1
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Erster O, Bar-Or I, Azar R, Assraf H, Kabat A, Mannasse B, Moshayoff V, Fleishon S, Preis SA, Yishai R, Teijman-Yarden N, Aguvaev I, Matar R, Aydenzon A, Mandelboim M, Zuckerman NS, Sofer D, Lustig Y. Incursion of SARS-CoV-2 BA.2.86.1 variant into Israel: National-scale wastewater surveillance using a novel quantitative real-time PCR assay. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173164. [PMID: 38735317 DOI: 10.1016/j.scitotenv.2024.173164] [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: 01/14/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
The emergence of the SARS-CoV-2 variant BA.2.86.1 raised a considerable concern, due to the large number of potentially virulent mutations. In this study, we developed a novel assay that specifically detects variant BA.2.86.1, and used it to screen environmental samples from wastewater treatment sites across Israel. By using a multiplex assay that included a general SARS-CoV-2 reaction, together with the BA.2.86.1-specific reaction and a control reaction, we quantified the absolute number of viral copies in each sample and its relative abundance, compared with the total copy number of circulating SARS-CoV-2. Evaluation of the new reactions showed that they are both sensitive and specific, detecting down to four copies per reaction, and maintain specificity in the presence of Omicron variants BA.1, 2 and 4 RNA. Examination of 279 samples from 30 wastewater collection sites during August-September 2023 showed that 35 samples (12.5 %) were positive, from 18 sites. Quantitative analysis of the samples showed that the relative abundance of variant BA.2.86.1 with respect to the total viral load of SARS-CoV-2 was very low and consisted between 0.01 % and 0.6 % of the total SARS-CoV-2 circulation. This study demonstrates the importance of combining wastewater surveillance with the development of specialized diagnostic assays, when clinical testing is insufficient. This approach may be useful for timely response by public health authorities in future outbreaks.
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Affiliation(s)
- Oran Erster
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel.
| | - Itay Bar-Or
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Roberto Azar
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Hadar Assraf
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Areej Kabat
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Batya Mannasse
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Vardit Moshayoff
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Shay Fleishon
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Ruth Yishai
- Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Irina Aguvaev
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Roaa Matar
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Alex Aydenzon
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Danit Sofer
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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2
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Margulis M, Rohana H, Erster O, Mandelboim M, Biber A, Schwartz E, Peretz A, Danielli A. Highly sensitive extraction-free saliva-based molecular assay for rapid diagnosis of SARS-CoV-2. J Clin Microbiol 2024; 62:e0060024. [PMID: 38785448 DOI: 10.1128/jcm.00600-24] [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: 04/19/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024] Open
Abstract
The COVID-19 pandemic highlighted the necessity of fast, sensitive, and efficient methods to test large populations for respiratory viruses. The "gold standard" molecular assays for detecting respiratory viruses, such as quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR), rely on invasive swab samples and require time-consuming and labor-intensive extraction processes. Moreover, the turnaround time for RT-qPCR-based assays is too lengthy for rapid screening. Extraction-free saliva-based methods provide a non-invasive sampling process with a fast turnaround time and are suitable for high-throughput applications. However, when used with a standard RT-qPCR system, the absence of extraction significantly reduces the assays' sensitivity. Here, using a novel optical modulation biosensing (OMB) platform, we developed a rapid and highly sensitive extraction-free saliva-based molecular assay. We blindly tested 364 paired nasopharyngeal swabs and saliva samples from suspected SARS-CoV-2 cases in Israel. Compared with the gold standard swab-based RT-qPCR assay, the sensitivity of the extraction-free saliva-based OMB assay is 90.7%, much higher than the sensitivity of extraction-free saliva-based RT-qPCR assay (77.8%) with similar specificity (95.3% and 97.6%, respectively). Moreover, out of 12 samples identified by the OMB-based assay as positive, 8 samples were collected from hospitalized patients in a COVID-19 ward and were verified to be SARS-CoV-2-positive upon admission, indicating that the actual clinical sensitivity and specificity of the OMB assay are higher. Considering its user-friendly saliva-based protocol, short and cost-effective extraction-free process, and high clinical accuracy, the OMB-based molecular assay is very suitable for high-throughput testing of large populations for respiratory viruses. IMPORTANCE Three years after the SARS-CoV-2 outbreak, there are no molecular tests that combine low-cost and straightforward sample preparation, effective sample handling, minimal reagent and disposable requirements, high sensitivity, and high throughput required for mass screening. Existing rapid molecular techniques typically sacrifice certain requirements to meet others. Yet, localized outbreaks of novel viral diseases happen daily in different parts of the world. In this context, respiratory diseases are of specific importance, as they are frequently airborne and highly contagious, with the potential for a rapid global spread. The widely accepted opinion is that another pandemic is just a question of time. To ensure that the containment efforts for the upcoming "disease X" are successful, introducing rapid, high-throughput, and highly sensitive diagnostic methods for detecting and identifying pathogens is critical. A few months into the pandemic, saliva was suggested as a diagnostic matrix for SARS-CoV-2 detection. The collection of saliva does not require swabs and is minimally invasive. In particular, extraction-free saliva-based assays require fewer reagents and disposables, and therefore are faster and cheaper, offering an appealing alternative for low-income countries. Unfortunately, current extraction-free saliva-based detection methods, such as direct RT-qPCR or isothermal amplification, have either low sensitivity or low throughput. Therefore, we believe that the presented highly sensitive ht-OMBi platform and the extraction-free saliva-based molecular assay can become an essential tool in the infectious disease monitoring toolbox.
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Affiliation(s)
- Michael Margulis
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Hanan Rohana
- Clinical Microbiology Laboratory, The Tzafon Medical Center, Poriya, Tiberias, Israel
| | - Oran Erster
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Centre, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Centre, Ramat Gan, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Asaf Biber
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- The Center for Geographic Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Eli Schwartz
- The Center for Geographic Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Avi Peretz
- Clinical Microbiology Laboratory, The Tzafon Medical Center, Poriya, Tiberias, Israel
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Amos Danielli
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
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3
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Perry WB, Chrispim MC, Barbosa MRF, de Souza Lauretto M, Razzolini MTP, Nardocci AC, Jones O, Jones DL, Weightman A, Sato MIZ, Montagner C, Durance I. Cross-continental comparative experiences of wastewater surveillance and a vision for the 21st century. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170842. [PMID: 38340868 DOI: 10.1016/j.scitotenv.2024.170842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
The COVID-19 pandemic has brought the epidemiological value of monitoring wastewater into sharp focus. The challenges of implementing and optimising wastewater monitoring vary significantly from one region to another, often due to the array of different wastewater systems around the globe, as well as the availability of resources to undertake the required analyses (e.g. laboratory infrastructure and expertise). Here we reflect on the local and shared challenges of implementing a SARS-CoV-2 monitoring programme in two geographically and socio-economically distinct regions, São Paulo state (Brazil) and Wales (UK), focusing on design, laboratory methods and data analysis, and identifying potential guiding principles for wastewater surveillance fit for the 21st century. Our results highlight the historical nature of region-specific challenges to the implementation of wastewater surveillance, including previous experience of using wastewater surveillance, stakeholders involved, and nature of wastewater infrastructure. Building on those challenges, we then highlight what an ideal programme would look like if restrictions such as resource were not a constraint. Finally, we demonstrate the value of bringing multidisciplinary skills and international networks together for effective wastewater surveillance.
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Affiliation(s)
| | - Mariana Cardoso Chrispim
- Environmental and Biosciences Department, School of Business, Innovation and Sustainability, Halmstad University, Kristian IV:s väg 3, 30118 Halmstad, Sweden
| | - Mikaela Renata Funada Barbosa
- Environmental Analysis Department, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil; NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Marcelo de Souza Lauretto
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Arts, Sciences and Humanities, University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo CEP 03828-000, Brazil
| | - Maria Tereza Pepe Razzolini
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Public Health, University of Sao Paulo, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Adelaide Cassia Nardocci
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Public Health, University of Sao Paulo, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Owen Jones
- School of Mathematics, Cardiff University, Cardiff CF24 4AG, UK
| | - Davey L Jones
- Environment Centre Wales, Bangor University, Bangor LL57 2UW, UK; Food Futures Institute, Murdoch University, Murdoch WA 6105, Australia
| | | | - Maria Inês Zanoli Sato
- Environmental Analysis Department, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil; NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Cassiana Montagner
- Environmental Chemistry Laboratory, Institute of Chemistry, University of Campinas, Campinas, São Paulo 13083970, Brazil
| | - Isabelle Durance
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.
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4
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Baz Lomba JA, Pires J, Myrmel M, Arnø JK, Madslien EH, Langlete P, Amato E, Hyllestad S. Effectiveness of environmental surveillance of SARS-CoV-2 as an early-warning system: Update of a systematic review during the second year of the pandemic. JOURNAL OF WATER AND HEALTH 2024; 22:197-234. [PMID: 38295081 PMCID: wh_2023_279 DOI: 10.2166/wh.2023.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The aim of this updated systematic review was to offer an overview of the effectiveness of environmental surveillance (ES) of SARS-CoV-2 as a potential early-warning system (EWS) for COVID-19 and new variants of concerns (VOCs) during the second year of the pandemic. An updated literature search was conducted to evaluate the added value of ES of SARS-CoV-2 for public health decisions. The search for studies published between June 2021 and July 2022 resulted in 1,588 publications, identifying 331 articles for full-text screening. A total of 151 publications met our inclusion criteria for the assessment of the effectiveness of ES as an EWS and early detection of SARS-CoV-2 variants. We identified a further 30 publications among the grey literature. ES confirms its usefulness as an EWS for detecting new waves of SARS-CoV-2 infection with an average lead time of 1-2 weeks for most of the publication. ES could function as an EWS for new VOCs in areas with no registered cases or limited clinical capacity. Challenges in data harmonization and variant detection require standardized approaches and innovations for improved public health decision-making. ES confirms its potential to support public health decision-making and resource allocation in future outbreaks.
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Affiliation(s)
- Jose Antonio Baz Lomba
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway E-mail:
| | - João Pires
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway; ECDC fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jorunn Karterud Arnø
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Elisabeth Henie Madslien
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Petter Langlete
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Ettore Amato
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Susanne Hyllestad
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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5
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Galani A, Markou A, Dimitrakopoulos L, Kontou A, Kostakis M, Kapes V, Diamantopoulos MA, Adamopoulos PG, Avgeris M, Lianidou E, Scorilas A, Paraskevis D, Tsiodras S, Dimopoulos MA, Thomaidis N. Delta SARS-CoV-2 variant is entirely substituted by the omicron variant during the fifth COVID-19 wave in Attica region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159062. [PMID: 36181801 PMCID: PMC9519360 DOI: 10.1016/j.scitotenv.2022.159062] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Abstract
Wastewater analysis is the most attractive alternative way for the quantification and variant profiling of SARS-CoV-2. Infection dynamics can be monitored by RT-qPCR assays while NGS can provide evidence for the presence of existing or new emerging SARS-CoV-2 variants. Herein, apart from the infection dynamic in Attica since June 1st, 2021, the monitoring of 9 mutations of the omicron and 4 mutations of the delta SARS-CoV-2 variants, utilizing both novel Nested-Seq and RT-PCR, is reported and the substitution of the delta variant (B.1.617.2) by the omicron variant (B.1.1.529) in Attica, Greece within approximately one month is highlighted. The key difference between the two methodologies is discovery power. RT-PCR can only detect known sequences cost-effectively, while NGS is a hypothesis-free approach that does not require prior knowledge to detect novel genes. Overall, the potential of wastewater genomic surveillance for the early discovery and monitoring of variants important for disease management at the community level is underlined. This is the first study, reporting the SARS-CoV-2 infection dynamic for an extended time period and the first attempt to monitor two of the most severe variants with two different methodologies in Greece.
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Affiliation(s)
- Aikaterini Galani
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Athina Markou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Lampros Dimitrakopoulos
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Aikaterini Kontou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Marios Kostakis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Vasileios Kapes
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece; Laboratory of Clinical Biochemistry - Molecular Diagnostics, Second Department of Pediatrics, "P. & A. Kyriakou" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Sotirios Tsiodras
- Fourth Department of Internal Medicine, School of Medicine, University General Hospital Attikon, National and Kapodistrian University of Athens, Greece
| | | | - Nikolaos Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, University Campus, Zografou, 15771 Athens, Greece.
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6
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Clark JR, Terwilliger A, Avadhanula V, Tisza M, Cormier J, Javornik-Cregeen S, Ross MC, Hoffman KL, Troisi C, Hanson B, Petrosino J, Balliew J, Piedra PA, Rios J, Deegan J, Bauer C, Wu F, Mena KD, Boerwinkle E, Maresso AW. Wastewater pandemic preparedness: Toward an end-to-end pathogen monitoring program. Front Public Health 2023; 11:1137881. [PMID: 37026145 PMCID: PMC10070845 DOI: 10.3389/fpubh.2023.1137881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/09/2023] [Indexed: 04/08/2023] Open
Abstract
Molecular analysis of public wastewater has great potential as a harbinger for community health and health threats. Long-used to monitor the presence of enteric viruses, in particular polio, recent successes of wastewater as a reliable lead indicator for trends in SARS-CoV-2 levels and hospital admissions has generated optimism and emerging evidence that similar science can be applied to other pathogens of pandemic potential (PPPs), especially respiratory viruses and their variants of concern (VOC). However, there are substantial challenges associated with implementation of this ideal, namely that multiple and distinct fields of inquiry must be bridged and coordinated. These include engineering, molecular sciences, temporal-geospatial analytics, epidemiology and medical, and governmental and public health messaging, all of which present their own caveats. Here, we outline a framework for an integrated, state-wide, end-to-end human pathogen monitoring program using wastewater to track viral PPPs.
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Affiliation(s)
- Justin R. Clark
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Austen Terwilliger
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Michael Tisza
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Juwan Cormier
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Sara Javornik-Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Matthew Clayton Ross
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Kristi Louise Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Catherine Troisi
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Blake Hanson
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - John Balliew
- El Paso Water Utility, El Paso, TX, United States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Pediatrics Department, Baylor College of Medicine, Houston, TX, United States
| | - Janelle Rios
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Jennifer Deegan
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Cici Bauer
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Department of Biostatistics and Data Science, UTHealth School of Public Health, Houston, TX, United States
| | - Fuqing Wu
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Kristina D. Mena
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Eric Boerwinkle
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Anthony W. Maresso
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Anthony W. Maresso
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