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Tian Y, Dong L. On-The-Spot Sampling and Detection of Viral Particles on Solid Surfaces Using a Sponge Virus Sensor Incorporated with Finger-Press Fluid Release. ACS Sens 2024. [PMID: 38564767 DOI: 10.1021/acssensors.3c02766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
This paper presents a sponge-based electrochemical sensor for rapid, on-site collection and analysis of infectious viruses on solid surfaces. The device utilizes a conducting porous sponge modified with graphene, graphene oxide, and specific antibodies. The sponge serves as a hydrophilic porous electrode capable of liquid collection and electrochemical measurements. The device operation involves spraying an aqueous solution on a target surface, swiping the misted surface using the sponge, discharging an electrolyte solution with a simple finger press, and performing in situ incubation and electrochemical measurements. By leveraging the water-absorbing ability of the biofunctionalized conducting sponge, the sensor can effectively collect and quantify virus particles from the surface. The portability of the device is enhanced by introducing a push-release feature that dispenses the liquid electrolyte from a miniature reservoir onto the sensor surface. This reservoir has sharp edges to rupture a liquid sealing film with a finger press. The ability of the device to sample and quantify viral particles is demonstrated by using influenza A virus as the model. The sensor provided a calculated limit of detection of 0.4 TCID50/mL for H1N1 virus, along with a practical concentration range from 1-106 TCID50/mL. Additionally, it achieves a 15% collection efficiency from single-run swiping on a tabletop surface. This versatile device allows for convenient on-site virus detection within minutes, eliminating the need for sample pretreatment and simplifying the entire sample collecting and measuring process. This device presents significant potential for rapid virus detection on solid surfaces.
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Affiliation(s)
- Yang Tian
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Liang Dong
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011, United States
- Microelectronics Research Center, Iowa State University, Ames, Iowa 50011, United States
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2
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Ahuja S, Tallur S, Kondabagil K. Simultaneous microbial capture and nucleic acid extraction from wastewater with minimal pre-processing and high recovery efficiency. Sci Total Environ 2024; 918:170347. [PMID: 38336063 DOI: 10.1016/j.scitotenv.2024.170347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/22/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
The COVID-19 pandemic accelerated research towards developing low-cost assays for automated urban wastewater monitoring assay that can be integrated into an environmental surveillance system for early warning of frequent disease outbreaks and future pandemics. Microbial concentration is one of the most challenging steps in wastewater surveillance, due to the sample heterogeneity and low pathogen load. Keeping in mind the requirements of large-scale testing in densely populated low- or middle-income countries (LMICs), such assays would need to be low-cost and have rapid turnaround time with high recovery efficiency. In this study, two such methods are presented and evaluated against commercially available kits for pathogen detection in wastewater. The first method utilizes paper dipsticks while the second method comprises of a PTFE membrane filter (PMF) integrated with a peristaltic pump. Both methods were used to concentrate and isolate nucleic acids from different microbes such as SARS-CoV-2, pepper mild mottle virus (PMMoV), bacteriophage Phi6, and E. coli from wastewater samples with minimal or no sample pre-processing. While the paper dipstick method is suitable for sub-milliliter sample volume, the PMF method can be used with larger volumes of wastewater sample (40 mL) and can detect multiple microbes with recovery efficiency comparable to commercially available kits.
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Affiliation(s)
- Shruti Ahuja
- Centre for Research in Nanotechnology & Science (CRNTS), IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
| | - Siddharth Tallur
- Department of Electrical Engineering, IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
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3
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Amirali A, Babler KM, Sharkey ME, Beaver CC, Boone MM, Comerford S, Cooper D, Currall BB, Goodman KW, Grills GS, Kobetz E, Kumar N, Laine J, Lamar WE, Mason CE, Reding BD, Roca MA, Ryon K, Schürer SC, Shukla BS, Solle NS, Stevenson M, Tallon JJ, Vidović D, Williams SL, Yin X, Solo-Gabriele HM. Wastewater based surveillance can be used to reduce clinical testing intensity on a university campus. Sci Total Environ 2024; 918:170452. [PMID: 38296085 PMCID: PMC10923133 DOI: 10.1016/j.scitotenv.2024.170452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/30/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024]
Abstract
Clinical testing has been a vital part of the response to and suppression of the COVID-19 pandemic; however, testing imposes significant burdens on a population. College students had to contend with clinical testing while simultaneously dealing with health risks and the academic pressures brought on by quarantines, changes to virtual platforms, and other disruptions to daily life. The objective of this study was to analyze whether wastewater surveillance can be used to decrease the intensity of clinical testing while maintaining reliable measurements of diseases incidence on campus. Twelve months of human health and wastewater surveillance data for eight residential buildings on a university campus were analyzed to establish how SARS-CoV-2 levels in the wastewater can be used to minimize clinical testing burden on students. Wastewater SARS-CoV-2 levels were used to create multiple scenarios, each with differing levels of testing intensity, which were compared to the actual testing volumes implemented by the university. We found that scenarios in which testing intensity fluctuations matched rise and falls in SARS-CoV-2 wastewater levels had stronger correlations between SARS-CoV-2 levels and recorded clinical positives. In addition to stronger correlations, most scenarios resulted in overall fewer weekly clinical tests performed. We suggest the use of wastewater surveillance to guide COVID-19 testing as it can significantly increase the efficacy of COVID-19 surveillance while reducing the burden placed on college students during a pandemic. Future efforts should be made to integrate wastewater surveillance into clinical testing strategies implemented on college campuses.
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Affiliation(s)
- Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Kristina M Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Mark E Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136, FL, USA
| | - Cynthia C Beaver
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Melinda M Boone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Samuel Comerford
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136, FL, USA
| | | | - Benjamin B Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Kenneth W Goodman
- Frost Institute for Data Science & Computing, University of Miami, Coral Gables, FL 33146, USA; Institute for Bioethics and Health Policy, University of Miami Miller School of Medicine, Miami, 33136, FL, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Erin Kobetz
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136, FL, USA
| | - Naresh Kumar
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Walter E Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL 33136, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Brian D Reding
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Matthew A Roca
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA
| | - Stephan C Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL 33146, USA
| | - Bhavarth S Shukla
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136, FL, USA
| | - Natasha Schaefer Solle
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136, FL, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mario Stevenson
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - John J Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL 33146, USA
| | - Dušica Vidović
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Sion L Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xue Yin
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Rishan ST, Kline RJ, Rahman MS. New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review. Environ Sci Pollut Res Int 2024; 31:11406-11427. [PMID: 38183542 DOI: 10.1007/s11356-023-31776-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024]
Abstract
Ecosystems are multifaceted and complex systems and understanding their composition is crucial for the implementation of efficient conservation and management. Conventional approaches to biodiversity surveys can have limitations in detecting the complete range of species present. In contrast, the study of environmental RNA (eRNA) offers a non-invasive and comprehensive method for monitoring and evaluating biodiversity across different ecosystems. Similar to eDNA, the examination of genetic material found in environmental samples can identify and measure many species, including ones that pose challenges to traditional methods. However, eRNA is degraded quickly and therefore shows promise in detection of living organisms closer to their actual location than eDNA methods. This method provides a comprehensive perspective on the well-being of ecosystems, facilitating the development of focused conservation approaches to save at-risk species and uphold ecological equilibrium. Furthermore, eRNA has been recognized as a valuable method for the identification of COVID-19 in the environment, besides its established uses in biodiversity protection. The SARS-CoV-2 virus, which is accountable for the worldwide epidemic, releases RNA particles into the surrounding environment via human waste, providing insights into the feasibility of detecting it in wastewater and other samples taken from the environment. In this article, we critically reviewed the recent research activities that use the eRNA method, including its utilization in biodiversity conservation, ecological surveillance, and ecotoxicological monitoring as well as its innovative potential in identifying COVID-19. Through this review, the reader can understand the recent developments, prospects, and challenges of eRNA research in ecosystem management and biodiversity conservation.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, TX, USA.
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Long A, Loethen K, Behzadnezhad A, Zhang W. A snapshot of SARS-CoV-2 viral RNA throughout wastewater treatment plants in Arkansas. Water Environ Res 2024; 96:e10992. [PMID: 38291790 DOI: 10.1002/wer.10992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can spread the viral RNA in wastewater by the feces of those experience COVID-19 symptoms. While wastewater monitoring of SARS-CoV-2 in the raw sewage has been confirmed as an effective tool to predict COVID-19 infection, the goal of this study is to assess the presence of SARS-CoV-2 viral RNA throughout various wastewater treatment processes. Wastewater samples were collected from wastewater treatment plants (WWTPs) in the state of Arkansas from August 2020 to June 2021 and measured for the relative concentration of SARS-CoV-2 viral RNA using RT-qPCR. The gene concentrations in the raw wastewater measured in this study were similar to other published studies, targeting the N1 and N2 genes of the virus. The viral RNA concentration was measured after each wastewater treatment step within WWTPs, including primary sedimentation, activated sludge, filtration and disinfection. Results show the most viral RNA removal occurred in the secondary treatment (activated sludge). The viral RNA was only occasionally detected after disinfection (chlorination or UV disinfection). Overall, WWTPs can remove the SARS-CoV-2 viral RNA at an average of 98.7%, while complete removal was achieved on 82% of the sampling days. Further investigation is required to ensure complete viral RNA removal from wastewater such as improving existing treatment process or supplementing with additional treatment steps. PRACTITIONER POINTS: The viral RNA of SARS-CoV-2 was detected in Arkansas wastewater treatment plants. SARS-CoV-2 was rarely detected in treated effluent from wastewater treatment plants. Activated sludge was effective removing SARS-CoV-2 viral RNA from wastewater. This study was limited by the direct RNA extraction from wastewater, which lowered the sensitivity of detection.
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Affiliation(s)
- Aaron Long
- Department of Civil Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Katie Loethen
- Department of Biological Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Asal Behzadnezhad
- Department of Civil Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Wen Zhang
- Department of Civil Engineering, University of Arkansas, Fayetteville, Arkansas, USA
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7
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Kumar M, Joshi M, Prajapati B, Sirikanchana K, Mongkolsuk S, Kumar R, Gallage TP, Joshi C. Early warning of statewide COVID-19 Omicron wave by sentineled urbanized sewer network monitoring using digital PCR in a province capital city, of Gujarat, India. Sci Total Environ 2023; 905:167060. [PMID: 37709091 DOI: 10.1016/j.scitotenv.2023.167060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/15/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Wastewater-based epidemiology (WBE) has been implemented globally. However, there remains confusion about the number and frequency of samples to be collected, as well as which types of treatment systems can provide reliable specific details about the virus prevalence in specific areas or communities, enabling prompt management and intervention measures. More research is necessary to fully comprehend the possibility of deploying sentinel locations in sewer networks in larger geographic areas. The present study introduces the first report on wastewater-based surveillance in Gandhinagar City using digital PCR (d-PCR) as a SARS-Cov-2 quantification tool, which describes the viral load from five pumping stations in Gandhinagar from October 2021 to March 2022. Raw wastewater samples (n = 119) were received and analyzed weekly to detect SARS-CoV-2 RNA, 109 of which were positive for N1 or N2 genes. The monthly variation analysis in viral genome copies depicted the highest concentrations in January 2022 and February 2022 (p < 0.05; Wilcoxon signed rank test) coincided with the Omicron wave, which contributed mainly from Vavol and Jaspur pumping stations. Cross-correlation analysis indicated that WBE from five stations in Gandhinagar, i.e., capital city sewer networks, provided two-week lead times to the citywide and statewide active cases (time-series cross-correlation function [CCF]; 0.666 and 0.648, respectively), mainly from individual contributions of the urbanized Kudasan and Vavol stations (CCF; 0.729 and 0.647, respectively). These findings suggest that sewer pumping stations in urbanized neighborhoods can be used as sentinel sites for statewide clinical surveillance and that WBE surveillance using digital PCR can be an efficient monitoring and management tool.
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Affiliation(s)
- Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India; Escuela de Ingeniería y Ciencias, Technologico de Monterrey, Campus Monterey, Monterrey 64849, Nuevo Leon, Mexico.
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Bhumika Prajapati
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Rakesh Kumar
- School of Ecology and Environment Studies, Nalanda University, Rajgir 803116, India; Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA
| | - Tharindu Pollwatta Gallage
- Program in Environmental Toxicology, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
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8
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Triggiano F, De Giglio O, Apollonio F, Brigida S, Fasano F, Mancini P, Bonanno Ferraro G, Veneri C, La Rosa G, Suffredini E, Lucentini L, Ungaro N, Di Vittorio G, Mongelli O, Albano N, Montagna MT. Wastewater-based Epidemiology and SARS-CoV-2: Variant Trends in the Apulia Region (Southern Italy) and Effect of Some Environmental Parameters. Food Environ Virol 2023; 15:331-341. [PMID: 37735299 PMCID: PMC10654208 DOI: 10.1007/s12560-023-09565-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
During the COVID-19 pandemic, wastewater monitoring has been used to monitor the levels of SARS-CoV-2 RNA entering the sewerage system. In Italy, the Istituto Superiore di Sanità coordinated the SARI project (Sorveglianza Ambientale Reflue in Italia) to detect SARS-CoV-2 and its variants. In this study, the concentration of SARS-CoV-2 and its variants in raw wastewater against COVID-19 cases was evaluated together with the effect of temperature and precipitation on virus spread. We validated a predictive model, proposed by De Giglio et al., 2021, to establish the number of COVID-19 cases/100,000 inhabitants. A receiver operating characteristic curve model was applied to predict the number of COVID-19 cases and Poisson regression was applied to study the effect of temperature and rainfall on viral load. In Apulia, from October 2021 to December 2022, we analyzed 1041 samples, of which 985 (94.6%) tested positive for SARS-CoV-2. Median atmospheric temperature was inversely proportional to viral load in wastewater; no correlation was found with precipitation. The predictive model confirmed that at least 11 cases/100,000 inhabitants would occur in the 15 days following the detection of the virus in wastewater. Environmental surveillance of SARS-CoV-2 can be used to map the virus and its variants.
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Affiliation(s)
- Francesco Triggiano
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Osvalda De Giglio
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy.
| | - Francesca Apollonio
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Silvia Brigida
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Campus Ecotekne, Monteroni di Lecce, Lecce, 73047, Italy
| | - Fabrizio Fasano
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Giusy Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Carolina Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Luca Lucentini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | - Nicola Ungaro
- Agency for the Environmental Prevention and Protection (ARPA Puglia), Corso Trieste 27, Bari, 70126, Italy
| | | | - Onofrio Mongelli
- Department of Health Promotion and Animal Welfare, Apulia Region, Bari, Italy
| | - Nelhudoff Albano
- Department of Health Promotion and Animal Welfare, Apulia Region, Bari, Italy
| | - Maria Teresa Montagna
- Interdisciplinary Department of Medicine, University of Bari Aldo Moro, Piazza G. Cesare 11, Bari, 70124, Italy
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9
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Babler KM, Sharkey ME, Amirali A, Boone MM, Comerford S, Currall BB, Grills GS, Laine J, Mason CE, Reding B, Schürer S, Stevenson M, Vidović D, Williams SL, Solo-Gabriele HM. Expanding a Wastewater-Based Surveillance Methodology for DNA Isolation from a Workflow Optimized for SARS-CoV-2 RNA Quantification. J Biomol Tech 2023; 34:3fc1f5fe.dfa8d906. [PMID: 38268997 PMCID: PMC10805363 DOI: 10.7171/3fc1f5fe.dfa8d906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Wastewater-based surveillance (WBS) is a noninvasive, epidemiological strategy for assessing the spread of COVID-19 in communities. This strategy was based upon wastewater RNA measurements of the viral target, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The utility of WBS for assessing the spread of COVID-19 has motivated research to measure targets beyond SARS-CoV-2, including pathogens containing DNA. The objective of this study was to establish the necessary steps for isolating DNA from wastewater by modifying a long-standing RNA-specific extraction workflow optimized for SARS-CoV-2 detection. Modifications were made to the sample concentration process and included an evaluation of bead bashing prior to the extraction of either DNA or RNA. Results showed that bead bashing reduced detection of RNA from wastewater but improved recovery of DNA as assessed by quantitative polymerase chain reaction (qPCR). Bead bashing is therefore not recommended for the quantification of RNA viruses using qPCR. Whereas for Mycobacterium bacterial DNA isolation, bead bashing was necessary for improving qPCR quantification. Overall, we recommend 2 separate workflows, one for RNA viruses that does not include bead bashing and one for other microbes that use bead bashing for DNA isolation. The experimentation done here shows that current-standing WBS program methodologies optimized for SARS-CoV-2 need to be modified and reoptimized to allow for alternative pathogens to be readily detected and monitored, expanding its utility as a tool for public health assessment.
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Affiliation(s)
- Kristina M. Babler
- Department of ChemicalEnvironmental and Materials
EngineeringUniversity of MiamiCoral GablesFlorida33124USA
| | - Mark E. Sharkey
- Department of MedicineUniversity of Miami Miller School
of MedicineMiamiFlorida33136USA
| | - Ayaaz Amirali
- Department of ChemicalEnvironmental and Materials
EngineeringUniversity of MiamiCoral GablesFlorida33124USA
| | - Melinda M. Boone
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - Samuel Comerford
- Department of MedicineUniversity of Miami Miller School
of MedicineMiamiFlorida33136USA
| | - Benjamin B. Currall
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - George S. Grills
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - Jennifer Laine
- Environmental Health and SafetyUniversity of MiamiMiamiFlorida33136USA
| | - Christopher E. Mason
- Department of Physiology and BiophysicsWeill Cornell
MedicineNew YorkNew York10065USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud
Institute for Computational BiomedicineWeill Cornell MedicineNew
YorkNew York10065USA
- The WorldQuant Initiative for Quantitative PredictionWeill Cornell MedicineNew YorkNew YorkUSA 10065USA
| | - Brian Reding
- Environmental Health and SafetyUniversity of MiamiMiamiFlorida33136USA
| | - Stephan Schürer
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
- Department of Molecular and Cellular PharmacologyUniversity of Miami Miller School of MedicineMiamiFlorida33136USA
- Institute for Data Science & Computing, University of
MiamiCoral GablesFlorida33146USA
| | - Mario Stevenson
- Department of MedicineUniversity of Miami Miller School
of MedicineMiamiFlorida33136USA
| | - Dušica Vidović
- Department of Molecular and Cellular PharmacologyUniversity of Miami Miller School of MedicineMiamiFlorida33136USA
| | - Sion L. Williams
- Sylvester Comprehensive Cancer CenterUniversity of Miami
Miller School of MedicineMiamiFlorida33136USA
| | - Helena M. Solo-Gabriele
- Department of ChemicalEnvironmental and Materials
EngineeringUniversity of MiamiCoral GablesFlorida33124USA
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10
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Yang J, Sun D, Xia T, Shi S, Suo J, Kuang H, Sun N, Hu H, Zheng Z, Zhou Y, Li X, Chen S, Huang H, Yan Z. Monitoring Prevalence and Persistence of Environmental Contamination by SARS-CoV-2 RNA in a Makeshift Hospital for Asymptomatic and Very Mild COVID-19 Patients. Int J Public Health 2023; 68:1605994. [PMID: 37767017 PMCID: PMC10520216 DOI: 10.3389/ijph.2023.1605994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Objective: To investigate the details of environmental contamination status by SARS-CoV-2 in a makeshift COVID-19 hospital. Methods: Environmental samples were collected from a makeshift hospital. The extent of contamination was assessed by quantitative reverse transcription polymerase chain reaction (RT-qPCR) for SARS-CoV-2 RNA from various samples. Results: There was a wide range of total collected samples contaminated with SARS-CoV-2 RNA, ranging from 8.47% to 100%. Results revealed that 70.00% of sewage from the bathroom and 48.19% of air samples were positive. The highest rate of contamination was found from the no-touch surfaces (73.07%) and the lowest from frequently touched surfaces (33.40%). The most contaminated objects were the top surfaces of patient cubic partitions (100%). The median Ct values among strongly positive samples were 33.38 (IQR, 31.69-35.07) and 33.24 (IQR, 31.33-34.34) for ORF1ab and N genes, respectively. SARS-CoV-2 relic RNA can be detected on indoor surfaces for up to 20 days. Conclusion: The findings show a higher prevalence and persistence in detecting the presence of SARS-CoV-2 in the makeshift COVID-19 hospital setting. The contamination mode of droplet deposition may be more common than contaminated touches.
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Affiliation(s)
- Jinyan Yang
- Department of Disease Prevention and Control, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Dan Sun
- Department of Disease Prevention and Control, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Tingting Xia
- Department of Disease Prevention and Control, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Shi Shi
- Department of Disease Prevention and Control, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Jijiang Suo
- Department of Disease Prevention and Control, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Huihui Kuang
- Department of Laboratory Medicine, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Nana Sun
- Department of Laboratory Medicine, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Hongyan Hu
- Department of Laboratory Medicine, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Zhecheng Zheng
- Department of Health Economics Management, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Yang Zhou
- Department of Health Economics Management, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Xiaocui Li
- Department of Cardiology, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Shaojuan Chen
- Department of Cardiology, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Haiqiang Huang
- Department of Radiotherapy, Hainan Hospital of People’s Liberation Army of China General Hospital, Sanya, China
| | - Zhongqiang Yan
- Department of Disease Prevention and Control, The Second Medical Center of People’s Liberation Army of China General Hospital, Beijing, China
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11
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Zhan Q, Solo-Gabriele HM, Sharkey ME, Amirali A, Beaver CC, Boone MM, Comerford S, Cooper D, Cortizas EM, Cosculluela GA, Currall BB, Grills GS, Kobetz E, Kumar N, Laine J, Lamar WE, Lyu J, Mason CE, Reding BD, Roca MA, Schürer SC, Shukla BS, Solle NS, Suarez MM, Stevenson M, Tallon JJ, Thomas C, Vidović D, Williams SL, Yin X, Zarnegarnia Y, Babler KM. Correlative analysis of wastewater trends with clinical cases and hospitalizations through five dominant variant waves of COVID-19. ACS ES T Water 2023; 3:2849-2862. [PMID: 38487696 PMCID: PMC10936583 DOI: 10.1021/acsestwater.3c00032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Wastewater-based epidemiology (WBE) has been utilized to track community infections of Coronavirus Disease 2019 (COVID-19) by detecting RNA of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), within samples collected from wastewater. The correlations between community infections and wastewater measurements of the RNA can potentially change as SARS-CoV-2 evolves into new variations by mutating. This study analyzed SARS-CoV-2 RNA, and indicators of human waste in wastewater from two sewersheds of different scales (University of Miami (UM) campus and Miami-Dade County Central District wastewater treatment plant (CDWWTP)) during five internally defined COVID-19 variant dominant periods (Initial, Pre-Delta, Delta, Omicron and Post-Omicron wave). SARS-CoV-2 RNA quantities were compared against COVID-19 clinical cases and hospitalizations to evaluate correlations with wastewater SARS-CoV-2 RNA. Although correlations between documented clinical cases and hospitalizations were high, prevalence for a given wastewater SARS-CoV-2 level varied depending upon the variant analyzed. The correlative relationship was significantly steeper (more cases per level found in wastewater) for the Omicron-dominated period. For hospitalization, the relationships were steepest for the Initial wave, followed by the Delta wave with flatter slopes during all other waves. Overall results were interpreted in the context of SARS-CoV-2 virulence and vaccination rates among the community.
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Affiliation(s)
- Qingyu Zhan
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Helena Maria Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Mark E. Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Cynthia C. Beaver
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Melinda M. Boone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Samuel Comerford
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | | | - Elena M. Cortizas
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Gabriella A. Cosculluela
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Benjamin B. Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Erin Kobetz
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Naresh Kumar
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL 33136 USA
| | - Walter E. Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL 33136 USA
| | - Jiangnan Lyu
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021 USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Brian D. Reding
- Environmental Health and Safety, University of Miami, Miami, FL 33136 USA
| | - Matthew A. Roca
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Stephan C. Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL 33136 USA
- Institute for Data Science & Computing, University of Miami, Coral Gables, FL 33146 USA
| | - Bhavarth S. Shukla
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Natasha Schaefer Solle
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Maritza M. Suarez
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Mario Stevenson
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - John J. Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL 33146 USA
| | - Collette Thomas
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Dušica Vidović
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL 33136 USA
| | - Sion L. Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Xue Yin
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Yalda Zarnegarnia
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Kristina Marie Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
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12
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Abelson S, Penso J, Alsuliman B, Babler K, Sharkey M, Stevenson M, Grills G, Mason CE, Solo-Gabriele H, Kumar N. COVID-19 Case and Mortality Surveillance using Daily SARS-CoV-2 in Wastewater Samples adjusting for Meteorological Conditions and Sample pH. medRxiv 2023:2023.07.12.23292570. [PMID: 37502918 PMCID: PMC10370245 DOI: 10.1101/2023.07.12.23292570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background Wastewater monitoring is increasingly used for community surveillance of infectious diseases, especially after the COVID-19 pandemic as the genomic footprints of pathogens shed by infected individuals can be traced in the environment. However, detection and concentration of pathogens in the environmental samples and their efficacy in predicting infectious diseases can be influenced by meteorological conditions and quality of samples. Objectives This research examines whether meteorological conditions and sample pH affect SARS-CoV-2 concentrations in wastewater samples, and whether the association of SARS-CoV-2 with COVID-19 cases and mortality improves when adjusted for meteorological conditions and sample pH value in Miami-Dade County, FL. Methods Daily wastewater samples were collected from Miami-Dade Wastewater Treatment Plant in Key Biscayne, Florida from August 2021 to August 2022. The samples were analyzed for pH and spiked with OC43. RNA was extracted from the concentrated wastewater sample and SARS-CoV-2 was quantified using qPCR. COVID-19 and mortality data were acquired from the Centers for Disease Control and Prevention (CDC) and meteorological data from the National Climatic Data Center. COVID-19 case and mortality rates were modelled with respect to time-lagged wastewater SARS-CoV-2 adjusting for meteorological conditions, and sample pH value and OC43 recovery. Results Temperature, dew point, pH values and OC43 recovery showed significant associations with wastewater SARS-CoV-2. Time-lagged wastewater SARS-CoV-2 showed significant associations with COVID-19 case and mortality incidence rates. This association improved when wastewater SARS-CoV-2 levels were adjusted for (or instrumented on) meteorological conditions, OC43 recovery, and sample pH. A 0.47% change in COVID-19 case incidence rate was associated with 1% change in wastewater SARS-CoV-2 (β ~ 0.47; 95% CI = 0.29 - 0.64; p < 0.001). A 0.12 % change in COVID-19 mortality rate was associated with 1 % change in SARS-CoV-2 in wastewater 44 days prior. A 0.07% decline in COVID-19 mortality rate was associated with a unit increase in ambient temperature 28 days prior. Discussion Time lagged wastewater SARS-CoV-2 (and its adjustment for sample pH and RNA recovery) and meteorological conditions can be used for the surveillance of COVID-19 case and mortality. These findings can be extrapolated to improve the surveillance of other infectious diseases by proactive measurements of infectious agent(s) in the wastewater samples, adjusting for meteorological conditions and sample pH value.
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Affiliation(s)
- Samantha Abelson
- Department of Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Johnathon Penso
- Department of Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Bader Alsuliman
- Department of Public Health, University of Miami Miller School of Medicine, Miami, Florida
| | - Kristina Babler
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, Florida
| | - Mark Sharkey
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, US
| | - Mario Stevenson
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, US
| | - George Grills
- Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, US
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University
| | - Helena Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami, Coral Gables, Florida
| | - Naresh Kumar
- Department of Public Health, University of Miami Miller School of Medicine, Miami, Florida
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13
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Khan M, Li L, Haak L, Payen SH, Carine M, Adhikari K, Uppal T, Hartley PD, Vasquez-Gross H, Petereit J, Verma SC, Pagilla K. Significance of wastewater surveillance in detecting the prevalence of SARS-CoV-2 variants and other respiratory viruses in the community - A multi-site evaluation. One Health 2023; 16:100536. [PMID: 37041760 PMCID: PMC10074727 DOI: 10.1016/j.onehlt.2023.100536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/13/2023] Open
Abstract
Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome in wastewater has proven to be useful for tracking the trends of virus prevalence within the community. The surveillance also provides precise and early detection of any new and circulating variants, which aids in response to viral outbreaks. Site-specific monitoring of SARS-CoV-2 variants provides valuable information on the prevalence of new or emerging variants in the community. We sequenced the genomic RNA of viruses present in the wastewater samples and analyzed for the prevalence of SARS-CoV-2 variants as well as other respiratory viruses for a period of one year to account for seasonal variations. The samples were collected from the Reno-Sparks metropolitan area on a weekly basis between November 2021 to November 2022. Samples were analyzed to detect the levels of SARS-CoV-2 genomic copies and variants identification. This study confirmed that wastewater monitoring of SARS-CoV-2 variants can be used for community surveillance and early detection of circulating variants and supports wastewater-based epidemiology (WBE) as a complement to clinical respiratory virus testing as a healthcare response effort. Our study showed the persistence of the SARS-CoV-2 virus throughout the year compared to a seasonal presence of other respiratory viruses, implicating SARS-CoV-2's broad genetic diversity and strength to persist and infect susceptible hosts. Through secondary analysis, we further identified antimicrobial resistance (AMR) genes in the same wastewater samples and found WBE to be a feasible tool for community AMR detection and monitoring.
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Affiliation(s)
- Majid Khan
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Lin Li
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Laura Haak
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Shannon Harger Payen
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Madeline Carine
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
| | - Kabita Adhikari
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Timsy Uppal
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Paul D. Hartley
- Nevada Genomics Center, University of Nevada, Reno, NV 89557, USA
| | - Hans Vasquez-Gross
- Nevada Bioinformatics Center (RRID:SCR_017802), University of Nevada, Reno, NV 89557, USA
| | - Juli Petereit
- Nevada Bioinformatics Center (RRID:SCR_017802), University of Nevada, Reno, NV 89557, USA
| | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, MS320, Reno, NV 89557, USA
| | - Krishna Pagilla
- Department of Civil and Environmental Engineering, University of Nevada, MS258, Reno, NV 89557, USA
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14
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Tierney BT, Foox J, Ryon KA, Butler D, Damle N, Young BG, Mozsary C, Babler KM, Yin X, Carattini Y, Andrews D, Solle NS, Kumar N, Shukla B, Vidovic D, Currall B, Williams SL, Schürer SC, Stevenson M, Amirali A, Beaver CC, Kobetz E, Boone MM, Reding B, Laine J, Comerford S, Lamar WE, Tallon JJ, Hirschberg JW, Proszynski J, Sharkey ME, Church GM, Grills GS, Solo-Gabriele HM, Mason CE. Geospatially-resolved public-health surveillance via wastewater sequencing. medRxiv 2023:2023.05.31.23290781. [PMID: 37398062 PMCID: PMC10312847 DOI: 10.1101/2023.05.31.23290781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Wastewater, which contains everything from pathogens to pollutants, is a geospatially-and temporally-linked microbial fingerprint of a given population. As a result, it can be leveraged for monitoring multiple dimensions of public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (n=1,419 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County from 2020-2022. First, we used targeted amplicon sequencing (n=966) to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with clinical caseloads from University students (N = 1,503) and Miami-Dade County hospital patients (N = 3,939 patients), as well as an 8-day earlier detection of the Delta variant in wastewater vs. in patients. Additionally, in 453 metatranscriptomic samples, we demonstrate that different wastewater sampling locations have clinically and public-health-relevant microbiota that vary as a function of the size of the human population they represent. Through assembly, alignment-based, and phylogenetic approaches, we also detect multiple clinically important viruses (e.g., norovirus ) and describe geospatial and temporal variation in microbial functional genes that indicate the presence of pollutants. Moreover, we found distinct profiles of antimicrobial resistance (AMR) genes and virulence factors across campus buildings, dorms, and hospitals, with hospital wastewater containing a significant increase in AMR abundance. Overall, this effort lays the groundwork for systematic characterization of wastewater to improve public health decision making and a broad platform to detect emerging pathogens.
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Babler KM, Sharkey ME, Abelson S, Amirali A, Benitez A, Cosculluela GA, Grills GS, Kumar N, Laine J, Lamar W, Lamm ED, Lyu J, Mason CE, McCabe PM, Raghavender J, Reding BD, Roca MA, Schürer SC, Stevenson M, Szeto A, Tallon JJ, Vidović D, Zarnegarnia Y, Solo-Gabriele HM. Degradation rates influence the ability of composite samples to represent 24-hourly means of SARS-CoV-2 and other microbiological target measures in wastewater. Sci Total Environ 2023; 867:161423. [PMID: 36623667 PMCID: PMC9817413 DOI: 10.1016/j.scitotenv.2023.161423] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/25/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
The utility of using severe-acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA for assessing the prevalence of COVID-19 within communities begins with the design of the sample collection program. The objective of this study was to assess the utility of 24-hour composites as representative samples for measuring multiple microbiological targets in wastewater, and whether normalization of SARS-CoV-2 by endogenous targets can be used to decrease hour to hour variability at different watershed scales. Two sets of experiments were conducted, in tandem with the same wastewater, with samples collected at the building, cluster, and community sewershed scales. The first set of experiments focused on evaluating degradation of microbiological targets: SARS-CoV-2, Simian Immunodeficiency Virus (SIV) - a surrogate spiked into the wastewater, plus human waste indicators of Pepper Mild Mottle Virus (PMMoV), Beta-2 microglobulin (B2M), and fecal coliform bacteria (FC). The second focused on the variability of these targets from samples, collected each hour on the hour. Results show that SARS-CoV-2, PMMoV, and B2M were relatively stable, with minimal degradation over 24-h. SIV, which was spiked-in prior to analysis, degraded significantly and FC increased significantly over the course of 24 h, emphasizing the possibility for decay and growth within wastewater. Hour-to-hour variability of the source wastewater was large between each hour of sampling relative to the variability of the SARS-CoV-2 levels calculated between sewershed scales; thus, differences in SARS-CoV-2 hourly variability were not statistically significant between sewershed scales. Results further provided that the quantified representativeness of 24-h composite samples (i.e., statistical equivalency compared against hourly collected grabs) was dependent upon the molecular target measured. Overall, improvements made by normalization were minimal within this study. Degradation and multiplication for other targets should be evaluated when deciding upon whether to collect composite or grab samples in future studies.
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Affiliation(s)
- Kristina M Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Mark E Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Samantha Abelson
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Aymara Benitez
- Miami-Dade Water and Sewer Department, Miami, FL 33149, USA
| | - Gabriella A Cosculluela
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Naresh Kumar
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Walter Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL 33136, USA
| | - Erik D Lamm
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Jiangnan Lyu
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Philip M McCabe
- Department of Psychology, University of Miami, Coral Gables, FL 33146, USA; Department of Biomedical Engineering, University of Miami, Coral Gables, FL 33146, USA
| | | | - Brian D Reding
- Environmental Health and Safety, University of Miami, Miami, FL 33136, USA
| | - Matthew A Roca
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Stephan C Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL, USA
| | - Mario Stevenson
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Angela Szeto
- Department of Psychology, University of Miami, Coral Gables, FL 33146, USA
| | - John J Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL 33146, USA
| | - Dusica Vidović
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yalda Zarnegarnia
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Helena M Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146, USA.
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Westover C, Rahmatulloev S, Danko D, Afshin EE, O’Hara NB, Ounit R, Bezdan D, Mason CE. Ozone Disinfection for Elimination of Bacteria and Degradation of SARS-CoV2 RNA for Medical Environments. Genes (Basel) 2022; 14:85. [PMID: 36672826 PMCID: PMC9858956 DOI: 10.3390/genes14010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Pathogenic bacteria and viruses in medical environments can lead to treatment complications and hospital-acquired infections. Current disinfection protocols do not address hard-to-access areas or may be beyond line-of-sight treatment, such as with ultraviolet radiation. The COVID-19 pandemic further underscores the demand for reliable and effective disinfection methods to sterilize a wide array of surfaces and to keep up with the supply of personal protective equipment (PPE). We tested the efficacy of Sani Sport ozone devices to treat hospital equipment and surfaces for killing Escherichia coli, Enterococcus faecalis, Bacillus subtilis, and Deinococcus radiodurans by assessing Colony Forming Units (CFUs) after 30 min, 1 h, and 2 h of ozone treatment. Further gene expression analysis was conducted on live E. coli K12 immediately post treatment to understand the oxidative damage stress response transcriptome profile. Ozone treatment was also used to degrade synthetic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA as assessed by qPCR CT values. We observed significant and rapid killing of medically relevant and environmental bacteria across four surfaces (blankets, catheter, remotes, and syringes) within 30 min, and up to a 99% reduction in viable bacteria at the end of 2 h treatment cycles. RNA-seq analysis of E. coli K12 revealed 447 differentially expressed genes in response to ozone treatment and an enrichment for oxidative stress response and related pathways. RNA degradation of synthetic SARS-CoV-2 RNA was seen an hour into ozone treatment as compared to non-treated controls, and a non-replicative form of the virus was shown to have significant RNA degradation at 30 min. These results show the strong promise of ozone treatment of surfaces for reducing the risk of hospital-acquired infections and as a method for degradation of SARS-CoV-2 RNA.
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Affiliation(s)
- Craig Westover
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Savlatjon Rahmatulloev
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - David Danko
- Jacobs Technion-Cornell Institute, Cornell Tech, New York, NY 10044, USA
| | - Evan E. Afshin
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
- The World Quant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Niamh B. O’Hara
- Jacobs Technion-Cornell Institute, Cornell Tech, New York, NY 10044, USA
| | - Rachid Ounit
- Department of Computer Science & Engineering, University of California, Riverside, CA 92521, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72074 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72074 Tübingen, Germany
- Yuri GmbH, 88074 Meckenbeuren, Germany
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
- Jacobs Technion-Cornell Institute, Cornell Tech, New York, NY 10044, USA
- The Feil Family Brain and Mind Research Institute, New York, NY 10065, USA
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