394 (S.C.); +86-0371-67781453 (Y.J.); +86-0371-67789797 (G.D.)
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (S.C.); (Y.J.); (G.D.); Tel.: +86-13523408394 (S.C.); +86-0371-67781453 (Y.J.); +86-0371-67789797 (G.D.)
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
- Henan Key Laboratory of Molecular Medicine, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (S.C.); (Y.J.); (G.D.); Tel.: +86-13523408394 (S.C.); +86-0371-67781453 (Y.J.); +86-0371-67789797 (G.D.)
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26
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Oloye FF, Xie Y, Asadi M, Cantin J, Challis JK, Brinkmann M, McPhedran KN, Kristian K, Keller M, Sadowski M, Jones PD, Landgraff C, Mangat C, Fuzzen M, Servos MR, Giesy JP. Rapid transition between SARS-CoV-2 variants of concern Delta and Omicron detected by monitoring municipal wastewater from three Canadian cities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156741. [PMID: 35716745 PMCID: PMC9212401 DOI: 10.1016/j.scitotenv.2022.156741] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 05/21/2023]
Abstract
Monitoring the communal incidence of COVID-19 is important for both government and residents of an area to make informed decisions. However, continuous reliance on one means of monitoring might not be accurate because of biases introduced by government policies or behaviours of residents. Wastewater surveillance was employed to monitor concentrations of SARS-CoV-2 RNA in raw influent wastewater from wastewater treatment plants serving three Canadian Prairie cities with different population sizes. Data obtained from wastewater are not directly influenced by government regulations or behaviours of individuals. The means of three weekly samples collected using 24 h composite auto-samplers were determined. Viral loads were determined by RT-qPCR, and whole-genome sequencing was used to charaterize variants of concern (VOC). The dominant VOCs in the three cities were the same but with different proportions of sub-lineages. Sub-lineages of Delta were AY.12, AY.25, AY.27 and AY.93 in 2021, while the major sub-lineage of Omicron was BA.1 in January 2022, and BA.2 subsequently became a trace-level sub-variant then the predominant VOC. When each VOC was first detected varied among cities; However, Saskatoon, with the largest population, was always the first to present new VOCs. Viral loads varied among cities, but there was no direct correlation with population size, possibly because of differences in flow regimes. Population is one of the factors that affects trends in onset and development of local outbreaks during the pandemic. This might be due to demography or the fact that larger populations had greater potential for inter- and intra-country migration. Hence, wastewater surveillance data from larger cities can typically be used to indicate what to expect in smaller communities.
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Affiliation(s)
- Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jonathan K Challis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kevin Kristian
- Wastewater Treatment Plant, Public Work Department, City of Prince Albert, Prince Albert, SK, Canada
| | - Mark Keller
- Wastewater Treatment Plant, City Operations, City of North Battleford, North Battleford, SK, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department, City of Saskatoon, Saskatoon, SK, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chand Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory Winnipeg, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
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27
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Oloye FF, Xie Y, Asadi M, Cantin J, Challis JK, Brinkmann M, McPhedran KN, Kristian K, Keller M, Sadowski M, Jones PD, Landgraff C, Mangat C, Fuzzen M, Servos MR, Giesy JP. Rapid transition between SARS-CoV-2 variants of concern Delta and Omicron detected by monitoring municipal wastewater from three Canadian cities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 35716745 PMCID: PMC8887651 DOI: 10.1021/acsestwater.1c00349&ref=pdf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Monitoring the communal incidence of COVID-19 is important for both government and residents of an area to make informed decisions. However, continuous reliance on one means of monitoring might not be accurate because of biases introduced by government policies or behaviours of residents. Wastewater surveillance was employed to monitor concentrations of SARS-CoV-2 RNA in raw influent wastewater from wastewater treatment plants serving three Canadian Prairie cities with different population sizes. Data obtained from wastewater are not directly influenced by government regulations or behaviours of individuals. The means of three weekly samples collected using 24 h composite auto-samplers were determined. Viral loads were determined by RT-qPCR, and whole-genome sequencing was used to charaterize variants of concern (VOC). The dominant VOCs in the three cities were the same but with different proportions of sub-lineages. Sub-lineages of Delta were AY.12, AY.25, AY.27 and AY.93 in 2021, while the major sub-lineage of Omicron was BA.1 in January 2022, and BA.2 subsequently became a trace-level sub-variant then the predominant VOC. When each VOC was first detected varied among cities; However, Saskatoon, with the largest population, was always the first to present new VOCs. Viral loads varied among cities, but there was no direct correlation with population size, possibly because of differences in flow regimes. Population is one of the factors that affects trends in onset and development of local outbreaks during the pandemic. This might be due to demography or the fact that larger populations had greater potential for inter- and intra-country migration. Hence, wastewater surveillance data from larger cities can typically be used to indicate what to expect in smaller communities.
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Affiliation(s)
- Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jonathan K Challis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kevin Kristian
- Wastewater Treatment Plant, Public Work Department, City of Prince Albert, Prince Albert, SK, Canada
| | - Mark Keller
- Wastewater Treatment Plant, City Operations, City of North Battleford, North Battleford, SK, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department, City of Saskatoon, Saskatoon, SK, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chand Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory Winnipeg, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
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28
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Hubert CRJ, Acosta N, Waddell BJM, Hasing ME, Qiu Y, Fuzzen M, Harper NBJ, Bautista MA, Gao T, Papparis C, Van Doorn J, Du K, Xiang K, Chan L, Vivas L, Pradhan P, McCalder J, Low K, England WE, Kuzma D, Conly J, Ryan MC, Achari G, Hu J, Cabaj JL, Sikora C, Svenson L, Zelyas N, Servos M, Meddings J, Hrudey SE, Frankowski K, Parkins MD, Pang XL, Lee BE. Tracking Emergence and Spread of SARS-CoV-2 Omicron Variant in Large and Small Communities by Wastewater Monitoring in Alberta, Canada. Emerg Infect Dis 2022. [PMID: 35867051 DOI: 10.1101/2022.03.07.22272055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Wastewater monitoring of SARS-CoV-2 enables early detection and monitoring of the COVID-19 disease burden in communities and can track specific variants of concern. We determined proportions of the Omicron and Delta variants across 30 municipalities covering >75% of the province of Alberta (population 4.5 million), Canada, during November 2021-January 2022. Larger cities Calgary and Edmonton exhibited more rapid emergence of Omicron than did smaller and more remote municipalities. Notable exceptions were Banff, a small international resort town, and Fort McMurray, a medium-sized northern community that has many workers who fly in and out regularly. The integrated wastewater signal revealed that the Omicron variant represented close to 100% of SARS-CoV-2 burden by late December, before the peak in newly diagnosed clinical cases throughout Alberta in mid-January. These findings demonstrate that wastewater monitoring offers early and reliable population-level results for establishing the extent and spread of SARS-CoV-2 variants.
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29
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Viveros ML, Azimi S, Pichon E, Roose-Amsaleg C, Bize A, Durandet F, Rocher V. Wild type and variants of SARS-COV-2 in Parisian sewage: presence in raw water and through processes in wastewater treatment plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67442-67449. [PMID: 36029443 PMCID: PMC9418656 DOI: 10.1007/s11356-022-22665-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 08/18/2022] [Indexed: 05/30/2023]
Abstract
The presence of SARS-CoV-2 RNA has been extensively reported at the influent of wastewater treatment plants (WWTPs) worldwide, and its monitoring has been proposed as a potential surveillance tool to early alert of epidemic outbreaks. However, the fate of the SARS-CoV-2 RNA in the treatment process of WWTP has not been widely studied yet; therefore, in this study, we aimed to evaluate the efficiency of treatment processes in reducing SARS-CoV-2 RNA levels in wastewater. The treatment process of three WWTPs of the Parisian area in France was monitored on six different weeks over a period of 2 months (from April 14 to June 9, 2021). SARS-CoV-2 RNA copies were detected using digital polymerase chain reaction (dPCR). Investigation on the presence of variants of concern (Del69-70, E484K, and L452R) was also performed. Additionally, SARS-CoV-2 RNA loads in the WWTPs influents were expressed as the viral concentration in per population equivalent (PE) and showed a good correlation with French public health indicators (incidence rate). SARS-CoV-2 RNA loads were notably reduced along the water treatment lines of the three WWTPs studied (2.5-3.4 log reduction). Finally, very low SARS-CoV-2 RNA loads were detected in effluents (non-detected in over half of the samples) which indicated that the potential risk of the release of wastewater effluents to the environment is probably insignificant, in the case of WWTPs enabling an efficient biological removal of nitrogen.
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Affiliation(s)
| | - Sam Azimi
- SIAAP - Direction Innovation, 82 avenue Kléber, 92700, Colombes, France
| | - Elodie Pichon
- GEOBIOMICS, 335 rue Louis Lépine, 34000, Montpellier, France
| | | | - Ariane Bize
- PRocédés biOtechnologiques Au Service de L'Environnement, INRAE Université Paris-Saclay, INRAE, 92761, Antony, France
| | | | - Vincent Rocher
- SIAAP - Direction Innovation, 82 avenue Kléber, 92700, Colombes, France
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de Sousa ARV, do Carmo Silva L, de Curcio JS, da Silva HD, Eduardo Anunciação C, Maria Salem Izacc S, Neto FOS, de Paula Silveira Lacerda E. "pySewage": a hybrid approach to predict the number of SARS-CoV-2-infected people from wastewater in Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67260-67269. [PMID: 35524091 PMCID: PMC9075719 DOI: 10.1007/s11356-022-20609-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/30/2022] [Indexed: 05/21/2023]
Abstract
It is well known that the new coronavirus pandemic has global environmental, public health, and economic implications. In this sense, this study aims to monitor SARS-CoV-2 in the largest wastewater treatment plant of Goiânia, which processes wastewater from more than 700,000 inhabitants, and to correlate the molecular and clinical data collected. Influent and effluent samples were collected at Dr. Helio de Seixo Britto's wastewater treatment plant from January to August 2021. Viral concentration was performed with polyethylene glycol before viral RNA extraction. Real-time qPCR (N1 and N2 gene assays) was performed to detect and quantify the viral RNA present in the samples. The results showed that 43.63% of the samples were positive. There is no significant difference between the detection of primers N1 (mean 3.23 log10 genome copies/L, std 0.23) and N2 (mean 2.95 log10 genome copies/L, std 0.29); also, there is no significant difference between the detection of influent and effluent samples. Our molecular data revealed a positive correlation with clinical data, and infection prevalence was higher than clinical data. In addition, we developed a user-friendly web application to predict the number of infected people based on the detection of viral load present in wastewater samples and may be applied as a public policy strategy for monitoring ongoing outbreaks.
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Affiliation(s)
| | - Lívia do Carmo Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Juliana Santana de Curcio
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Hugo Delleon da Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
- Universitary Center of Goiás (UNIGOIÁS), Goiânia, Goiás, Brazil
| | - Carlos Eduardo Anunciação
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Silvia Maria Salem Izacc
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
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Hubert CRJ, Acosta N, Waddell BJM, Hasing ME, Qiu Y, Fuzzen M, Harper NBJ, Bautista MA, Gao T, Papparis C, Van Doorn J, Du K, Xiang K, Chan L, Vivas L, Pradhan P, McCalder J, Low K, England WE, Kuzma D, Conly J, Ryan MC, Achari G, Hu J, Cabaj JL, Sikora C, Svenson L, Zelyas N, Servos M, Meddings J, Hrudey SE, Frankowski K, Parkins MD, Pang XL, Lee BE. Tracking Emergence and Spread of SARS-CoV-2 Omicron Variant in Large and Small Communities by Wastewater Monitoring in Alberta, Canada. Emerg Infect Dis 2022; 28:1770-1776. [PMID: 35867051 PMCID: PMC9423933 DOI: 10.3201/eid2809.220476] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Wastewater monitoring of SARS-CoV-2 enables early detection and monitoring of the COVID-19 disease burden in communities and can track specific variants of concern. We determined proportions of the Omicron and Delta variants across 30 municipalities covering >75% of the province of Alberta (population 4.5 million), Canada, during November 2021-January 2022. Larger cities Calgary and Edmonton exhibited more rapid emergence of Omicron than did smaller and more remote municipalities. Notable exceptions were Banff, a small international resort town, and Fort McMurray, a medium-sized northern community that has many workers who fly in and out regularly. The integrated wastewater signal revealed that the Omicron variant represented close to 100% of SARS-CoV-2 burden by late December, before the peak in newly diagnosed clinical cases throughout Alberta in mid-January. These findings demonstrate that wastewater monitoring offers early and reliable population-level results for establishing the extent and spread of SARS-CoV-2 variants.
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Xu X, Deng Y, Ding J, Zheng X, Li S, Liu L, Chui HK, Poon LLM, Zhang T. Real-time allelic assays of SARS-CoV-2 variants to enhance sewage surveillance. WATER RESEARCH 2022; 220:118686. [PMID: 35679788 PMCID: PMC9148393 DOI: 10.1016/j.watres.2022.118686] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 05/21/2023]
Abstract
To effectively control the ongoing outbreaks of fast-spreading SARS-CoV-2 variants, there is an urgent need to add rapid variant detection and discrimination methods to the existing sewage surveillance systems established worldwide. We designed eight assays based on allele-specific RT-qPCR for real-time allelic discrimination of eight SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Omicron, Lambda, Mu, and Kappa) in sewage. In silico analysis of the designed assays for identifying SARS-CoV-2 variants using more than four million SARS-CoV-2 variant sequences yielded ∼100% specificity and >90% sensitivity. All assays could sensitively discriminate and quantify target variants at levels as low as 10 viral RNA copy/µL with minimal cross-reactivity to the corresponding nontarget genotypes, even for sewage samples containing mixtures of SARS-CoV-2 variants with differential abundances. Integration of this method into the routine sewage surveillance in Hong Kong successfully identified the Beta variant in a community sewage. Complete concordance was observed between the results of viral whole-genome sequencing and those of our novel assays in sewage samples that contained exclusively the Delta variant discharged by a clinically diagnosed COVID-19 patient living in a quarantine hotel. Our assays in this method also provided real-time discrimination of the newly emerging Omicron variant in sewage two days prior to clinical test results in another quarantine hotel in Hong Kong. These novel allelic discrimination assays offer a rapid, sensitive, and specific way for detecting multiple SARS-CoV-2 variants in sewage and can be directly integrated into the existing sewage surveillance systems.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - Lei Liu
- 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
| | - Ho-Kwong Chui
- Environmental Protection Department, The Government of Hong Kong SAR, Tamar, 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.
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Peng J, Sun J, Yang MI, Gibson RM, Arts EJ, Olabode AS, Poon AFY, Wang X, Wheeler AR, Edwards EA, Peng H. Early Warning Measurement of SARS-CoV-2 Variants of Concern in Wastewaters by Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2022; 9:638-644. [PMID: 37552744 PMCID: PMC9236213 DOI: 10.1021/acs.estlett.2c00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/15/2022] [Indexed: 05/24/2023]
Abstract
Wastewater surveillance has rapidly emerged as an early warning tool to track COVID-19. However, the early warning measurement of new SARS-CoV-2 variants of concern (VOCs) in wastewaters remains a major challenge. We herein report a rapid analytical strategy for quantitative measurement of VOCs, which couples nested polymerase chain reaction and liquid chromatography-mass spectrometry (nPCR-LC-MS). This method showed a greater selectivity than the current allele-specific quantitative PCR (AS-qPCR) for tracking new VOC and allowed the detection of multiple signature mutations in a single measurement. By measuring the Omicron variant in wastewaters across nine Ontario wastewater treatment plants serving over a three million population, the nPCR-LC-MS method demonstrated a better quantification accuracy than next-generation sequencing (NGS), particularly at the early stage of community spreading of Omicron. This work addresses a major challenge for current SARS-CoV-2 wastewater surveillance by rapidly and accurately measuring VOCs in wastewaters for early warning.
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Affiliation(s)
- Jiaxi Peng
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College Street, Toronto,
Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering,
University of Toronto, 164 College Street, Toronto, Ontario
M5S 3G9, Canada
| | - Jianxian Sun
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
| | - Minqing Ivy Yang
- Department of Chemical Engineering and Applied
Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario M5S 3E5, Canada
| | - Richard M. Gibson
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Eric J. Arts
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Abayomi S. Olabode
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Art F. Y. Poon
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Xianyao Wang
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College Street, Toronto,
Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering,
University of Toronto, 164 College Street, Toronto, Ontario
M5S 3G9, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied
Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario M5S 3E5, Canada
| | - Hui Peng
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
- School of the Environment, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
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Bar-Or I, Indenbaum V, Weil M, Elul M, Levi N, Aguvaev I, Cohen Z, Levy V, Azar R, Mannasse B, Shirazi R, Bucris E, Mor O, Sela Brown A, Sofer D, Zuckerman NS, Mendelson E, Erster O. National Scale Real-Time Surveillance of SARS-CoV-2 Variants Dynamics by Wastewater Monitoring in Israel. Viruses 2022; 14:1229. [PMID: 35746700 PMCID: PMC9227326 DOI: 10.3390/v14061229] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
In this report, we describe a national-scale monitoring of the SARS-CoV-2 (SC-2) variant dynamics in Israel, using multiple-time sampling of 13 wastewater treatment plants. We used a combination of inclusive and selective quantitative PCR assays that specifically identify variants A19/A20 or B.1.1.7 and tested each sample for the presence and relative viral RNA load of each variant. We show that between December 2020 and March 2021, a complete shift in the SC-2 variant circulation was observed, where the B.1.1.7 replaced the A19 in all examined test points. We further show that the normalized viral load (NVL) values and the average new cases per week reached a peak in January 2021 and then decreased gradually in almost all test points, in parallel with the progression of the national vaccination campaign, during February-March 2021. This study demonstrates the importance of monitoring SC-2 variant by using a combination of inclusive and selective PCR tests on a national scale through wastewater sampling, which is far more amendable for high-throughput monitoring compared with sequencing. This approach may be useful for real-time dynamics surveillance of current and future variants, such as the Omicron (BA.1, BA.2) and other variants.
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Affiliation(s)
- Itay Bar-Or
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Victoria Indenbaum
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Merav Weil
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Michal Elul
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Nofar Levi
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Irina Aguvaev
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Zvi Cohen
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Virginia Levy
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Roberto Azar
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Batya Mannasse
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Rachel Shirazi
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Efrat Bucris
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
- Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Alin Sela Brown
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Danit Sofer
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
| | - Ella Mendelson
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
- Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Oran Erster
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Ramat Gan 5262000, Israel; (I.B.-O.); (V.I.); (M.W.); (M.E.); (N.L.); (I.A.); (Z.C.); (V.L.); (R.A.); (B.M.); (R.S.); (E.B.); (O.M.); (A.S.B.); (D.S.); (N.S.Z.); (E.M.)
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35
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Borillo GA, Kagan RM, Marlowe EM. Rapid and Accurate Identification of SARS-CoV-2 Variants Using Real Time PCR Assays. Front Cell Infect Microbiol 2022; 12:894613. [PMID: 35619652 PMCID: PMC9127862 DOI: 10.3389/fcimb.2022.894613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/07/2022] [Indexed: 12/16/2022] Open
Abstract
Background Genomic surveillance efforts for SARS-CoV-2 are needed to understand the epidemiology of the COVID-19 pandemic. Viral variants may impact routine diagnostic testing, increase viral transmissibility, cause differences in disease severity, have decreased susceptibility to therapeutics, and/or confer the ability to evade host immunity. While viral whole-genome sequencing (WGS) has played a leading role in surveillance programs, many laboratories lack the expertise and resources for performing WGS. This study describes the performance of multiplexed real-time reverse transcription-PCR (RT-PCR) assays for identification of SARS-CoV-2 variants. Methods SARS-CoV-2 specimens were tested for spike-gene variants using a combination of allele-specific primer and allele-specific detection technology (PlexPrime® and PlexZyme®). Targeted detection of spike gene mutations by RT-PCR was compared to variant detection in positive specimens by WGS, including the recently emerged SARS-CoV-2 Omicron variant. Results A total of 398 SAR-CoV-2 RT-PCR positive and 39 negative specimens previously tested by WGS were re-tested by RT-PCR genotyping. PCR detection of spike gene mutations N501Y, E484K, and S982A correlated 100% with WGS for the 29 lineages represented, including Alpha (B.1.1.7), Beta (B.1.351), and Gamma (P.1). Incorporating the P681R spike gene mutation also allowed screening for the SARS-CoV-2 Delta variant (B.1.617.2 and AY sublineages). Further sampling of 664 specimens that were screened by WGS between June and August 2021 and then re-tested by RT-PCR showed strong agreement for Delta variant positivity: 34.5% for WGS vs 32.9% for RT-PCR in June; 100% vs 97.8% in August. In a blinded panel of 16 Omicron and 16 Delta specimens, results of RT-PCR were 100% concordant with WGS results. Conclusions These data demonstrate that multiplexed real-time RT-PCR genotyping has strong agreement with WGS and may provide additional SARS-CoV-2 variant screening capabilities when WGS is unavailable or cost-prohibitive. RT-PCR genotyping assays may also supplement existing sequencing efforts while providing rapid results at or near the time of diagnosis to help guide patient management.
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Boogaerts T, Van den Bogaert S, Van Poelvoorde LAE, El Masri D, De Roeck N, Roosens NHC, Lesenfants M, Lahousse L, Van Hoorde K, van Nuijs ALN, Delputte P. Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. Viruses 2022; 14:610. [PMID: 35337017 PMCID: PMC8953730 DOI: 10.3390/v14030610] [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] [Received: 02/08/2022] [Revised: 02/24/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Since the beginning of the COVID-19 pandemic, the wastewater-based epidemiology (WBE) of SARS-CoV-2 has been used as a complementary indicator to follow up on the trends in the COVID-19 spread in Belgium and in many other countries. To further develop the use of WBE, a multiplex digital polymerase chain reaction (dPCR) assay was optimized, validated and applied for the measurement of emerging SARS-CoV-2 variants of concern (VOC) in influent wastewater (IWW) samples. Key mutations were targeted in the different VOC strains, including SΔ69/70 deletion, N501Y, SΔ241 and SΔ157. The presented bioanalytical method was able to distinguish between SARS-CoV-2 RNA originating from the wild-type and B.1.1.7, B.1.351 and B.1.617.2 variants. The dPCR assay proved to be sensitive enough to detect low concentrations of SARS-CoV-2 RNA in IWW since the limit of detection of the different targets ranged between 0.3 and 2.9 copies/µL. This developed WBE approach was applied to IWW samples originating from different Belgian locations and was able to monitor spatio-temporal changes in the presence of targeted VOC strains in the investigated communities. The present dPCR assay developments were realized to bring added-value to the current national WBE of COVID-19 by also having the spatio-temporal proportions of the VoC in presence in the wastewaters.
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Affiliation(s)
- Tim Boogaerts
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium;
| | - Siel Van den Bogaert
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
| | - Laura A. E. Van Poelvoorde
- Scientific Directorate of Biological Health Risks, Service Transerversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (L.A.E.V.P.); (N.H.C.R.)
| | - Diala El Masri
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
| | - Naomi De Roeck
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
| | - Nancy H. C. Roosens
- Scientific Directorate of Biological Health Risks, Service Transerversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium; (L.A.E.V.P.); (N.H.C.R.)
| | - Marie Lesenfants
- Scientific Directorate of Epidemiology and Public Health, Service Epidemiology of Infectious Diseases, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium;
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium;
| | - Koenraad Van Hoorde
- Scientific Directorate of Infectious Diseases in Humans, Service Foodborne Pathogens, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium;
| | | | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (D.E.M.); (N.D.R.); (P.D.)
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A Sensitive and Rapid Wastewater Test for SARS-COV-2 and Its Use for the Early Detection of a Cluster of Cases in a Remote Community. Appl Environ Microbiol 2022; 88:e0174021. [PMID: 34985977 PMCID: PMC8904056 DOI: 10.1128/aem.01740-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Throughout the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has been used to monitor trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prevalence in the community. A major challenge in establishing wastewater surveillance programs, especially in remote areas, is the need for a well-equipped laboratory for sample analysis. Currently, no options exist for rapid, sensitive, mobile, and easy-to-use wastewater tests for SARS-CoV-2. The performance of the GeneXpert system, which offers cartridge-based, rapid molecular clinical testing for SARS-CoV-2 in a portable platform, was evaluated using wastewater as the input. The GeneXpert demonstrated a SARS-CoV-2 limit of detection in wastewater below 32 copies/mL with a sample processing time of less than an hour. Using wastewater samples collected from multiple sites across Canada during February and March 2021, a high overall agreement (97.8%) was observed between the GeneXpert assay and laboratory-developed tests regarding the presence or absence of SARS-CoV-2. Additionally, with the use of centrifugal filters, the detection threshold of the GeneXpert system was improved to <10 copies/mL in wastewater. Finally, to support on-site wastewater surveillance, GeneXpert testing was implemented in Yellowknife, a remote community in Northern Canada, where its use successfully alerted public health authorities to undetected transmission of COVID-19. The identification of SARS-CoV-2 in wastewater triggered clinical testing of recent travelers and identification of new COVID-19 cases/clusters. Taken together, these results suggest that GeneXpert is a viable option for surveillance of SARS-CoV-2 in wastewater in locations that do not have access to established testing laboratories. IMPORTANCE Wastewater-based surveillance is a powerful tool that provides an unbiased measure of COVID-19 prevalence in a community. This work describes a sensitive wastewater rapid test for SARS-CoV-2 based on a widely distributed technology, the GeneXpert. The advantages of an easy-to-use wastewater test for SARS-CoV-2 are clear: it supports surveillance in remote communities, improves access to testing, and provides faster results allowing for an immediate public health response. The application of wastewater rapid testing in a remote community facilitated the detection of a COVID-19 cluster and triggered public health action, clearly demonstrating the utility of this technology. Wastewater surveillance will become increasingly important in the postvaccination pandemic landscape as individuals with asymptomatic/mild infections continue transmitting SARS-CoV-2 but are unlikely to be tested.
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Hrudey SE, Bischel HN, Charrois J, Chik AHS, Conant B, Delatolla R, Dorner S, Graber TE, Hubert C, Isaac-Renton J, Pons W, Safford H, Servos M, Sikora C. Wastewater Surveillance for SARS-CoV-2 RNA in Canada. Facets (Ott) 2022. [DOI: 10.1139/facets-2022-0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Wastewater surveillance for SARS-CoV-2 RNA is a relatively recent adaptation of long-standing wastewater surveillance for infectious and other harmful agents. Individuals infected with COVID-19 were found to shed SARS-CoV-2 in their faeces. Researchers around the world confirmed that SARS-CoV-2 RNA fragments could be detected and quantified in community wastewater. Canadian academic researchers, largely as volunteer initiatives, reported proof-of-concept by April 2020. National collaboration was initially facilitated by the Canadian Water Network. Many public health officials were initially skeptical about actionable information being provided by wastewater surveillance even though experience has shown that public health surveillance for a pandemic has no single, perfect approach. Rather, different approaches provide different insights, each with its own strengths and limitations. Public health science must triangulate among different forms of evidence to maximize understanding of what is happening or may be expected. Well-conceived, resourced, and implemented wastewater-based platforms can provide a cost-effective approach to support other conventional lines of evidence. Sustaining wastewater monitoring platforms for future surveillance of other disease targets and health states is a challenge. Canada can benefit from taking lessons learned from the COVID-19 pandemic to develop forward-looking interpretive frameworks and capacity to implement, adapt, and expand such public health surveillance capabilities.
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Affiliation(s)
- Steve E. Hrudey
- Professor Emeritus, Analytical & Environmental Toxicology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2G3 Canada
| | - Heather N. Bischel
- Associate Professor, Department of Civil & Environmental Engineering, University of California, Davis, Davis, CA 95616 USA
| | - Jeff Charrois
- Senior Manager, Analytical Operations and Process Development Teams, EPCOR Water Services Inc, Edmonton, AB T5K 0A5 Canada
| | - Alex H. S. Chik
- Project Manager, Wastewater Surveillance Initiative, Ontario Clean Water Agency, Mississauga, ON L5A 4G1 Canada
| | - Bernadette Conant
- Past Chief Executive Officer, Canadian Water Network, Waterloo, ON N2L 3G1 Canada
| | - Rob Delatolla
- Professor, Civil Engineering, University of Ottawa, Ottawa, ON K1N 6N5 Canada
| | - Sarah Dorner
- Professor, Civil, Geological & Mining Engineering, Polytechnique Montréal, Montréal, PQ H3T 1J4 Canada
| | - Tyson E. Graber
- Associate Scientist, Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1 Canada
| | - Casey Hubert
- Professor, Campus Alberta Innovates Program Chair in Geomicrobiology, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Judy Isaac-Renton
- Professor Emerita, Dept. Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Calgary, AB, T2N 3V9 Canada
| | - Wendy Pons
- Professor, Bachelor of Environmental Health Program Conestoga College Institute of Technology and Advanced Learning, Kitchener, ON N2P 2N6 Canada
| | - Hannah Safford
- Associate Director of Science Policy, Federation of American Scientists, Arlington, VA 22205 USA
| | - Mark Servos
- Professor & Canada Research Chair, Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1 Canada
| | - Christopher Sikora
- Medical Officer of Health, Edmonton Region, Alberta Health Services, Edmonton, AB T5J 3E4 Canada
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