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Chaqroun A, El Soufi G, Gerber Z, Loutreul J, Cluzel N, Delafoy D, Sandron F, Di Jorio L, Raffestin S, Maréchal V, Gantzer C, Olaso R, Deleuze JF, Rohr O, Boudaud N, Wallet C, Bertrand I. Definition of a concentration and RNA extraction protocol for optimal whole genome sequencing of SARS-CoV-2 in wastewater (ANRS0160). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:175823. [PMID: 39197764 DOI: 10.1016/j.scitotenv.2024.175823] [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: 06/06/2024] [Revised: 07/26/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
Monitoring the presence of RNA from emerging pathogenic viruses, such as SARS-CoV-2, in wastewater (WW) samples requires suitable methods to ensure an effective response. Genome sequencing of WW is one of the crucial methods, but it requires high-quality RNA in sufficient quantities, especially for monitoring emerging variants. Consequently, methods for viral concentration and RNA extraction from WW samples have to be optimized before sequencing. The purpose of this study was to achieve high coverage (≥ 90 %) and sequencing depth (at least ≥200×) even for low initial RNA concentrations (< 105 genome copies (GC)/L) in WW. A further objective was to determine the range of SARS-CoV-2 RNA concentrations that allow high-quality sequencing, and the optimal sample volume for analysis. Ultrafiltration (UF) methods were used to concentrate viral particles from large influent samples (up to 500 mL). An RNA extraction protocol using silica beads, neutral phenol-chloroform treatment, and a PCR inhibitor removal kit was chosen for its effectiveness in extracting RNA and eliminating PCR inhibitors, as well as its adaptability for use with large influent samples. Recovery rates ranged from 24 % to 63 % (N = 17) for SARS-CoV-2 naturally present in WW samples. 200 mL WW samples can be enough for UF concentration, as they showed high quality sequencing analyses with between 5 × 104 GC/L and 6 × 103 GC/L. Below 6 × 103 GC/L, high-quality sequencing was also achieved for ∼40 % of the samples using 500 mL of WW. Sequencing analysis for variant detection was performed on 200 mL WW samples with coverage of >95 % and sequencing depth of >1000×. Analyses revealed the predominance of variant EG.5, known as Eris (66 %-100 %). The use of UF methods in combination with a suitable RNA extraction protocol appear promising for sequencing enveloped viruses in WW in a context of viral emergence.
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Affiliation(s)
- Ahlam Chaqroun
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France; OBEPINE consortium, Paris, France
| | - Ghina El Soufi
- Université de Strasbourg, UPR CNRS 9002 ARN, F-67300 Schiltigheim, France; Université de Strasbourg, IUT Louis Pasteur, F-67300 Schiltigheim, France; OBEPINE consortium, Paris, France
| | - Zuzana Gerber
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, F-91057 Evry, France
| | - Julie Loutreul
- ACTALIA, F-50000 Saint Lô, France; OBEPINE consortium, Paris, France
| | - Nicolas Cluzel
- Maison des Modélisations Ingénieries et Technologies (SUMMIT), Sorbonne Université, Paris 75005, France; OBEPINE consortium, Paris, France
| | - Damien Delafoy
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, F-91057 Evry, France
| | - Florian Sandron
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, F-91057 Evry, France
| | - Léo Di Jorio
- Université de Strasbourg, UPR CNRS 9002 ARN, F-67300 Schiltigheim, France; Université de Strasbourg, IUT Louis Pasteur, F-67300 Schiltigheim, France; OBEPINE consortium, Paris, France
| | - Stéphanie Raffestin
- Institut Pasteur de la Guyane, French Guiana, Cayenne 97300, France; OBEPINE consortium, Paris, France
| | - Vincent Maréchal
- INSERM, Centre de Recherche Saint-Antoine, Sorbonne Université, Paris 75012, France; OBEPINE consortium, Paris, France
| | - Christophe Gantzer
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France; OBEPINE consortium, Paris, France
| | - Robert Olaso
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, F-91057 Evry, France
| | - Jean-François Deleuze
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, F-91057 Evry, France
| | - Olivier Rohr
- Université de Strasbourg, UPR CNRS 9002 ARN, F-67300 Schiltigheim, France; Université de Strasbourg, IUT Louis Pasteur, F-67300 Schiltigheim, France; OBEPINE consortium, Paris, France
| | - Nicolas Boudaud
- ACTALIA, F-50000 Saint Lô, France; OBEPINE consortium, Paris, France
| | - Clémentine Wallet
- Université de Strasbourg, UPR CNRS 9002 ARN, F-67300 Schiltigheim, France; Université de Strasbourg, IUT Louis Pasteur, F-67300 Schiltigheim, France; OBEPINE consortium, Paris, France
| | - Isabelle Bertrand
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France; OBEPINE consortium, Paris, France.
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Devianto LA, Amarasiri M, Wang L, Iizuka T, Sano D. Identification of protein biomarkers in wastewater linked to the incidence of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175649. [PMID: 39168326 DOI: 10.1016/j.scitotenv.2024.175649] [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: 10/31/2023] [Revised: 07/19/2024] [Accepted: 08/17/2024] [Indexed: 08/23/2024]
Abstract
Wastewater-based epidemiological (WBE) surveillance is a viable disease surveillance technique capable of monitoring the spread of infectious disease agents in sewershed communities. In addition to detecting viral genomes in wastewater, WBE surveillance can identify other endogenous biomarkers that are significantly elevated and excreted in the saliva, urine, and/or stool of infected individuals. Human protein biomarkers allow the realization of real-time WBE surveillance using highly sensitive biosensors. In this study, we analyzed endogenous protein biomarkers present in wastewater influent through liquid chromatography-tandem mass spectrophotometry and scaffold data-independent acquisition to identify candidate target protein biomarkers for WBE surveillance of SARS-CoV-2. We found that out of the 1382 proteins observed in the wastewater samples, 44 were human proteins associated with infectious diseases. These included immune response substances such as immunoglobulins, cytokine-chemokines, and complements, as well as proteins belonging to antimicrobial and antiviral groups. A significant correlation was observed between the intensity of human infectious disease-related protein biomarkers in wastewater and COVID-19 case numbers. Real-time WBE surveillance using biosensors targeting immune response proteins, such as antibodies or immunoglobulins, in wastewater holds promise for expediting the implementation of relevant policies for the effective prevention of infectious diseases in the near future.
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Affiliation(s)
- Luhur Akbar Devianto
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8579, Japan; Department of Environmental Engineering, Faculty of Agriculture Technology, Brawijaya University, Malang 65145, Indonesia
| | - Mohan Amarasiri
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Luyao Wang
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Takehito Iizuka
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Daisuke Sano
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8579, Japan; Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan; Wastewater Information Research Center, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan; New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi 980-8579, Japan.
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3
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Kumar M, Mahapatra DM. First reporting of BA.1* and BA.2* recombinant SARS-CoV-2 lineage XAP from Indian wastewaters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174756. [PMID: 39004359 DOI: 10.1016/j.scitotenv.2024.174756] [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: 05/22/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
Tracking new variants of SARS-CoV-2 is vital for managing COVID-19 spread and allocating resources. Domestic antigen testing has created surveillance gaps that make it hard to identify new viral variants. We conducted whole genome sequencing of wastewater viral genes from major and minor treatment facilities in Dehradun from March 2022 onwards. Based on our analysis, the samples that achieved higher sequencing depth and covered >90 % of the viral genome uncovered a major variant pattern resembling the XAP recombinant lineage that is reported for the first time in the City of Dehradun, Uttrakhand and is the first ever records in India as on date. This novel XAP recombinant lineage had 9, 2, 30, 1, 2, 5, 1, 1, 1 aminoacid changes (total 54 mutations) in Orf1a, Orf1b, S, E, M, N, Orf3a, Orf6 and Orf8 regions of the gene respectively that shares 49 mutations common to the ancestral lineages BA.1* and BA.2*, with 6 unique mutations. Subsequent comparison and analysis of the clinical sequence data from the region post-detection of this rare and unusual variant showed no causalities infected with the newly detected XAP lineage. These findings are indicative of future alarming situation with plausible threats of fresh spur of Omicron variant led infections in the urban community.
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Affiliation(s)
- Manish Kumar
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterrey, Eugenio Garza Sada 2501 Sur, Monterrey 64849, Mexico; School of Advance Engineering, University of Petroleum and Energy Studies, Dehradun, Uttarakhand 248007, India.
| | - Durga Madhab Mahapatra
- School of Advance Engineering, University of Petroleum and Energy Studies, Dehradun, Uttarakhand 248007, India; Department of Biological and Ecological Engineering, School of Engineering, Oregon State University, Corvallis, OR, USA
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Eren AM, Banfield JF. Modern microbiology: Embracing complexity through integration across scales. Cell 2024; 187:5151-5170. [PMID: 39303684 DOI: 10.1016/j.cell.2024.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/14/2024] [Accepted: 08/14/2024] [Indexed: 09/22/2024]
Abstract
Microbes were the only form of life on Earth for most of its history, and they still account for the vast majority of life's diversity. They convert rocks to soil, produce much of the oxygen we breathe, remediate our sewage, and sustain agriculture. Microbes are vital to planetary health as they maintain biogeochemical cycles that produce and consume major greenhouse gases and support large food webs. Modern microbiologists analyze nucleic acids, proteins, and metabolites; leverage sophisticated genetic tools, software, and bioinformatic algorithms; and process and integrate complex and heterogeneous datasets so that microbial systems may be harnessed to address contemporary challenges in health, the environment, and basic science. Here, we consider an inevitably incomplete list of emergent themes in our discipline and highlight those that we recognize as the archetypes of its modern era that aim to address the most pressing problems of the 21st century.
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Affiliation(s)
- A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany; Marine Biological Laboratory, Woods Hole, MA, USA; Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Environmental Science Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
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5
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Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Peacock TP, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. Cell 2024; 187:5468-5482.e11. [PMID: 39303692 DOI: 10.1016/j.cell.2024.08.010] [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: 09/13/2023] [Revised: 05/01/2024] [Accepted: 08/07/2024] [Indexed: 09/22/2024]
Abstract
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.
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Affiliation(s)
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA
| | - Jonathan E Pekar
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, San Diego, CA, USA
| | - Stephen A Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Reema Singh
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, Av. da República, Oeiras, Lisbon 2780-157, Portugal
| | - Karthik Gangavarapu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Matthew B Rogers
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, San Diego, CA, USA
| | - Robert F Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marion P G Koopmans
- Department of Viroscience, and Pandemic and Disaster Preparedness Centre, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Thomas P Peacock
- The Pirbright Institute, Woking GU24 0NF, Surrey, UK; Department of Infectious Disease, Imperial College London, London W2 1P, UK
| | - Saskia Popescu
- University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow G61 1QH, UK
| | - Marc A Suchard
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, San Diego, CA, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA.
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
| | - Florence Débarre
- Institut d'Écologie et des Sciences de l'Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France.
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Merrett JE, Nolan M, Hartman L, John N, Flynn B, Baker L, Schang C, McCarthy D, Lister D, Cheng NN, Crosbie N, Poon R, Jex A. Highly sensitive wastewater surveillance of SARS-CoV-2 variants by targeted next-generation amplicon sequencing provides early warning of incursion in Victoria, Australia. Appl Environ Microbiol 2024; 90:e0149723. [PMID: 39012098 PMCID: PMC11337797 DOI: 10.1128/aem.01497-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 06/06/2024] [Indexed: 07/17/2024] Open
Abstract
The future of the COVID pandemic and its public health and societal impact will be determined by the profile and spread of emerging variants and the timely identification and response to them. Wastewater surveillance of SARS-CoV-2 has been widely adopted in many countries across the globe and has played an important role in tracking infection levels and providing useful epidemiological information that cannot be adequately captured by clinical testing alone. However, novel variants can emerge rapidly, spread globally, and markedly alter the trajectory of the pandemic, as exemplified by the Delta and Omicron variants. Most mutations linked to the emergence of new SARS-CoV-2 variants are found within variable regions of the SARS-CoV-2 Spike protein. We have developed a duplex hemi-nested PCR method that, coupled with short amplicon sequencing, allows simultaneous typing of two of the most highly variable and informative regions of the Spike gene: the N-terminal domain and the receptor binding motif. Using this method in an operationalized public health program, we identified the first known incursion of Omicron BA.1 into Victoria, Australia and demonstrated how sensitive amplicon sequencing methods can be combined with wastewater surveillance as a relatively low-cost solution for early warning of variant incursion and spread.IMPORTANCEThis study offers a rapid, cost-effective, and sensitive approach for monitoring SARS-CoV-2 variants in wastewater. The method's flexibility permits timely modifications, enabling the integration of emerging variants and adaptations to evolving SARS-CoV-2 genetics. Of particular significance for low- and middle-income regions with limited surveillance capabilities, this technique can potentially be utilized to study a range of pathogens or viruses that possess diverse genetic sequences, similar to influenza.
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Affiliation(s)
- James E. Merrett
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Monica Nolan
- Victorian Department of Health, Melbourne, Victoria, Australia
| | - Leon Hartman
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Nijoy John
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Brianna Flynn
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Louise Baker
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Christelle Schang
- Environmental and Public Health Microbiology Lab, Monash University, Clayton, Victoria, Australia
| | - David McCarthy
- Environmental and Public Health Microbiology Lab, Monash University, Clayton, Victoria, Australia
- School of Civil and Environmental Engineering, Queensland University of Technology, Brisbane, Queensland, Australia
| | - David Lister
- Victorian Department of Health, Melbourne, Victoria, Australia
| | - Ngai Ning Cheng
- Victorian Department of Health, Melbourne, Victoria, Australia
- South Australian Water Corporation, Adelaide, South Australia, Australia
| | - Nick Crosbie
- Melbourne Water Corporation, Docklands, Victoria, Australia
| | - Rachael Poon
- Victorian Department of Health, Melbourne, Victoria, Australia
| | - Aaron Jex
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
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Tang L, Guo Z, Lu X, Zhao J, Li Y, Yang K. Wastewater multiplex PCR amplicon sequencing revealed community transmission of SARS-CoV-2 lineages during the outbreak of infection in Chinese Mainland. Heliyon 2024; 10:e35332. [PMID: 39166043 PMCID: PMC11334792 DOI: 10.1016/j.heliyon.2024.e35332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/22/2024] Open
Abstract
During the COVID-19, wastewater-based epidemiology (WBE) has become a powerful epidemic surveillance tool widely used worldwide. However, the development and application of this technology in Chinese Mainland are relatively lagging. Herein, we for the first time monitored the community circulation of SARS-CoV-2 lineages using WBE methods in Chinese Mainland. During the peak period of infection outbreak at the end of 2022, six precious sewage samples were collected from the manhole in the student dormitory area on Wangjiang Campus of Sichuan University. RT-qPCR revealed that the six sewage samples were all positive for SARS-CoV-2 RNA. Multiplex PCR amplicon sequencing of the sewage samples reflected the local transmission of SARS-CoV-2 variants. The results of two deconvolution methods indicate that the main virus lineages have clear evolutionary genetic correlations. Furthermore, the sampling time is consistent with the timeline of concern for these virus lineages, as well as the timeline of uploading the nucleic acid sequences from the corresponding lineages in Sichuan to the database. These results demonstrate the reliability of the sewage sequencing results. Multiplex PCR amplicon sequencing is by far the most powerful analytical tool of WBE, enabling quantitative detection of virus lineages transmission and evolution at the community level.
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Affiliation(s)
| | | | - Xiaoyi Lu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Junqiao Zhao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Yonghong Li
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
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Singh S, Ahmed AI, Almansoori S, Alameri S, Adlan A, Odivilas G, Chattaway MA, Salem SB, Brudecki G, Elamin W. A narrative review of wastewater surveillance: pathogens of concern, applications, detection methods, and challenges. Front Public Health 2024; 12:1445961. [PMID: 39139672 PMCID: PMC11319304 DOI: 10.3389/fpubh.2024.1445961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024] Open
Abstract
Introduction The emergence and resurgence of pathogens have led to significant global health challenges. Wastewater surveillance has historically been used to track water-borne or fecal-orally transmitted pathogens, providing a sensitive means of monitoring pathogens within a community. This technique offers a comprehensive, real-time, and cost-effective approach to disease surveillance, especially for diseases that are difficult to monitor through individual clinical screenings. Methods This narrative review examines the current state of knowledge on wastewater surveillance, emphasizing important findings and techniques used to detect potential pathogens from wastewater. It includes a review of literature on the detection methods, the pathogens of concern, and the challenges faced in the surveillance process. Results Wastewater surveillance has proven to be a powerful tool for early warning and timely intervention of infectious diseases. It can detect pathogens shed by asymptomatic and pre-symptomatic individuals, providing an accurate population-level view of disease transmission. The review highlights the applications of wastewater surveillance in tracking key pathogens of concern, such as gastrointestinal pathogens, respiratory pathogens, and viruses like SARS-CoV-2. Discussion The review discusses the benefits of wastewater surveillance in public health, particularly its role in enhancing existing systems for infectious disease surveillance. It also addresses the challenges faced, such as the need for improved detection methods and the management of antimicrobial resistance. The potential for wastewater surveillance to inform public health mitigation strategies and outbreak response protocols is emphasized. Conclusion Wastewater surveillance is a valuable tool in the fight against infectious diseases. It offers a unique perspective on the spread and evolution of pathogens, aiding in the prevention and control of disease epidemics. This review underscores the importance of continued research and development in this field to overcome current challenges and maximize the potential of wastewater surveillance in public health.
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Affiliation(s)
- Surabhi Singh
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Amina Ismail Ahmed
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Sumayya Almansoori
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Shaikha Alameri
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Ashraf Adlan
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Giovanni Odivilas
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Marie Anne Chattaway
- United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Laboratory, London, United Kingdom
| | - Samara Bin Salem
- Central Testing Laboratory, Abu Dhabi Quality and Conformity Council, Abu Dhabi, United Arab Emirates
| | - Grzegorz Brudecki
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
| | - Wael Elamin
- Microbiology Lab, Reference and Surveillance Intelligence Department, Abu Dhabi, United Arab Emirates
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9
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Liang R, Liu K, Li Y, Zhang X, Duan L, Huang M, Sun L, Yuan F, Zhao J, Zhao Y, Zhang G. Adaptive truncation of the S gene in IBV during chicken embryo passaging plays a crucial role in its attenuation. PLoS Pathog 2024; 20:e1012415. [PMID: 39078847 PMCID: PMC11315334 DOI: 10.1371/journal.ppat.1012415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 08/09/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Like all coronaviruses, infectious bronchitis virus, the causative agent of infectious bronchitis in chickens, exhibits a high mutation rate. Adaptive mutations that arise during the production of live attenuated vaccines against IBV often decrease virulence. The specific impact of these mutations on viral pathogenicity, however, has not been fully elucidated. In this study, we identified a mutation at the 3' end of the S gene in an IBV strain that was serially passaged in chicken embryos, and showed that this mutation resulted in a 9-aa truncation of the cytoplasmic tail (CT) of the S protein. This phenomenon of CT truncation has previously been observed in the production of attenuated vaccines against other coronaviruses such as the porcine epidemic diarrhea virus. We next discovered that the 9-aa truncation in the S protein CT resulted in the loss of the endoplasmic-reticulum-retention signal (KKSV). Rescue experiments with recombinant viruses confirmed that the deletion of the KKSV motif impaired the localization of the S protein to the endoplasmic-reticulum-Golgi intermediate compartment (ERGIC) and increased its expression on the cell surface. This significantly reduced the incorporation of the S protein into viral particles, impaired early subgenomic RNA and protein synthesis, and ultimately reduced viral invasion efficiency in CEK cells. In vivo experiments in chickens confirmed the reduced pathogenicity of the mutant IBV strains. Additionally, we showed that the adaptive mutation altered the TRS-B of ORF3 and impacted the transcriptional regulation of this gene. Our findings underscore the significance of this adaptive mutation in the attenuation of IBV infection and provide a novel strategy for the development of live attenuated IBV vaccines.
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Affiliation(s)
- Rong Liang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kangchengyin Liu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yingfei Li
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xuehui Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Linqing Duan
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Min Huang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lu Sun
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Fang Yuan
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jing Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ye Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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10
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Morecchiato F, Coppi M, Niccolai C, Antonelli A, Di Gloria L, Calà P, Mancuso F, Ramazzotti M, Lotti T, Lubello C, Rossolini GM. Evaluation of different molecular systems for detection and quantification of SARS-CoV-2 RNA from wastewater samples. J Virol Methods 2024; 328:114956. [PMID: 38796134 DOI: 10.1016/j.jviromet.2024.114956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
Wastewater-based epidemiology has proved to be a suitable approach for tracking the spread of epidemic agents including SARS-CoV-2 RNA. Different protocols have been developed for quantitative detection of SARS-CoV-2 RNA from wastewater samples, but little is known on their performance. In this study we compared three protocols based on Reverse Transcription Real Time-PCR (RT-PCR) and one based on Droplet Digital PCR (ddPCR) for SARS-CoV-2 RNA detection from 35 wastewater samples. Overall, SARS-CoV-2 RNA was detected by at least one method in 85.7 % of samples, while 51.4 %, 22.8 % and 8.6 % resulted positive with two, three or all four methods, respectively. Protocols based on commercial RT-PCR assays and on Droplet Digital PCR showed an overall higher sensitivity vs. an in-house assay. The use of more than one system, targeting different genes, could be helpful to increase detection sensitivity.
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Affiliation(s)
- Fabio Morecchiato
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Claudia Niccolai
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Leandro Di Gloria
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50, Firenze (FI) 50134, Italy
| | - Piergiuseppe Calà
- Tuscany Region, Department of Prevention Local Health Authority Tuscany Center, Via S. Salvi, 12, Firenze (FI) 50135, Italy
| | - Fabrizio Mancuso
- Ingegnerie Toscane - Area R&D, Via Bellatalla, 1, Pisa (PI) 56121, Italy
| | - Matteo Ramazzotti
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50, Firenze (FI) 50134, Italy
| | - Tommaso Lotti
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3, Firenze (FI) 50139, Italy
| | - Claudio Lubello
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3, Firenze (FI) 50139, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy.
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11
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Timme RE, Woods J, Jones JL, Calci KR, Rodriguez R, Barnes C, Leard E, Craven M, Chen H, Boerner C, Grim C, Windsor AM, Ramachandran P, Muruvanda T, Rand H, Tesfaldet B, Amirzadegan J, Kayikcioglu T, Walsky T, Allard M, Balkey M, Bias CH, Brown E, Judy K, Pfefer T, Tallent SM, Hoffmann M, Pettengill J. SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA's GenomeTrakr network. mSystems 2024; 9:e0141523. [PMID: 38819130 PMCID: PMC11326115 DOI: 10.1128/msystems.01415-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/05/2024] [Indexed: 06/01/2024] Open
Abstract
Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA's genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject, PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA's GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA. IMPORTANCE This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA's laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.
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Affiliation(s)
- Ruth E Timme
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Jacquelina Woods
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Jessica L Jones
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Kevin R Calci
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Rachel Rodriguez
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Candace Barnes
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Elizabeth Leard
- Gulf Coast Seafood Laboratory, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Dauphin Island, Alabama, USA
| | - Mark Craven
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, USA
| | - Haifeng Chen
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, USA
| | - Cameron Boerner
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, USA
| | - Christopher Grim
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Amanda M Windsor
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Padmini Ramachandran
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Tim Muruvanda
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Hugh Rand
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Bereket Tesfaldet
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Jasmine Amirzadegan
- Oak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, Tennessee, USA
| | - Tunc Kayikcioglu
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, USA
| | - Tamara Walsky
- Oak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, Tennessee, USA
| | - Marc Allard
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Maria Balkey
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - C Hope Bias
- Oak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, Tennessee, USA
| | - Eric Brown
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Kathryn Judy
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Tina Pfefer
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Sandra M Tallent
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Maria Hoffmann
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - James Pettengill
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
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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. 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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13
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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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14
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Girón-Guzmán I, Cuevas-Ferrando E, Barranquero R, Díaz-Reolid A, Puchades-Colera P, Falcó I, Pérez-Cataluña A, Sánchez G. Urban wastewater-based epidemiology for multi-viral pathogen surveillance in the Valencian region, Spain. WATER RESEARCH 2024; 255:121463. [PMID: 38537489 DOI: 10.1016/j.watres.2024.121463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 04/24/2024]
Abstract
Wastewater-based epidemiology (WBE) has lately arised as a promising tool for monitoring and tracking viral pathogens in communities. In this study, we analysed WBE's role as a multi-pathogen surveillance strategy to detect the presence of several viral illness causative agents. Thus, an epidemiological study was conducted from October 2021 to February 2023 to estimate the weekly levels of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Respiratory Syncytial virus (RSV), and Influenza A virus (IAV) in influent wastewater samples (n = 69). In parallel, a one-year study (October 2021 to October 2022) was performed to assess the presence of pathogenic human enteric viruses. Besides, monitoring of proposed viral fecal contamination indicators crAssphage and Pepper mild mottle virus (PMMoV) was also assessed, along with plaque counting of somatic coliphages. Genetic material of rotavirus (RV), human astrovirus (HAStV), and norovirus genogroup I (GI) and GII was found in almost all samples, while hepatitis A and E viruses (HAV and HEV) only tested positive in 3.77 % and 22.64 % of the samples, respectively. No seasonal patterns were overall found for enteric viruses, although RVs had a peak prevalence in the winter months. All samples tested positive for SARS-CoV-2 RNA, with a mean concentration of 5.43 log genome copies per liter (log GC/L). The tracking of the circulating SARS-CoV-2 variants of concern (VOCs) was performed by both duplex RT-qPCR and next generation sequencing (NGS). Both techniques reliably showed how the dominant VOC transitioned from Delta to Omicron during two weeks in Spain in December 2021. RSV and IAV viruses peaked in winter months with mean concentrations 6.40 and 4.10 log GC/L, respectively. Moreover, the three selected respiratory viruses strongly correlated with reported clinical data when normalised by wastewater physico-chemical parameters and presented weaker correlations when normalising sewage concentration levels with crAssphage or somatic coliphages titers. Finally, predictive models were generated for each respiratory virus, confirming high reliability on WBE data as an early-warning system and communities illness monitoring system. Overall, this study presents WBE as an optimal tool for multi-pathogen tracking reflecting viral circulation and diseases trends within a selected area, its value as a multi-pathogen early-warning tool stands out due to its public health interest.
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Affiliation(s)
- Inés Girón-Guzmán
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Enric Cuevas-Ferrando
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain.
| | - Regino Barranquero
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Azahara Díaz-Reolid
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Pablo Puchades-Colera
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Irene Falcó
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain; Department of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Alba Pérez-Cataluña
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Gloria Sánchez
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain.
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15
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Jiang M, Wang ALW, Be NA, Mulakken N, Nelson KL, Kantor RS. Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8239-8250. [PMID: 38690747 PMCID: PMC11097627 DOI: 10.1021/acs.est.4c00580] [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: 01/16/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024]
Abstract
Sequencing human viruses in wastewater is challenging due to their low abundance compared to the total microbial background. This study compared the impact of four virus concentration/extraction methods (Innovaprep, Nanotrap, Promega, and Solids extraction) on probe-capture enrichment for human viruses followed by sequencing. Different concentration/extraction methods yielded distinct virus profiles. Innovaprep ultrafiltration (following solids removal) had the highest sequencing sensitivity and richness, resulting in the successful assembly of several near-complete human virus genomes. However, it was less sensitive in detecting SARS-CoV-2 by digital polymerase chain reaction (dPCR) compared to Promega and Nanotrap. Across all preparation methods, astroviruses and polyomaviruses were the most highly abundant human viruses, and SARS-CoV-2 was rare. These findings suggest that sequencing success can be increased using methods that reduce nontarget nucleic acids in the extract, though the absolute concentration of total extracted nucleic acid, as indicated by Qubit, and targeted viruses, as indicated by dPCR, may not be directly related to targeted sequencing performance. Further, using broadly targeted sequencing panels may capture viral diversity but risks losing signals for specific low-abundance viruses. Overall, this study highlights the importance of aligning wet lab and bioinformatic methods with specific goals when employing probe-capture enrichment for human virus sequencing from wastewater.
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Affiliation(s)
- Minxi Jiang
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Audrey L. W. Wang
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Nicholas A. Be
- Physical
and Life Sciences Directorate, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Nisha Mulakken
- Computing
and Global Security Directorates, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Rose S. Kantor
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
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16
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Kantor RS, Jiang M. Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8161-8168. [PMID: 38691513 PMCID: PMC11097388 DOI: 10.1021/acs.est.4c02638] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Until recently, wastewater-based monitoring for pathogens of public health concern primarily used PCR-based quantification methods and targeted sequencing for specific pathogens (e.g., SARS-CoV-2). In the past three years, researchers have expanded sequencing to monitor a broad range of pathogens, applying probe capture enrichment to wastewater. The goals of those studies included (1) monitoring and expanding fundamental knowledge of disease dynamics for known pathogens and (2) evaluating the potential for early detection of emerging diseases resulting from zoonotic spillover or novel viral variants. Several studies using off-the-shelf probe panels designed for clinical and environmental surveillance reported that enrichment increased virus relative abundance but did not recover complete genomes for most nonenteric viruses. Based on our experience and recent results reported by others using these panels for wastewater, clinical, and synthetic samples, we discuss challenges and technical factors that affect the rates of false positive and false negative results. We identify trade-offs and opportunities throughout the workflow, including in wastewater sample processing, probe panel design, and bioinformatic analysis. We suggest tailored methods of virus concentration and background removal, carefully designed probe panels, and multithresholded bioinformatics analysis.
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Affiliation(s)
- Rose S. Kantor
- Department of Civil and Environmental
Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Minxi Jiang
- Department of Civil and Environmental
Engineering, University of California, Berkeley, Berkeley, California 94720, United States
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17
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Folkes M, Castro-Gutierrez V, Lundy L, Bajón-Fernández Y, Soares A, Jeffrey P, Hassard F. Campus source to sink wastewater surveillance of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100240. [PMID: 38774836 PMCID: PMC11106825 DOI: 10.1016/j.crmicr.2024.100240] [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] [Indexed: 05/24/2024] Open
Abstract
Wastewater-based surveillance (WBS) offers an aggregate, and cost-effective approach for tracking infectious disease outbreak prevalence within communities, that provides data on community health complementary to individual clinical testing. This study reports on a 16-month WBS initiative on a university campus in England, UK, assessing the presence of SARS-CoV-2 in sewers from large buildings, downstream sewer locations, raw wastewater, partially treated and treated effluents. Key findings include the detection of the Alpha (B.1.1.7) variant in wastewater, with 70 % of confirmed campus cases correlating with positive wastewater samples. Notably, ammonium nitrogen (NH4-N) levels showed a positive correlation (ρ = 0.543, p < 0.01) with virus levels at the large building scale, a relationship not observed at the sewer or wastewater treatment works (WWTW) levels due to dilution. The WWTW was compliant to wastewater standards, but the secondary treatment processes were not efficient for virus removal as SARS-CoV-2 was consistently detected in treated discharges. Tools developed through WBS can also be used to enhance traditional environmental monitoring of aquatic systems. This study provides a detailed source-to-sink evaluation, emphasizing the critical need for the widespread application and improvement of WBS. It showcases WBS utility and reinforces the ongoing challenges posed by viruses to receiving water quality.
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Affiliation(s)
- M. Folkes
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - V.M. Castro-Gutierrez
- Center for Research on Environmental Pollution (CICA), Universidad de Costa Rica, Montes de Oca, 11501, Costa Rica
| | - L. Lundy
- Department of Natural Sciences, Middlesex University, NW4 4BT, UK
| | - Y. Bajón-Fernández
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - A. Soares
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - P. Jeffrey
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - F. Hassard
- Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
- Institute for Nanotechnology and Water Sustainability, College of Science, Engineering and Technology, University of South Africa, Johannesburg, South Africa
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18
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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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19
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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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20
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Vigil K, D'Souza N, Bazner J, Cedraz FMA, Fisch S, Rose JB, Aw TG. Long-term monitoring of SARS-CoV-2 variants in wastewater using a coordinated workflow of droplet digital PCR and nanopore sequencing. WATER RESEARCH 2024; 254:121338. [PMID: 38430753 DOI: 10.1016/j.watres.2024.121338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/12/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024]
Abstract
Quantitative polymerase chain reaction (PCR) and genome sequencing are important methods for wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The reverse transcription-droplet digital PCR (RT-ddPCR) is a highly sensitive method for quantifying SARS-CoV-2 RNA in wastewater samples to track the trends of viral activity levels but cannot identify new variants. It also takes time to develop new PCR-based assays targeting variants of interest. Whole genome sequencing (WGS) can be used to monitor known and new SARS-CoV-2 variants, but it is generally not quantitative. Several short-read sequencing techniques can be expensive and might experience delayed turnaround times when outsourced due to inadequate in-house resources. Recently, a portable nanopore sequencing system offers an affordable and real-time method for sequencing SARS-CoV-2 variants in wastewater. This technology has the potential to enable swift response to disease outbreaks without relying on clinical sequencing results. In addressing concerns related to rapid turnaround time and accurate variant analysis, both RT-ddPCR and nanopore sequencing methods were employed to monitor the emergence of SARS-CoV-2 variants in wastewater. This surveillance was conducted at 23 sewer maintenance hole sites and five wastewater treatment plants in Michigan from 2020 to 2022. In 2020, the wastewater samples were dominated by the parental variants (20A, 20C and 20 G), followed by 20I (Alpha, B.1.1.7) in early 2021 and the Delta variant of concern (VOC) in late 2021. For the year 2022, Omicron variants dominated. Nanopore sequencing has the potential to validate suspected variant cases that were initially undetermined by RT-ddPCR assays. The concordance rate between nanopore sequencing and RT-ddPCR assays in identifying SARS-CoV-2 variants to the clade-level was 76.9%. Notably, instances of disagreement between the two methods were most prominent in the identification of the parental and Omicron variants. We also showed that sequencing wastewater samples with SARS-CoV-2 N gene concentrations of >104 GC/100 ml as measured by RT-ddPCR improve genome recovery and coverage depth using MinION device. RT-ddPCR was better at detecting key spike protein mutations A67V, del69-70, K417N, L452R, N501Y, N679K, and R408S (p-value <0.05) as compared to nanopore sequencing. It is suggested that RT-ddPCR and nanopore sequencing should be coordinated in wastewater surveillance where RT-ddPCR can be used as a preliminary quantification method and nanopore sequencing as the confirmatory method for the detection of variants or identification of new variants. The RT-ddPCR and nanopore sequencing methods reported here can be adopted as a reliable in-house analysis of SARS-CoV-2 in wastewater for rapid community level surveillance and public health response.
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Affiliation(s)
- Katie Vigil
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States
| | - Julia Bazner
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States
| | - Fernanda Mac-Allister Cedraz
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States
| | - Samuel Fisch
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States.
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21
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Gaston JM, Alm EJ, Zhang AN. Fast and accurate variant identification tool for sequencing-based studies. BMC Biol 2024; 22:90. [PMID: 38644496 PMCID: PMC11034086 DOI: 10.1186/s12915-024-01891-4] [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: 11/03/2023] [Accepted: 04/17/2024] [Indexed: 04/23/2024] Open
Abstract
BACKGROUND Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, and disease diagnosis. Genetic studies into microbiomes often require processing numerous sequencing datasets, necessitating variant identifiers with high speed, accuracy, and robustness. RESULTS We present QuickVariants, a bioinformatics tool that effectively summarizes variant information from read alignments and identifies variants. When tested on diverse bacterial sequencing data, QuickVariants demonstrates a ninefold higher median speed than bcftools, a widely used variant identifier, with higher accuracy in identifying both point mutations and indels. This accuracy extends to variant identification in virus samples, including SARS-CoV-2, particularly with significantly fewer false negative indels than bcftools. The high accuracy of QuickVariants is further demonstrated by its detection of a greater number of Omicron-specific indels (5 versus 0) and point mutations (61 versus 48-54) than bcftools in sewage metagenomes predominated by Omicron variants. Much of the reduced accuracy of bcftools was attributable to its misinterpretation of indels, often producing false negative indels and false positive point mutations at the same locations. CONCLUSIONS We introduce QuickVariants, a fast, accurate, and robust bioinformatics tool designed for identifying genetic variants for microbial studies. QuickVariants is available at https://github.com/caozhichongchong/QuickVariants .
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Affiliation(s)
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, USA
| | - An-Ni Zhang
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, USA.
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22
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Reis AC, Pinto D, Monteiro S, Santos R, Martins JV, Sousa A, Páscoa R, Lourinho R, Cunha MV. Systematic SARS-CoV-2 S-gene sequencing in wastewater samples enables early lineage detection and uncovers rare mutations in Portugal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:170961. [PMID: 38367735 DOI: 10.1016/j.scitotenv.2024.170961] [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: 10/29/2023] [Revised: 12/23/2023] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
As the COVID-19 pandemic reached its peak, many countries implemented genomic surveillance systems to track the evolution and transmission of SARS-CoV-2. Transition from the pandemic to the endemic phase prioritized alternative testing strategies to maintain effective epidemic surveillance at the population level, with less intensive sequencing efforts. One such promising approach was Wastewater-Based Surveillance (WBS), which offers non-invasive, cost-effective means for analysing virus trends at the sewershed level. From 2020 onwards, wastewater has been recognized as an instrumental source of information for public health, with national and international authorities exploring options to implement national wastewater surveillance systems and increasingly relying on WBS as early warning of potential pathogen outbreaks. In Portugal, several pioneer projects joined the academia, water utilities and Public Administration around WBS. To validate WBS as an effective genomic surveillance strategy, it is crucial to collect long term performance data. In this work, we present one year of systematic SARS-CoV-2 wastewater surveillance in Portugal, representing 35 % of the mainland population. We employed two complementary methods for lineage determination - allelic discrimination by RT-PCR and S-gene sequencing. This combination allowed us to monitor variant evolution in near-real-time and identify low-frequency mutations. Over the course of this year-long study, spanning from May 2022 to April 2023, we successfully tracked the dominant Omicron sub-lineages, their progression and evolution, which aligned with concurrent clinical surveillance data. Our results underscore the effectiveness of WBS as a tracking system for virus variants, with the ability to unveil mutations undetected via massive sequencing of clinical samples from Portugal, demonstrating the ability of WBS to uncover new mutations and detect rare genetic variants. Our findings emphasize that knowledge of the genetic diversity of SARS-CoV-2 at the population level can be extended far beyond via the combination of routine clinical genomic surveillance with wastewater sequencing and genotyping.
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Affiliation(s)
- Ana C Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Daniela Pinto
- Centre for Ecology, Evolution and Environmental Changes (cE3c), CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Sílvia Monteiro
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; CERIS - Civil Engineering Research and Innovation for Sustainability, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; DECN - Department of Nuclear Sciences and Engineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Ricardo Santos
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; CERIS - Civil Engineering Research and Innovation for Sustainability, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; DECN - Department of Nuclear Sciences and Engineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | | | | | | | | | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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23
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Lipponen A, Kolehmainen A, Oikarinen S, Hokajärvi AM, Lehto KM, Heikinheimo A, Halkilahti J, Juutinen A, Luomala O, Smura T, Liitsola K, Blomqvist S, Savolainen-Kopra C, Pitkänen T. Detection of SARS-COV-2 variants and their proportions in wastewater samples using next-generation sequencing in Finland. Sci Rep 2024; 14:7751. [PMID: 38565591 PMCID: PMC10987589 DOI: 10.1038/s41598-024-58113-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants may have different characteristics, e.g., in transmission, mortality, and the effectiveness of vaccines, indicating the importance of variant detection at the population level. Wastewater-based surveillance of SARS-CoV-2 RNA fragments has been shown to be an effective way to monitor the COVID-19 pandemic at the population level. Wastewater is a complex sample matrix affected by environmental factors and PCR inhibitors, causing insufficient coverage in sequencing, for example. Subsequently, results where part of the genome does not have sufficient coverage are not uncommon. To identify variants and their proportions in wastewater over time, we utilized next-generation sequencing with the ARTIC Network's primer set and bioinformatics pipeline to evaluate the presence of variants in partial genome data. Based on the wastewater data from November 2021 to February 2022, the Delta variant was dominant until mid-December in Helsinki, Finland's capital, and thereafter in late December 2022 Omicron became the most common variant. At the same time, the Omicron variant of SARS-CoV-2 outcompeted the previous Delta variant in Finland in new COVID-19 cases. The SARS-CoV-2 variant findings from wastewater are in agreement with the variant information obtained from the patient samples when visually comparing trends in the sewerage network area. This indicates that the sequencing of wastewater is an effective way to monitor temporal and spatial trends of SARS-CoV-2 variants at the population level.
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Affiliation(s)
- Anssi Lipponen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland.
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.
| | - Aleksi Kolehmainen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anna-Maria Hokajärvi
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Microbiology Unit, Laboratory and Research Division, Finnish Food Authority, Helsinki, Finland
| | - Jani Halkilahti
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aapo Juutinen
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Oskari Luomala
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kirsi Liitsola
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Soile Blomqvist
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Carita Savolainen-Kopra
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Tarja Pitkänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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24
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Parkins MD, Lee BE, Acosta N, Bautista M, Hubert CRJ, Hrudey SE, Frankowski K, Pang XL. Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond. Clin Microbiol Rev 2024; 37:e0010322. [PMID: 38095438 PMCID: PMC10938902 DOI: 10.1128/cmr.00103-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024] Open
Abstract
Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.
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Affiliation(s)
- Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O’Brien Institute of Public Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole Acosta
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maria Bautista
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Provincial Health Laboratory, Alberta Health Services, Calgary, Alberta, Canada
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25
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Dostálková A, Zdeňková K, Bartáčková J, Čermáková E, Kapisheva M, Lopez Marin MA, Kouba V, Sýkora P, Chmel M, Bartoš O, Dresler J, Demnerová K, Rumlová M, Bartáček J. Prevalence of SARS-CoV-2 variants in Prague wastewater determined by nanopore-based sequencing. CHEMOSPHERE 2024; 351:141162. [PMID: 38218235 DOI: 10.1016/j.chemosphere.2024.141162] [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: 06/30/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
The early detection of upcoming disease outbreaks is essential to avoid both health and economic damage. The last four years of COVID-19 pandemic have proven wastewater-based epidemiology is a reliable system for monitoring the spread of SARS-CoV-2, a causative agent of COVID-19, in an urban population. As this monitoring enables the identification of the prevalence of spreading variants of SARS-CoV-2, it could provide a critical tool in the fight against this viral disease. In this study, we evaluated the presence of variants and subvariants of SARS-CoV-2 in Prague wastewater using nanopore-based sequencing. During August 2021, the data clearly showed that the number of identified SARS-CoV-2 RNA copies increased in the wastewater earlier than in clinical samples indicating the upcoming wave of the Delta variant. New SARS-CoV-2 variants consistently prevailed in wastewater samples around a month after they already prevailed in clinical samples. We also analyzed wastewater samples from smaller sub-sewersheds of Prague and detected significant differences in SARS-CoV-2 lineage progression dynamics among individual localities studied, e.g., suggesting faster prevalence of new variants among the sites with highest population density and mobility.
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Affiliation(s)
- Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology Prague, Czech Republic; National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Kamila Zdeňková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic.
| | - Jana Bartáčková
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
| | - Eliška Čermáková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Marina Kapisheva
- National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Marco A Lopez Marin
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Vojtěch Kouba
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
| | - Petr Sýkora
- PVK a.s., Prague Water Supply and Sewerage Company, Czech Republic
| | - Martin Chmel
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic; Military Health Institute, Military Medical Agency, Czech Republic
| | - Oldřich Bartoš
- Military Health Institute, Military Medical Agency, Czech Republic
| | - Jiří Dresler
- Military Health Institute, Military Medical Agency, Czech Republic
| | - Kateřina Demnerová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology Prague, Czech Republic; National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Jan Bartáček
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
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26
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Tavera Gonzales A, Bazalar Gonzales J, Silvestre Espejo T, Leiva Galarza M, Rodríguez Cueva C, Carhuaricra Huamán D, Luna Espinoza L, Maturrano Hernández A. Possible Spreading of SARS-CoV-2 from Humans to Captive Non-Human Primates in the Peruvian Amazon. Animals (Basel) 2024; 14:732. [PMID: 38473117 DOI: 10.3390/ani14050732] [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: 12/10/2023] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 03/14/2024] Open
Abstract
Human-to-animal transmission events of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) have been reported in both domestic and wild species worldwide. Despite the high rates of contagion and mortality during the COVID-19 (Coronavirus Diseases 2019) pandemic in Peru, no instances of natural virus infection have been documented in wild animals, particularly in the Amazonian regions where human-wildlife interactions are prevalent. In this study, we conducted a surveillance investigation using viral RNA sequencing of fecal samples collected from 76 captive and semi-captive non-human primates (NHPs) in the Loreto, Ucayali, and Madre de Dios regions between August 2022 and February 2023. We detected a segment of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 by metagenomic sequencing in a pooled fecal sample from captive white-fronted capuchins (Cebus unicolor) at a rescue center in Bello Horizonte, Ucayali. Phylogenetic analysis further confirmed that the retrieved partial sequence of the RdRp gene matched the SARS-CoV-2 genome. This study represents the first documented instance of molecular SARS-CoV-2 detection in NHPs in the Peruvian Amazon, underscoring the adverse impact of anthropic activities on the human-NHP interface and emphasizing the importance of ongoing surveillance for early detection and prediction of future emergence of new SARS-CoV-2 variants in animals.
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Affiliation(s)
- Andrea Tavera Gonzales
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Jhonathan Bazalar Gonzales
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
- Asociación Equipo Primatológico del Perú, Iquitos 16008, Peru
| | - Thalía Silvestre Espejo
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Milagros Leiva Galarza
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Carmen Rodríguez Cueva
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Dennis Carhuaricra Huamán
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
- Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão 1010, São Paulo 05508-090, Brazil
| | - Luis Luna Espinoza
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Abelardo Maturrano Hernández
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
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27
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Van Dusen J, LeBlanc H, Nastasi N, Panescu J, Shamblin A, Smith JW, Sovic MG, Williams A, Quam MBM, Faith S, Dannemiller KC. Identification of SARS-CoV-2 variants in indoor dust. PLoS One 2024; 19:e0297172. [PMID: 38335205 PMCID: PMC10857703 DOI: 10.1371/journal.pone.0297172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/30/2023] [Indexed: 02/12/2024] Open
Abstract
Environmental surveillance of pathogens underlying infectious disease is critical to ensure public health. Recent efforts to track SARS-CoV-2 have utilized wastewater sampling to infer community trends in viral abundance and variant composition. Indoor dust has also been used for building-level inferences, though to date no sequencing data providing variant-scale resolution have been reported from dust samples, and strategies to monitor circulating variants in dust are needed to help inform public health decisions. In this study, we demonstrate that SARS-CoV-2 lineages can be detected and sequenced from indoor bulk dust samples. We collected 93 vacuum bags from April 2021 to March 2022 from buildings on The Ohio State University's (OSU) Columbus campus, and the dust was used to develop and apply an amplicon-based whole-genome sequencing protocol to identify the variants present and estimate their relative abundances. Three variants of concern were detected in the dust: Alpha, Delta, and Omicron. Alpha was found in our earliest sample in April 2021 with an estimated frequency of 100%. Delta was the primary variant present from October of 2021 to January 2022, with an average estimated frequency of 91% (±1.3%). Omicron became the primary variant in January 2022 and was the dominant strain in circulation through March with an estimated frequency of 87% (±3.2%). The detection of these variants on OSU's campus correlates with the circulation of these variants in the surrounding population (Delta p<0.0001 and Omicron p = 0.02). Overall, these results support the hypothesis that dust can be used to track COVID-19 variants in buildings.
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Affiliation(s)
- John Van Dusen
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Haley LeBlanc
- Genetic Counseling Program, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Nicholas Nastasi
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, The Ohio State University, Columbus, Ohio, United States of America
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
| | - Jenny Panescu
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, The Ohio State University, Columbus, Ohio, United States of America
| | - Austin Shamblin
- Applied Microbiology Services Lab, The Ohio State University, Columbus, Ohio, United States of America
| | - Jacob W. Smith
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Michael G. Sovic
- Applied Microbiology Services Lab, The Ohio State University, Columbus, Ohio, United States of America
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Amanda Williams
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Mikkel B. M. Quam
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
- Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
- Section of Sustainable Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Seth Faith
- Applied Microbiology Services Lab, The Ohio State University, Columbus, Ohio, United States of America
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Karen C. Dannemiller
- Department of Civil, Environmental & Geodetic Engineering, College of Engineering, The Ohio State University, Columbus, Ohio, United States of America
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
- Sustainability Institute, The Ohio State University, Columbus, Ohio, United States of America
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28
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Champredon D, Becker D, Peterson SW, Mejia E, Hizon N, Schertzer A, Djebli M, Oloye FF, Xie Y, Asadi M, Cantin J, Pu X, Osunla CA, Brinkmann M, McPhedran KN, Servos MR, Giesy JP, Mangat C. Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data. BMC Infect Dis 2024; 24:139. [PMID: 38287244 PMCID: PMC10823614 DOI: 10.1186/s12879-024-08997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND The spread of SARS-CoV-2 has been studied at unprecedented levels worldwide. In jurisdictions where molecular analysis was performed on large scales, the emergence and competition of numerous SARS-CoV-2lineages have been observed in near real-time. Lineage identification, traditionally performed from clinical samples, can also be determined by sampling wastewater from sewersheds serving populations of interest. Variants of concern (VOCs) and SARS-CoV-2 lineages associated with increased transmissibility and/or severity are of particular interest. METHOD Here, we consider clinical and wastewater data sources to assess the emergence and spread of VOCs in Canada retrospectively. RESULTS We show that, overall, wastewater-based VOC identification provides similar insights to the surveillance based on clinical samples. Based on clinical data, we observed synchrony in VOC introduction as well as similar emergence speeds across most Canadian provinces despite the large geographical size of the country and differences in provincial public health measures. CONCLUSION In particular, it took approximately four months for VOC Alpha and Delta to contribute to half of the incidence. In contrast, VOC Omicron achieved the same contribution in less than one month. This study provides significant benchmarks to enhance planning for future VOCs, and to some extent for future pandemics caused by other pathogens, by quantifying the rate of SARS-CoV-2 VOCs invasion in Canada.
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Affiliation(s)
- David Champredon
- Public Health Agency of Canada, National Microbiology Laboratory, Public Health Risk Sciences Division, Guelph, ON, Canada.
| | - Devan Becker
- Public Health Agency of Canada, National Microbiology Laboratory, Public Health Risk Sciences Division, Guelph, ON, Canada
| | - Shelley W Peterson
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
| | - Edgard Mejia
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
| | - Nikho Hizon
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
| | - Andrea Schertzer
- Public Health Agency of Canada, Centre for Immunization and Respiratory Infectious Diseases, Ottawa, ON, Canada
| | - Mohamed Djebli
- Public Health Agency of Canada, Centre for Immunization and Respiratory Infectious Diseases, Ottawa, ON, Canada
| | - Femi F Oloye
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Chemistry, Division of Physical and Computational Sciences, University of Pittsburgh at Bradford, Bradford, United States.
| | - Yuwei Xie
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Xia Pu
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Charles A Osunla
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Markus Brinkmann
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
- Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - John P Giesy
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Environmental Sciences, Baylor University, Waco, TX, USA.
- Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Chand Mangat
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
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29
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Kanchan S, Ogden E, Kesheri M, Skinner A, Miliken E, Lyman D, Armstrong J, Sciglitano L, Hampikian G. COVID-19 hospitalizations and deaths predicted by SARS-CoV-2 levels in Boise, Idaho wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167742. [PMID: 37852488 DOI: 10.1016/j.scitotenv.2023.167742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/22/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023]
Abstract
The viral load of COVID-19 in untreated wastewater from Idaho's capital city Boise, ID (Ada County) has been used to predict changes in hospital admissions (statewide in Idaho) and deaths (Ada County) using distributed fixed lag modeling and artificial neural networks (ANN). The wastewater viral counts were used to determine the lag time between peaks in wastewater viral counts and COVID-19 hospitalizations as well as deaths (14 and 23 days, respectively). Quantitative measurement of SARS-CoV-2 viral RNA counts in the untreated wastewater was determined three times a week using RT-qPCR over a span of 13 months. To mitigate the effects of PCR inhibitors in wastewater, a series of dilution tests were conducted, and the 1/4 dilution was used to generate the most successful model. Wastewater SARS-CoV-2 viral RNA counts and hospitalization from June 7, 2021 to December 29, 2021 were used as training data to predict hospitalizations; and wastewater SARS-CoV-2 viral RNA counts and deaths from June 7, 2021 to December 20, 2021 were used as training data to predict deaths. These training data were used to make predictive ANN models for future hospitalizations and deaths. To the best of our knowledge, this is the first report of prediction of deaths from COVID-19 based on wastewater SARS-CoV-2 viral RNA counts using machine learning-based multilayered ANN. The applied modeling demonstrates that wastewater surveillance data can be combined with hospitalizations and death data to generate machine learning-based ANN models that predict future COVID-19 hospital admissions and deaths, providing an early warning for medical response teams and healthcare policymakers.
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Affiliation(s)
- Swarna Kanchan
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America; Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, 25701, United States of America
| | - Ernie Ogden
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Minu Kesheri
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America; Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, 25701, United States of America
| | - Alexis Skinner
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Erin Miliken
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Devyn Lyman
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Jacob Armstrong
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Lawrence Sciglitano
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Greg Hampikian
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America.
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30
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Cuevas-Ferrando E, Sánchez G, Pérez-Cataluña A. SARS-CoV-2 Detection and Genome Sequencing in Urban Wastewaters. Methods Mol Biol 2024; 2732:119-131. [PMID: 38060121 DOI: 10.1007/978-1-0716-3515-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Due to the excretion of SARS-CoV-2 in faeces, the use of wastewater-based epidemiology (WBE) is a useful tool for virus surveillance in large populations. The analysis of this virus includes a concentration step prior to virus detection by RT-qPCR. In addition, the use of massive sequencing allows the detection of specific mutations of clinical importance, as well as the detection of the introduction of new lineages in a specific population. In this chapter, we describe the analysis of SARS-CoV-2 in urban wastewater by the concentration of the samples by precipitation with aluminum chloride, the detection, and quantification of SARS-CoV-2 RNA by RT-qPCR and the genomic sequencing using two different sequencing platforms.
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Affiliation(s)
- Enric Cuevas-Ferrando
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain
| | - Gloria Sánchez
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain
| | - Alba Pérez-Cataluña
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain.
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31
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Parsons RJ, Acharya P. Evolution of the SARS-CoV-2 Omicron spike. Cell Rep 2023; 42:113444. [PMID: 37979169 PMCID: PMC10782855 DOI: 10.1016/j.celrep.2023.113444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/21/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern, first identified in November 2021, rapidly spread worldwide and diversified into several subvariants. The Omicron spike (S) protein accumulated an unprecedented number of sequence changes relative to previous variants. In this review, we discuss how Omicron S protein structural features modulate host cell receptor binding, virus entry, and immune evasion and highlight how these structural features differentiate Omicron from previous variants. We also examine how key structural properties track across the still-evolving Omicron subvariants and the importance of continuing surveillance of the S protein sequence evolution over time.
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Affiliation(s)
- Ruth J Parsons
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA.
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA.
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32
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Maal-Bared R, Brisolara K, Knight M, Mansfeldt C. To sample or not to sample: A governance-focused decision tree for wastewater service providers considering participation in wastewater-based epidemiology (WBE) in support of public health programs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167128. [PMID: 37722431 DOI: 10.1016/j.scitotenv.2023.167128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
Wastewater-based epidemiology (WBE) provides value to public health monitoring and protection. Participation of public and private wastewater system operators in WBE efforts is critical to public health surveillance program success and sustainability. However, given the number of WBE solicitations wastewater service providers receive, the limitation of service provider resources, the concerns around privacy, ethics, and equity, and the fatigue associated with responding to COVID-19, operators are becoming more hesitant to participate in WBE efforts. While various ethical concerns and sustainability challenges associated with WBE have been documented, no efforts to date have investigated what factors should systematically influence the decision to provide samples to a WBE effort. Therefore, this study develops a decision-making tool for WBE teams to proactively monitor, manage, and avoid wastewater system operators' operational risks and potential liabilities. Ultimately, using this tool allows WBE program partners in academia, government, and industry to better understand wastewater system operators' needs and challenges surrounding data quality and use, public health ethics, and daily wastewater infrastructure operation.
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Affiliation(s)
| | - Kari Brisolara
- LSUHSC, School of Public Health, 2020 Gravier St, New Orleans, LA, USA.
| | - Mark Knight
- LuminUltra Technologies Ltd, 520 King St, Fredericton, NB E3B 6G3, Canada.
| | - Cresten Mansfeldt
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO, USA; Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO, USA.
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33
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Child HT, Airey G, Maloney DM, Parker A, Wild J, McGinley S, Evens N, Porter J, Templeton K, Paterson S, van Aerle R, Wade MJ, Jeffries AR, Bassano I. Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater. mBio 2023; 14:e0146823. [PMID: 37877702 PMCID: PMC10746264 DOI: 10.1128/mbio.01468-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
IMPORTANCE Most public health initiatives that monitor viruses in wastewater have utilized quantitative polymerase chain reaction (PCR) and whole genome PCR sequencing, mirroring techniques used for viral epidemiology in individuals. These techniques require prior knowledge of the target viral genome and are limited to monitoring individual or small groups of viruses. Metagenomic sequencing may offer an alternative strategy for monitoring a broad spectrum of viruses in wastewater, including novel and emerging pathogens. In this study, while amplicon sequencing gave high viral genome coverage, untargeted shotgun sequencing of total nucleic acid samples was unable to detect human pathogenic viruses with enough sensitivity for use in genomic epidemiology. Enrichment of shotgun libraries for respiratory viruses using hybrid-capture technology provided genotypic information on a range of viruses simultaneously, indicating strong potential for wastewater surveillance. This type of targeted metagenomics could be used for monitoring diverse targets, such as pathogens or antimicrobial resistance genes, in environmental samples.
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Affiliation(s)
- Harry T. Child
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - George Airey
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Daniel M. Maloney
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Suzie McGinley
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Nicholas Evens
- Environment Agency, National Monitoring, Starcross, Exeter, United Kingdom
| | - Jonathan Porter
- Environment Agency, National Monitoring, Starcross, Exeter, United Kingdom
| | - Kate Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas, Weymouth, United Kingdom
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Matthew J. Wade
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Aaron R. Jeffries
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Irene Bassano
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
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34
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Yan T, Zheng R, Li Y, Sun S, Zeng X, Yue Z, Liao Y, Hu Q, Xu Y, Li Q. Epidemiological Insights into the Omicron Outbreak via MeltArray-Assisted Real-Time Tracking of SARS-CoV-2 Variants. Viruses 2023; 15:2397. [PMID: 38140638 PMCID: PMC10748191 DOI: 10.3390/v15122397] [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: 11/02/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
The prolonged course of the COVID-19 pandemic necessitates sustained surveillance of emerging variants. This study aimed to develop a multiplex real-time polymerase chain reaction (rt-PCR) suitable for the real-time tracking of Omicron subvariants in clinical and wastewater samples. Plasmids containing variant-specific mutations were used to develop a MeltArray assay. After a comprehensive evaluation of both analytical and clinical performance, the established assay was used to detect Omicron variants in clinical and wastewater samples, and the results were compared with those of next-generation sequencing (NGS) and droplet digital PCR (ddPCR). The MeltArray assay identified 14 variant-specific mutations, enabling the detection of five Omicron sublineages (BA.2*, BA.5.2*, BA.2.75*, BQ.1*, and XBB.1*) and eight subvariants (BF.7, BN.1, BR.2, BQ.1.1, XBB.1.5, XBB.1.16, XBB.1.9, and BA.4.6). The limit of detection (LOD) of the assay was 50 copies/reaction, and no cross-reactivity was observed with 15 other respiratory viruses. Using NGS as the reference method, the clinical evaluation of 232 swab samples exhibited a clinical sensitivity of > 95.12% (95% CI 89.77-97.75%) and a specificity of > 95.21% (95% CI, 91.15-97.46%). When used to evaluate the Omicron outbreak from late 2022 to early 2023, the MeltArray assay performed on 1408 samples revealed that the epidemic was driven by BA.5.2* (883, 62.71%) and BF.7 (525, 37.29%). Additionally, the MeltArray assay demonstrated potential for estimating variant abundance in wastewater samples. The MeltArray assay is a rapid and scalable method for identifying SARS-CoV-2 variants. Integrating this approach with NGS and ddPCR will improve variant surveillance capabilities and ensure preparedness for future variants.
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Affiliation(s)
- Ting Yan
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (T.Y.); (S.S.); (Y.L.)
| | - Rongrong Zheng
- Xiamen Centre for Disease Control and Prevention, Xiamen 361021, China; (R.Z.); (X.Z.)
| | - Yinghui Li
- Shenzhen Centre for Disease Control and Prevention, Shenzhen 518055, China; (Y.L.); (Z.Y.); (Q.H.)
| | - Siyang Sun
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (T.Y.); (S.S.); (Y.L.)
| | - Xiaohong Zeng
- Xiamen Centre for Disease Control and Prevention, Xiamen 361021, China; (R.Z.); (X.Z.)
| | - Zhijiao Yue
- Shenzhen Centre for Disease Control and Prevention, Shenzhen 518055, China; (Y.L.); (Z.Y.); (Q.H.)
| | - Yiqun Liao
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (T.Y.); (S.S.); (Y.L.)
| | - Qinghua Hu
- Shenzhen Centre for Disease Control and Prevention, Shenzhen 518055, China; (Y.L.); (Z.Y.); (Q.H.)
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (T.Y.); (S.S.); (Y.L.)
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; (T.Y.); (S.S.); (Y.L.)
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35
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Rajput V, Pramanik R, Malik V, Yadav R, Samson R, Kadam P, Bhalerao U, Tupekar M, Deshpande D, Shah P, Shashidhara LS, Boargaonkar R, Patil D, Kale S, Bhalerao A, Jain N, Kamble S, Dastager S, Karmodiya K, Dharne M. Genomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:118976-118988. [PMID: 37922087 DOI: 10.1007/s11356-023-30709-z] [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: 06/27/2023] [Accepted: 10/23/2023] [Indexed: 11/05/2023]
Abstract
The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods to detect and monitor the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool for proactive analysis and quantification of infectious pathogens within a population before clinical cases emerge. In the present study, we aimed to assess the trend and dynamics of SARS-CoV-2 variants using a longitudinal approach. Our objective included early detection and monitoring of these variants to enhance our understanding of their prevalence and potential impact. To achieve our goals, we conducted real-time quantitative polymerase chain reaction (RT-qPCR) and Illumina sequencing on 442 wastewater (WW) samples collected from 10 sewage treatment plants (STPs) in Pune city, India, spanning from November 2021 to April 2022. Our comprehensive analysis identified 426 distinct lineages representing 17 highly transmissible variants of SARS-CoV-2. Notably, fragments of Omicron variant were detected in WW samples prior to its first clinical detection in Botswana. Furthermore, we observed highly contagious sub-lineages of the Omicron variant, including BA.1 (~28%), BA.1.X (1.0-72%), BA.2 (1.0-18%), BA.2.X (1.0-97.4%) BA.2.12 (0.8-0.25%), BA.2.38 (0.8-1.0%), BA.2.75 (0.01-0.02%), BA.3 (0.09-6.3%), BA.4 (0.24-0.29%), and XBB (0.01-21.83%), with varying prevalence rates. Overall, the present study demonstrated the practicality of WBE in the early detection of SARS-CoV-2 variants, which could help track future outbreaks of SARS-CoV-2. Such approaches could be implicated in monitoring infectious agents before they appear in clinical cases.
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Affiliation(s)
- Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rinka Pramanik
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinita Malik
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
| | - Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Pradnya Kadam
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Unnati Bhalerao
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Manisha Tupekar
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Dipti Deshpande
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Priyanki Shah
- The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India
| | - L S Shashidhara
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
- The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India
| | | | - Dhawal Patil
- Ecosan Services Foundation (ESF), Pune, Maharashtra, 411030, India
| | - Saurabh Kale
- Ecosan Services Foundation (ESF), Pune, Maharashtra, 411030, India
| | - Asim Bhalerao
- Fluid Robotics Private Limited (FRPL), Pune, Maharashtra, 411052, India
| | - Nidhi Jain
- Fluid Robotics Private Limited (FRPL), Pune, Maharashtra, 411052, India
| | - Sanjay Kamble
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India
| | - Syed Dastager
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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36
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Rosario P, Seenivasan T, Viswash R, Ramalingam S, Barani V, Welling CM, Grego S. Impact of heat-treatment on wastewater analytical parameters. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 88:2931-2939. [PMID: 38096079 PMCID: wst_2023_359 DOI: 10.2166/wst.2023.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Raw wastewater analysis is an important step in treatment assessment; however, it is associated with risks of personnel exposure to pathogens. Such risks are enhanced during virus outbreaks, such as the COVID pandemic, and heat-treatment is a commonly used mitigation measure. We examined whether heat-treatment compromises wastewater analytical parameters results. We found that heat-treatment of blackwater at 60 °C for 90 min in capped containers yielded no statistically different values (p > 0.05) for pH, chemical oxygen demand (COD), ammonia (NH3), total nitrogen (TN), total suspended solids (TSS), and turbidity for specimens from three different sources. This heat-treatment inactivated coliform bacteria (>4 log10 reduction) thus compromising the measurement of commonly used fecal contamination indicators. The observation of intact helminth eggs in heat-treated specimens suggests that the helminth egg enumeration assay is not compromised. These findings indicate that heat-treatment for the safe handling of wastewater, as may be needed in future virus outbreaks, does not affect the measurements of many common wastewater physico-chemical properties.
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Affiliation(s)
| | | | - Ramya Viswash
- PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, India
| | - Sudha Ramalingam
- PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, India
| | - Viswa Barani
- Duke India Services Private Ltd, Bangalore, India
| | | | - Sonia Grego
- Center for WaSH-AID, Duke University, Durham, NC 27701, USA
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37
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Brunner FS, Payne A, Cairns E, Airey G, Gregory R, Pickwell ND, Wilson M, Carlile M, Holmes N, Hill V, Child H, Tomlinson J, Ahmed S, Denise H, Rowe W, Frazer J, Aerle RV, Evens N, Porter J, Templeton K, Jeffries AR, Loose M, Paterson S. Utility of wastewater genomic surveillance compared to clinical surveillance to track the spread of the SARS-CoV-2 Omicron variant across England. WATER RESEARCH 2023; 247:120804. [PMID: 37925861 DOI: 10.1016/j.watres.2023.120804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
The world has moved into a new stage of managing the SARS-CoV-2 pandemic with minimal restrictions and reduced testing in the population, leading to reduced genomic surveillance of virus variants in individuals. Wastewater-based epidemiology (WBE) can provide an alternative means of tracking virus variants in the population but decision-makers require confidence that it can be applied to a national scale and is comparable to individual testing data. We analysed 19,911 samples from 524 wastewater sites across England at least twice a week between November 2021 and February 2022, capturing sewage from >70% of the English population. We used amplicon-based sequencing and the phylogeny based de-mixing tool Freyja to estimate SARS-CoV-2 variant frequencies and compared these to the variant dynamics observed in individual testing data from clinical and community settings. We show that wastewater data can reconstruct the spread of the Omicron variant across England since November 2021 in close detail and aligns closely with epidemiological estimates from individual testing data. We also show the temporal and spatial spread of Omicron within London. Our wastewater data further reliably track the transition between Omicron subvariants BA1 and BA2 in February 2022 at regional and national levels. Our demonstration that WBE can track the fast-paced dynamics of SARS-CoV-2 variant frequencies at a national scale and closely match individual testing data in time shows that WBE can reliably fill the monitoring gap left by reduced individual testing in a more affordable way.
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Affiliation(s)
- Franziska S Brunner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - Alexander Payne
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Edward Cairns
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - George Airey
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - Richard Gregory
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK
| | - Natalie D Pickwell
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Myles Wilson
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Matthew Carlile
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Nadine Holmes
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Harry Child
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Jasmine Tomlinson
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Suhel Ahmed
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Hubert Denise
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK
| | - William Rowe
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK
| | - Jacob Frazer
- Environmental Monitoring for Health Protection, UK Health Security Agency, Nobel House, London SW1P 3HX, UK
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas, Barrack Road, Weymouth, DT 8UB, UK
| | - Nicholas Evens
- Monitoring Laboratories, National Monitoring, Environment Agency EX6 8FD, UK
| | - Jonathan Porter
- Monitoring Laboratories, National Monitoring, Environment Agency EX6 8FD, UK
| | - Kate Templeton
- NHS Lothian, Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Aaron R Jeffries
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Matt Loose
- Deep Seq, Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool L69 7ZB, UK.
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38
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Hasing ME, Lee BE, Gao T, Li Q, Qiu Y, Ellehoj E, Graber TE, Fuzzen M, Servos M, Landgraff C, Delatolla R, Tipples G, Zelyas N, Hinshaw D, Maal-Bared R, Sikora C, Parkins M, Hubert CRJ, Frankowski K, Hrudey SE, Pang XL. Wastewater surveillance monitoring of SARS-CoV-2 variants of concern and dynamics of transmission and community burden of COVID-19. Emerg Microbes Infect 2023; 12:2233638. [PMID: 37409382 PMCID: PMC10408568 DOI: 10.1080/22221751.2023.2233638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/04/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Wastewater-based surveillance is a valuable approach for monitoring COVID-19 at community level. Monitoring SARS-CoV-2 variants of concern (VOC) in wastewater has become increasingly relevant when clinical testing capacity and case-based surveillance are limited. In this study, we ascertained the turnover of six VOC in Alberta wastewater from May 2020 to May 2022. Wastewater samples from nine wastewater treatment plants across Alberta were analysed using VOC-specific RT-qPCR assays. The performance of the RT-qPCR assays in identifying VOC in wastewater was evaluated against next generation sequencing. The relative abundance of each VOC in wastewater was compared to positivity rate in COVID-19 testing. VOC-specific RT-qPCR assays performed comparatively well against next generation sequencing; concordance rates ranged from 89% to 98% for detection of Alpha, Beta, Gamma, Omicron BA.1 and Omicron BA.2, with a slightly lower rate of 85% for Delta (p < 0.01). Elevated relative abundance of Alpha, Delta, Omicron BA.1 and BA.2 were each associated with increased COVID-19 positivity rate. Alpha, Delta and Omicron BA.2 reached 90% relative abundance in wastewater within 80, 111 and 62 days after their initial detection, respectively. Omicron BA.1 increased more rapidly, reaching a 90% relative abundance in wastewater after 35 days. Our results from VOC surveillance in wastewater correspond with clinical observations that Omicron is the VOC with highest disease burden over the shortest period in Alberta to date. The findings suggest that changes in relative abundance of a VOC in wastewater can be used as a supplementary indicator to track and perhaps predict COVID-19 burden in a population.
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Affiliation(s)
- Maria E. Hasing
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Bonita E. Lee
- Department of Paediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Tiejun Gao
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Qiaozhi Li
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Erik Ellehoj
- Ellehoj Redmond Consulting, Edmonton, Alberta, Canada
| | - Tyson E. Graber
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mark Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Graham Tipples
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Nathan Zelyas
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Deena Hinshaw
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Christopher Sikora
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaoli L. Pang
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
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39
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Barnes KG, Levy JI, Gauld J, Rigby J, Kanjerwa O, Uzzell CB, Chilupsya C, Anscombe C, Tomkins-Tinch C, Mbeti O, Cairns E, Thole H, McSweeney S, Chibwana MG, Ashton PM, Jere KC, Meschke JS, Diggle P, Cornick J, Chilima B, Jambo K, Andersen KG, Kawalazira G, Paterson S, Nyirenda TS, Feasey N. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems. Nat Commun 2023; 14:7883. [PMID: 38036496 PMCID: PMC10689440 DOI: 10.1038/s41467-023-43047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
The COVID-19 pandemic has profoundly impacted health systems globally and robust surveillance has been critical for pandemic control, however not all countries can currently sustain community pathogen surveillance programs. Wastewater surveillance has proven valuable in high-income settings, but less is known about the utility of water surveillance of pathogens in low-income countries. Here we show how wastewater surveillance of SAR-CoV-2 can be used to identify temporal changes and help determine circulating variants quickly. In Malawi, a country with limited community-based COVID-19 testing capacity, we explore the utility of rivers and wastewater for SARS-CoV-2 surveillance. From May 2020-May 2022, we collect water from up to 112 river or defunct wastewater treatment plant sites, detecting SARS-CoV-2 in 8.3% of samples. Peak SARS-CoV-2 detection in water samples predate peaks in clinical cases. Sequencing of water samples identified the Beta, Delta, and Omicron variants, with Delta and Omicron detected well in advance of detection in patients. Our work highlights how wastewater can be used to detect emerging waves, identify variants of concern, and provide an early warning system in settings with no formal sewage systems.
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Affiliation(s)
- Kayla G Barnes
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Joshua I Levy
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jillian Gauld
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan Rigby
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Oscar Kanjerwa
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Christopher B Uzzell
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Chisomo Chilupsya
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Catherine Anscombe
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Christopher Tomkins-Tinch
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Omar Mbeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Herbert Thole
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Shannon McSweeney
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Marah G Chibwana
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Philip M Ashton
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
| | - Khuzwayo C Jere
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - John Scott Meschke
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Peter Diggle
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Jennifer Cornick
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
| | - Benjamin Chilima
- CHICAS, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Kondwani Jambo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Public Health Institute of Malawi, Lilongwe, Malawi
| | - Kristian G Andersen
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Scripps Research Translational Institute, La Jolla, CA, USA
| | - Gift Kawalazira
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Tonney S Nyirenda
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Nicholas Feasey
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
- School of Medicine, University of St Andrews, St Andrews, UK
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40
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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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Zhakparov D, Quirin Y, Xiao Y, Battaglia N, Holzer M, Bühler M, Kistler W, Engel D, Zumthor JP, Caduff A, Baerenfaller K. Sequencing of SARS-CoV-2 RNA Fragments in Wastewater Detects the Spread of New Variants during Major Events. Microorganisms 2023; 11:2660. [PMID: 38004672 PMCID: PMC10672834 DOI: 10.3390/microorganisms11112660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The sequencing of SARS-CoV-2 RNA in wastewater is an unbiased method to detect the spread of emerging variants and to track regional infection dynamics, which is especially useful in case of limited testing and clinical sequencing. To test how major international events influence the spread of new variants we have sequenced SARS-CoV-2 RNA in the wastewater samples of Davos, Landquart, Lostallo, and St. Moritz in the Swiss canton of Grisons in the time around the international sports competitions in Davos and St. Moritz in December 2021, and additionally in May 2022 and January 2023 in Davos and St. Moritz during the World Economic Forum (WEF) in Davos. The prevalence of the variants identified from the wastewater sequencing data showed that the Omicron variant BA.1 had spread in Davos and St. Moritz during the international sporting events hosted there in December 2021. This spread was associated with an increase in case numbers, while it was not observed in Landquart and Lostallo. Another instance of new variant spread occurred during the WEF in January 2023, when the Omicron variant BA.2.75 arrived in Davos but not in St. Moritz. We can therefore conclude that major international events promote the spread of new variants in the respective host region, which has important implications for the protective measures that should be taken.
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Affiliation(s)
- Damir Zhakparov
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland; (D.Z.)
- Swiss Institute of Bioinformatics (SIB), 1005 Lausanne, Switzerland
| | - Yves Quirin
- Cantonal Office for Nature and Environment, 7000 Chur, Switzerland
| | - Yi Xiao
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland; (D.Z.)
- Swiss Institute of Bioinformatics (SIB), 1005 Lausanne, Switzerland
| | - Nicole Battaglia
- Cantonal Office for Food Security and Animal Health, 7000 Chur, Switzerland
| | - Michael Holzer
- Cantonal Office for Nature and Environment, 7000 Chur, Switzerland
| | - Martin Bühler
- Cantonal Office for Military and Civil Protection, 7000 Chur, Switzerland (A.C.)
| | | | | | - Jon Paulin Zumthor
- Cantonal Office for Food Security and Animal Health, 7000 Chur, Switzerland
| | - Alexa Caduff
- Cantonal Office for Military and Civil Protection, 7000 Chur, Switzerland (A.C.)
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland; (D.Z.)
- Swiss Institute of Bioinformatics (SIB), 1005 Lausanne, Switzerland
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42
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Tisza M, Javornik Cregeen S, Avadhanula V, Zhang P, Ayvaz T, Feliz K, Hoffman KL, Clark JR, Terwilliger A, Ross MC, Cormier J, Moreno H, Wang L, Payne K, Henke D, Troisi C, Wu F, Rios J, Deegan J, Hansen B, Balliew J, Gitter A, Zhang K, Li R, Bauer CX, Mena KD, Piedra PA, Petrosino JF, Boerwinkle E, Maresso AW. Wastewater sequencing reveals community and variant dynamics of the collective human virome. Nat Commun 2023; 14:6878. [PMID: 37898601 PMCID: PMC10613200 DOI: 10.1038/s41467-023-42064-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/25/2023] [Indexed: 10/30/2023] Open
Abstract
Wastewater is a discarded human by-product, but its analysis may help us understand the health of populations. Epidemiologists first analyzed wastewater to track outbreaks of poliovirus decades ago, but so-called wastewater-based epidemiology was reinvigorated to monitor SARS-CoV-2 levels while bypassing the difficulties and pit falls of individual testing. Current approaches overlook the activity of most human viruses and preclude a deeper understanding of human virome community dynamics. Here, we conduct a comprehensive sequencing-based analysis of 363 longitudinal wastewater samples from ten distinct sites in two major cities. Critical to detection is the use of a viral probe capture set targeting thousands of viral species or variants. Over 450 distinct pathogenic viruses from 28 viral families are observed, most of which have never been detected in such samples. Sequencing reads of established pathogens and emerging viruses correlate to clinical data sets of SARS-CoV-2, influenza virus, and monkeypox viruses, outlining the public health utility of this approach. Viral communities are tightly organized by space and time. Finally, the most abundant human viruses yield sequence variant information consistent with regional spread and evolution. We reveal the viral landscape of human wastewater and its potential to improve our understanding of outbreaks, transmission, and its effects on overall population health.
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Affiliation(s)
- Michael Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sara Javornik Cregeen
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ping Zhang
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tulin Ayvaz
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Karen Feliz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kristi L Hoffman
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Justin R Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- TAILOR Labs, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Austen Terwilliger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- TAILOR Labs, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew C Ross
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juwan Cormier
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hannah Moreno
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Li Wang
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Katelyn Payne
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Catherine Troisi
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Fuqing Wu
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | - Janelle Rios
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
| | - Jennifer Deegan
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
| | - Blake Hansen
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | | | - Anna Gitter
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | - Kehe Zhang
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Biostatistics and Data Science, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
- Center for Spatial-temporal Modeling for Applications in Population Sciences, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
| | - Runze Li
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Biostatistics and Data Science, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
- Center for Spatial-temporal Modeling for Applications in Population Sciences, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
| | - Cici X Bauer
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Biostatistics and Data Science, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
- Center for Spatial-temporal Modeling for Applications in Population Sciences, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
| | - Kristina D Mena
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA.
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA.
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
- TAILOR Labs, Baylor College of Medicine, Houston, TX, 77030, USA.
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Wadford DA, Baumrind N, Baylis EF, Bell JM, Bouchard EL, Crumpler M, Foote EM, Gilliam S, Glaser CA, Hacker JK, Ledin K, Messenger SL, Morales C, Smith EA, Sevinsky JR, Corbett-Detig RB, DeRisi J, Jacobson K. Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance. Front Public Health 2023; 11:1249614. [PMID: 37937074 PMCID: PMC10627185 DOI: 10.3389/fpubh.2023.1249614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/27/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these challenges and to characterize the virus over time, the State of California established the California SARS-CoV-2 Whole Genome Sequencing (WGS) Initiative, or "California COVIDNet". This initiative constituted an unprecedented multi-sector collaborative effort to achieve large-scale genomic surveillance of SARS-CoV-2 across California to monitor the spread of variants within the state, to detect new and emerging variants, and to characterize outbreaks in congregate, workplace, and other settings. Methods California COVIDNet consists of 50 laboratory partners that include public health laboratories, private clinical diagnostic laboratories, and academic sequencing facilities as well as expert advisors, scientists, consultants, and contractors. Data management, sample sourcing and processing, and computational infrastructure were major challenges that had to be resolved in the midst of the pandemic chaos in order to conduct SARS-CoV-2 genomic surveillance. Data management, storage, and analytics needs were addressed with both conventional database applications and newer cloud-based data solutions, which also fulfilled computational requirements. Results Representative and randomly selected samples were sourced from state-sponsored community testing sites. Since March of 2021, California COVIDNet partners have contributed more than 450,000 SARS-CoV-2 genomes sequenced from remnant samples from both molecular and antigen tests. Combined with genomes from CDC-contracted WGS labs, there are currently nearly 800,000 genomes from all 61 local health jurisdictions (LHJs) in California in the COVIDNet sequence database. More than 5% of all reported positive tests in the state have been sequenced, with similar rates of sequencing across 5 major geographic regions in the state. Discussion Implementation of California COVIDNet revealed challenges and limitations in the public health system. These were overcome by engaging in novel partnerships that established a successful genomic surveillance program which provided valuable data to inform the COVID-19 public health response in California. Significantly, California COVIDNet has provided a foundational data framework and computational infrastructure needed to respond to future public health crises.
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Affiliation(s)
- Debra A. Wadford
- California Department of Public Health, Richmond, CA, United States
| | - Nikki Baumrind
- California Department of Public Health, Richmond, CA, United States
| | | | - John M. Bell
- California Department of Public Health, Richmond, CA, United States
| | | | - Megan Crumpler
- Orange County Public Health Laboratory, Santa Ana, CA, United States
| | - Eric M. Foote
- California Department of Public Health, Richmond, CA, United States
| | - Sabrina Gilliam
- California Department of Public Health, Richmond, CA, United States
| | - Carol A. Glaser
- California Department of Public Health, Richmond, CA, United States
| | - Jill K. Hacker
- California Department of Public Health, Richmond, CA, United States
| | - Katya Ledin
- California Department of Public Health, Richmond, CA, United States
| | | | | | | | | | | | - Joseph DeRisi
- University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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44
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Haver A, Theijn R, Grift ID, Raaijmakers G, Poorter E, Laros JFJ, van Dissel JT, Lodder WJ. Regional reemergence of a SARS-CoV-2 Delta lineage amid an Omicron wave detected by wastewater sequencing. Sci Rep 2023; 13:17870. [PMID: 37857658 PMCID: PMC10587120 DOI: 10.1038/s41598-023-44500-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
The implementation and integration of wastewater-based epidemiology constitutes a valuable addition to existing pathogen surveillance systems, such as clinical surveillance for SARS-CoV-2. In the Netherlands, SARS-CoV-2 variant circulation is monitored by performing whole-genome sequencing on wastewater samples. In this manuscript, we describe the detection of an AY.43 lineage (Delta variant) amid a period of BA.5 (Omicron variant) dominance in wastewater samples from two wastewater treatment plants (WWTPs) during the months of August and September of 2022. Our results describe a temporary emergence, which was absent in samples from other WWTPs, and which coincided with peaks in viral load. We show how these lineage estimates can be traced back to lineage-specific substitution patterns. The absence of this variant from reported clinical data, but high associated viral loads suggest cryptic transmission. Our findings highlight the additional value of wastewater surveillance for generating insights into circulating pathogens.
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Affiliation(s)
- Auke Haver
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Human Genetics (HG), Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Rick Theijn
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ivo D Grift
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Gino Raaijmakers
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Elsa Poorter
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics (HG), Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of BioInformatics and Computational Services (BIR), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jaap T van Dissel
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Willemijn J Lodder
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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Yousif M, Rachida S, Taukobong S, Ndlovu N, Iwu-Jaja C, Howard W, Moonsamy S, Mhlambi N, Gwala S, Levy JI, Andersen KG, Scheepers C, von Gottberg A, Wolter N, Bhiman JN, Amoako DG, Ismail A, Suchard M, McCarthy K. SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses. Nat Commun 2023; 14:6325. [PMID: 37816740 PMCID: PMC10564906 DOI: 10.1038/s41467-023-41369-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/30/2023] [Indexed: 10/12/2023] Open
Abstract
As global SARS-CoV-2 burden and testing frequency have decreased, wastewater surveillance has emerged as a key tool to support clinical surveillance efforts. The aims of this study were to identify and characterize SARS-CoV-2 variants in wastewater samples collected from urban centers across South Africa. Here we show that wastewater sequencing analyses are temporally concordant with clinical genomic surveillance and reveal the presence of multiple lineages not detected by clinical surveillance. We show that wastewater genomics can support SARS-CoV-2 epidemiological investigations by reliably recovering the prevalence of local circulating variants, even when clinical samples are not available. Further, we find that analysis of mutations observed in wastewater can provide a signal of upcoming lineage transitions. Our study demonstrates the utility of wastewater genomics to monitor evolution and spread of endemic viruses.
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Affiliation(s)
- Mukhlid Yousif
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa.
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Said Rachida
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Setshaba Taukobong
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nkosenhle Ndlovu
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Chinwe Iwu-Jaja
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wayne Howard
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Shelina Moonsamy
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nompilo Mhlambi
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Sipho Gwala
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Cathrine Scheepers
- SAMRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel Gyamfi Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa
| | - Melinda Suchard
- Department of Chemical Pathology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Kerrigan McCarthy
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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47
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Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557637. [PMID: 37745602 PMCID: PMC10515900 DOI: 10.1101/2023.09.13.557637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.
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Affiliation(s)
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan E. Pekar
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Reema Singh
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da Republica, 2780-157, Oeiras, Portugal
| | - Karthik Gangavarapu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Matthew B. Rogers
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Robert F. Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marion P. G. Koopmans
- Department of Viroscience, and Pandemic and Disaster Preparedness Centre., Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Saskia Popescu
- University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L. Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow, G61 1QH, UK
| | - Marc A. Suchard
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Florence Débarre
- Institut d’Écologie et des Sciences de l’Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France
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48
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Bowes D, Darling A, Driver EM, Kaya D, Maal-Bared R, Lee LM, Goodman K, Adhikari S, Aggarwal S, Bivins A, Bohrerova Z, Cohen A, Duvallet C, Elnimeiry RA, Hutchison JM, Kapoor V, Keenum I, Ling F, Sills D, Tiwari A, Vikesland P, Ziels R, Mansfeldt C. Structured Ethical Review for Wastewater-Based Testing in Support of Public Health. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12969-12980. [PMID: 37611169 PMCID: PMC10484207 DOI: 10.1021/acs.est.3c04529] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Wastewater-based testing (WBT) for SARS-CoV-2 has rapidly expanded over the past three years due to its ability to provide a comprehensive measurement of disease prevalence independent of clinical testing. The development and simultaneous application of WBT measured biomarkers for research activities and for the pursuit of public health goals, both areas with well-established ethical frameworks. Currently, WBT practitioners do not employ a standardized ethical review process, introducing the potential for adverse outcomes for WBT professionals and community members. To address this deficiency, an interdisciplinary workshop developed a framework for a structured ethical review of WBT. The workshop employed a consensus approach to create this framework as a set of 11 questions derived from primarily public health guidance. This study retrospectively applied these questions to SARS-CoV-2 monitoring programs covering the emergent phase of the pandemic (3/2020-2/2022 (n = 53)). Of note, 43% of answers highlight a lack of reported information to assess. Therefore, a systematic framework would at a minimum structure the communication of ethical considerations for applications of WBT. Consistent application of an ethical review will also assist in developing a practice of updating approaches and techniques to reflect the concerns held by both those practicing and those being monitored by WBT supported programs.
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Affiliation(s)
- Devin
A. Bowes
- Biodesign
Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, United States
- Center on
Forced Displacement, Boston University, 111 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Amanda Darling
- Department
of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, 415 Durham Hall; Blacksburg, Virginia 24061, United States
| | - Erin M. Driver
- Biodesign
Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, United States
| | - Devrim Kaya
- School of
Chemical, Biological, and Environmental Engineering, Oregon State University, 105 26th St, Corvallis, Oregon 97331, United States
- School of
Public Health, San Diego State University, San Diego and Imperial Valley, California 92182, United States
| | - Rasha Maal-Bared
- Quality
Assurance and Environment, EPCOR Water Services Inc., EPCOR Tower, 2000−10423 101
Street NW, Edmonton, Alberta T5H 0E7, Canada
| | - Lisa M. Lee
- Department
of Population Health Sciences and Division of Scholarly Integrity
and Research Compliance, Virginia Tech, 300 Turner St. NW, Suite 4120 (0497), Blacksburg, Virginia 24061, United States
| | - Kenneth Goodman
- Institute
for Bioethics and Health Policy, Miller School of Medicine, University of Miami, Miami, Florida 33101, United States
| | - Sangeet Adhikari
- Biodesign
Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, 1001 S. McAllister Ave, Tempe, Arizona 85287, United States
| | - Srijan Aggarwal
- Department
of Civil, Geological, and Environmental Engineering, University of Alaska Fairbanks, 1764 Tanana Loop, Fairbanks, Alaska 99775, United States
| | - Aaron Bivins
- Department
of Civil & Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, Louisiana 70803, United States
| | - Zuzana Bohrerova
- The Ohio
State University, Department of Civil, Environmental
and Geodetic Engineering, 2070 Neil Avenue, 470 Hitchcock Hall, Columbus, Ohio 43210, United States
| | - Alasdair Cohen
- Department
of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, 415 Durham Hall; Blacksburg, Virginia 24061, United States
- Department
of Population Health Sciences, Virginia
Tech, 205 Duck Pond Drive, Blacksburg, Virginia 24061, United States
| | - Claire Duvallet
- Biobot
Analytics, Inc., 501
Massachusetts Avenue; Cambridge, Massachusetts 02139, United States
| | - Rasha A. Elnimeiry
- Public
Health Outbreak Coordination, Informatics, Surveillance (PHOCIS) Office—Surveillance
Section, Division of Disease Control and Health Statistics, Washington State Department of Health, 111 Israel Rd SE, Tumwater, Washington 98501, United States
| | - Justin M. Hutchison
- Department
of Civil, Environmental, and Architectural Engineering, University of Kansas, 1530 W 15th St, Lawrence, Kansas 66045, United States
| | - Vikram Kapoor
- School
of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, 1 UTSA Circle, San Antonio, Texas 78249, United States
| | - Ishi Keenum
- Complex
Microbial Systems Group, National Institute
of Standards and Technology, 100 Bureau Dr, Gaithersburg, Maryland 20899, United States
| | - Fangqiong Ling
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Deborah Sills
- Department
of Civil and Environmental Engineering, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Ananda Tiwari
- Department
of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöberginkatu 2,
P.O. Box 66, FI 00014 Helsinki, Finland
- Expert
Microbiology Unit, Finnish Institute for
Health and Welfare, FI 70600 Kuopio, Finland
| | - Peter Vikesland
- Department
of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, 415 Durham Hall; Blacksburg, Virginia 24061, United States
| | - Ryan Ziels
- Department
of Civil Engineering, The University of
British Columbia, 6250
Applied Science Ln #2002, Vancouver, BC V6T 1Z4, Canada
| | - Cresten Mansfeldt
- Department
of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, UCB 428, Boulder, Colorado 80309, United States
- Environmental
Engineering Program, University of Colorado
Boulder, UCB 607, Boulder, Colorado 80309, United States
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49
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Phan T, Brozak S, Pell B, Oghuan J, Gitter A, Hu T, Ribeiro RM, Ke R, Mena KD, Perelson AS, Kuang Y, Wu F. Making waves: Integrating wastewater surveillance with dynamic modeling to track and predict viral outbreaks. WATER RESEARCH 2023; 243:120372. [PMID: 37494742 DOI: 10.1016/j.watres.2023.120372] [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: 03/26/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 07/28/2023]
Abstract
Wastewater surveillance has proved to be a valuable tool to track the COVID-19 pandemic. However, most studies using wastewater surveillance data revolve around establishing correlations and lead time relative to reported case data. In this perspective, we advocate for the integration of wastewater surveillance data with dynamic within-host and between-host models to better understand, monitor, and predict viral disease outbreaks. Dynamic models overcome emblematic difficulties of using wastewater surveillance data such as establishing the temporal viral shedding profile. Complementarily, wastewater surveillance data bypasses the issues of time lag and underreporting in clinical case report data, thus enhancing the utility and applicability of dynamic models. The integration of wastewater surveillance data with dynamic models can enhance real-time tracking and prevalence estimation, forecast viral transmission and intervention effectiveness, and most importantly, provide a mechanistic understanding of infectious disease dynamics and the driving factors. Dynamic modeling of wastewater surveillance data will advance the development of a predictive and responsive monitoring system to improve pandemic preparedness and population health.
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Affiliation(s)
- Tin Phan
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Samantha Brozak
- School of Mathematical and Statistical Sciences, Arizona State University, AZ 85281, USA
| | - Bruce Pell
- Department of Mathematics and Computer Science, Lawrence Technological University, MI 48075, USA
| | - Jeremiah Oghuan
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Anna Gitter
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Tao Hu
- Department of Geography, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Kristina D Mena
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Texas Epidemic Public Health Institute, Houston, TX 77030, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, AZ 85281, USA
| | - Fuqing Wu
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Texas Epidemic Public Health Institute, Houston, TX 77030, USA.
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50
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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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