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Han D, Linares P, Holm RH, Chandran K, Smith T. Wastewater threshold as an indicator of COVID-19 cases in correctional facilities for public health response: A modeling study. WATER RESEARCH 2024; 260:121934. [PMID: 38908309 DOI: 10.1016/j.watres.2024.121934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/24/2024]
Abstract
Although prison facilities are not fully isolated from the communities in which they are located, most of the population is confined and requires high levels of health vigilance and protection. This study aimed to examine the dynamic relationship between facility-level wastewater viral concentrations and the probability of at least one positive COVID-19 case within the facility. The study period was from January 11, 2021 to May 8, 2023. Wastewater samples were collected and analyzed for SARS-CoV-2 (N1) and pepper mild mottle virus (PMMoV) three times weekly across 14 prison facilities in Kentucky (USA). Positive clinical case reports were also provided. A hierarchical Bayesian facility-level temporal model with a latent lagged process was developed. We modeled facility-specific SARS-CoV-2 (N1) normalized by the PMMoV wastewater concentration ratio threshold associated with at least one COVID-19 clinical case at an 80 % probability. The threshold differed among facilities. Across the 14 facilities, our model demonstrates a mean capture rate of 94.95 % via the N1/PMMoV ratio threshold with pts≥0.5. However, as the pts threshold was set higher, such as at ≥0.9, the mean capture rate of the model was reduced to 60 %. This robust performance underscores the effectiveness of the model for accurately detecting the presence of positive COVID-19 cases among incarcerated people. The findings of this study provide a facility-specific threshold model for public health response based on frequent wastewater surveillance.
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Affiliation(s)
- Dan Han
- Department of Mathematics, College of Arts & Sciences, University of Louisville, 2301 S. 3rd St., Louisville, KY 40292, USA
| | - Pamela Linares
- Department of Mathematics, College of Arts & Sciences, University of Louisville, 2301 S. 3rd St., Louisville, KY 40292, USA
| | - Rochelle H Holm
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA.
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, 500 W. 120th St., New York, NY 10027, USA
| | - Ted Smith
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA
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2
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Chen C, Kaur G, Adiga A, Espinoza B, Venkatramanan S, Warren A, Lewis B, Crow J, Singh R, Lorentz A, Toney D, Marathe M. Wastewater-based Epidemiology for COVID-19 Surveillance: A Survey. ARXIV 2024:arXiv:2403.15291v1. [PMID: 38562450 PMCID: PMC10984000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The pandemic of COVID-19 has imposed tremendous pressure on public health systems and social economic ecosystems over the past years. To alleviate its social impact, it is important to proactively track the prevalence of COVID-19 within communities. The traditional way to estimate the disease prevalence is to estimate from reported clinical test data or surveys. However, the coverage of clinical tests is often limited and the tests can be labor-intensive, requires reliable and timely results, and consistent diagnostic and reporting criteria. Recent studies revealed that patients who are diagnosed with COVID-19 often undergo fecal shedding of SARS-CoV-2 virus into wastewater, which makes wastewater-based epidemiology (WBE) for COVID-19 surveillance a promising approach to complement traditional clinical testing. In this paper, we survey the existing literature regarding WBE for COVID-19 surveillance and summarize the current advances in the area. Specifically, we have covered the key aspects of wastewater sampling, sample testing, and presented a comprehensive and organized summary of wastewater data analytical methods. Finally, we provide the open challenges on current wastewater-based COVID-19 surveillance studies, aiming to encourage new ideas to advance the development of effective wastewater-based surveillance systems for general infectious diseases.
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Affiliation(s)
- Chen Chen
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Gursharn Kaur
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Aniruddha Adiga
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Baltazar Espinoza
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Srinivasan Venkatramanan
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Andrew Warren
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Bryan Lewis
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
| | - Justin Crow
- Virginia Department of Health, Richmond, 23219, United States
| | - Rekha Singh
- Virginia Department of Health, Richmond, 23219, United States
| | - Alexandra Lorentz
- Division of Consolidated Laboratory Services, Department of General Services, Richmond, 23219, United States
| | - Denise Toney
- Division of Consolidated Laboratory Services, Department of General Services, Richmond, 23219, United States
| | - Madhav Marathe
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States
- Department of Computer Science, University of Virginia, Charlottesville, 22904, United States
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3
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Anupong S, Chadsuthi S, Hongsing P, Hurst C, Phattharapornjaroen P, Rad S.M. AH, Fernandez S, Huang AT, Vatanaprasan P, Saethang T, Luk-in S, Storer RJ, Ounjai P, Devanga Ragupathi NK, Kanthawee P, Ngamwongsatit N, Badavath VN, Thuptimdang W, Leelahavanichkul A, Kanjanabuch T, Miyanaga K, Cui L, Nanbo A, Shibuya K, Kupwiwat R, Sano D, Furukawa T, Sei K, Higgins PG, Kicic A, Singer AC, Chatsuwan T, Trowsdale S, Abe S, Ishikawa H, Amarasiri M, Modchang C, Wannigama DL. Exploring indoor and outdoor dust as a potential tool for detection and monitoring of COVID-19 transmission. iScience 2024; 27:109043. [PMID: 38375225 PMCID: PMC10875567 DOI: 10.1016/j.isci.2024.109043] [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: 11/09/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
This study investigated the potential of using SARS-CoV-2 viral concentrations in dust as an additional surveillance tool for early detection and monitoring of COVID-19 transmission. Dust samples were collected from 8 public locations in 16 districts of Bangkok, Thailand, from June to August 2021. SARS-CoV-2 RNA concentrations in dust were quantified, and their correlation with community case incidence was assessed. Our findings revealed a positive correlation between viral concentrations detected in dust and the relative risk of COVID-19. The highest risk was observed with no delay (0-day lag), and this risk gradually decreased as the lag time increased. We observed an overall decline in viral concentrations in public places during lockdown, closely associated with reduced human mobility. The effective reproduction number for COVID-19 transmission remained above one throughout the study period, suggesting that transmission may persist in locations beyond public areas even after the lockdown measures were in place.
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Affiliation(s)
- Suparinthon Anupong
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sudarat Chadsuthi
- Department of Physics, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Parichart Hongsing
- Mae Fah Luang University Hospital, Chiang Rai, Thailand
- School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, Thailand
| | - Cameron Hurst
- Molly Wardaguga Research Centre, Charles Darwin University, Brisbane, QLD, Australia
- Statistics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Phatthranit Phattharapornjaroen
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Academy, Gothenburg University, 40530 Gothenburg, Sweden
| | - Ali Hosseini Rad S.M.
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago 9010, New Zealand
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Stefan Fernandez
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Angkana T. Huang
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Sirirat Luk-in
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Robin James Storer
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Naveen Kumar Devanga Ragupathi
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries, The University of Sheffield, Sheffield, UK
- Division of Microbial Interactions, Department of Research and Development, Bioberrys Healthcare and Research Centre, Vellore 632009, India
| | - Phitsanuruk Kanthawee
- Public Health Major, School of Health Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Natharin Ngamwongsatit
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Vishnu Nayak Badavath
- School of Pharmacy & Technology Management, SVKM’s Narsee Monjee Institute of Management Studies (NMIMS), Hyderabad 509301, India
| | - Wanwara Thuptimdang
- Institute of Biomedical Engineering, Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Talerngsak Kanjanabuch
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Dialysis Policy and Practice Program (DiP3), School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Peritoneal Dialysis Excellence Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Kazuhiko Miyanaga
- Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Longzhu Cui
- Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Asuka Nanbo
- The National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Kenji Shibuya
- Tokyo Foundation for Policy Research, Minato-ku, Tokyo, Japan
| | - Rosalyn Kupwiwat
- Department of Dermatology. Faculty of Medicine Siriraj Hospital. Mahidol University, Bangkok, Thailand
| | - Daisuke Sano
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, Japan
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Takashi Furukawa
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Minato City, Tokyo 108-8641, Japan
| | - Kazunari Sei
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Minato City, Tokyo 108-8641, Japan
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands WA 6009, Australia
- School of Population Health, Curtin University, Bentley WA 6102, Australia
| | | | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sam Trowsdale
- Department of Environmental Science, University of Auckland, Auckland 1010, New Zealand
| | - Shuichi Abe
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Hitoshi Ishikawa
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata 990-2212, Japan
| | - Mohan Amarasiri
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Minato City, Tokyo 108-8641, Japan
| | - Charin Modchang
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Centre of Excellence in Mathematics, MHESI, Bangkok 10400, Thailand
- Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, 328 Si Ayutthaya Road, Bangkok 10400, Thailand
| | - Dhammika Leshan Wannigama
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries, The University of Sheffield, Sheffield, UK
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata 990-2212, Japan
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Pathogen Hunter’s Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
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Haskell BR, Dhiyebi HA, Srikanthan N, Bragg LM, Parker WJ, Giesy JP, Servos MR. Implementing an adaptive, two-tiered SARS-CoV-2 wastewater surveillance program on a university campus using passive sampling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168998. [PMID: 38040360 DOI: 10.1016/j.scitotenv.2023.168998] [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: 10/13/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023]
Abstract
Building-level wastewater-based surveillance (WBS) has been increasingly applied upstream from wastewater treatment plants to conduct targeted monitoring for SARS-CoV-2. In this study, a two-tiered, trigger-based wastewater surveillance program was developed on a university campus to monitor dormitory wastewater. The objective was to determine if passive sampling with cotton gauze as a sampling medium could be used to support institution-level public health action. Two nucleocapsid gene targets (N1 and N2) of SARS-CoV-2 as well as the endogenous fecal indicator pepper mild mottle virus (PMMoV) were quantified using RT-qPCR. >500 samples were analyzed during two contrasting surveillance periods. In the Fall of 2021 community viral burden was low and a tiered sampling network was able to isolate individual clinical cases at the building-scale. In the Winter of 2022 wastewater signals were quickly elevated by the emergence of the highly transmissible SARS-CoV-2 Omicron (B.1.1.529) variant. Prevalence of SARS-CoV-2 shifted surveillance objectives from isolating cases to monitoring trends, revealing both the benefits and limitations of a tiered surveillance design under different public health situations. Normalization of SARS-CoV-2 by PMMoV was not reflective of upstream population differences, suggesting saturation of the material occurred during the exposure period. The passive sampling method detected nearly all known clinical cases and in one instance was able to identify one pre-symptomatic individual days prior to confirmation by clinical test. Comparisons between campus samplers and municipal wastewater influent suggests that the spread of COVID-19 on the campus was similar to that of the broader community. The results demonstrate that passive sampling is an effective tool that can produce semi-quantitative data capable of tracking temporal trends to guide targeted public health decision-making at an institutional level. Practitioners of WBS can utilize these results to inform surveillance program designs that prioritize efficient resource use and rapid reporting.
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Affiliation(s)
- Blake R Haskell
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada.
| | - Hadi A Dhiyebi
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada.
| | - Nivetha Srikanthan
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
| | - Leslie M Bragg
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada.
| | - Wayne J Parker
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada.
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, 44 Campus Dr., Saskatoon, Saskatchewan S7N 5B3, Canada; Department of Environmental Science, Baylor University, 1 Bear Trail, Waco, TX 76798, USA
| | - Mark R Servos
- Department of Biology, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada.
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5
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Germano ER, Flores T, Freed GS, Kim K, Tulinsky GH, Yang A, Rose OJ, Ray CA, Autry A, Catallozzi M, Mailloux BJ, Miranda JJL. Building-level wastewater surveillance localizes interseasonal influenza variation. mSphere 2024; 9:e0060023. [PMID: 38168676 PMCID: PMC10826355 DOI: 10.1128/msphere.00600-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024] Open
Abstract
Influenza virus poses a recurring threat to public health and infects many populations in annual waves of generally unpredictable magnitude and timing. We aimed to detect the arrival and estimate the case magnitude of seasonal influenza A in urban New York City college dormitory buildings. Our wastewater-based surveillance (WBS) program measured viral RNA in the sewage outflow of three dormitories at Barnard College in 2021 and 2022. Wastewater test positivity strongly correlated with New York County clinical cases (Kendall's τ = 0.58). Positive wastewater samples are also associated with campus clinical cases. The 2022 data stand in stark contrast to the 2021 results by revealing the more frequent and earlier presence of influenza A. The increase in positive tests is significant (P < 0.01). It is further noteworthy that positive samples were not evenly distributed among buildings. Surveillance additionally identified the influenza A H3 subtype but did not detect any influenza B. We also systematically analyzed our viral purification protocol to identify in which fraction influenza can be found. While virus can be found in solid fractions, a substantial quantity remains in the final liquid fraction. Our work focuses on individual buildings rather than larger sewersheds because buildings may localize interseasonal influenza variation to specific subpopulations. Our results highlight the potential value of building-level WBS in measuring influenza incidence to help guide public health intervention.IMPORTANCESeasonal influenza remains a major public health burden. We monitored influenza A in dormitory wastewater of a New York City college in 2021 and 2022. Longitudinal samples acquired over consecutive years allowed measurement of individual buildings between seasons. We uncovered building-level changes in the magnitude and timing of test positivity concordant with clinical cases. Surveillance also localized the heterogeneity of influenza variation during the large 2022 seasonal surge. The ability to detect such changes could be leveraged as part of a public health response.
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Affiliation(s)
- Emma R. Germano
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
| | - Tiffany Flores
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
| | - Grace S. Freed
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
| | - Kang Kim
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
| | - Grace H. Tulinsky
- Environmental Science Department, Barnard College, Columbia University, New York, New York, USA
| | - Annie Yang
- Environmental Science Department, Barnard College, Columbia University, New York, New York, USA
| | - Oliver J. Rose
- Office of Facilities Services, Barnard College, Columbia University, New York, New York, USA
| | - Caroline A. Ray
- Office of Health and Wellness, Barnard College, Columbia University, New York, New York, USA
| | - April Autry
- Office of Health and Wellness, Barnard College, Columbia University, New York, New York, USA
- Heilbrunn Department of Population and Family Health, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Marina Catallozzi
- Office of Health and Wellness, Barnard College, Columbia University, New York, New York, USA
- Heilbrunn Department of Population and Family Health, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Brian J. Mailloux
- Environmental Science Department, Barnard College, Columbia University, New York, New York, USA
| | - JJ L. Miranda
- Department of Biology, Barnard College, Columbia University, New York, New York, USA
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6
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Conway MJ, Yang H, Revord LA, Novay MP, Lee RJ, Ward AS, Abel JD, Williams MR, Uzarski RL, Alm EW. Chronic shedding of a SARS-CoV-2 Alpha variant in wastewater. BMC Genomics 2024; 25:59. [PMID: 38218804 PMCID: PMC10787452 DOI: 10.1186/s12864-024-09977-7] [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: 08/15/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Central Michigan University (CMU) participated in a state-wide SARS-CoV-2 wastewater monitoring program since 2021. Wastewater samples were collected from on-campus sites and nine off-campus wastewater treatment plants servicing small metropolitan and rural communities. SARS-CoV-2 genome copies were quantified using droplet digital PCR and results were reported to the health department. RESULTS One rural, off-campus site consistently produced higher concentrations of SARS-CoV-2 genome copies. Samples from this site were sequenced and contained predominately a derivative of Alpha variant lineage B.1.1.7, detected from fall 2021 through summer 2023. Mutational analysis of reconstructed genes revealed divergence from the Alpha variant lineage sequence over time, including numerous mutations in the Spike RBD and NTD. CONCLUSIONS We discuss the possibility that a chronic SARS-CoV-2 infection accumulated adaptive mutations that promoted long-term infection. This study reveals that small wastewater treatment plants can enhance resolution of rare events and facilitate reconstruction of viral genomes due to the relative lack of contaminating sequences.
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Affiliation(s)
- Michael J Conway
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA.
- Institute for Great Lakes Research, Central Michigan University, Mt. Pleasant, MI, USA.
| | - Hannah Yang
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Lauren A Revord
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Michael P Novay
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Rachel J Lee
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Avery S Ward
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Jackson D Abel
- Foundational Sciences, Central Michigan University, College of Medicine, Mt. Pleasant, MI, USA
| | - Maggie R Williams
- School of Engineering & Technology, Central Michigan University, Mt. Pleasant, MI, USA
- Institute for Great Lakes Research, Central Michigan University, Mt. Pleasant, MI, USA
| | - Rebecca L Uzarski
- Department of Biology and Herbert H. and Grace A. Dow College of Health, Professions, Central Michigan University, Mt. Pleasant, MI, USA
| | - Elizabeth W Alm
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, USA
- Institute for Great Lakes Research, Central Michigan University, Mt. Pleasant, MI, USA
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