1
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John A, Dreifuss D, Kang S, Bratus-Neuenschwander A, Zajac N, Topolsky I, Dondi A, Aquino C, Julian TR, Beerenwinkel N. Assessing different next-generation sequencing technologies for wastewater-based epidemiology. WATER RESEARCH 2024; 267:122465. [PMID: 39388978 DOI: 10.1016/j.watres.2024.122465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 09/02/2024] [Accepted: 09/16/2024] [Indexed: 10/12/2024]
Abstract
Wastewater-based epidemiology has proven to be an important public health asset during the COVID-19 pandemic. It can provide less biassed and more cost-effective population-level monitoring of the disease burden as compared to clinical testing. An essential component of SARS-CoV-2 wastewater monitoring is next-generation sequencing, providing genomic data to identify and quantify circulating viral strains rapidly. However, the specific choice of sequencing method influences the quality and timeliness of generated data and hence its usefulness for wastewater-based pathogen surveillance. Here, we systematically benchmarked Illumina Novaseq 6000, Element Aviti, ONT R9.4.1 MinION flow cell, and ONT R9.4.1 Flongle flow cell sequencing data to facilitate the selection of sequencing technology. Using a time series of wastewater samples from influent of six wastewater treatment plants throughout Switzerland, along with spike-in experiments, we show that higher sequencing error rates of ONT Nanopore sequencing reduce the accuracy of estimates of the relative abundance of viral variants, but the overall trend is in good concordance among all technologies. We find that the sequencing runtime for ONT Nanopore flow cells can be reduced to as little as five hours without significant impact on the quality of variant estimates. Our findings suggest that SARS-CoV-2 variant tracking is readily achievable with all tested technologies, albeit with different tradeoffs in terms of cost, timeliness and accuracy.
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Affiliation(s)
- Anika John
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Seju Kang
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | | | - Natalia Zajac
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, CH-8057, Zurich, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Arthur Dondi
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, CH-8057, Zurich, Switzerland
| | - Timothy R Julian
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland; Swiss Tropical and Public Health Institute, CH-4123 Allschwil, Switzerland; University of Basel, CH-4055 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4056 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
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2
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Han E, Kim J, Kim YJ, Choi HJ, Bae MH. Clinical performance of a rapid RT-PCR assay using STANDARD™ M10 SARS-CoV-2 between July 2022 and January 2023 in Korea. Diagn Microbiol Infect Dis 2024; 110:116523. [PMID: 39244844 DOI: 10.1016/j.diagmicrobio.2024.116523] [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: 05/19/2024] [Revised: 08/05/2024] [Accepted: 09/01/2024] [Indexed: 09/10/2024]
Abstract
Rapid detection of SARS-CoV-2 is essential for clinical management in the emergency department during the COVID-19 pandemic. We evaluated the clinical performance of the recently developed cartridge-based rapid RT-PCR assay (STANDARD M10 SARS-CoV-2) in patients visiting the emergency department from July 2022 to January 2023, which was when the Omicron BA.5 sublineage was predominant in Korea. A total of 534 specimens were subjected to the STANDARD M10 and standard RT-PCR (Allplex SARS-CoV-2) assays. The overall, positive, and negative percent agreements between these two assays were 99.6%, 100%, and 99.6%, respectively. The results showed that compared with the established RT-PCR assay, the STANDARD M10 SARS-CoV-2 assay is a reliable and useful tool for SARS-CoV-2 detection during the study period. The new rapid RT-PCR will expand the diversity in rapid diagnostics and can help resolve the global imbalance associated with the supply of diagnostic resources.
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Affiliation(s)
- Eunhee Han
- Department of Laboratory Medicine, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jinyeong Kim
- Division of Infectious Disease, Department of Internal Medicine, Hanyang University Guri Hospital, Guri, South Korea
| | - Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, South Korea
| | - Hyuk Joong Choi
- Department of Emergency Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Mi Hyun Bae
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Gyeongchun-ro 153, Guri, 11923, South Korea.
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3
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Shempela DM, Muleya W, Mudenda S, Daka V, Sikalima J, Kamayani M, Sandala D, Chipango C, Muzala K, Musonda K, Chizimu JY, Mulenga C, Kapona O, Kwenda G, Kasanga M, Njuguna M, Cham F, Simwaka B, Morrison L, Muma JB, Saasa N, Sichinga K, Simulundu E, Chilengi R. Wastewater Surveillance of SARS-CoV-2 in Zambia: An Early Warning Tool. Int J Mol Sci 2024; 25:8839. [PMID: 39201525 PMCID: PMC11354861 DOI: 10.3390/ijms25168839] [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: 06/24/2024] [Revised: 08/10/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
Wastewater-based surveillance has emerged as an important method for monitoring the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This study investigated the presence of SARS-CoV-2 in wastewater in Zambia. We conducted a longitudinal study in the Copperbelt and Eastern provinces of Zambia from October 2023 to December 2023 during which 155 wastewater samples were collected. The samples were subjected to three different concentration methods, namely bag-mediated filtration, skimmed milk flocculation, and polythene glycol-based concentration assays. Molecular detection of SARS-CoV-2 nucleic acid was conducted using real-time Polymerase Chain Reaction (PCR). Whole genome sequencing was conducted using Illumina COVIDSEQ assay. Of the 155 wastewater samples, 62 (40%) tested positive for SARS-CoV-2. Of these, 13 sequences of sufficient length to determine SARS-CoV-2 lineages were obtained and 2 sequences were phylogenetically analyzed. Various Omicron subvariants were detected in wastewater including BA.5, XBB.1.45, BA.2.86, and JN.1. Some of these subvariants have been detected in clinical cases in Zambia. Interestingly, phylogenetic analysis positioned a sequence from the Copperbelt Province in the B.1.1.529 clade, suggesting that earlier Omicron variants detected in late 2021 could still be circulating and may not have been wholly replaced by newer subvariants. This study stresses the need for integrating wastewater surveillance of SARS-CoV-2 into mainstream strategies for monitoring SARS-CoV-2 circulation in Zambia.
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Affiliation(s)
- Doreen Mainza Shempela
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (M.K.); (D.S.); (C.C.); (K.S.)
| | - Walter Muleya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia;
| | - Steward Mudenda
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia;
| | - Victor Daka
- Public Health Department, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola 21692, Zambia;
| | - Jay Sikalima
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (M.K.); (D.S.); (C.C.); (K.S.)
| | - Mapeesho Kamayani
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (M.K.); (D.S.); (C.C.); (K.S.)
| | - Dickson Sandala
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (M.K.); (D.S.); (C.C.); (K.S.)
| | - Chilufya Chipango
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (M.K.); (D.S.); (C.C.); (K.S.)
| | - Kapina Muzala
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (K.M.); (J.Y.C.); (C.M.); (O.K.); (R.C.)
| | - Kunda Musonda
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (K.M.); (J.Y.C.); (C.M.); (O.K.); (R.C.)
| | - Joseph Yamweka Chizimu
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (K.M.); (J.Y.C.); (C.M.); (O.K.); (R.C.)
| | - Chilufya Mulenga
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (K.M.); (J.Y.C.); (C.M.); (O.K.); (R.C.)
| | - Otridah Kapona
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (K.M.); (J.Y.C.); (C.M.); (O.K.); (R.C.)
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia;
| | - Maisa Kasanga
- Department of Epidemiology and Biostatistics, School of Public Health, Zhengzhou University, Zhengzhou 450001, China;
| | - Michael Njuguna
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (M.N.); (F.C.); (B.S.); (L.M.)
| | - Fatim Cham
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (M.N.); (F.C.); (B.S.); (L.M.)
| | - Bertha Simwaka
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (M.N.); (F.C.); (B.S.); (L.M.)
| | - Linden Morrison
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (M.N.); (F.C.); (B.S.); (L.M.)
| | - John Bwalya Muma
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (J.B.M.); (N.S.)
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (J.B.M.); (N.S.)
| | - Karen Sichinga
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (M.K.); (D.S.); (C.C.); (K.S.)
| | | | - Roma Chilengi
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (K.M.); (J.Y.C.); (C.M.); (O.K.); (R.C.)
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4
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Liu Y, Sapoval N, Gallego-García P, Tomás L, Posada D, Treangen TJ, Stadler LB. Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater. Nat Commun 2024; 15:4545. [PMID: 38806450 PMCID: PMC11133379 DOI: 10.1038/s41467-024-48334-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
Wastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants of concerns and can be used to screen for novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that are rare, or entirely missing, in existing SARS-CoV-2 databases. While previous approaches have focused on specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and investigating their potential origin. We present Crykey, a tool for rapidly identifying rare linked-read mutations across the genome of SARS-CoV-2. We evaluated the utility of Crykey on over 3,000 wastewater and over 22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations in wastewater that represent potential circulating cryptic lineages, serving as a new computational tool for wastewater surveillance of SARS-CoV-2.
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Affiliation(s)
- Yunxi Liu
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Pilar Gallego-García
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Laura Tomás
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - David Posada
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310, Vigo, Spain
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, 77005, USA.
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA.
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5
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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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6
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Wang Y, Ni G, Tian W, Wang H, Li J, Thai P, Choi PM, Jackson G, Hu S, Yang B, Guo J. Wastewater tiling amplicon sequencing in sentinel sites reveals longitudinal dynamics of SARS-CoV-2 variants prevalence. WATER RESEARCH X 2024; 23:100224. [PMID: 38711798 PMCID: PMC11070618 DOI: 10.1016/j.wroa.2024.100224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/08/2024]
Abstract
The ongoing evolution of SARS-CoV-2 is a significant concern, especially with the decrease in clinical sequencing efforts, which impedes the ability of public health sectors to prepare for the emergence of new variants and potential COVID-19 outbreaks. Wastewater-based epidemiology (WBE) has been proposed as a surveillance program to detect and monitor the SARS-CoV-2 variants being transmitted in communities. However, research is limited in evaluating the effectiveness of wastewater collection at sentinel sites for monitoring disease prevalence and variant dynamics, especially in terms of inferring the epidemic patterns on a broader scale, such as at the state/province level. This study utilized a multiplexed tiling amplicon-based sequencing (ATOPlex) to track the longitudinal dynamics of variant of concern (VOC) in wastewater collected from municipalities in Queensland, Australia, spanning from 2020 to 2022. We demonstrated that wastewater epidemiology measured by ATOPlex exhibited a strong and consistent correlation with the number of daily confirmed cases. The VOC dynamics observed in wastewater closely aligned with the dynamic profile reported by clinical sequencing. Wastewater sequencing has the potential to provide early warning information for emerging variants. These findings suggest that WBE at sentinel sites, coupled with sensitive sequencing methods, provides a reliable and long-term disease surveillance strategy.
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Affiliation(s)
- Yu Wang
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Gaofeng Ni
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Wei Tian
- MGI Australia Pty Ltd, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Haofei Wang
- MGI Australia Pty Ltd, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Jiaying Li
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane, Queensland, Australia
| | - Phong Thai
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane, Queensland, Australia
| | - Phil M. Choi
- Water Unit, Health Protection Branch, Queensland Public Health and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Greg Jackson
- Water Unit, Health Protection Branch, Queensland Public Health and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Bicheng Yang
- MGI Australia Pty Ltd, 300 Herston Road, Herston, Brisbane, QLD 4006, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
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7
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Sutcliffe SG, Kraemer SA, Ellmen I, Knapp JJ, Overton AK, Nash D, Nissimov JI, Charles TC, Dreifuss D, Topolsky I, Baykal PI, Fuhrmann L, Jablonski KP, Beerenwinkel N, Levy JI, Olabode AS, Becker DG, Gugan G, Brintnell E, Poon AF, Valieris R, Drummond RD, Defelicibus A, Dias-Neto E, Rosales RA, Tojal da Silva I, Orfanou A, Psomopoulos F, Pechlivanis N, Pipes L, Chen Z, Baaijens JA, Baym M, Shapiro BJ. Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data. Microb Genom 2024; 10:001249. [PMID: 38785221 PMCID: PMC11165662 DOI: 10.1099/mgen.0.001249] [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: 02/21/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic 'novel' lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1 % frequency, results were more reliable above a 5 % threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of error or bias in wastewater sequencing analysis and to appreciate the commonalities and differences across methods.
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Affiliation(s)
- Steven G. Sutcliffe
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Susanne A. Kraemer
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Environment and Climate Change Canada, Montreal, QC, Canada
| | - Isaac Ellmen
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | | | - Delaney Nash
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | | | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Pelin I. Baykal
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Kim P. Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Abayomi S. Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Devan G. Becker
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Gopi Gugan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erin Brintnell
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Art F.Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Renan Valieris
- Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | | | | | | | | | | | - Aspasia Orfanou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Nikolaos Pechlivanis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Lenore Pipes
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Zihao Chen
- School of Mathematical Sciences, Peking University, Beijing, BJ, PR China
| | - Jasmijn A. Baaijens
- Delft University of Technology, Delft, ZH, Netherlands
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
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8
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Ryon MG, Langan LM, Brennan C, O'Brien ME, Bain FL, Miller AE, Snow CC, Salinas V, Norman RS, Bojes HK, Brooks BW. Influences of 23 different equations used to calculate gene copies of SARS-CoV-2 during wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170345. [PMID: 38272099 DOI: 10.1016/j.scitotenv.2024.170345] [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: 10/01/2023] [Revised: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
Following the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the use of wastewater-based surveillance (WBS) has increased dramatically along with associated infrastructure globally. However, due to the global nature of its application, and various workflow adaptations (e.g., sample collection, water concentration, RNA extraction kits), numerous methods for back-calculation of gene copies per volume (gc/L) of sewage have also emerged. Many studies have considered the comparability of processing methods (e.g., water concentration, RNA extraction); however, for equations used to calculate gene copies in a wastewater sample and subsequent influences on monitoring viral trends in a community and its association with epidemiological data, less is known. Due to limited information on how many formulas exist for the calculation of SARS-CoV-2 gene copies in wastewater, we initially attempted to quantify how many equations existed in the referred literature. We identified 23 unique equations, which were subsequently applied to an existing wastewater dataset. We observed a range of gene copies based on use of different equations, along with variability of AUC curve values, and results from correlation and regression analyses. Though a number of individual laboratories appear to have independently converged on a similar formula for back-calculation of viral load in wastewater, and share similar relationships with epidemiological data, differential influences of various equations were observed for variation in PCR volumes, RNA extraction volumes, or PCR assay parameters. Such observations highlight challenges when performing comparisons among WBS studies when numerous methodologies and back-calculation methods exist. To facilitate reproducibility among studies, the different gc/L equations were packaged as an R Shiny app, which provides end users the ability to investigate variability within their datasets and support comparisons among studies.
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Affiliation(s)
- Mia G Ryon
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Laura M Langan
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA.
| | - Christopher Brennan
- Department of Entomology, Texas A&M University, TAMU 2475, College Station, TX 77843-2475, USA
| | - Megan E O'Brien
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Fallon L Bain
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Aubree E Miller
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Christine C Snow
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA
| | - Victoria Salinas
- Environmental Epidemiology and Disease Registries, Texas Department of State Health Services, Austin, TX 78756, USA
| | - R Sean Norman
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, 921 Assembly St., Columbia, SC 28208, USA
| | - Heidi K Bojes
- Environmental Epidemiology and Disease Registries, Texas Department of State Health Services, Austin, TX 78756, USA
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA; Department of Public Health, Baylor University, One Bear Place #97343, Waco, TX 76798, USA.
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9
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Kim KH, Ryu E, Khaleel ZH, Seo SE, Kim L, Kim YH, Park HG, Kwon OS. Plasmonic digital PCR for discriminative detection of SARS-CoV-2 variants. Biosens Bioelectron 2024; 246:115859. [PMID: 38011776 DOI: 10.1016/j.bios.2023.115859] [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: 10/30/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
We developed a novel strategy for discriminative detection of SARS-CoV-2 variants based on the plasmonic photothermal effect of gold nanofilms and digital polymerase chain reaction (dPCR) technology. This method consists of the gold nanofilm-based dPCR chip fabrication for ultrafast heating and cooling cycles by the plasmonic photothermal effect, the LED quencher immobilization through the interfacing compound on the surface of the gold nanofilm to prevent photoquenching of PCR signaling dye, and the discriminative detection of the variant viruses from the COVID-19 clinical samples by photothermal cycles with fabricated dPCR chips and a portable plasmonic PCR device. Compared to conventional sequencing or RT-qPCR-based variant detection methods, this technology can be effectively applied to point-of-care testing by enabling ultrafast quantitative analysis with a small device. With this method, we successfully detected the delta variant and the omicron variant with a high sensitivity of 10 copies from COVID-19 patients' clinical samples within 25 min, including reverse transcription. This method can be applied universally to rapid and accurate point-of-care testing for various pandemic viruses as well as the coronavirus.
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Affiliation(s)
- Kyung Ho Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Eunsu Ryu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Zinah Hilal Khaleel
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Science and Technology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sung Eun Seo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Lina Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Science and Technology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Oh Seok Kwon
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Science and Technology, Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
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10
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Anand A, Long C, Chandran K. NYC metropolitan wastewater reveals links between SARS-CoV-2 amino acid mutations and disease outcomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:167971. [PMID: 37914132 DOI: 10.1016/j.scitotenv.2023.167971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
Since late 2020, diverse SARS-CoV-2 variants with enhanced infectivity and transmissibility have emerged. In contrast to the focus on amino acid mutations in the spike protein, mutations in non-spike proteins and their associated impacts remain relatively understudied. New York City metropolitan wastewater revealed over 60 % of the most frequently occurring amino acid mutations in regions outside the spike protein. Strikingly, ~50 % of the mutations detected herein remain uncharacterized for functional impacts. Our results suggest that there are several understudied mutations within non-spike proteins N, ORF1a, ORF1b, ORF9b, and ORF9c, that could increase transmissibility, and infectivity among human populations. We also demonstrate significant correlations of P314L, D614G, T95I, G50E, G50R, G204R, R203K, G662S, P10S, and P13L with documented mortality rates, hospitalization rates, and percent positivity suggesting that amino acid mutations are likely to be indicators of COVID-19 infection outcomes.
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Affiliation(s)
- Archana Anand
- Department of Earth and Environmental Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, United States of America
| | - Chenghua Long
- Department of Earth and Environmental Engineering, Columbia University, 500 W. 120th Street, New York, NY 10027, United States of America
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, 500 W. 120th Street, New York, NY 10027, United States of America.
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11
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Baz Lomba JA, Pires J, Myrmel M, Arnø JK, Madslien EH, Langlete P, Amato E, Hyllestad S. Effectiveness of environmental surveillance of SARS-CoV-2 as an early-warning system: Update of a systematic review during the second year of the pandemic. JOURNAL OF WATER AND HEALTH 2024; 22:197-234. [PMID: 38295081 PMCID: wh_2023_279 DOI: 10.2166/wh.2023.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The aim of this updated systematic review was to offer an overview of the effectiveness of environmental surveillance (ES) of SARS-CoV-2 as a potential early-warning system (EWS) for COVID-19 and new variants of concerns (VOCs) during the second year of the pandemic. An updated literature search was conducted to evaluate the added value of ES of SARS-CoV-2 for public health decisions. The search for studies published between June 2021 and July 2022 resulted in 1,588 publications, identifying 331 articles for full-text screening. A total of 151 publications met our inclusion criteria for the assessment of the effectiveness of ES as an EWS and early detection of SARS-CoV-2 variants. We identified a further 30 publications among the grey literature. ES confirms its usefulness as an EWS for detecting new waves of SARS-CoV-2 infection with an average lead time of 1-2 weeks for most of the publication. ES could function as an EWS for new VOCs in areas with no registered cases or limited clinical capacity. Challenges in data harmonization and variant detection require standardized approaches and innovations for improved public health decision-making. ES confirms its potential to support public health decision-making and resource allocation in future outbreaks.
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Affiliation(s)
- Jose Antonio Baz Lomba
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway E-mail:
| | - João Pires
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway; ECDC fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jorunn Karterud Arnø
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Elisabeth Henie Madslien
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Petter Langlete
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Ettore Amato
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Susanne Hyllestad
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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12
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Liu Y, Sapoval N, Gallego-García P, Tomás L, Posada D, Treangen TJ, Stadler LB. Crykey: Rapid Identification of SARS-CoV-2 Cryptic Mutations in Wastewater. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.16.23291524. [PMID: 37986916 PMCID: PMC10659477 DOI: 10.1101/2023.06.16.23291524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
We present Crykey, a computational tool for rapidly identifying cryptic mutations of SARS-CoV-2. Specifically, we identify co-occurring single nucleotide mutations on the same sequencing read, called linked-read mutations, that are rare or entirely missing in existing databases, and have the potential to represent novel cryptic lineages found in wastewater. While previous approaches exist for identifying cryptic linked-read mutations from specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and for tens of thousands of samples and with increased scrutiny, given their potential to represent either artifacts or hidden SARS-CoV-2 lineages. Crykey fills this gap by identifying rare linked-read mutations that pass stringent computational filters to limit the potential for artifacts. We evaluate the utility of Crykey on >3,000 wastewater and >22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over a three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations representing potential cryptic lineages in wastewater.
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Affiliation(s)
- Yunxi Liu
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Pilar Gallego-García
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
| | - Laura Tomás
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Lauren B. Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA
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13
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Harrison K, Snead D, Kilts A, Ammerman ML, Wigginton KR. The Protective Effect of Virus Capsids on RNA and DNA Virus Genomes in Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13757-13766. [PMID: 37656816 PMCID: PMC10516120 DOI: 10.1021/acs.est.3c03814] [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: 05/22/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
Virus concentrations measured in municipal wastewater help inform both the water treatment necessary to protect human health and wastewater-based epidemiology. Wastewater measurements are typically PCR-based, and interpreting gene copy concentrations requires an understanding of the form and stability of the nucleic acids. Here, we study the persistence of model virus genomes in wastewater, the protective effects provided by the virus capsids, and the relative decay rates of the genome and infectious viruses. In benchtop batch experiments in wastewater influent at 25 °C, extraviral (+)ssRNA and dsDNA amplicons degraded by 90% within 15-19 min and 1.6-1.9 h, respectively. When encapsidated, the T90 for MS2 (+)ssRNA increased by 424× and the T90 for T4 dsDNA increased by 52×. The (+)ssRNA decay rates were similar for a range of amplicon sizes. For our model phages MS2 and T4, the nucleic acid signal in untreated wastewater disappeared shortly after the viruses lost infectivity. Combined, these results suggest that most viral genome copies measured in wastewater are encapsidated, that measured concentrations are independent of assay amplicon sizes, and that the virus genome decay rates of nonenveloped (i.e., naked) viruses are similar to inactivation rates. These findings are valuable for the interpretation of wastewater virus measurements.
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Affiliation(s)
- Katherine
R. Harrison
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Delaney Snead
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna Kilts
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Michelle L. Ammerman
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
| | - Krista R. Wigginton
- Department of Civil &
Environmental Engineering, University of
Michigan, Ann Arbor, Michigan 48109, United States
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14
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Kumblathan T, Liu Y, Pang X, Hrudey SE, Le XC, Li XF. Quantification and Differentiation of SARS-CoV-2 Variants in Wastewater for Surveillance. ENVIRONMENT & HEALTH (WASHINGTON, D.C.) 2023; 1:203-213. [PMID: 37736345 PMCID: PMC10510104 DOI: 10.1021/envhealth.3c00089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 09/23/2023]
Abstract
Wastewater surveillance plays an important role in the monitoring of infections of SARS-CoV-2 at the community level. We report here the determination of SARS-CoV-2 and differentiation of its variants of concern in 294 wastewater samples collected from two major Canadian cities from May 2021 to March 2023. The overall method of analysis involved extraction of the virus and viral components using electronegative membranes, in situ stabilization and concentration of the viral RNA onto magnetic beads, and direct analysis of the viral RNA on the magnetic beads. Multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays, targeting specific and naturally selected mutations in SARS-CoV-2, enabled detection and differentiation of the Alpha, Beta, Gamma, Delta, and Omicron variants. An Omicron triplex RT-qPCR assay targeting three mutations, HV 69-70 deletion, K417N, and L452R, was able to detect and differentiate the Omicron BA.1/BA.3, BA.2/XBB, and BA.4/5. This assay had efficiencies of 90-104% for all three mutation targets and a limit of detection of 28 RNA copies per reaction. Analyses of 294 wastewater samples collected over a two-year span showed the concentrations and trends of Alpha, Beta, Gamma, Delta, and Omicron variants as they emerge in two major Canadian cities participating in the wastewater surveillance program. The trends of specific variants were consistent with clinical reports for the same period. At the beginning of each wave, the corresponding variants were detectable in wastewater. For example, RNA concentrations of the BA.2 variant were as high as 104 copies per 100 mL of wastewater collected in January 2022, when approximately only 50-60 clinical cases of BA.2 infection were reported in Canada. These results show that the strategy and highly sensitive assays for the variants of concern in wastewater are potentially useful for the detection of newly emerging SARS-CoV-2 variants and other viruses for future community biomonitoring.
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Affiliation(s)
- Teresa Kumblathan
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Yanming Liu
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Xiaoli Pang
- Division
of Diagnostic and Applied Microbiology, Department of Laboratory Medicine
and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2B7
- Public
Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada T6G 2J2
| | - Steve E. Hrudey
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - X. Chris Le
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
- Division
of Diagnostic and Applied Microbiology, Department of Laboratory Medicine
and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2B7
- Public
Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada T6G 2J2
| | - Xing-Fang Li
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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15
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Sharkey ME, Babler KM, Shukla BS, Abelson SM, Alsuliman B, Amirali A, Comerford S, Grills GS, Kumar N, Laine J, Lee J, Lamar WE, Mason CE, Penso J, Reding BD, Schürer SC, Stevenson M, Vidović D, Solo-Gabriele HM. Monkeypox viral nucleic acids detected using both DNA and RNA extraction workflows. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 890:164289. [PMID: 37216988 PMCID: PMC10213602 DOI: 10.1016/j.scitotenv.2023.164289] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023]
Abstract
Molecular methods have been used to detect human pathogens in wastewater with sampling typically performed at wastewater treatment plants (WWTP) and upstream locations within the sewer system. A wastewater-based surveillance (WBS) program was established at the University of Miami (UM) in 2020, which included measurements of SARS-CoV-2 levels in wastewater from its hospital and within the regional WWTP. In addition to the development of a SARS-CoV-2 quantitative PCR (qPCR) assay, qPCR assays to detect other human pathogens of interest were also developed at UM. Here we report on the use of a modified set of reagents published by the CDC to detect nucleic acids of Monkeypox virus (MPXV) which emerged during May of 2022 to become a concern worldwide. Samples collected from the University hospital and from the regional WWTP were processed through DNA and RNA workflows and analyzed by qPCR to detect a segment of the MPXV CrmB gene. Results show positive detections of MPXV nucleic acids in the hospital and wastewater treatment plant wastewater which coincided with clinical cases in the community and mirrored the overall trend of nationwide MPXV cases reported to the CDC. We recommend the expansion of current WBS programs' methods to detect a broader range of pathogens of concern in wastewater and present evidence that viral RNA in human cells infected by a DNA virus can be detected in wastewater.
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Affiliation(s)
- Mark E Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kristina M Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA
| | - Bhavarth S Shukla
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Samantha M Abelson
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bader Alsuliman
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA
| | - Samuel Comerford
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Naresh Kumar
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL, USA
| | - Jisue Lee
- University of Miami Health System, Miami, FL, USA
| | - Walter E Lamar
- Facilities Safety & Compliance, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, USA
| | - Johnathon Penso
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Brian D Reding
- Environmental Health and Safety, University of Miami, Miami, FL, USA
| | - Stephan C Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL, USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Dušica Vidović
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL, USA.
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16
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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] [MESH Headings] [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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17
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Kadonsky KF, Naughton CC, Susa M, Olson R, Singh GL, Daza-Torres ML, Montesinos-López JC, Garcia YE, Gafurova M, Gushgari A, Cosgrove J, White BJ, Boehm AB, Wolfe MK, Nuño M, Bischel HN. Expansion of wastewater-based disease surveillance to improve health equity in California's Central Valley: sequential shifts in case-to-wastewater and hospitalization-to-wastewater ratios. Front Public Health 2023; 11:1141097. [PMID: 37457240 PMCID: PMC10348812 DOI: 10.3389/fpubh.2023.1141097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Over a third of the communities (39%) in the Central Valley of California, a richly diverse and important agricultural region, are classified as disadvantaged-with inadequate access to healthcare, lower socio-economic status, and higher exposure to air and water pollution. The majority of racial and ethnic minorities are also at higher risk of COVID-19 infection, hospitalization, and death according to the Centers for Disease Control and Prevention. Healthy Central Valley Together established a wastewater-based disease surveillance (WDS) program that aims to achieve greater health equity in the region through partnership with Central Valley communities and the Sewer Coronavirus Alert Network. WDS offers a cost-effective strategy to monitor trends in SARS-CoV-2 community infection rates. Methods In this study, we evaluated correlations between public health and wastewater data (represented as SARS-CoV-2 target gene copies normalized by pepper mild mottle virus target gene copies) collected for three Central Valley communities over two periods of COVID-19 infection waves between October 2021 and September 2022. Public health data included clinical case counts at county and sewershed scales as well as COVID-19 hospitalization and intensive care unit admissions. Lag-adjusted hospitalization:wastewater ratios were also evaluated as a retrospective metric of disease severity and corollary to hospitalization:case ratios. Results Consistent with other studies, strong correlations were found between wastewater and public health data. However, a significant reduction in case:wastewater ratios was observed for all three communities from the first to the second wave of infections, decreasing from an average of 4.7 ± 1.4 over the first infection wave to 0.8 ± 0.4 over the second. Discussion The decline in case:wastewater ratios was likely due to reduced clinical testing availability and test seeking behavior, highlighting how WDS can fill data gaps associated with under-reporting of cases. Overall, the hospitalization:wastewater ratios remained more stable through the two waves of infections, averaging 0.5 ± 0.3 and 0.3 ± 0.4 over the first and second waves, respectively.
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Affiliation(s)
- Krystin F. Kadonsky
- Department of Civil and Environmental Engineering, University of California, Merced, Merced, CA, United States
| | - Colleen C. Naughton
- Department of Civil and Environmental Engineering, University of California, Merced, Merced, CA, United States
| | - Mirjana Susa
- Department of Public Health Sciences, University of California, Davis, Davis, CA, United States
| | - Rachel Olson
- Department of Civil and Environmental Engineering, University of California, Davis, Davis, CA, United States
| | - Guadalupe L. Singh
- Department of Civil and Environmental Engineering, University of California, Merced, Merced, CA, United States
| | - Maria L. Daza-Torres
- Department of Public Health Sciences, University of California, Davis, Davis, CA, United States
| | | | - Yury Elena Garcia
- Department of Public Health Sciences, University of California, Davis, Davis, CA, United States
| | - Maftuna Gafurova
- Eurofins Environment Testing US, West Sacramento, CA, United States
| | - Adam Gushgari
- Eurofins Environment Testing US, West Sacramento, CA, United States
| | - John Cosgrove
- Eurofins Environment Testing US, West Sacramento, CA, United States
| | | | - Alexandria B. Boehm
- Department of Civil & Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, CA, United States
| | - Marlene K. Wolfe
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Miriam Nuño
- Department of Public Health Sciences, University of California, Davis, Davis, CA, United States
| | - Heather N. Bischel
- Department of Civil and Environmental Engineering, University of California, Davis, Davis, CA, United States
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18
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Gupta P, Liao S, Ezekiel M, Novak N, Rossi A, LaCross N, Oakeson K, Rohrwasser A. Wastewater Genomic Surveillance Captures Early Detection of Omicron in Utah. Microbiol Spectr 2023; 11:e0039123. [PMID: 37154725 PMCID: PMC10269515 DOI: 10.1128/spectrum.00391-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
Wastewater-based epidemiology has emerged as a powerful public health tool to trace new outbreaks, detect trends in infection, and provide an early warning of COVID-19 community spread. Here, we investigated the spread of SARS-CoV-2 infections across Utah by characterizing lineages and mutations detected in wastewater samples. We sequenced over 1,200 samples from 32 sewersheds collected between November 2021 and March 2022. Wastewater sequencing confirmed the presence of Omicron (B.1.1.529) in Utah in samples collected on November 19, 2021, up to 10 days before its corresponding detection via clinical sequencing. Analysis of diversity of SARS-CoV-2 lineages revealed Delta as the most frequently detected lineage during November 2021 (67.71%), but it started declining in December 2021 with the onset of Omicron (B.1.1529) and its sublineage BA.1 (6.79%). The proportion of Omicron increased to ~58% by January 4, 2022, and completely displaced Delta by February 7, 2022. Wastewater genomic surveillance revealed the presence of Omicron sublineage BA.3, a lineage that was not identified from Utah's clinical surveillance. Interestingly, several Omicron-defining mutations began to appear in early November 2021 and increased in prevalence across sewersheds from December to January, aligning with the surge in clinical cases. Our study highlights the importance of tracking epidemiologically relevant mutations in detecting emerging lineages in the early stages of an outbreak. Wastewater genomic epidemiology provides an unbiased representation of community-wide infection dynamics and is an excellent complementary tool to SARS-CoV-2 clinical surveillance, with the potential of guiding public health action and policy decisions. IMPORTANCE SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has had a significant impact on public health. Global emergence of novel SARS-CoV-2 variants, shift to at-home tests, and reduction in clinical tests demonstrate the need for a reliable and effective surveillance strategy to contain COVID-19 spread. Monitoring of SARS-CoV-2 viruses in wastewater is an effective way to trace new outbreaks, establish baseline levels of infection, and complement clinical surveillance efforts. Wastewater genomic surveillance, in particular, can provide valuable insights into the evolution and spread of SARS-CoV-2 variants. We characterized the diversity of SARS-CoV-2 mutations and lineages using whole-genome sequencing to trace the introduction of lineage B.1.1.519 (Omicron) in Utah. Our data showed that Omicron appeared in Utah on November 19, 2021, up to 10 days prior to its detection in patient samples, indicating that wastewater surveillance provides an early warning signal. Our findings are important from a public health perspective as timely identification of communities with high COVID-19 transmission could help guide public health interventions.
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Affiliation(s)
- Pooja Gupta
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Stefan Liao
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Maleea Ezekiel
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Nicolle Novak
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Alessandro Rossi
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Nathan LaCross
- Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Kelly Oakeson
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Andreas Rohrwasser
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
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19
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Tangwangvivat R, Wacharapluesadee S, Pinyopornpanish P, Petcharat S, Hearn SM, Thippamom N, Phiancharoen C, Hirunpatrawong P, Duangkaewkart P, Supataragul A, Chaiden C, Wechsirisan W, Wandee N, Srimuang K, Paitoonpong L, Buathong R, Klungthong C, Pawun V, Hinjoy S, Putcharoen O, Iamsirithaworn S. SARS-CoV-2 Variants Detection Strategies in Wastewater Samples Collected in the Bangkok Metropolitan Region. Viruses 2023; 15:v15040876. [PMID: 37112855 PMCID: PMC10145351 DOI: 10.3390/v15040876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Wastewater surveillance is considered a promising approach for COVID-19 surveillance in communities. In this study, we collected wastewater samples between November 2020 and February 2022 from twenty-three sites in the Bangkok Metropolitan Region to detect the presence of SARS-CoV-2 and its variants for comparison to standard clinical sampling. A total of 215 wastewater samples were collected and tested for SARS-CoV-2 RNA by real-time PCR with three targeted genes (N, E, and ORF1ab); 102 samples were positive (42.5%). The SARS-CoV-2 variants were determined by a multiplex PCR MassARRAY assay to distinguish four SARS-CoV-2 variants, including Alpha, Beta, Delta, and Omicron. Multiple variants of Alpha-Delta and Delta-Omicron were detected in the wastewater samples in July 2021 and January 2022, respectively. These wastewater variant results mirrored the country data from clinical specimens deposited in GISAID. Our results demonstrated that wastewater surveillance using multiple signature mutation sites for SARS-CoV-2 variant detection is an appropriate strategy to monitor the presence of SARS-CoV-2 variants in the community at a low cost and with rapid turn-around time. However, it is essential to note that sequencing surveillance of wastewater samples should be considered complementary to whole genome sequencing of clinical samples to detect novel variants.
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Affiliation(s)
- Ratanaporn Tangwangvivat
- Division of Communicable Diseases, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Supaporn Wacharapluesadee
- Thai Red Cross Emerging Infectious Disease Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok 10330, Thailand
- School of Global Health, Faculty of Medicine, Chulalongkorn University, Rama IV Road, Pathumwan, Bangkok 10330, Thailand
| | - Papassorn Pinyopornpanish
- Division of Communicable Diseases, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Sininat Petcharat
- Thai Red Cross Emerging Infectious Disease Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok 10330, Thailand
| | - Suthida Muangnoicharoen Hearn
- Division of Epidemiology, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Nattakarn Thippamom
- Thai Red Cross Emerging Infectious Disease Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok 10330, Thailand
| | - Chadaporn Phiancharoen
- Division of Communicable Diseases, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Piyapha Hirunpatrawong
- Thai Red Cross Emerging Infectious Disease Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok 10330, Thailand
| | - Phattra Duangkaewkart
- Division of Communicable Diseases, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Ananporn Supataragul
- Thai Red Cross Emerging Infectious Disease Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok 10330, Thailand
| | - Chadaporn Chaiden
- Division of Communicable Diseases, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Wiriyachayon Wechsirisan
- Division of Epidemiology, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Nantaporn Wandee
- National Institute of Animal Health, Department of Livestock Development, Ministry of Agriculture and Cooperatives, Chatuchak, Bangkok 10900, Thailand
| | - Krongkan Srimuang
- Thai Red Cross Emerging Infectious Disease Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok 10330, Thailand
| | - Leilani Paitoonpong
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Rama IV Road, Pathumwan, Bangkok 10330, Thailand
| | - Rome Buathong
- Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Vichan Pawun
- Division of Communicable Diseases, Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Soawapak Hinjoy
- Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Opass Putcharoen
- Thai Red Cross Emerging Infectious Disease Clinical Center, King Chulalongkorn Memorial Hospital, Rama IV Road, Pathumwan, Bangkok 10330, Thailand
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Rama IV Road, Pathumwan, Bangkok 10330, Thailand
| | - Sopon Iamsirithaworn
- Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
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20
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Agrawal S, Orschler L, Zachmann K, Lackner S. Comprehensive mutation profiling from wastewater in southern Germany extends evidence of circulating SARS-CoV-2 diversity beyond mutations characteristic for Omicron. FEMS MICROBES 2023; 4:xtad006. [PMID: 37333432 PMCID: PMC10117852 DOI: 10.1093/femsmc/xtad006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 02/11/2023] [Accepted: 03/02/2023] [Indexed: 03/19/2024] Open
Abstract
Tracking SARS-CoV-2 variants in wastewater is primarily performed by detecting characteristic mutations of the variants. Unlike the Delta variant, the emergence of the Omicron variant and its sublineages as variants of concern has posed a challenge in using characteristic mutations for wastewater surveillance. In this study, we monitored the temporal and spatial variation of SARS-CoV-2 variants by including all the detected mutations and compared whether limiting the analyses to characteristic mutations for variants like Omicron impact the outcomes. We collected 24-hour composite samples from 15 wastewater treatment plants (WWTP) in Hesse and sequenced 164 wastewater samples with a targeted sequencing approach from September 2021 to March 2022. Our results show that comparing the number of all the mutations against the number of the characteristic mutations reveals a different outcome. A different temporal variation was observed for the ORF1a and S gene. As Omicron became dominant, we observed an increase in the overall number of mutations. Based on the characteristic mutations of the SARS-CoV-2 variants, a decreasing trend for the number of ORF1a and S gene mutations was noticed, though the number of known characteristic mutations in both genes is higher in Omicron than Delta.
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Affiliation(s)
- Shelesh Agrawal
- Technical University of Darmstadt, Institute IWAR, Chair of Water and Environmental Biotechnology, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - Laura Orschler
- Technical University of Darmstadt, Institute IWAR, Chair of Water and Environmental Biotechnology, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - Kira Zachmann
- Technical University of Darmstadt, Institute IWAR, Chair of Water and Environmental Biotechnology, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - Susanne Lackner
- Technical University of Darmstadt, Institute IWAR, Chair of Water and Environmental Biotechnology, Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
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21
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Yang WW, Hsu CW, Chan YJ, Su SB, Feng IJ, Hou CY, Huang CY. Using Real-Time PCR Fluorescence Reaction Values to Improve SARS-CoV-2 Virus Detection and Benefit Clinical Decision-Making. Life (Basel) 2023; 13:life13030683. [PMID: 36983837 PMCID: PMC10057560 DOI: 10.3390/life13030683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/05/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
This study aimed to compare the SARS-CoV-2 nucleic acid detection results of the BD MAX™ System and other platforms to formulate an optimized laboratory verification process. The re-examination of 400 samples determined as positive by BD MAX™ indicated that the inconsistency rate between BD MAX™ and the other platforms was 65.8%; the inconsistency rate of single-gene-positive results was as high as 99.2%. A receiver operating characteristic curve was drawn for the relative light unit (RLU) values of samples positive for a single gene, and RLU 800 was used as the cutoff. After setting the retest standard as single-gene positive and RLU ≥ 800, the number of the 260 BD MAX™ single-gene positives that needed to be confirmed again was 36 (13.8%) and the number that could be directly reported as negative was 224 (86.2%). This verification process can shorten the reporting period and speed up the epidemic adjustment time and turnover rate of special wards, thereby improving SARS-CoV-2 detection efficiency and clinical decision-making.
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Affiliation(s)
- Wan-Wen Yang
- Department of Clinical Pathology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Chin-Wen Hsu
- Department of Family Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Yu-Ju Chan
- Department of Family Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Shih-Bin Su
- Division of Occupational Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
- Division of Occupational Medicine, Chi-Mei Medical Center, Tainan 710402, Taiwan
| | - I-Jung Feng
- Institute of Precision Medicine, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Chia-Yi Hou
- Department of Clinical Pathology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
- Correspondence: (C.-Y.H.); (C.-Y.H.)
| | - Chien-Yuan Huang
- Division of Occupational Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
- Division of Occupational Medicine, Chi-Mei Medical Center, Tainan 710402, Taiwan
- Correspondence: (C.-Y.H.); (C.-Y.H.)
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22
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Sangsanont J, Rattanakul S, Makkaew P, Precha N, Rukthanapitak P, Sresung M, Siri Y, Kitajima M, Takeda T, Haramoto E, Puenpa J, Wanlapakorn N, Poovorawan Y, Mongkolsuk S, Sirikanchana K. Wastewater monitoring in tourist cities as potential sentinel sites for near real-time dynamics of imported SARS-CoV-2 variants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160317. [PMID: 36436629 PMCID: PMC9691270 DOI: 10.1016/j.scitotenv.2022.160317] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/29/2022] [Accepted: 11/16/2022] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) complements the clinical surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants' distribution in populations. Many developed nations have established national and regional WBE systems; however, governance and budget constraints could be obstacles for low- and middle-income countries. An urgent need thus exists to identify hotspots to serve as sentinel sites for WBE. We hypothesized that representative wastewater treatment plants (WWTPs) in two international gateway cities, Bangkok and Phuket, Thailand, could be sentineled for SARS-CoV-2 and its variants to reflect the clinical distribution patterns at city level and serve as early indicators of new variants entering the country. Municipal wastewater samples (n = 132) were collected from eight representative municipal WWTPs in Bangkok and Phuket during 19 sampling events from October 2021 to March 2022, which were tested by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) using the US CDC N1 and N2 multiplex and variant (Alpha, Delta, and Omicron BA.1 and BA.2) singleplex assays. The variant detection ratios from Bangkok and Phuket followed similar trends to the national clinical testing data, and each variant's viral loads agreed with the daily new cases (3-d moving average). Omicron BA.1 was detected in Phuket wastewater prior to Bangkok, possibly due to Phuket's WWTPs serving tourist communities. We found that the Omicron BA.1 and BA.2 viral loads predominantly drove the SARS-CoV-2 resurgence. We also noted a shifting pattern in the Bangkok WBE from a 22-d early warning in early 2021 to a near real-time pattern in late 2021. The potential application of tourist hotspots for WBE to indicate the arrival of new variants and re-emerging or unprecedented infectious agents could support tourism-dependent economies by complementing the reduced clinical regulations while maintaining public health protection via wastewater surveillance.
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Affiliation(s)
- Jatuwat Sangsanont
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Water Science and Technology for Sustainable Environmental Research Group, Chulalongkorn University, Bangkok 10330, Thailand
| | - Surapong Rattanakul
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Prasert Makkaew
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Nopadol Precha
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Pratchaya Rukthanapitak
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Montakarn Sresung
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Yadpiroon Siri
- Environmental, Safety Technology and Health Program, School of Public Health, Walailak University, Thaiburi, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Hokkaido 060-8628, Japan
| | - Tomoko Takeda
- Department of Earth and Planetary Science, The University of Tokyo, 113-0033, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi 400-8511, Japan
| | - Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand.
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23
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Galani A, Markou A, Dimitrakopoulos L, Kontou A, Kostakis M, Kapes V, Diamantopoulos MA, Adamopoulos PG, Avgeris M, Lianidou E, Scorilas A, Paraskevis D, Tsiodras S, Dimopoulos MA, Thomaidis N. Delta SARS-CoV-2 variant is entirely substituted by the omicron variant during the fifth COVID-19 wave in Attica region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159062. [PMID: 36181801 PMCID: PMC9519360 DOI: 10.1016/j.scitotenv.2022.159062] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Abstract
Wastewater analysis is the most attractive alternative way for the quantification and variant profiling of SARS-CoV-2. Infection dynamics can be monitored by RT-qPCR assays while NGS can provide evidence for the presence of existing or new emerging SARS-CoV-2 variants. Herein, apart from the infection dynamic in Attica since June 1st, 2021, the monitoring of 9 mutations of the omicron and 4 mutations of the delta SARS-CoV-2 variants, utilizing both novel Nested-Seq and RT-PCR, is reported and the substitution of the delta variant (B.1.617.2) by the omicron variant (B.1.1.529) in Attica, Greece within approximately one month is highlighted. The key difference between the two methodologies is discovery power. RT-PCR can only detect known sequences cost-effectively, while NGS is a hypothesis-free approach that does not require prior knowledge to detect novel genes. Overall, the potential of wastewater genomic surveillance for the early discovery and monitoring of variants important for disease management at the community level is underlined. This is the first study, reporting the SARS-CoV-2 infection dynamic for an extended time period and the first attempt to monitor two of the most severe variants with two different methodologies in Greece.
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Affiliation(s)
- Aikaterini Galani
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Athina Markou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Lampros Dimitrakopoulos
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Aikaterini Kontou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Marios Kostakis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Vasileios Kapes
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece; Laboratory of Clinical Biochemistry - Molecular Diagnostics, Second Department of Pediatrics, "P. & A. Kyriakou" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Sotirios Tsiodras
- Fourth Department of Internal Medicine, School of Medicine, University General Hospital Attikon, National and Kapodistrian University of Athens, Greece
| | | | - Nikolaos Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece.
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Lei N, Li BX, Zhang KF, Bao H, Ding J, Wang Y. Analysis of the Protective Effect of Infection Controllers Supervising Third-Party Personnel Entering and Leaving Shanghai Fangcang Shelter Hospital. Infect Drug Resist 2022; 15:7519-7527. [PMID: 36570712 PMCID: PMC9788835 DOI: 10.2147/idr.s388707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Objective To analyze the impact of the new supervision and management methods of infection controllers on the protection of third-party personnel entering and leaving Shanghai Fangcang shelter hospital, to provide a reference for the management of third-party personnel in Fangcang shelter hospitals. Methods A total of 200 third-party personnel received with traditional supervision and management methods, and 156 received new supervision and management methods from the Fangcang shelter hospital of the Shanghai International Convention and Exhibition Center. The sociodemographic characteristics of third-party personnel, including gender, age, education level, work experience in fighting the epidemic with safety awareness, was analyzed. The effects of the two different management modes on the protection of third-party personnel were statistically analyzed by the Chi-square test or logistic regression analysis. Results There were statistically significant differences in the incidence of infection among third-party personnel in terms of age, education level, work experience in fighting the epidemic in traditional supervision and management group, and whether they accepted the new supervision and management model had statistically significant differences (p <0.05). The main causes of incorrect put on and take off protective clothing, such as wrong way to detach the face screen, wrong way to remove goggles, wrong way to undress protective clothing, wrong way to take off the shoe cover, hand washing steps omitted, are that causes infection of third-party personnel (p <0.05). Conclusion The new supervision and management model can reduce the infection rate of third-party personnel in Fangcang shelter hospitals through planned and purposeful training in terms of different age groups, education levels, work experience, and acceptance of protection knowledge.
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Affiliation(s)
- Na Lei
- Department of Disinfection and Supply, General Hospital of Central Theater Command of the People’s Liberation Army, Wuhan, People’s Republic of China
| | - Bi-Xi Li
- Department of Anesthesiology, General Hospital of Central Theater Command of the People’s Liberation Army, Wuhan, People’s Republic of China
| | - Kai-Fen Zhang
- Department of Outpatient, General Hospital of Central Theater Command of the People’s Liberation Army, Wuhan, People’s Republic of China
| | - Hui Bao
- Department of Urology, General Hospital of Central Theater Command of the People’s Liberation Army, Wuhan, People’s Republic of China
| | - Jian Ding
- Department of Disinfection and Supply, General Hospital of Central Theater Command of the People’s Liberation Army, Wuhan, People’s Republic of China,Correspondence: Jian Ding; Yan Wang, Department of Disinfection and Supply, General Hospital of Central Theater Command of the People’s Liberation Army, 627#, Wuluo Road, Wuchang District, Wuhan, 430070, People’s Republic of China, Tel +86-18971123442, Fax +86-27-50772953, Email ;
| | - Yan Wang
- Department of Disinfection and Supply, General Hospital of Central Theater Command of the People’s Liberation Army, Wuhan, People’s Republic of China
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25
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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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26
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Langan LM, O’Brien M, Lovin LM, Scarlett KR, Davis H, Henke AN, Seidel SE, Archer N, Lawrence E, Norman RS, Bojes HK, Brooks BW. Quantitative Reverse Transcription PCR Surveillance of SARS-CoV-2 Variants of Concern in Wastewater of Two Counties in Texas, United States. ACS ES&T WATER 2022; 2:2211-2224. [PMID: 37552718 PMCID: PMC9291321 DOI: 10.1021/acsestwater.2c00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 06/02/2023]
Abstract
After its emergence in late November/December 2019, the severe acute respiratory syndrome coronavirus 2 virus (SARS-CoV-2) rapidly spread globally. Recognizing that this virus is shed in feces of individuals and that viral RNA is detectable in wastewater, testing for SARS-CoV-2 in sewage collections systems has allowed for the monitoring of a community's viral burden. Over a 9 month period, the influents of two regional wastewater treatment facilities were concurrently examined for wild-type SARS-CoV-2 along with variants B.1.1.7 and B.1.617.2 incorporated as they emerged. Epidemiological data including new confirmed COVID-19 cases and associated hospitalizations and fatalities were tabulated within each location. RNA from SARS-CoV-2 was detectable in 100% of the wastewater samples, while variant detection was more variable. Quantitative reverse transcription PCR (RT-qPCR) results align with clinical trends for COVID-19 cases, and increases in COVID-19 cases were positively related with increases in SARS-CoV-2 RNA load in wastewater, although the strength of this relationship was location specific. Our observations demonstrate that clinical and wastewater surveillance of SARS-CoV-2 wild type and constantly emerging variants of concern can be combined using RT-qPCR to characterize population infection dynamics. This may provide an early warning for at-risk communities and increases in COVID-19 related hospitalizations.
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Affiliation(s)
- Laura M. Langan
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Megan O’Brien
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Public Health, Baylor
University, One Bear Place #97343, Waco, Texas 76798, United
States
| | - Lea M. Lovin
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Kendall R. Scarlett
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Haley Davis
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Abigail N. Henke
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Biology, Baylor
University, One Bear Place #97388, Waco, Texas 76798, United
States
| | - Sarah E. Seidel
- Center for Health
Statistics, Texas Department of State Health Services, Austin, Texas
78756, United States
| | - Natalie Archer
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - Eric Lawrence
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - R. Sean Norman
- Department of Environmental Health Sciences, Arnold School of
Public Health, University of South Carolina, 921 Assembly
Street Columbia, South Carolina 29208, United States
| | - Heidi K. Bojes
- Environmental Epidemiology and Disease Registries
Section, Texas Department of State Health Services, Austin,
Texas 78756, United States
| | - Bryan W. Brooks
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Public Health, Baylor
University, One Bear Place #97343, Waco, Texas 76798, United
States
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27
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Wartell BA, Proano C, Bakalian L, Kaya D, Croft K, McCreary M, Lichtenstein N, Miske V, Arcellana P, Boyer J, Benschoten IV, Anderson M, Crabb A, Gilson S, Gourley A, Wheeler T, Trest B, Bowman G, Kjellerup BV. Implementing wastewater surveillance for SARS-CoV-2 on a university campus: Lessons learned. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2022; 94:e10807. [PMID: 36372781 PMCID: PMC9827968 DOI: 10.1002/wer.10807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Wastewater surveillance, also known as wastewater-based epidemiology (WBE), has been successfully used to detect SARS-CoV-2 and other viruses in sewage in many locations in the United States and globally. This includes implementation of the surveillance on college and university campuses. A two-phase study was conducted during the 2020-2021 academic year to test the feasibility of a WBE system on campus and to supplement the clinical COVID-19 testing performed for the student, staff, and faculty body. The primary objective during the Fall 2020 semester was to monitor a large portion of the on-campus population and to obtain an understanding of the spreading of the SARS-CoV-2 virus. The Spring 2021 objective was focused on selected residence halls and groups of residents on campus, as this was more efficient and relevant for an effective follow-up response. Logistical problems and planning oversights initially occurred but were corrected with improved communication and experience. Many lessons were learned, including effective mapping, site planning, communication, personnel organization, and equipment management, and obtained along the way, thereby paving an opportune guide for future planning efforts. PRACTITIONER POINTS: WBE was successful in the detection of many SARS-CoV-2 variants incl. Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron. Careful planning and contingencies were essential for a successful implementation of a SARS-CoV-2 monitoring program. A surveillance program may be important for detection and monitoring of other public health relevant targets in wastewater incl. bacteria, viruses, fungi and viruses. Diverse lessons were learned incl. effective mapping, site planning, communication, personnel organization, and equipment management, thereby providing a guide for future planning efforts.
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Affiliation(s)
- Brian A. Wartell
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Camila Proano
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Lena Bakalian
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Devrim Kaya
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Kristen Croft
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Michael McCreary
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Naomi Lichtenstein
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Victoria Miske
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Patricia Arcellana
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Jessica Boyer
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Isabelle Van Benschoten
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Marya Anderson
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Andrea Crabb
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Susan Gilson
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Anthony Gourley
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Tim Wheeler
- Department of Residential FacilitiesUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Brian Trest
- Facilities ManagementUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Glynnis Bowman
- Facilities ManagementUniversity of Maryland College ParkCollege ParkMarylandUSA
| | - Birthe V. Kjellerup
- Department of Civil and Environmental EngineeringUniversity of Maryland College ParkCollege ParkMarylandUSA
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28
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The Detection of Periodic Reemergence Events of SARS-CoV-2 Delta Strain in Communities Dominated by Omicron. Pathogens 2022; 11:pathogens11111249. [PMID: 36365000 PMCID: PMC9697103 DOI: 10.3390/pathogens11111249] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/14/2022] [Accepted: 10/24/2022] [Indexed: 12/01/2022] Open
Abstract
Despite entering an endemic phase, SARS-CoV-2 remains a significant burden to public health across the global community. Wastewater sampling has consistently proven utility to understanding SARS-CoV-2 prevalence trends and genetic variation as it represents a less biased assessment of the corresponding communities. Here, we report that ongoing monitoring of SARS-CoV-2 genetic variation in samples obtained from the wastewatersheds of the city of Louisville in Jefferson county Kentucky has revealed the periodic reemergence of the Delta strain in the presence of the presumed dominant Omicron strain. Unlike previous SARS-CoV-2 waves/emergence events, the Delta reemergence events were geographically restricted in the community and failed to spread into other areas as determined by wastewater analyses. Moreover, the reemergence of the Delta strain did not correlate with vaccination rates as communities with lower relative vaccination have been, to date, not affected. Importantly, Delta reemergence events correlate with increased public health burdens, as indicated by increased daily case rates and mortality relative to non-Delta wastewatershed communities. While the underlying reasons for the reemergence of the Delta variant remain unclear, these data reaffirm the ongoing importance of wastewater genomic analyses towards understanding SARS-CoV-2 as it enters the endemic phase.
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29
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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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30
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Soni V, Paital S, Raizada P, Ahamad T, Khan AAP, Thakur S, Singh P, Hussain CM, Sharma S, Nadda AK. Surveillance of omicron variants through wastewater epidemiology: Latest developments in environmental monitoring of pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:156724. [PMID: 35716753 PMCID: PMC9197784 DOI: 10.1016/j.scitotenv.2022.156724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/09/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
WBE has been a monitoring system that can give purposeful and inclusive real-time assessments of civic society as well as environmental health. This concept review introduces WBE as a surveillance scheme and initial warning outbreaks of contagious diseases caused by harmful SARS-CoV-2 with pandemic potential. Examining biomarkers of contagious diseases as evidence in polluted water taken from wastewater treatment plants suggests that these systems can be examined to get epidemiological data for checking the transmission of infectious B.1.1.529 to different areas. Thereafter, various benefits of surveillance are provided to analyse health information and pinpoint different problems that may be occurring in the workstation. Surveillance is followed by intervention steps that improved the work environment and prevent further progression of the disease. This information will help to improve early detection strategies, designing a prevention strategy to reduce their spread, infection control and therapies, thus, strengthening our global preparedness to fight future epidemics. In the end, a comprehensive discussion on the remaining challenges and opportunities for epidemiology has been given for future research perspectives.
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Affiliation(s)
- Vatika Soni
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India
| | - Shilpa Paital
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India
| | - Pankaj Raizada
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India
| | - Tansir Ahamad
- Department of Chemistry, College of Science, King Saud University, Saudi Arabia.
| | - Aftab Aslam Parwaz Khan
- Center of Excellence for Advanced Materials Research, King Abdulaziz University, P. O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Sourbh Thakur
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland.
| | - Pardeep Singh
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India.
| | - Chaudhery Mustansar Hussain
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA.
| | - Swati Sharma
- University Institute of Biotechnology, Chandigarh University, Chandigarh-Ludhiana Highway, Mohali, Punjab, India
| | - Ashok Kumar Nadda
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173234, Himachal Pradesh, India
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Tsao J, Kussman A, Segovia NA, Abrams GD, Boehm AB, Hwang CE. Prevalence of Positive Rapid Antigen Tests After 7-Day Isolation Following SARS-CoV-2 Infection in College Athletes During Omicron Variant Predominance. JAMA Netw Open 2022; 5:e2237149. [PMID: 36255722 PMCID: PMC9579911 DOI: 10.1001/jamanetworkopen.2022.37149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE The US Centers for Disease Control and Prevention shortened the recommended isolation period for SARS-CoV-2 infection from 10 days to 5 days in December 2021. It is unknown whether an individual with the infection may still have a positive result to a rapid antigen test and potentially be contagious at the end of this shortened isolation period. OBJECTIVE To estimate the proportion of individuals with SARS-CoV-2 infection whose rapid antigen test is still positive starting 7 days postdiagnosis. DESIGN, SETTING, AND PARTICIPANTS This case series analyzed student athletes at a National Collegiate Athletic Association Division I university campus who tested positive for SARS-CoV-2 between January 3 and May 6, 2022. Individuals underwent rapid antigen testing starting 7 days postdiagnosis to determine whether they could end their isolation period. EXPOSURES Rapid antigen testing 7 days after testing positive for SARS-CoV-2. MAIN OUTCOMES AND MEASURES Rapid antigen test results, symptom status, and SARS-CoV-2 variant identification via campus wastewater analysis. RESULTS A total of 264 student athletes (140 [53%] female; mean [SD] age, 20.1 [1.2] years; range, 18-25 years) representing 268 infections (177 [66%] symptomatic, 91 [34%] asymptomatic) were included in the study. Of the 248 infections in individuals who did a day 7 test, 67 (27%; 95% CI, 21%-33%) tests were still positive. Patients with symptomatic infections were significantly more likely to test positive on day 7 vs those who were asymptomatic (35%; 95% CI, 28%-43% vs 11%; 95% CI, 5%-18%; P < .001). Patients with the BA.2 variant were also significantly more likely to test positive on day 7 compared with those with the BA.1 variant (40%; 95% CI, 29%-51% vs 21%; 95% CI, 15%-27%; P = .007). CONCLUSIONS AND RELEVANCE In this case series, rapid antigen tests remained positive in 27% of the individuals after 7 days of isolation, suggesting that the Centers for Disease Control and Prevention-recommended 5-day isolation period may be insufficient in preventing ongoing spread of disease. Further studies are needed to determine whether these findings are present in a more heterogeneous population and in subsequent variants.
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Affiliation(s)
- Jessica Tsao
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, California
| | - Andrea Kussman
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, California
| | - Nicole A. Segovia
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, California
| | - Geoffrey D. Abrams
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, California
| | - Alexandria B. Boehm
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California
| | - Calvin E. Hwang
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, California
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32
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Dhawan M, Saied AA, Mitra S, Alhumaydhi FA, Emran TB, Wilairatana P. Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2? Biomed Pharmacother 2022; 154:113522. [PMID: 36030585 PMCID: PMC9376347 DOI: 10.1016/j.biopha.2022.113522] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/19/2022] Open
Abstract
Since the start of the COVID-19 pandemic, numerous variants of SARS-CoV-2 have been reported worldwide. The advent of variants of concern (VOCs) raises severe concerns amid the serious containment efforts against COVID-19 that include physical measures, pharmacological repurposing, immunization, and genomic/community surveillance. Omicron variant (B.1.1.529) has been identified as a highly modified, contagious, and crucial variant among the five VOCs of SARS-CoV-2. The increased affinity of the spike protein (S-protein), and host receptor, angiotensin converting enzyme-2 (ACE-2), due to a higher number of mutations in the receptor-binding domain (RBD) of the S-protein has been proposed as the primary reason for the decreased efficacy of majorly available vaccines against the Omicron variant and the increased transmissible nature of the Omicron variant. Because of its significant competitive advantage, the Omicron variant and its sublineages swiftly surpassed other variants to become the dominant circulating lineages in a number of nations. The Omicron variant has been identified as a prevalent strain in the United Kingdom and South Africa. Furthermore, the emergence of recombinant variants through the conjunction of the Omicron variant with other variants or by the mixing of the Omicron variant's sublineages/subvariants poses a major threat to humanity. This raises various issues and hazards regarding the Omicron variant and its sublineages, such as an Omicron variant breakout in susceptible populations among fully vaccinated persons. As a result, understanding the features and genetic implications of this variant is crucial. Hence, we explained in depth the evolution and features of the Omicron variant and analyzed the repercussions of spike mutations on infectiousness, dissemination ability, viral entry mechanism, and immune evasion. We also presented a viewpoint on feasible strategies for precluding and counteracting any future catastrophic emergence and spread of the omicron variant and its sublineages that could result in a detrimental wave of COVID-19 cases.
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Affiliation(s)
- Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, Punjab, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
| | - AbdulRahman A Saied
- National Food Safety Authority (NFSA), Aswan Branch, Aswan 81511, Egypt; Ministry of Tourism and Antiquities, Aswan Office, Aswan 81511, Egypt
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh; Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh.
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
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Lee WL, Armas F, Guarneri F, Gu X, Formenti N, Wu F, Chandra F, Parisio G, Chen H, Xiao A, Romeo C, Scali F, Tonni M, Leifels M, Chua FJD, Kwok GW, Tay JY, Pasquali P, Thompson J, Alborali GL, Alm EJ. Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater. WATER RESEARCH 2022; 221:118809. [PMID: 35841797 PMCID: PMC9250349 DOI: 10.1016/j.watres.2022.118809] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/18/2022] [Accepted: 07/01/2022] [Indexed: 05/06/2023]
Abstract
On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for clinical community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect SARS-CoV-2 variants (Alpha and Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets the stretch of mutations from Q493R to Q498R for quantitative detection of the Omicron variant in wastewater. We report their validation against 10-month longitudinal samples from the influent of a wastewater treatment plant in Italy. SARS-CoV-2 RNA concentrations and variant frequencies in wastewater determined using these variant assays agree with clinical cases, revealing rapid displacement of the Delta variant by the Omicron variant within three weeks. These variant trends, when mapped against vaccination rates, support clinical studies that found the rapid emergence of SARS-CoV-2 Omicron variant being associated with an infection advantage over Delta in vaccinated persons. These data reinforce the versatility, utility and accuracy of these open-sourced methods using allele-specific RT-qPCR for tracking the dynamics of variant displacement in communities through wastewater for informed public health responses.
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Affiliation(s)
- Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Flavia Guarneri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Nicoletta Formenti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Fuqing Wu
- Center for Infectious Disease, Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Giovanni Parisio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Department of Biological Engineering, Massachusetts Institute of Technology, USA
| | - Claudia Romeo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Federico Scali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Matteo Tonni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Feng Jun Desmond Chua
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Germaine Wc Kwok
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Joey Yr Tay
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Paolo Pasquali
- Dipartimento di Sicurezza Alimentare, Nutrizione e Sanità Pubblica Veterinaria, Istituto Superiore di Sanità, Italy
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore.
| | - Giovanni Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Department of Biological Engineering, Massachusetts Institute of Technology, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Wu F, Lee WL, Chen H, Gu X, Chandra F, Armas F, Xiao A, Leifels M, Rhode SF, Wuertz S, Thompson J, Alm EJ. Making waves: Wastewater surveillance of SARS-CoV-2 in an endemic future. WATER RESEARCH 2022; 219:118535. [PMID: 35605390 PMCID: PMC9062764 DOI: 10.1016/j.watres.2022.118535] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 05/28/2023]
Abstract
Wastewater-based surveillance (WBS) has been widely used as a public health tool to monitor the emergence and spread of SARS-CoV-2 infections in populations during the COVID-19 pandemic. Coincident with the global vaccination efforts, the world is also enduring new waves of SARS-CoV-2 variants. Reinfections and vaccine breakthroughs suggest an endemic future where SARS-CoV-2 continues to persist in the general population. In this treatise, we aim to explore the future roles of wastewater surveillance. Practically, WBS serves as a relatively affordable and non-invasive tool for mass surveillance of SARS-CoV-2 infection while minimizing privacy concerns, attributes that make it extremely suited for its long-term usage. In an endemic future, the utility of WBS will include 1) monitoring the trend of viral loads of targets in wastewater for quantitative estimate of changes in disease incidence; 2) sampling upstream for pinpointing infections in neighborhoods and at the building level; 3) integrating wastewater and clinical surveillance for cost-efficient population surveillance; and 4) genome sequencing wastewater samples to track circulating and emerging variants in the population. We further discuss the challenges and future developments of WBS to reduce inconsistencies in wastewater data worldwide, improve its epidemiological inference, and advance viral tracking and discovery as a preparation for the next viral pandemic.
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Affiliation(s)
- Fuqing Wu
- Center for Infectious Disease, Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA.
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | | | - Stefan Wuertz
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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35
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Boehm AB, Hughes B, Wolfe MK, White BJ, Duong D, Chan-Herur V. Regional Replacement of SARS-CoV-2 Variant Omicron BA.1 with BA.2 as Observed through Wastewater Surveillance. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2022; 9:575-580. [PMID: 35711323 PMCID: PMC9159514 DOI: 10.1021/acs.estlett.2c00266] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 05/06/2023]
Abstract
Greater knowledge of circulating SARS-CoV-2 variants can inform pandemic response, vaccine development, disease epidemiology, and use of monoclonal antibody treatments. We developed custom assays targeting characteristic mutations in SARS-CoV-2 variants Omicron BA.1 and BA.2 and confirmed their sensitivity and specificity in silico and in vitro. We then applied these assays to daily wastewater solid samples from eight publicly owned treatment works in the greater Bay Area of California, United States, over four months to obtain a spatially and temporally intensive data set. We documented regional replacement of BA.1 with BA.2 in agreement with, and ahead of, clinical sequencing data. This study highlights the utility of wastewater surveillance for real-time tracking of SARS-CoV-2 sublineage circulation. The results suggest that concerted efforts to design RT-PCR assays that target variant and variant sublineage characteristic mutations for wide-scale wastewater monitoring implementation will be informative for pandemic response.
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Affiliation(s)
- Alexandria B. Boehm
- Department
of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, California 94305, United States
- . Phone; 650-724-9128
| | - Bridgette Hughes
- Verily
Life Sciences, South
San Francisco, California 94080, United States
| | - Marlene K. Wolfe
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd., Atlanta, Georgia 30322, United States
| | - Bradley J. White
- Verily
Life Sciences, South
San Francisco, California 94080, United States
| | - Dorothea Duong
- Verily
Life Sciences, South
San Francisco, California 94080, United States
| | - Vikram Chan-Herur
- Verily
Life Sciences, South
San Francisco, California 94080, United States
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36
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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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