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Chai X, Liu S, Liu C, Bai J, Meng J, Tian H, Han X, Han G, Xu X, Li Q. Surveillance of SARS-CoV-2 in wastewater by quantitative PCR and digital PCR: a case study in Shijiazhuang city, Hebei province, China. Emerg Microbes Infect 2024; 13:2324502. [PMID: 38465692 DOI: 10.1080/22221751.2024.2324502] [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: 12/13/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024]
Abstract
In this study, we reported the first long-term monitoring of SARS-CoV-2 in wastewater in Mainland China from November 2021 to October 2023. The city of Shijiazhuang was employed for this case study. We developed a triple reverse transcription droplet digital PCR (RT-ddPCR) method using triple primer-probes for simultaneous detection of the N1 gene, E gene, and Pepper mild mottle virus (PMMoV) to achieve accurate quantification of SARS-CoV-2 RNA in wastewater. Both the RT-ddPCR method and the commercial multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) method were implemented for the detection of SARS-CoV-2 in wastewater in Shijiazhuang City over a 24-month period. Results showed that SARS-CoV-2 was detected for the first time in the wastewater of Shijiazhuang City on 10 November 2022. The peak of COVID-19 cases occurred in the middle of December 2022, when the concentration of SARS-CoV-2 in the wastewater was highest. The trend of virus concentration increases and decreases forming a "long-tailed" shape in the COVID-19 outbreak and recession cycle. The results indicated that both multiplex RT-ddPCR and RT-qPCR are effective in detecting SARS-CoV-2 in wastewater, but RT-ddPCR is capable of detecting low concentrations of SARS-CoV-2 in wastewater which is more efficient. The SARS-CoV-2 abundance in wastewater is correlated to clinical data, outlining the public health utility of this work.HighlightsFirst long-term monitoring of SARS-CoV-2 in wastewater in Mainland ChinaCOVID-19 outbreak was tracked in Shijiazhuang City from outbreak to containmentWastewater was monitored simultaneously using RT-ddPCR and RT-qPCR methodsTriple primer-probe RT-ddPCR detects N1 and E genes of SARS-CoV-2 and PMMoV.
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Affiliation(s)
- Xiaoru Chai
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Shiyou Liu
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Chao Liu
- Shijiazhuang Qiaodong Sewage Treatment Plant, Shijiazhuang, People's Republic of China
| | - Jiaxuan Bai
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Juntao Meng
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Hong Tian
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Xu Han
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Guangyue Han
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Xiangdong Xu
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, People's Republic of China
| | - Qi Li
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
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do Nascimento MCA, Smith WJM, Liu Y, Simpson SL, Bivins A, Rahal P, Ahmed W. Development and comparative assessment of RT-qPCR and duplex RT-LAMP assays for the monitoring of Aichi virus A (AiV-A) in untreated wastewater samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:175440. [PMID: 39153611 DOI: 10.1016/j.scitotenv.2024.175440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 08/08/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024]
Abstract
Diverse enteric pathogens, transmitted through human and animal feces, can cause gastroenteritis. Enteric viruses, such as human Aichi virus, specifically genotype A (AiV-A), are emerging pathogens that cause illnesses even at low doses and are spreading globally. This research developed a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay targeting the 3CD junction and a reverse transcription colorimetric loop-mediated isothermal amplification (RT-cLAMP) duplex assay targeting junctions 2BC and 3CD of the AiV-A genome for rapid and sensitive detection of this virus in metropolitan and regional wastewater samples in Queensland, Australia. The performance of these assays was evaluated using control materials and by analyzing wastewater samples. In serially diluted control materials, RT-qPCR provided quantifiable data (mean 1.51 log10 GC/2 μL of nucleic acid) down to a dilution of 1 × 10-5 pg/μL. In comparison, the duplex RT-cLAMP assay detected down to 1 × 10-4 pg/μL, indicating that its sensitivity was one order of magnitude less than that of RT-qPCR. Of the 38 wastewater samples from 38 metropolitan and regional wastewater treatment plants (WWTPs) in Queensland, Australia, 21 (55.3 %) tested positive by RT-qPCR with concentrations ranging from 3.60 to 6.23 log10 GC/L. In contrast, only 15 (39.5 %) of 38 wastewater samples were positive using the duplex RT-cLAMP assay. The methods demonstrated substantial qualitative agreement (κ = 0.730), with a concordance of 86.5 %, demonstrating the reliability of RT-cLAMP for detecting AiV-A in wastewater samples. The duplex RT-cLAMP assay, despite demonstrating reduced detection sensitivity, has proven effective and holds promise as a supplementary approach, especially in settings with limited resources where rapid and affordable testing is crucial.
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Affiliation(s)
- Mariah C A do Nascimento
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.; Department of Biology, São Paulo State University - UNESP, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.; State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Stuart L Simpson
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Paula Rahal
- Department of Biology, São Paulo State University - UNESP, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia..
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Chen C, Wang Y, 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 and beyond: A survey. Epidemics 2024; 49:100793. [PMID: 39357172 DOI: 10.1016/j.epidem.2024.100793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024] Open
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 for COVID-19 surveillance a promising approach to complement traditional clinical testing. In this paper, we survey the existing literature regarding wastewater-based epidemiology 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
- Department of Computer Science, University of Virginia, Charlottesville, 22904, United States.
| | - Yunfan Wang
- Department of Computer Science, 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
- Department of Computer Science, University of Virginia, Charlottesville, 22904, United States; Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, 22904, United States.
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Chen X, Balliew J, Bauer CX, Deegan J, Gitter A, Hanson BM, Maresso AW, Tisza MJ, Troisi CL, Rios J, Mena KD, Boerwinkle E, Wu F. Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater. J Infect 2024; 89:106284. [PMID: 39341403 DOI: 10.1016/j.jinf.2024.106284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/06/2024] [Accepted: 09/20/2024] [Indexed: 10/01/2024]
Abstract
OBJECTIVES Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study aimed to monitor the SARS-CoV-2 variant community dynamics and evolution using receptor-binding domain (RBD) amplicon sequencing of wastewater samples. METHODS We sequenced wastewater from El Paso, Texas, over 17 months, compared the sequencing data with clinical genome data, and performed biodiversity analysis to reveal SARS-CoV-2 variant dynamics and evolution. RESULTS We identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Comparison with clinical genome sequencing data revealed earlier detection of variants and identification of unreported outbreaks. Our results also showed strong consistency with clinical data for dominant variants at the local, state, and national levels. Alpha diversity analyses revealed significant seasonal variations, with the highest diversity observed in winter. By segmenting the outbreak into lag, growth, stationary, and decline phases, we found higher variant diversity during the lag phase, likely due to lower inter-variant competition preceding outbreak growth. CONCLUSIONS Our findings underscore the importance of low transmission periods in facilitating rapid mutation and variant evolution. Our approach, integrating RBD amplicon sequencing with wastewater surveillance, demonstrates effectiveness in tracking viral evolution and understanding variant emergence, thus enhancing public health preparedness.
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Affiliation(s)
- Xingwen Chen
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA; Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | | | - Cici X Bauer
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA; Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Jennifer Deegan
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA; Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Anna Gitter
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA; Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Blake M Hanson
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA; Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Anthony W Maresso
- TAILOR Labs, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Michael J Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Catherine L Troisi
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA; Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Janelle Rios
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA; Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Kristina D Mena
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA; Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA; Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Fuqing Wu
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA; Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA.
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Sanjak JS, McAuley EM, Raybern J, Pinkham R, Tarnowski J, Miko N, Rasmussen B, Manalo CJ, Goodson M, Stamps B, Necciai B, Sozhamannan S, Maier EJ. Wastewater Surveillance Pilot at US Military Installations: Cost Model Analysis. JMIR Public Health Surveill 2024; 10:e54750. [PMID: 39240545 PMCID: PMC11396592 DOI: 10.2196/54750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 09/07/2024] Open
Abstract
Background The COVID-19 pandemic highlighted the need for pathogen surveillance systems to augment both early warning and outbreak monitoring/control efforts. Community wastewater samples provide a rapid and accurate source of environmental surveillance data to complement direct patient sampling. Due to its global presence and critical missions, the US military is a leader in global pandemic preparedness efforts. Clinical testing for COVID-19 on US Air Force (USAF) bases (AFBs) was effective but costly with respect to direct monetary costs and indirect costs due to lost time. To remain operating at peak capacity, such bases sought a more passive surveillance option and piloted wastewater surveillance (WWS) at 17 AFBs to demonstrate feasibility, safety, utility, and cost-effectiveness from May 2021 to January 2022. Objective We model the costs of a wastewater program for pathogens of public health concern within the specific context of US military installations using assumptions based on the results of the USAF and Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense pilot program. The objective was to determine the cost of deploying WWS to all AFBs relative to clinical swab testing surveillance regimes. Methods A WWS cost projection model was built based on subject matter expert input and actual costs incurred during the WWS pilot program at USAF AFBs. Several SARS-CoV-2 circulation scenarios were considered, and the costs of both WWS and clinical swab testing were projected. Analysis was conducted to determine the break-even point and how a reduction in swab testing could unlock funds to enable WWS to occur in parallel. Results Our model confirmed that WWS is complementary and highly cost-effective when compared to existing alternative forms of biosurveillance. We found that the cost of WWS was between US $10.5-$18.5 million less expensive annually in direct costs as compared to clinical swab testing surveillance. When the indirect cost of lost work was incorporated, including lost work associated with required clinical swab testing, we estimated that over two-thirds of clinical swab testing could be maintained with no additional costs upon implementation of WWS. Conclusions Our results support the adoption of WWS across US military installations as part of a more comprehensive and early warning system that will enable adaptive monitoring during disease outbreaks in a more cost-effective manner than swab testing alone.
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Affiliation(s)
- Jaleal S Sanjak
- Booz Allen Hamilton, 4747 Bethesda Ave, Bethesda, MD, United States, 1 5712413499
| | - Erin M McAuley
- Booz Allen Hamilton, 4747 Bethesda Ave, Bethesda, MD, United States, 1 5712413499
| | - Justin Raybern
- Booz Allen Hamilton, 4747 Bethesda Ave, Bethesda, MD, United States, 1 5712413499
| | - Richard Pinkham
- Booz Allen Hamilton, 4747 Bethesda Ave, Bethesda, MD, United States, 1 5712413499
| | - Jacob Tarnowski
- Booz Allen Hamilton, 4747 Bethesda Ave, Bethesda, MD, United States, 1 5712413499
| | - Nicole Miko
- Booz Allen Hamilton, 4747 Bethesda Ave, Bethesda, MD, United States, 1 5712413499
| | - Bridgette Rasmussen
- Booz Allen Hamilton, 4747 Bethesda Ave, Bethesda, MD, United States, 1 5712413499
| | - Christian J Manalo
- Booz Allen Hamilton, 4747 Bethesda Ave, Bethesda, MD, United States, 1 5712413499
| | - Michael Goodson
- United State Air Force Research Laboratory, Wright Patterson Air Force Base, OH, United States
| | - Blake Stamps
- United State Air Force Research Laboratory, Wright Patterson Air Force Base, OH, United States
| | - Bryan Necciai
- Chemical, Biological, Radiological and Nuclear Defense Enabling Biotechnologies, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense, Frederick, MD, United States
| | - Shanmuga Sozhamannan
- Chemical, Biological, Radiological and Nuclear Defense Enabling Biotechnologies, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense, Frederick, MD, United States
- Joint Research and Development, Inc, Stafford, VA, United States
| | - Ezekiel J Maier
- Booz Allen Hamilton, 4747 Bethesda Ave, Bethesda, MD, United States, 1 5712413499
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Pang X, Lee BE, Gao T, Rosychuk RJ, Immaraj L, Qiu JY, Wen J, Zelyas N, Howden K, Wallace J, Risling E, Little LA, Kim J, Wood H, Robinson A, Parkins M, Hubert CRJ, Frankowski K, Hrudey SE, Sikora C. Early warning COVID-19 outbreak in long-term care facilities using wastewater surveillance: correlation, prediction, and interaction with clinical and serological statuses. THE LANCET. MICROBE 2024:100894. [PMID: 39182502 DOI: 10.1016/s2666-5247(24)00126-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND The unprecedented COVID-19 pandemic has highlighted the strategic value of wastewater-based surveillance (WBS) of SARS-CoV-2. This multisite 28-month-long study focused on WBS for older residents in 12 long-term care facilities (LTCFs) in Edmonton (AB, Canada) by assessing relationships between COVID-19, WBS, and serostatus during the pandemic. METHODS Wastewater samples collected two to three times per week were tested for SARS-CoV-2 using RT-quantitative PCR. The serostatus of antibodies was examined using immunoassays. The data of clinical COVID-19 outbreaks based on extensive testing were obtained from local public health officials. Analyses included calculating correlations between 7-day rolling averages for WBS and COVID-19 cases and investigating whether WBS led or lagged confirmed outbreaks using a multinomial test. FINDINGS Wastewater results correlated well with clinical COVID-19 infections and outbreaks at participating LTCFs. 1058 (36·0%) of 2936 collected wastewater samples were SARS-CoV-2 positive, compared with 1247 people (resident n=671, staff n=572, and unknown n=4) reporting positive test results of 21 673 clinical samples assessed (5·8%). WBS led clinical testing in 32 (60·4%) confirmed outbreaks, which was significantly different from WBS lagged (12 outbreaks [22·6%, 95% CI 11·3-33·7]). Non-detection of WBS SARS-CoV-2 served as a negative predictor for outbreaks. WBS results attested protective immunity in vaccinated individuals before the omicron wave. A parallel increase in the proportions of positive WBS SARS-CoV-2 and anti-nucleocapsid antibodies underlined that omicron was an immunity-evading variant despite high seropositivity of neutralising antibodies after multiple doses of vaccine. INTERPRETATION Implementation of WBS could enable targeted clinical investigations and improve cost-effectiveness of COVID-19 outbreak management in LTCFs. WBS and serostatus provided informed dynamic changes of infections and immunity. Critical evidence was that LTCF WBS is an effective early warning system to support rapid public health outbreak management and protect vulnerable older populations. FUNDING Canadian Immunity Task Force for COVID-19 and Alberta Health.
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Affiliation(s)
- Xiaoli Pang
- Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada; Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.
| | - Bonita E Lee
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada; Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Tiejun Gao
- Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Rhonda J Rosychuk
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Linnet Immaraj
- Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Judy Y Qiu
- Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada; Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada
| | - Jiabi Wen
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Nathan Zelyas
- Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada; Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada
| | - Krista Howden
- Edmonton Zone, Alberta Health Services, Edmonton, AB, Canada
| | - Janelle Wallace
- Edmonton Zone, Alberta Health Services, Edmonton, AB, Canada
| | - Eleanor Risling
- Edmonton Zone, Alberta Health Services, Edmonton, AB, Canada
| | - Lorie A Little
- Edmonton Zone, Alberta Health Services, Edmonton, AB, Canada
| | - John Kim
- National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Heidi Wood
- National Microbiology Laboratory, Winnipeg, MB, Canada
| | | | - Michael Parkins
- Department of Medicine and Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, AB, Canada
| | - Steve E Hrudey
- Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Christopher Sikora
- Department of Medicine, University of Alberta, Edmonton, AB, Canada; School of Public Health, University of Alberta, Edmonton, AB, Canada; Edmonton Zone, Alberta Health Services, Edmonton, AB, Canada
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Sartirano D, Morecchiato F, Antonelli A, Lotti T, Morelli D, Ramazzotti M, Rossolini GM, Lubello C. Verifying the feasibility of wastewater-based epidemiological monitoring for the small catchment and sewage networks with significant pretreatment. JOURNAL OF WATER AND HEALTH 2024; 22:1516-1526. [PMID: 39212284 DOI: 10.2166/wh.2024.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 07/14/2024] [Indexed: 09/04/2024]
Abstract
Wastewater-based epidemiology (WBE) has emerged as a valuable tool for COVID-19 monitoring, especially as the frequency of clinical testing diminishes. Beyond COronaVIrus Disease 19 (COVID-19), the tool's versatility extends to addressing various public health concerns, including antibiotic resistance and drug consumption. However, the complexity of sewage systems introduces noise when measuring chemical tracer concentrations, potentially compromising their applicability for modeling. In our study, we detail the approach adopted to determine the concentration of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) ribonucleiec acid (RNA) in wastewater from the Ponte a Niccheri wastewater treatment plant in Tuscany (Italy), with a sample size of N = 13,935 inhabitants. The unique characteristics of this wastewater system, including mandatory pretreatment in septic tanks with extended retention times, the presence of a hospital for COVID-19 patients, and mixed sewage networks, posed additional challenges. Nevertheless, our results highlight a robust and significant correlation between our measurements and the number of infections within the wastewater treatment plant's catchment area at the time of sampling. A simple linear model also shows promising results in estimating the number of infected people within the area.
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Affiliation(s)
- Daniele Sartirano
- Department of Civil and Environmental Engineering, University of Florence, Florence, Italy E-mail:
| | - Fabio Morecchiato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Microbiology and Virology Unit, Careggi University Hospital, University of Florence, Florence, Italy
| | - Tommaso Lotti
- Department of Civil and Environmental Engineering, University of Florence, Florence, Italy
| | | | - Matteo Ramazzotti
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', University of Florence, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Microbiology and Virology Unit, Careggi University Hospital, University of Florence, Florence, Italy
| | - Claudio Lubello
- Department of Civil and Environmental Engineering, University of Florence, Florence, Italy
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Corchis-Scott R, Beach M, Geng Q, Podadera A, Corchis-Scott O, Norton J, Busch A, Faust RA, McFarlane S, Withington S, Irwin B, Aloosh M, Ng KKS, McKay RM. Wastewater Surveillance to Confirm Differences in Influenza A Infection between Michigan, USA, and Ontario, Canada, September 2022-March 2023. Emerg Infect Dis 2024; 30:1580-1588. [PMID: 39043398 PMCID: PMC11286066 DOI: 10.3201/eid3008.240225] [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] [Indexed: 07/25/2024] Open
Abstract
Wastewater surveillance is an effective way to track the prevalence of infectious agents within a community and, potentially, the spread of pathogens between jurisdictions. We conducted a retrospective wastewater surveillance study of the 2022-23 influenza season in 2 communities, Detroit, Michigan, USA, and Windsor-Essex, Ontario, Canada, that form North America's largest cross-border conurbation. We observed a positive relationship between influenza-related hospitalizations and the influenza A virus (IAV) wastewater signal in Windsor-Essex (ρ = 0.785; p<0.001) and an association between influenza-related hospitalizations in Michigan and the IAV wastewater signal for Detroit (ρ = 0.769; p<0.001). Time-lagged cross correlation and qualitative examination of wastewater signal in the monitored sewersheds showed the peak of the IAV season in Detroit was delayed behind Windsor-Essex by 3 weeks. Wastewater surveillance for IAV reflects regional differences in infection dynamics which may be influenced by many factors, including the timing of vaccine administration between jurisdictions.
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D'Arpino MC, Sineli PE, Goroso G, Watanabe W, Saavedra ML, Hebert EM, Martínez MA, Migliavacca J, Gerstenfeld S, Chahla RE, Bellomio A, Albarracín VH. Wastewater monitoring of SARS-CoV-2 gene for COVID-19 epidemiological surveillance in Tucumán, Argentina. J Basic Microbiol 2024; 64:e2300773. [PMID: 38712352 DOI: 10.1002/jobm.202300773] [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: 12/29/2023] [Revised: 03/12/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024]
Abstract
Wastewater-based epidemiology provides temporal and spatial information about the health status of a population. The objective of this study was to analyze and report the epidemiological dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the province of Tucumán, Argentina during the second and third waves of coronavirus disease 2019 (COVID-19) between April 2021 and March 2022. The study aimed to quantify SARS-CoV-2 RNA in wastewater, correlating it with clinically reported COVID-19 cases. Wastewater samples (n = 72) were collected from 16 sampling points located in three cities of Tucumán (San Miguel de Tucumán, Yerba Buena y Banda del Río Salí). Detection of viral nucleocapsid markers (N1 gene) was carried out using one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Viral loads were determined for each positive sample using a standard curve. A positive correlation (p < 0.05) was observed between viral load (copies/mL) and the clinically confirmed COVID-19 cases reported at specific sampling points in San Miguel de Tucumán (SP4, SP7, and SP8) in both months, May and June. Indeed, the high viral load concurred with the peaks of COVID-19 cases. This method allowed us to follow the behavior of SARS-CoV-2 infection during epidemic outbreaks. Thus, wastewater monitoring is a valuable epidemiological indicator that enables the anticipation of increases in COVID-19 cases and tracking the progress of the pandemic. SARS-CoV-2 genome-based surveillance should be implemented as a routine practice to prepare for any future surge in infections.
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Affiliation(s)
- María Cecilia D'Arpino
- Laboratory of Molecular and Ultraestructural Microbiology, Centro Integral de Microscopía Electrónica, (CIME-UNT-CONICET), Facultad de Agronomía, Zootecnia y Veterinaria, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Pedro Eugenio Sineli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina
| | - Gustavo Goroso
- Laboratorio de Processamento de Sinais e Modelagem de Sistemas Biológicos. Núcleo de Pesquisas Tecnológicas, Universidade Mogi das Cruzes, Sao Paulo, Brasil
| | - William Watanabe
- Laboratorio de Processamento de Sinais e Modelagem de Sistemas Biológicos. Núcleo de Pesquisas Tecnológicas, Universidade Mogi das Cruzes, Sao Paulo, Brasil
| | | | | | | | | | | | | | - Augusto Bellomio
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-Universidad Nacional de Tucumán), Tucumán, Argentina
| | - Virginia Helena Albarracín
- Laboratory of Molecular and Ultraestructural Microbiology, Centro Integral de Microscopía Electrónica, (CIME-UNT-CONICET), Facultad de Agronomía, Zootecnia y Veterinaria, Universidad Nacional de Tucumán, Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional Tucumán, Tucumán, Argentina
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10
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Chen X, Balliew J, Bauer CX, Deegan J, Gitter A, Hanson BM, Maresso AW, Tisza MJ, Troisi CL, Rios J, Mena KD, Boerwinkle E, Wu F. RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.12.24310301. [PMID: 39040200 PMCID: PMC11261926 DOI: 10.1101/2024.07.12.24310301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study utilized receptor-binding domain (RBD) amplicon sequencing of wastewater samples to monitor the SARS-CoV-2 community dynamics and evolution in El Paso, TX. Over 17 months, we identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Our findings demonstrated early detection of variants and identification of unreported outbreaks, while showing strong consistency with clinical genome sequencing data at the local, state, and national levels. Alpha diversity analyses revealed significant periodical variations, with the highest diversity observed in winter and the outbreak lag phases, likely due to lower competition among variants before the outbreak growth phase. The data underscores the importance of low transmission periods for rapid mutation and variant evolution. This study highlights the effectiveness of integrating RBD amplicon sequencing with wastewater surveillance in tracking viral evolution, understanding variant emergence, and enhancing public health preparedness.
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Affiliation(s)
- Xingwen Chen
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - John Balliew
- El Paso Water Utility, El Paso, TX, United States
| | - Cici X Bauer
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Jennifer Deegan
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Anna Gitter
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Blake M Hanson
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Anthony W Maresso
- TAILOR Labs, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Michael J Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Catherine L Troisi
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Janelle Rios
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Kristina D Mena
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
| | - Fuqing Wu
- School of Public Health, University of Texas Health Science Center at Houston, TX, USA
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, USA
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11
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Ahmed W, Liu Y, Smith W, Ingall W, Belby M, Bivins A, Bertsch P, Williams DT, Richards K, Simpson S. Leveraging wastewater surveillance to detect viral diseases in livestock settings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172593. [PMID: 38642765 DOI: 10.1016/j.scitotenv.2024.172593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/14/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Wastewater surveillance has evolved into a powerful tool for monitoring public health-relevant analytes. Recent applications in tracking severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection highlight its potential. Beyond humans, it can be extended to livestock settings where there is increasing demand for livestock products, posing risks of disease emergence. Wastewater surveillance may offer non-invasive, cost-effective means to detect potential outbreaks among animals. This approach aligns with the "One Health" paradigm, emphasizing the interconnectedness of animal, human, and ecosystem health. By monitoring viruses in livestock wastewater, early detection, prevention, and control strategies can be employed, safeguarding both animal and human health, economic stability, and international trade. This integrated "One Health" approach enhances collaboration and a comprehensive understanding of disease dynamics, supporting proactive measures in the Anthropocene era where animal and human diseases are on the rise.
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Affiliation(s)
- Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia; State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Wendy Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wayne Ingall
- Wide Bay Public Health Unit, 14 Branyan Street, Bundaberg, West Qld 4670, Australia
| | - Michael Belby
- Wide Bay Public Health Unit, 14 Branyan Street, Bundaberg, West Qld 4670, Australia
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Paul Bertsch
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - David T Williams
- CSIRO Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong, VIC 3220, Australia
| | - Kirsty Richards
- SunPork Group, 1/6 Eagleview Place, Eagle Farm, QLD 4009, Australia
| | - Stuart Simpson
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
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12
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Xu L, Ceolotto N, Jagadeesan K, Standerwick R, Robertson M, Barden R, Kasprzyk-Hordern B. Antimicrobials and antimicrobial resistance genes in the shadow of COVID-19 pandemic: A wastewater-based epidemiology perspective. WATER RESEARCH 2024; 257:121665. [PMID: 38692256 DOI: 10.1016/j.watres.2024.121665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/21/2024] [Accepted: 04/21/2024] [Indexed: 05/03/2024]
Abstract
Higher usage of antimicrobial agents in both healthcare facilities and the communities has resulted in an increased spread of resistant bacteria. However, the improved infection prevention and control practices may also contribute to decreasing antimicrobial resistance (AMR). In the present study, wastewater-based epidemiology (WBE) approach was applied to explore the link between COVID-19 and the community usage of antimicrobials, as well as the prevalence of resistance genes. Longitudinal study has been conducted to monitor the levels of 50 antimicrobial agents (AAs), 24 metabolites, 5 antibiotic resistance genes (ARGs) and class 1 integrons (intI 1) in wastewater influents in 4 towns/cities over two years (April 2020 - March 2022) in the South-West of England (a total of 1,180 samples collected with 87,320 individual AA measurements and 8,148 ARG measurements). Results suggested higher loads of AAs and ARGs in 2021-22 than 2020-21, with beta-lactams, quinolones, macrolides and most ARGs showing statistical differences. In particular, the intI 1 gene (a proxy of environmental ARG pollution) showed a significant increase after the ease of the third national lockdown in England. Positive correlations for all quantifiable parent AAs and metabolites were observed, and consumption vs direct disposal of unused AAs has been identified via WBE. This work can help establish baselines for AMR status in communities, providing community-wide surveillance and evidence for informing public health interventions. Overall, studies focused on AMR from the start of the pandemic to the present, especially in the context of environmental settings, are of great importance to further understand the long-term impact of the pandemic on AMR.
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Affiliation(s)
- Like Xu
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK
| | - Nicola Ceolotto
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK; Institute for Sustainability, University of Bath, Bath BA2 7AY, UK
| | | | | | | | - Ruth Barden
- Wessex Water Service Ltd., Claverton Down, Bath BA2 7WW, UK
| | - Barbara Kasprzyk-Hordern
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK; Institute for Sustainability, University of Bath, Bath BA2 7AY, UK.
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13
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Robbins AA, Gallagher TL, Toledo DM, Hershberger KC, Salmela SM, Barney RE, Szczepiorkowski ZM, Tsongalis GJ, Martin IW, Hubbard JA, Lefferts JA. Analytical validation of a semi-automated methodology for quantitative measurement of SARS-CoV-2 RNA in wastewater collected in northern New England. Microbiol Spectr 2024; 12:e0112223. [PMID: 38747589 PMCID: PMC11323974 DOI: 10.1128/spectrum.01122-23] [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: 04/21/2023] [Accepted: 04/11/2024] [Indexed: 06/06/2024] Open
Abstract
Wastewater-based epidemiology (WBE) can be used to monitor the community presence of infectious disease pathogens of public health concern such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Viral nucleic acid has been detected in the stool of SARS-CoV-2-infected individuals. Asymptomatic SARS-CoV-2 infections make community monitoring difficult without extensive and continuous population screening. In this study, we validated a procedure that includes manual pre-processing, automated SARS-CoV-2 RNA extraction and detection workflows using both reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) and reverse transcriptase droplet digital PCR (RT-ddPCR). Genomic RNA and calibration materials were used to create known concentrations of viral material to determine the linearity, accuracy, and precision of the wastewater extraction and SARS-CoV-2 RNA detection. Both RT-qPCR and RT-ddPCR perform similarly in all the validation experiments, with a limit of detection of 50 copies/mL. A wastewater sample from a care facility with a known outbreak was assessed for viral content in replicate, and we showed consistent results across both assays. Finally, in a 2-week survey of two New Hampshire cities, we assessed the suitability of our methods for daily surveillance. This paper describes the technical validation of a molecular assay that can be used for long-term monitoring of SARS-CoV-2 in wastewater as a potential tool for community surveillance to assist with public health efforts.IMPORTANCEThis paper describes the technical validation of a molecular assay that can be used for the long-term monitoring of SARS-CoV-2 in wastewater as a potential tool for community surveillance to assist with public health efforts.
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Affiliation(s)
- Ashlee A. Robbins
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Torrey L. Gallagher
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Diana M. Toledo
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- The Broad Institute at MIT and Harvard, Cambridge, Massachusetts, USA
| | - K. Chase Hershberger
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Sabrina M. Salmela
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Rachael E. Barney
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Zbigniew M. Szczepiorkowski
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Gregory J. Tsongalis
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Isabella W. Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Jacqueline A. Hubbard
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Joel A. Lefferts
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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14
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Hadi M, Kheiri R, Baghban M, Sayahi A, Nasseri S, Alimohammadi M, Khastoo H, Aminabad MS, Vaghefi KA, Vakili B, Tashauoei H, Borji SH, Iravani E. The occurrence of SARS-CoV-2 in Tehran's municipal wastewater: performance of treatment systems and feasibility of wastewater-based epidemiology. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2024; 22:281-293. [PMID: 38887767 PMCID: PMC11180145 DOI: 10.1007/s40201-024-00897-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/29/2024] [Indexed: 06/20/2024]
Abstract
Analyzing municipal wastewater for the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) helps to evaluate the efficacy of treatment systems in mitigating virus-related health risks. This research investigates wastewater treatment plants' (WWTPs) performance in the reduction of SARS-CoV-2 from municipal wastewater in Tehran, Iran. SARS-CoV-2 RNA was measured within sewers, at the inlets, and after the primary and secondary treatment stages of three main WWTPs. Within sewers, the average virus titer stood at 58,600 gc/L, while at WWTP inlets, it measured 38,136 gc/L. A substantial 67% reduction in virus titer was observed at the inlets, accompanied by a 2-log reduction post-primary treatment. Remarkably, the biological treatment process resulted in complete virus elimination across all plants. Additionally, a notable positive correlation (r > 0.8) was observed between temperature and virus titer in wastewater. Using wastewater-based epidemiology (WBE) technique and the estimated SARS-CoV-2 RNA shedding rates, the infection prevalence among populations served by WWTPs found to be between 0.128% to 0.577%. In conclusion, this research not only advances our understanding of SARS-CoV-2 dynamics within wastewater treatment systems but also provides practical insights for enhancing treatment efficiency and implementing the feasibility of WBE strategies in Tehran. These implications contribute to the broader efforts to protect public health and mitigate the impact of future viral outbreaks. Graphical abstract
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Affiliation(s)
- Mahdi Hadi
- Center for Water Quality Research (CWQR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, Tehran, Iran
| | - Roohollah Kheiri
- Water Quality Control Office, Alborz Province Water and Wastewater Company, Karaj, Iran
| | - Mahtab Baghban
- Reference Laboratory of Water and Wastewater, Tehran Province Water and Wastewater Company, Tehran, Iran
| | - Ahmad Sayahi
- Office of R&D and Industrial Relations of Water and Wastewater Engineering Company, Tehran, Iran
| | - Simin Nasseri
- Center for Water Quality Research (CWQR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmood Alimohammadi
- Center for Water Quality Research (CWQR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, Tehran, Iran
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Khastoo
- Office of R&D and Industrial Relations of Water and Wastewater Engineering Company, Tehran, Iran
| | - Mehri Solaimany Aminabad
- Center for Water Quality Research (CWQR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, Tehran, Iran
| | - Kooshiar Azam Vaghefi
- Manager of Water Quality Control Bureau, National Water and Wastewater Engineering Company, Tehran, Iran
| | - Behnam Vakili
- Office of Improvement on Wastewater Operation Procedures, National Water and Wastewater Engineering Company, Tehran, Iran
| | - Hamidreza Tashauoei
- Department of Environmental Health Engineering, School of Health, Islamic Azad University, Tehran Medical Branch, Tehran, Iran
| | - Saeedeh Hemmati Borji
- Center for Water Quality Research (CWQR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, Tehran, Iran
| | - Elnaz Iravani
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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15
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Starke JC, Bell NS, Martinez CM, Friberg IK, Lawley C, Sriskantharajah V, Hirschberg DL. Measuring SARS-CoV-2 RNA concentrations in neighborhood wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172021. [PMID: 38552966 DOI: 10.1016/j.scitotenv.2024.172021] [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: 09/27/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
Longitudinal wastewater sampling during the COVID-19 pandemic was an important aspect of disease surveillance, adding to a more complete understanding of infection dynamics and providing important data for community public health monitoring and intervention planning. This was largely accomplished by testing SARS-CoV-2 RNA concentrations in samples from municipal wastewater treatment plants (WWTPs). We evaluated the utility of testing for virus levels upstream from WWTP within the residential neighborhoods that feed into the WWTP. We propose that monitoring virus dynamics across residential neighborhoods could reveal important public health-relevant information about community sub-group heterogeneity in virus concentrations. PRINCIPAL RESULTS: Virus concentration patterns display heterogeneity within neighborhoods and between neighborhoods over time. Sewage SARS-CoV-2 RNA concentrations as measured by RT-qPCR also corresponded closely to verified COVID-19 infection counts within individual neighborhoods. More importantly, our data suggest the loss of disease-relevant public health information when sampling occurs only at the level of WWTP instead of upstream in neighborhoods. Spikes in SARS-CoV-2 RNA concentrations in neighborhoods are often masked by dilution from other neighborhoods in the WWTP samples. MAJOR CONCLUSIONS: Wastewater-based epidemiology (WBE) employed at WWTP reliably detects SARS-CoV-2 in a city-sized population but provides less actionable public health information about neighborhoods experiencing greater viral infection and disease. Neighborhood sewershed sampling reveals important population-based information about local virus dynamics and improves opportunities for public health intervention. Longitudinally employed, neighborhood sewershed surveillance may provide a 3-6 day early warning of SARS-CoV-2 infection spikes and, importantly, highly specific information on subpopulations in a community particularly at higher risk at different points in time. Sampling in neighborhoods may thus provide timely and cost-saving information for targeted interventions within communities.
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Affiliation(s)
| | - Nicole S Bell
- RAIN Incubator, Tacoma, WA, USA; Squally Creek, LLC, Tacoma, WA, USA
| | - Chloe Mae Martinez
- RAIN Incubator, Tacoma, WA, USA; University of Washington-Tacoma, Tacoma, WA, USA
| | | | | | | | - David L Hirschberg
- RAIN Incubator, Tacoma, WA, USA; School of Engineering and Technology, University of Washington-Tacoma, Tacoma, WA, USA
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16
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Ma C, Zhou F, Lu D, Xu S, Luo J, Gan H, Gao D, Yao Z, He W, Kurup PU, Zhu DZ. Quantification and cultivation of Helicobacter pylori (H. pylori) from various urban water environments: A comprehensive analysis of precondition methods and sample characteristics. ENVIRONMENT INTERNATIONAL 2024; 187:108683. [PMID: 38735073 DOI: 10.1016/j.envint.2024.108683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/15/2024] [Accepted: 04/21/2024] [Indexed: 05/14/2024]
Abstract
Substantial evidence suggests that all types of water, such as drinking water, wastewater, surface water, and groundwater, can be potential sources of Helicobacter pylori (H. pylori) infection. Thus, it is critical to thoroughly investigate all possible preconditioning methods to enhance the recovery of H. pylori, improve the reproducibility of subsequent detection, and optimize the suitability for various water types and different detection purposes. In this study, we proposed and evaluated five distinct preconditioning methods for treating water samples collected from multiple urban water environments, aiming to maximize the quantitative qPCR readouts and achieve effective selective cultivation. According to the experimental results, when using the qPCR technique to examine WWTP influent, effluent, septic tank, and wetland water samples, the significance of having a preliminary cleaning step becomes more evident as it can profoundly influence qPCR detection results. In contrast, the simple, straightforward membrane filtration method could perform best when isolating and culturing H. pylori from all water samples. Upon examining the cultivation and qPCR results obtained from groundwater samples, the presence of infectious H. pylori (potentially other pathogens) in aquifers must represent a pressing environmental emergency demanding immediate attention. Furthermore, we believe groundwater can be used as a medium to reflect the H. pylori prevalence in a highly populated community due to its straightforward analytical matrix, consistent detection performance, and minimal interferences from human activities, temperature, precipitation, and other environmental fluctuations.
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Affiliation(s)
- Chen Ma
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo 315211, China
| | - Fangyuan Zhou
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo 315211, China
| | - Dingnan Lu
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo 315211, China; Department of Civil and Environmental Engineering, University of Massachusetts Lowell, One University Ave., Lowell, MA 01854, USA; Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China.
| | - Shengliang Xu
- Ningbo Municipal Engineering Construction Group Co., 315000, China
| | - Jiayue Luo
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo 315211, China; Department of Civil and Environmental Engineering, University of Massachusetts Lowell, One University Ave., Lowell, MA 01854, USA; Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China
| | - Huihui Gan
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo 315211, China; Department of Civil and Environmental Engineering, University of Massachusetts Lowell, One University Ave., Lowell, MA 01854, USA; Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China
| | - Doudou Gao
- Ningbo Municipal Engineering Construction Group Co., 315000, China
| | - Zhiyuan Yao
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo 315211, China; Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China
| | - Weidong He
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo 315211, China
| | - Pradeep U Kurup
- Department of Civil and Environmental Engineering, University of Massachusetts Lowell, One University Ave., Lowell, MA 01854, USA
| | - David Z Zhu
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo 315211, China; Institute of Ocean Engineering, Ningbo University, Ningbo 315211, China; Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
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17
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Shafer MM, Bobholz MJ, Vuyk WC, Gregory DA, Roguet A, Haddock Soto LA, Rushford C, Janssen KH, Emmen IE, Ries HJ, Pilch HE, Mullen PA, Fahney RB, Wei W, Lambert M, Wenzel J, Halfmann P, Kawaoka Y, Wilson NA, Friedrich TC, Pray IW, Westergaard R, O'Connor DH, Johnson MC. Tracing the origin of SARS-CoV-2 omicron-like spike sequences detected in an urban sewershed: a targeted, longitudinal surveillance study of a cryptic wastewater lineage. THE LANCET. MICROBE 2024; 5:e335-e344. [PMID: 38484748 PMCID: PMC11049544 DOI: 10.1016/s2666-5247(23)00372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 04/08/2024]
Abstract
BACKGROUND The origin of novel SARS-CoV-2 spike sequences found in wastewater, without corresponding detection in clinical specimens, remains unclear. We sought to determine the origin of one such cryptic wastewater lineage by tracking and characterising its persistence and genomic evolution over time. METHODS We first detected a cryptic lineage, WI-CL-001, in municipal wastewater in Wisconsin, USA, in January, 2022. To determine the source of WI-CL-001, we systematically sampled wastewater from targeted sub-sewershed lines and maintenance holes using compositing autosamplers. Viral concentrations in wastewater samples over time were measured by RT digital PCR. In addition to using metagenomic 12s rRNA sequencing to determine the virus's host species, we also sequenced SARS-CoV-2 spike receptor binding domains, and, where possible, whole viral genomes to identify and characterise the evolution of this lineage. FINDINGS We traced WI-CL-001 to its source at a single commercial building. There we detected the cryptic lineage at concentrations as high as 2·7 × 109 genome copies per L. The majority of 12s rRNA sequences detected in wastewater leaving the identified source building were human. Additionally, we generated over 100 viral receptor binding domain and whole-genome sequences from wastewater samples containing the cryptic lineage collected over the 13 consecutive months this virus was detectable (January, 2022, to January, 2023). These sequences contained a combination of fixed nucleotide substitutions characteristic of Pango lineage B.1.234, which circulated in humans in Wisconsin at low levels from October, 2020, to February, 2021. Despite this, mutations in the spike gene and elsewhere resembled those subsequently found in omicron variants. INTERPRETATION We propose that prolonged detection of WI-CL-001 in wastewater indicates persistent shedding of SARS-CoV-2 from a single human initially infected by an ancestral B.1.234 virus. The accumulation of convergent omicron-like mutations in WI-CL-001's ancestral B.1.234 genome probably reflects persistent infection and extensive within-host evolution. People who shed cryptic lineages could be an important source of highly divergent viruses that sporadically emerge and spread. FUNDING The Rockefeller Foundation, Wisconsin Department of Health Services, Centers for Disease Control and Prevention, National Institute on Drug Abuse, and the Center for Research on Influenza Pathogenesis and Transmission.
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Affiliation(s)
- Martin M Shafer
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Max J Bobholz
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - William C Vuyk
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Devon A Gregory
- School of Medicine, University of Missouri, Columbia, MO, USA
| | - Adelaide Roguet
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Luis A Haddock Soto
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Kayley H Janssen
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Isla E Emmen
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Hunter J Ries
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Hannah E Pilch
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Paige A Mullen
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Rebecca B Fahney
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew Lambert
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; Wisconsin Department of Health Services, Madison, WI, USA
| | - Jeff Wenzel
- Missouri Department of Health and Senior Services, Jefferson City, MO, USA
| | - Peter Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Nancy A Wilson
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Ian W Pray
- Wisconsin Department of Health Services, Madison, WI, USA
| | - Ryan Westergaard
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; Wisconsin Department of Health Services, Madison, WI, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc C Johnson
- School of Medicine, University of Missouri, Columbia, MO, USA.
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18
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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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19
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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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20
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Krogsgaard LW, Benedetti G, Gudde A, Richter SR, Rasmussen LD, Midgley SE, Qvesel AG, Nauta M, Bahrenscheer NS, von Kappelgaard L, McManus O, Hansen NC, Pedersen JB, Haimes D, Gamst J, Nørgaard LS, Jørgensen ACU, Ejegod DM, Møller SS, Clauson-Kaas J, Knudsen IM, Franck KT, Ethelberg S. Results from the SARS-CoV-2 wastewater-based surveillance system in Denmark, July 2021 to June 2022. WATER RESEARCH 2024; 252:121223. [PMID: 38310802 DOI: 10.1016/j.watres.2024.121223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/01/2023] [Accepted: 01/28/2024] [Indexed: 02/06/2024]
Abstract
The microbiological analysis of wastewater samples is increasingly used for the surveillance of SARS-CoV-2 globally. We described the setup process of the national SARS-CoV-2 wastewater-based surveillance system in Denmark, presented its main results during the first year of activities, from July 2021 to June 2022, and discussed their operational significance. The Danish SARS-CoV-2 wastewater-based surveillance system was designed to cover 85 % of the population in Denmark and it entailed taking three weekly samples from 230 sites. Samples were RT-qPCR tested for SARS-CoV-2 RNA, targeting the genetic markers N1, N2 and RdRp, and for two faecal indicators, Pepper Mild Mottle Virus and crAssphage. We calculated the weekly SARS-CoV-2 RNA concentration in the wastewater from each sampling site and monitored it in view of the results from individual testing, at the national and regional levels. We attempted to use wastewater results to identify potential local outbreaks, and we sequenced positive wastewater samples using Nanopore sequencing to monitor the circulation of viral variants in Denmark. The system reached its full implementation by October 2021 and covered up to 86.4 % of the Danish population. The system allowed for monitoring of the national and regional trends of SARS-CoV-2 infections in Denmark. However, the system contribution to the identification of potential local outbreaks was limited by the extensive information available from clinical testing. The sequencing of wastewater samples identified relevant variants of concern, in line with results from sequencing of human samples. Amidst the COVID-19 pandemic, Denmark implemented a nationwide SARS-CoV-2 wastewater-based surveillance system that integrated routine surveillance from individual testing. Today, while testing for COVID-19 at the community level has been discontinued, the system is on the frontline to monitor the occurrence and spread of SARS-CoV-2 in Denmark.
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Affiliation(s)
- Lene Wulff Krogsgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Guido Benedetti
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark.
| | - Aina Gudde
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Stine Raith Richter
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Lasse Dam Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Sofie Elisabeth Midgley
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Amanda Gammelby Qvesel
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Maarten Nauta
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Naja Stolberg Bahrenscheer
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Lene von Kappelgaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Oliver McManus
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, Gustav III: s Boulevard 40, 16973 Solna, Sweden
| | - Nicco Claudio Hansen
- Test Centre Denmark, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Jan Bryla Pedersen
- Department of Finance, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Danny Haimes
- Danish Patient Safety Authority, Islands Brygge 67, 2300 Copenhagen, Denmark
| | - Jesper Gamst
- Eurofins Environment, Ladelundvej 85, 6600 Vejen, Denmark
| | | | | | | | | | - Jes Clauson-Kaas
- HOFOR - Greater Copenhagen Utility, Ørestads Boulevard 35, 2300 Copenhagen, Denmark
| | - Ida Marie Knudsen
- HOFOR - Greater Copenhagen Utility, Ørestads Boulevard 35, 2300 Copenhagen, Denmark
| | - Kristina Træholt Franck
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; Department of Public Health, Global Health Section, University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen, Denmark
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21
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Cheng K, Lv Y, Li C, Cheng S, Xu S, Gao X, Xu H. Meta-analysis of the SARS-CoV-2 positivity rate in municipal wastewater. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:119. [PMID: 38483628 DOI: 10.1007/s10653-024-01895-7] [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: 12/20/2023] [Accepted: 01/29/2024] [Indexed: 03/19/2024]
Abstract
The aim of this study is to conduct a systematic analysis of the SARS-CoV-2 levels in urban sewage and evaluate the associated positivity rates, thereby developing comprehensive insights into the epidemic situation and providing valuable inputs for the development of effective disease prevention and control strategies. The PubMed, Scopus, Embase, China National Knowledge Infrastructure, Wanfang Database, and VIP databases were systematically searched based on the predefined retrieval strategy. The literature published up to February 2023 was meticulously screened according to the predetermined inclusion and exclusion criteria, and the relevant data were extracted for subsequent integration. The quality assessment of the included studies adhered to the rigorous Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement guidelines. The meta-analysis was conducted using Stata 17.0 software. The meta-analysis included a total of 34 studies, encompassing 8429 municipal wastewater samples. A random effects model was employed for the analysis, revealing an overall SARS-CoV-2 positivity rate of 53.7% in the municipal wastewater samples. The subgroup analyses demonstrated significant regional variations in the SARS-CoV-2 positivity rate in municipal wastewater, with Africa exhibiting the highest rate at 62.5% (95% confidence interval [CI] 47.4 ~ 76.0%) and Oceania displaying the lowest at 33.3% (95% CI 22.0 ~ 46.3%). However, the subgroup analyses based on the sampling site, strain prevalence period, and laboratory testing method did not yield any statistically significant differences. The SARS-CoV-2 positivity rate in wastewater is relatively high globally, although it exhibits regional disparities. Regions with larger populations and lower economic levels demonstrate higher viral detection rates in sewage. Different types of wastewater sampling sites can be employed to monitor distinct aspects of the COVID-19 pandemic. Continuous surveillance of SARS-CoV-2 in wastewater plays a pivotal role in complementing clinical data, helping to track outbreak progression across diverse regions.
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Affiliation(s)
- Keyi Cheng
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Ye Lv
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Chaokang Li
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Shi Cheng
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Shanshan Xu
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Xin Gao
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Hong Xu
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China.
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22
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Usmani M, Brumfield KD, Magers B, Zhou A, Oh C, Mao Y, Brown W, Schmidt A, Wu CY, Shisler JL, Nguyen TH, Huq A, Colwell R, Jutla A. Building Environmental and Sociological Predictive Intelligence to Understand the Seasonal Threat of SARS-CoV-2 in Human Populations. Am J Trop Med Hyg 2024; 110:518-528. [PMID: 38320317 PMCID: PMC10919182 DOI: 10.4269/ajtmh.23-0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/03/2023] [Indexed: 02/08/2024] Open
Abstract
Current modeling practices for environmental and sociological modulated infectious diseases remain inadequate to forecast the risk of outbreak(s) in human populations, partly due to a lack of integration of disciplinary knowledge, limited availability of disease surveillance datasets, and overreliance on compartmental epidemiological modeling methods. Harvesting data knowledge from virus transmission (aerosols) and detection (wastewater) of SARS-CoV-2, a heuristic score-based environmental predictive intelligence system was developed that calculates the risk of COVID-19 in the human population. Seasonal validation of the algorithm was uniquely associated with wastewater surveillance of the virus, providing a lead time of 7-14 days before a county-level outbreak. Using county-scale disease prevalence data from the United States, the algorithm could predict COVID-19 risk with an overall accuracy ranging between 81% and 98%. Similarly, using wastewater surveillance data from Illinois and Maryland, the SARS-CoV-2 detection rate was greater than 80% for 75% of the locations during the same time the risk was predicted to be high. Results suggest the importance of a holistic approach across disciplinary boundaries that can potentially allow anticipatory decision-making policies of saving lives and maximizing the use of available capacity and resources.
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Affiliation(s)
- Moiz Usmani
- GeoHealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida
| | - Kyle D. Brumfield
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland
| | - Bailey Magers
- GeoHealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois
| | - Chamteut Oh
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida
| | - Yuqing Mao
- Department of Civil and Environmental Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois
| | - William Brown
- Department of Pathobiology, University of Illinois at Urbana–Champaign, Urbana, Illinois
| | - Arthur Schmidt
- Department of Civil and Environmental Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois
| | - Chang-Yu Wu
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida
- Department of Chemical, Environmental and Materials Engineering, University of Miami, Florida
| | - Joanna L. Shisler
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland
| | - Rita Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland
| | - Antarpreet Jutla
- GeoHealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida
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23
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Rezaeitavabe F, Rezaie M, Modayil M, Pham T, Ice G, Riefler G, Coschigano KT. Beyond linear regression: Modeling COVID-19 clinical cases with wastewater surveillance of SARS-CoV-2 for the city of Athens and Ohio University campus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169028. [PMID: 38061656 DOI: 10.1016/j.scitotenv.2023.169028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 01/18/2024]
Abstract
Wastewater-based surveillance has emerged as a detection tool for population-wide infectious diseases, including coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infected individuals shed the virus, which can be detected in wastewater using molecular techniques such as reverse transcription-digital polymerase chain reaction (RT-dPCR). This study examined the association between the number of clinical cases and the concentration of SARS-CoV-2 in wastewater beyond linear regression and for various normalizations of viral loads. Viral loads were measured in a total of 446 wastewater samples during the period from August 2021 to April 2022. These samples were collected from nine different locations, with 220 samples taken from four specific sites within the city of Athens and 226 samples from five sites within Ohio University. The correlation between COVID-19 cases and wastewater viral concentrations, which was estimated using the Pearson correlation coefficient, was statistically significant and ranged from 0.6 to 0.9. In addition, time-lagged cross correlation was applied to identify the lag time between clinical and wastewater data, estimated 4 to 7 days. While we also explored the effect on the correlation coefficients of various normalizations of viral loads accounting for procedural loss or amount of fecal material and of estimated lag times, these alternative specifications did not change our substantive conclusions. Additionally, several linear and non-linear regression models were applied to predict the COVID-19 cases given wastewater data as input. The non-linear approach was found to yield the highest R-squared and Pearson correlation and lowest Mean Absolute Error values between the predicted and actual number of COVID-19 cases for both aggregated OHIO Campus and city data. Our results provide support for previous studies on correlation and time lag and new evidence that non-linear models, approximated with artificial neural networks, should be implemented for WBS of contagious diseases.
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Affiliation(s)
- Fatemeh Rezaeitavabe
- Ohio University, Russ College of Engineering, Department of Civil and Environmental Engineering, Athens, OH 45701, USA
| | - Mehdi Rezaie
- Kansas State University, Department of Physics, Manhattan, KS 66506, USA
| | - Maria Modayil
- Ohio University, Division of Diversity and Inclusion, Athens, OH 45701, USA; Ohio University, College of Health Sciences and Professions, Department of Interdisciplinary Health Studies, Athens, OH 45701, USA
| | - Tuyen Pham
- Ohio University, Voinovich School of Leadership and Public Service, Athens, OH 45701, USA
| | - Gillian Ice
- Ohio University, College of Health Sciences and Professions, Department of Interdisciplinary Health Studies, Athens, OH 45701, USA; Ohio University, Heritage College of Osteopathic Medicine, Department of Social Medicine, Athens, OH 45701, USA
| | - Guy Riefler
- Ohio University, Russ College of Engineering, Department of Civil and Environmental Engineering, Athens, OH 45701, USA
| | - Karen T Coschigano
- Ohio University, Heritage College of Osteopathic Medicine, Department of Biomedical Sciences, Athens, OH 45701, USA.
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24
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Tran DPH, You BC, Liu CW, Chen YN, Wang YF, Chung SN, Lee JJ, You SJ. Identifying spatiotemporal trends of SARS-CoV-2 RNA in wastewater: from the perspective of upstream and downstream wastewater-based epidemiology (WBE). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11576-11590. [PMID: 38221556 DOI: 10.1007/s11356-023-31769-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 12/25/2023] [Indexed: 01/16/2024]
Abstract
Recently, many efforts have been made to address the rapid spread of newly identified COVID-19 virus variants. Wastewater-based epidemiology (WBE) is considered a potential early warning tool for identifying the rapid spread of this virus. This study investigated the occurrence of SARS-CoV-2 in eight wastewater treatment plants (WWTPs) and their sewerage systems which serve most of the population in Taoyuan City, Taiwan. Across the entire study period, the wastewater viral concentrations were correlated with the number of COVID-19 cases in each WWTP (Spearman's r = 0.23-0.76). In addition, it is confirmed that several treatment technologies could effectively eliminate the virus RNA from WWTP influent (> 90%). On the other hand, further results revealed that an inverse distance weighted (IDW) interpolation and hotspot model combined with the geographic information system (GIS) method could be applied to analyze the spatiotemporal variations of SARS-CoV-2 in wastewater from the sewer system. In addition, socio-economic factors, namely, population density, land use, and income tax were successfully identified as the potential drivers which substantially affected the onset of the COVID-19 outbreak in Taiwan. Finally, the data obtained from this study can provide a powerful tool in public health decision-making not only in response to the current epidemic situation but also to other epidemic issues in the future.
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Affiliation(s)
- Duyen Phuc-Hanh Tran
- Department of Civil Engineering, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
- Center for Environmental Risk Management, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
| | - Bo-Cheng You
- Center for Environmental Risk Management, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
- Department of Environmental Engineering, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
| | - Chen-Wuing Liu
- Department of Water Resource, Taoyuan City Government, Taoyuan City, 320, Taiwan, Republic of China
| | - Yi-Ning Chen
- Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
| | - Ya-Fen Wang
- Center for Environmental Risk Management, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
- Department of Environmental Engineering, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China
| | - Shu-Nu Chung
- Department of Water Resource, Taoyuan City Government, Taoyuan City, 320, Taiwan, Republic of China
| | - Jin-Jing Lee
- Department of Water Resource, Taoyuan City Government, Taoyuan City, 320, Taiwan, Republic of China
| | - Sheng-Jie You
- Center for Environmental Risk Management, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China.
- Department of Environmental Engineering, Chung Yuan Christian University, Taoyuan City, 320, Taiwan, Republic of China.
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25
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Philo SE, De León KB, Noble RT, Zhou NA, Alghafri R, Bar-Or I, Darling A, D'Souza N, Hachimi O, Kaya D, Kim S, Gaardbo Kuhn K, Layton BA, Mansfeldt C, Oceguera B, Radniecki TS, Ram JL, Saunders LP, Shrestha A, Stadler LB, Steele JA, Stevenson BS, Vogel JR, Bibby K, Boehm AB, Halden RU, Delgado Vela J. Wastewater surveillance for bacterial targets: current challenges and future goals. Appl Environ Microbiol 2024; 90:e0142823. [PMID: 38099657 PMCID: PMC10807411 DOI: 10.1128/aem.01428-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
Wastewater-based epidemiology (WBE) expanded rapidly in response to the COVID-19 pandemic. As the public health emergency has ended, researchers and practitioners are looking to shift the focus of existing wastewater surveillance programs to other targets, including bacteria. Bacterial targets may pose some unique challenges for WBE applications. To explore the current state of the field, the National Science Foundation-funded Research Coordination Network (RCN) on Wastewater Based Epidemiology for SARS-CoV-2 and Emerging Public Health Threats held a workshop in April 2023 to discuss the challenges and needs for wastewater bacterial surveillance. The targets and methods used in existing programs were diverse, with twelve different targets and nine different methods listed. Discussions during the workshop highlighted the challenges in adapting existing programs and identified research gaps in four key areas: choosing new targets, relating bacterial wastewater data to human disease incidence and prevalence, developing methods, and normalizing results. To help with these challenges and research gaps, the authors identified steps the larger community can take to improve bacteria wastewater surveillance. This includes developing data reporting standards and method optimization and validation for bacterial programs. Additionally, more work is needed to understand shedding patterns for potential bacterial targets to better relate wastewater data to human infections. Wastewater surveillance for bacteria can help provide insight into the underlying prevalence in communities, but much work is needed to establish these methods.IMPORTANCEWastewater surveillance was a useful tool to elucidate the burden and spread of SARS-CoV-2 during the pandemic. Public health officials and researchers are interested in expanding these surveillance programs to include bacterial targets, but many questions remain. The NSF-funded Research Coordination Network for Wastewater Surveillance of SARS-CoV-2 and Emerging Public Health Threats held a workshop to identify barriers and research gaps to implementing bacterial wastewater surveillance programs.
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Affiliation(s)
- Sarah E. Philo
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kara B. De León
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Rachel T. Noble
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, North Carolina, USA
| | - Nicolette A. Zhou
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Rashed Alghafri
- International Center for Forensic Sciences, Dubai Police, Dubai, UAE
| | - Itay Bar-Or
- Israel Ministry of Health, Jerusalem, Israel
| | - Amanda Darling
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Oumaima Hachimi
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Devrim Kaya
- School of Public Health, San Diego State University, San Diego, California, USA
| | - Sooyeol Kim
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, California, USA
| | - Katrin Gaardbo Kuhn
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | - Cresten Mansfeldt
- Environmental Engineering Program, University of Colorado Boulder, Boulder, Colorado, USA
| | - Bethany Oceguera
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Tyler S. Radniecki
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Jeffrey L. Ram
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | | | - Abhilasha Shrestha
- Environmental and Occupational Health Sciences Division, University of Illinois Chicago School of Public Health, Chicago, Illinois, USA
| | - Lauren B. Stadler
- Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | - Joshua A. Steele
- Department of Microbiology, Southern California Coastal Research Project, Costa Mesa, California, USA
| | | | - Jason R. Vogel
- School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA
| | - Rolf U. Halden
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, Duke University, Durham, North Carolina, USA
- Department of Civil and Environmental Engineering, Howard University, Washington, District of Columbia, USA
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26
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Akter J, Smith WJ, Liu Y, Kim I, Simpson SL, Thai P, Korajkic A, Ahmed W. Comparison of adsorption-extraction (AE) workflows for improved measurements of viral and bacterial nucleic acid in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:167966. [PMID: 38476760 PMCID: PMC10927021 DOI: 10.1016/j.scitotenv.2023.167966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The lack of standardized methods and large differences in virus concentration and extraction workflows have hampered Severe Acute Respiratory Syndrome (SARS-CoV-2) wastewater surveillance and data reporting practices. Numerous studies have shown that adsorption-extraction (AE) method holds promise, yet several uncertainties remain regarding the optimal AE workflow. Several procedural components may influence the recovered concentrations of target nucleic acid, including membrane types, homogenization instruments, speed and duration, and lysis buffer. In this study, 42 different AE workflows that varied these components were compared to determine the optimal workflow by quantifying endogenous SARS-CoV-2, human adenovirus 40/41 (HAdV 40/41), and a bacterial marker gene of fecal contamination (Bacteroides HF183). Our findings suggest that the workflow chosen had a significant impact on SARS-CoV-2 concentrations, whereas it had minimal impact on HF183 and no effect on HAdV 40/41 concentrations. When comparing individual components in a workflow, such as membrane type (MF-Millipore™ 0.45 μm MCE vs. Isopore™ 0.40 μm), we found that they had no impact on SARS-CoV-2, HAdV 40/41, and HF183 concentrations. This suggests that at least some consumables and equipment are interchangeable. Buffer PM1 + TRIzol-based workflows yielded higher concentrations of SARS-CoV-2 than other workflows. HF183 concentrations were higher in workflows without chloroform. Similarly, higher homogenization speeds (5000-10,000 rpm) led to increased concentrations of SARS-CoV-2 and HF183 but had no effect on HAdV 40/41. Our findings indicate that minor enhancements to the AE workflow can improve the recovery of viruses and bacteria from the wastewater, leading to improved outcomes from wastewater surveillance efforts.
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Affiliation(s)
- Jesmin Akter
- Department of Civil and Environmental Engineering, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, Republic of Korea
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J.M. Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Ilho Kim
- Department of Civil and Environmental Engineering, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, Republic of Korea
| | | | - Phong Thai
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 4102 Brisbane, Australia
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
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27
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Akter J, Smith WJM, Gebrewold M, Kim I, Simpson SL, Bivins A, Ahmed W. Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167964. [PMID: 37865239 DOI: 10.1016/j.scitotenv.2023.167964] [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: 09/22/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARS-CoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 × 102 GC/reaction, with greater analytical sensitivity at 2 × 101 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 × 103 GC/reaction. For SARS-CoV-2 seeded wastewater samples, the US CDC N1 assay exhibited greater analytical sensitivity than the US CDC N2, E_Sarbeco, and RT-LAMP assays. Out of 30 wastewater samples, RT-qPCR detected endogenous SARS-CoV-2 RNA in 29 samples, while RT-LAMP identified 27 positive samples, with 20 displaying consistent amplifications in all three RT-LAMP technical replicates. Agreement analysis revealed a strong concordance between RT-LAMP and the US CDC N1 and E_Sarbeco RT-qPCR assays (κ = 0.474) but lower agreement with the US CDC N2 RT-qPCR assay (κ = 0.359). Quantification of SARS-CoV-2 RNA in positive samples revealed a strong correlation between the US CDC N1 and E_Sarbeco assays, while the US CDC N1 and US CDC N2 assays exhibited weak correlation. Logistic regression analysis indicated that RT-LAMP results correlated with RNA quantified by the US CDC N1 and E_Sarbeco assays, with 95 % limits of detection of 3.99 and 3.47 log10 GC/15 mL, respectively. In conclusion, despite lower sensitivity compared to RT-qPCR assays, RT-LAMP may offer advantages for wastewater surveillance, such as rapid results (estimated as twice as fast), and simplicity, making it a valuable tool in the shifting landscape of COVID-19 wastewater surveillance. Furthermore, LAMP positive wastewater samples might be prioritized for SARS-CoV-2 sequencing due to reduced analytical sensitivity. These findings support the use of RT-LAMP as a specific and efficient method for screening wastewater samples for SARS-CoV-2, particularly in resource-limited settings.
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Affiliation(s)
- Jesmin Akter
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea; CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Metasebia Gebrewold
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Ilho Kim
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea
| | | | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
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28
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Zammit I, Badia S, Mejías-Molina C, Rusiñol M, Bofill-Mas S, Borrego CM, Corominas L. Zooming in to the neighborhood level: A year-long wastewater-based epidemiology monitoring campaign for COVID-19 in small intraurban catchments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167811. [PMID: 37852481 DOI: 10.1016/j.scitotenv.2023.167811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/14/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
In recent years, wastewater-based epidemiology (WBE) has emerged as a valuable and cost-effective tool for monitoring the prevalence of COVID-19. Large-scale monitoring efforts have been implemented in numerous countries, primarily focusing on sampling at the entrance of wastewater treatment plants (WWTPs) to cover a large population. However, sampling at a finer spatial scale, such as at the neighborhood level (NGBs), pose new challenges, including the absence of composite sampling infrastructure and increased uncertainty due to the dynamics of small catchments. This study aims to investigate the feasibility and accuracy of WBE when deployed at the neighborhood level (sampling in sewers) compared to the city level (sampling at the entrance of a WWTP). To achieve this, we deployed specific WBE sampling stations at the intraurban scale within three NGBs in Barcelona, Spain. The study period covers the 5th and the 6th waves of COVID-19 in Spain, spanning from March 2021 to March 2022, along with the WWTP downstream from the NGBs. The results showed a strong correlation between the dynamics of COVID-19 clinical cases and wastewater SARS-CoV-2 loads at both the NGB and city levels. Notably, during the 5th wave, which was dominated by the Delta SARS-CoV-2 variant, wastewater loads were higher than during the 6th wave (Omicron variant), despite a lower number of clinical cases recorded during the 5th wave. The correlations between wastewater loads and clinical cases at the NGB level were stronger than at the WWTP level. However, the early warning potential varied across neighborhoods and waves, with some cases showing a one-week early warning and others lacking any significant early warning signal. Interestingly, the prevalence of COVID-19 did not exhibit major differences among NGBs with different socioeconomic statuses.
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Affiliation(s)
- Ian Zammit
- Catalan Institute for Water Research (ICRA-CERCA), Emili Grahit 101, 17003 Girona, Spain; University of Girona, Plaça de Sant Domènec 3, 17004 Girona, Spain
| | - Sergi Badia
- Catalan Institute for Water Research (ICRA-CERCA), Emili Grahit 101, 17003 Girona, Spain; University of Girona, Plaça de Sant Domènec 3, 17004 Girona, Spain
| | - Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA-CERCA), Emili Grahit 101, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Catalonia, Spain
| | - Lluís Corominas
- Catalan Institute for Water Research (ICRA-CERCA), Emili Grahit 101, 17003 Girona, Spain; University of Girona, Plaça de Sant Domènec 3, 17004 Girona, Spain.
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29
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Kuroita T, Yoshimura A, Iwamoto R, Ando H, Okabe S, Kitajima M. Quantitative analysis of SARS-CoV-2 RNA in wastewater and evaluation of sampling frequency during the downward period of a COVID-19 wave in Japan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:166526. [PMID: 37647962 DOI: 10.1016/j.scitotenv.2023.166526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/06/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Wastewater-based epidemiology (WBE) is a practical approach for detecting the presence of SARS-CoV-2 infections and assessing the epidemic trend of the coronavirus disease 2019 (COVID-19). The purpose of this study was to evaluate the minimum sampling frequency required to properly identify the COVID-19 trend during the downward epidemic period when using a highly sensitive RNA detection method. WBE was conducted using the Efficient and Practical virus Identification System with ENhanced Sensitivity for Solids (EPISENS-S), a highly sensitive SARS-CoV-2 RNA detection method, at nine neighboring wastewater treatment plants (WWTPs). These WWTPs were in the same prefecture in Japan, and they had different sewer types, sampling methods, and sampling frequencies. The overall detection rate of SARS-CoV-2 RNA was 97.8 % during the entire study period when the geometric means of new COVID-19 cases per 100,000 inhabitants were between 3.3 and 7.7 in each WWTP. The maximum SARS-CoV-2 RNA concentration in wastewater was 2.14 × 104 copies/L, which corresponded to pepper mild mottle virus (PMMoV)-normalized concentrations of 6.54 × 10-3. We evaluated the effect of sampling frequencies on the probability of a significant correlation with the number of newly reported COVID-19 cases by hypothetically reducing the sampling frequency in the same dataset. When the wastewater sampling frequency occurred 5, 3, 2, and 1 times per week, these results exhibited significant correlations of 100 % (5/5), 89 % (8/9), 85 % (23/27), and 48 % (13/27), respectively. To achieve significant correlation with a high probability of over 85 %, a minimum sampling frequency of twice per week is required, even if sampling methods and sewer types are different. WBE using the EPISENS-S method and a sampling frequency of more than twice a week can be used to properly monitor COVID-19 wave epidemic trends, even during downward periods.
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Affiliation(s)
- Tomohiro Kuroita
- AdvanSentinel Inc., 3-1-8, Doshomachi, Chuo-ku, Osaka 541-0045, Japan; Shionogi & Co., Ltd., 3-1-8, Doshomachi, Chuo-ku, Osaka 541-0045, Japan
| | - Akimasa Yoshimura
- Shionogi & Co., Ltd., 3-1-8, Doshomachi, Chuo-ku, Osaka 541-0045, Japan
| | - Ryo Iwamoto
- AdvanSentinel Inc., 3-1-8, Doshomachi, Chuo-ku, Osaka 541-0045, Japan; Shionogi & Co., Ltd., 3-1-8, Doshomachi, Chuo-ku, Osaka 541-0045, Japan
| | - Hiroki Ando
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
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30
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Ding J, Xu X, Deng Y, Zheng X, Zhang T. Circulation of SARS-CoV-2 Omicron sub-lineages revealed by multiplex genotyping RT-qPCR assays for sewage surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166300. [PMID: 37591390 DOI: 10.1016/j.scitotenv.2023.166300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023]
Abstract
Sewage surveillance has proven to be an essential complementary tool to clinical diagnosis in combating the COVID-19 pandemic by tracking the spread of the SARS-CoV-2 virus and evaluating infection levels in populations. With the striking spreading and continuous evolution of SARS-CoV-2 Omicron VOC that characterized with higher transmissibility and potential immune evasion, there is an urgent need for the rapid surveillance of this prevalent strain and its sub-lineages in sewage. In this study, based on three multiplex allele-specific (AS) RT-qPCR assays, we established a rapid and high-throughput detection workflow for the simultaneous discrimination of Omicron sub-lineages BA.2.2, BA.2.12.1, BA.4 and BA.5 (hereafter referred to as BA.4/BA.5) to track their community circulation in Hong Kong. All primer-probe sets in the multiplex assays could correctly discriminate and quantitate their target genotypes with high sensitivity and specificity, even when multiple variants co-existed in the sewage samples. Using the established multiplex assays, the trends of SARS-CoV-2 total viral load and variant dynamics in influent samples collected from 11 wastewater treatment plants (WWTPs) during June 2022 and September 2022, aligned with the clinical data, successfully unveiling the swift emergence and predominance of Omicron BA.4/BA.5 in Hong Kong. The study highlights the feasibility and applicability of multiplex RT-qPCR assays for monitoring epidemic trends and tracking variant displacement dynamics in sewage samples, providing a more rapid, high-throughput and cost-effective alternative to enhance the current sewage surveillance system.
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Affiliation(s)
- Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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Zhao B, Fujita T, Nihei Y, Yu Z, Chen X, Tanaka H, Ihara M. Tracking community infection dynamics of COVID-19 by monitoring SARS-CoV-2 RNA in wastewater, counting positive reactions by qPCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166420. [PMID: 37611711 DOI: 10.1016/j.scitotenv.2023.166420] [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: 11/10/2022] [Revised: 07/18/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Wastewater-based epidemiology has proved useful for monitoring the COVID-19 infection dynamics in communities. However, in regions of low prevalence, low concentrations of SARS-CoV-2 RNA in wastewater make this difficult. Here, we used real-time reverse-transcription PCR (RT-qPCR) to monitor SARS-CoV-2 RNA in wastewater from October 2020 to December 2022 during the third, fourth, fifth, sixth, seventh, and eighth waves of the COVID-19 outbreak in Japan. Viral RNA was below the limit of detection in all samples during the third and fourth waves. However, by counting the number of positive replicates in qPCR of each sample, we found that the positive ratio to all replicates in wastewater was significantly correlated with the number of clinically confirmed cases by the date of symptom onset during the third, fourth, and fifth waves. Time-step analysis indicated that, for 2 days either side of symptom onset, COVID-19 patients excreted in their feces large amounts of virus that wastewater surveillance could detect. We also demonstrated that the viral genome copy number in wastewater, as estimated from the positive ratio of SARSA-CoV-2 RNA, was correlated with the number of clinically confirmed cases. The positive count method is thus useful for tracing COVID-19 dynamics in regions of low prevalence.
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Affiliation(s)
- Bo Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China; Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Tomonori Fujita
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Yoshiaki Nihei
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan; Water Agency Inc., 3-25 Higashi-Goken-cho, Shinjuku-ku, Tokyo 162-0813, Japan
| | - Zaizhi Yu
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Xiaohan Chen
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan; Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe-Otsu, Nankoku city, Kochi 783-8502, Japan.
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32
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Lau M, King BJ, Keegan A, Drigo B, Donner E, Monis P. Comparison of kits for SARS-CoV-2 extraction in liquid and passive samples. Lett Appl Microbiol 2023; 76:ovad136. [PMID: 38066699 DOI: 10.1093/lambio/ovad136] [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: 09/04/2023] [Revised: 11/19/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
Abstract
Effective extraction and detection of viral nucleic acids from sewage are fundamental components of a successful SARS-CoV-2 sewage surveillance programme. As there is no standard method employed in sewage surveillance, understanding the performance of different extraction kits in the recovery of SARS-CoV-2 and the impact that PCR inhibitors have on quantification is essential to minimize data discrepancies caused by sample extraction. Three commercial nucleic acid extraction kits: the RNeasy PowerSoil Total RNA Kit (PS), the RNeasy PowerMicrobiome Kit (PMB), and the MagMAX™ Microbiome Ultra Nucleic Acid Isolation Kit (MM), with minor modifications, were evaluated. Their efficacy in recovering viral ribonucleic acid and removal of PCR inhibitors was assessed using two South Australian wastewater matrices-one from a major metropolitan site and one from a regional centre. Both had SARS-CoV-2 present due to active COVID-19 cases in these communities. Overall, the MM kit had a higher recovery of SARS-CoV-2 from the samples tested, followed by PMB and PS. The PMB kit performance was strongly influenced by the sample matrix when compared to the MM kit. It is recommended to assess the performance of extraction kits using different local wastewater matrices to ensure the accuracy and reliability of monitoring results to avoid false reporting.
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Affiliation(s)
- Melody Lau
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
| | - Brendon J King
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
| | - Alexandra Keegan
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
- UniSA STEM, University of South Australia, Adelaide, SA 5001, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
- Cooperative Research Centre for Solving Antimicrobial resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, SA 5001, Australia
| | - Paul Monis
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
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Hasing ME, Lee BE, Gao T, Li Q, Qiu Y, Ellehoj E, Graber TE, Fuzzen M, Servos M, Landgraff C, Delatolla R, Tipples G, Zelyas N, Hinshaw D, Maal-Bared R, Sikora C, Parkins M, Hubert CRJ, Frankowski K, Hrudey SE, Pang XL. Wastewater surveillance monitoring of SARS-CoV-2 variants of concern and dynamics of transmission and community burden of COVID-19. Emerg Microbes Infect 2023; 12:2233638. [PMID: 37409382 PMCID: PMC10408568 DOI: 10.1080/22221751.2023.2233638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/04/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Wastewater-based surveillance is a valuable approach for monitoring COVID-19 at community level. Monitoring SARS-CoV-2 variants of concern (VOC) in wastewater has become increasingly relevant when clinical testing capacity and case-based surveillance are limited. In this study, we ascertained the turnover of six VOC in Alberta wastewater from May 2020 to May 2022. Wastewater samples from nine wastewater treatment plants across Alberta were analysed using VOC-specific RT-qPCR assays. The performance of the RT-qPCR assays in identifying VOC in wastewater was evaluated against next generation sequencing. The relative abundance of each VOC in wastewater was compared to positivity rate in COVID-19 testing. VOC-specific RT-qPCR assays performed comparatively well against next generation sequencing; concordance rates ranged from 89% to 98% for detection of Alpha, Beta, Gamma, Omicron BA.1 and Omicron BA.2, with a slightly lower rate of 85% for Delta (p < 0.01). Elevated relative abundance of Alpha, Delta, Omicron BA.1 and BA.2 were each associated with increased COVID-19 positivity rate. Alpha, Delta and Omicron BA.2 reached 90% relative abundance in wastewater within 80, 111 and 62 days after their initial detection, respectively. Omicron BA.1 increased more rapidly, reaching a 90% relative abundance in wastewater after 35 days. Our results from VOC surveillance in wastewater correspond with clinical observations that Omicron is the VOC with highest disease burden over the shortest period in Alberta to date. The findings suggest that changes in relative abundance of a VOC in wastewater can be used as a supplementary indicator to track and perhaps predict COVID-19 burden in a population.
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Affiliation(s)
- Maria E. Hasing
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Bonita E. Lee
- Department of Paediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Tiejun Gao
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Qiaozhi Li
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Erik Ellehoj
- Ellehoj Redmond Consulting, Edmonton, Alberta, Canada
| | - Tyson E. Graber
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Meghan Fuzzen
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Mark Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Graham Tipples
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Nathan Zelyas
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - Deena Hinshaw
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Christopher Sikora
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaoli L. Pang
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
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Barnes KG, Levy JI, Gauld J, Rigby J, Kanjerwa O, Uzzell CB, Chilupsya C, Anscombe C, Tomkins-Tinch C, Mbeti O, Cairns E, Thole H, McSweeney S, Chibwana MG, Ashton PM, Jere KC, Meschke JS, Diggle P, Cornick J, Chilima B, Jambo K, Andersen KG, Kawalazira G, Paterson S, Nyirenda TS, Feasey N. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems. Nat Commun 2023; 14:7883. [PMID: 38036496 PMCID: PMC10689440 DOI: 10.1038/s41467-023-43047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
The COVID-19 pandemic has profoundly impacted health systems globally and robust surveillance has been critical for pandemic control, however not all countries can currently sustain community pathogen surveillance programs. Wastewater surveillance has proven valuable in high-income settings, but less is known about the utility of water surveillance of pathogens in low-income countries. Here we show how wastewater surveillance of SAR-CoV-2 can be used to identify temporal changes and help determine circulating variants quickly. In Malawi, a country with limited community-based COVID-19 testing capacity, we explore the utility of rivers and wastewater for SARS-CoV-2 surveillance. From May 2020-May 2022, we collect water from up to 112 river or defunct wastewater treatment plant sites, detecting SARS-CoV-2 in 8.3% of samples. Peak SARS-CoV-2 detection in water samples predate peaks in clinical cases. Sequencing of water samples identified the Beta, Delta, and Omicron variants, with Delta and Omicron detected well in advance of detection in patients. Our work highlights how wastewater can be used to detect emerging waves, identify variants of concern, and provide an early warning system in settings with no formal sewage systems.
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Affiliation(s)
- Kayla G Barnes
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Joshua I Levy
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jillian Gauld
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan Rigby
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Oscar Kanjerwa
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Christopher B Uzzell
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Chisomo Chilupsya
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Catherine Anscombe
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Christopher Tomkins-Tinch
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Omar Mbeti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Herbert Thole
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Shannon McSweeney
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Marah G Chibwana
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Philip M Ashton
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
| | - Khuzwayo C Jere
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - John Scott Meschke
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Peter Diggle
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Jennifer Cornick
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Blantyre District Health Office, Blantyre, Malawi
| | - Benjamin Chilima
- CHICAS, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Kondwani Jambo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Public Health Institute of Malawi, Lilongwe, Malawi
| | - Kristian G Andersen
- Department of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Scripps Research Translational Institute, La Jolla, CA, USA
| | - Gift Kawalazira
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Tonney S Nyirenda
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Pathology, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Nicholas Feasey
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
- School of Medicine, University of St Andrews, St Andrews, UK
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35
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Kumar M, Joshi M, Jiang G, Yamada R, Honda R, Srivastava V, Mahlknecht J, Barcelo D, Chidambram S, Khursheed A, Graham DW, Goswami R, Kuroda K, Tiwari A, Joshi C. Response of wastewater-based epidemiology predictor for the second wave of COVID-19 in Ahmedabad, India: A long-term data Perspective. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122471. [PMID: 37652227 DOI: 10.1016/j.envpol.2023.122471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/30/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
In this work, we present an eight-month longitudinal study of wastewater-based epidemiology (WBE) in Ahmedabad, India, where wastewater surveillance was introduced in September 2020 after the successful containment of the first wave of COVID-19 to predict the resurge of the infection during the second wave of the pandemic. The study aims to elucidate the weekly resolution of the SARS-CoV-2 RNA data for eight months in wastewater samples to predict the COVID-19 situation and identify hotspots in Ahmedabad. A total of 287 samples were analyzed for SARS-CoV-2 RNA using RT-PCR, and Spearman's rank correlation was applied to depict the early warning potential of WBE. During September 2020 to April 2021, the increasing number of positive wastewater influent samples correlated with the growing number of confirmed clinical cases. It also showed clear evidence of early detection of the second wave of COVID-19 in Ahmedabad (March 2021). 258 out of a total 287 samples were detected positive with at least two out of three SARS-CoV-2 genes (N, ORF- 1 ab, and S). Monthly variation represented a significant decline in all three gene copies in October compared to September 2020, followed by an abrupt increase in November 2020. A similar increment in the gene copies was observed in March and April 2021, which would be an indicator of the second wave of COVID-19. A lead time of 1-2 weeks was observed in the change of gene concentrations compared with clinically confirmed cases. Measured wastewater ORF- 1 ab gene copies ranged from 6.1 x 102 (October 2020) to 1.4 x 104 (November 2020) copies/mL, and wastewater gene levels typically lead to confirmed cases by one to two weeks. The study highlights the value of WBE as a monitoring tool to predict waves within a pandemic, identify local disease hotspots within a city, and guide rapid management interventions.
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Affiliation(s)
- Manish Kumar
- Sustainability Cluster, School of Advanced Engineering, UPES, Dehradun, Uttarakhand, 248007, India; Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterey, Monterrey, 64849, Nuevo Leon, Mexico.
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, 248007, India
| | - Guangming Jiang
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, Australia
| | - Rintaro Yamada
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, 920-1192, Japan; Yachiyo Engineering Co., Ltd. Tokyo, 111-8648, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Vaibhav Srivastava
- Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, 211002, India
| | - Jürgen Mahlknecht
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterey, Monterrey, 64849, Nuevo Leon, Mexico
| | - Damia Barcelo
- Sustainability Cluster, School of Advanced Engineering, UPES, Dehradun, Uttarakhand, 248007, India; Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona, 18-26, 08034, Barcelona, Spain; Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnol'ogic de la Universitat de Girona, c/Emili Grahit, 101, Edifici H2O, 17003, Girona, Spain
| | | | - Anwar Khursheed
- Department of Civil Engineering, College of Engineering, King Saud University, Riyadh, 11421, Saudi Arabia
| | - David W Graham
- Department of Civil and Environmental Engineering, Newcastle University, Newcastle, UK
| | - Ritusmita Goswami
- Centre for Ecology, Environment and Sustainable Development, Tata Institute of Social Sciences, Guwahati, India
| | - Keisuke Kuroda
- Department of Environmental and Civil Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, 939-0398, Japan
| | - Ananda Tiwari
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, 70701 Kuopio, Finland
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, 248007, India
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36
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Schmiege D, Kraiselburd I, Haselhoff T, Thomas A, Doerr A, Gosch J, Schoth J, Teichgräber B, Moebus S, Meyer F. Analyzing community wastewater in sub-sewersheds for the small-scale detection of SARS-CoV-2 variants in a German metropolitan area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165458. [PMID: 37454854 DOI: 10.1016/j.scitotenv.2023.165458] [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: 04/06/2023] [Revised: 06/09/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
Wastewater surveillance of SARS-CoV-2 proved useful, including for identifying the local appearance of newly identified virus variants. Previous studies focused on wastewater treatment plants (WWTP) with sewersheds of several hundred thousand people or at single building level, representing only a small number of people. Both approaches may prove inadequate for small-scale intra-urban inferences for early detection of emerging or novel virus variants. Our study aims (i) to analyze SARS-CoV-2 single nucleotide variants (SNVs) in wastewater of sub-sewersheds and WWTP using whole genome sequencing in order to (ii) investigate the potential of small-scale detection of novel known SARS-CoV-2 variants of concern (VOC) within a metropolitan wastewater system. We selected three sub-sewershed sampling sites, based on estimated population- and built environment-related indicators, and the inlet of the receiving WWTP in the Ruhr region, Germany. Untreated wastewater was sampled weekly between October and December 2021, with a total of 22 samples collected. SARS-CoV-2 RNA was analyzed by RT-qPCR and whole genome sequencing. For all samples, genome sequences were obtained, while only 13 samples were positive for RT-qPCR. We identified multiple specific SARS-CoV-2 SNVs in the wastewater samples of the sub-sewersheds and the WWTP. Identified SNVs reflected the dominance of VOC Delta at the time of sampling. Interestingly, we could identify an Omicron-specific SNV in one sub-sewershed. A concurrent wastewater study sampling the same WWTP detected the VOC Omicron one week later. Our observations suggest that the small-scale approach may prove particularly useful for the detection and description of spatially confined emerging or existing virus variants circulating in populations. Future studies applying small-scale sampling strategies taking into account the specific features of the wastewater system will be useful to analyze temporal and spatial variance in more detail.
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Affiliation(s)
- Dennis Schmiege
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130 Essen, Germany.
| | - Ivana Kraiselburd
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany
| | - Timo Haselhoff
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130 Essen, Germany
| | - Alexander Thomas
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany
| | - Adrian Doerr
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany
| | - Jule Gosch
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany
| | - Jens Schoth
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, 45128 Essen, Germany
| | | | - Susanne Moebus
- Institute for Urban Public Health (InUPH), University Hospital Essen, University of Duisburg-Essen, 45130 Essen, Germany
| | - Folker Meyer
- Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, 45131 Essen, Germany
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Zhou J, Pang Y, Wang H, Li W, Liu J, Luo Z, Shao W, Zhang H. Sewage network operational risks based on InfoWorks ICM with nodal flow diurnal patterns under NPIs for COVID-19. WATER RESEARCH 2023; 246:120708. [PMID: 37827041 DOI: 10.1016/j.watres.2023.120708] [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: 12/23/2022] [Revised: 09/18/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023]
Abstract
Non-Pharmaceutical Interventions (NPIs) have been widely employed globally over the past three years to control the rapid spread of coronavirus disease 2019 (COVID-19). These measures have imposed restrictions on urban residents' activities and significantly influenced sewage discharge characteristics within sewage network, particularly in densely populated cities in China. This study focused on the nodal flow diurnal patterns and sewage network operational risks before and after epidemic lockdown in Beijing from March to May in 2022. Nodal flow diurnal patterns on weekdays and weekends before and after NPIs were analyzed using measured data through statistical and mathematical methods. A sewage network model was established to simulate and analyze the operational risks based on InfoWorks ICM before and after epidemic lockdown. The main conclusions were as follows: (1) In predominantly residential areas, the total wastewater volume increased by approximately 28.76 % to 33.52 % after the implementation of strict NPIs. The morning and midday "M" peaks on normalized weekdays transformed into "N" peaks, and the morning peak time was delayed by 0.5 to 1 hour after the lockdown; (2) Following NPIs, More than 90 % of manholes' average water levels rose to varying degrees, approximately 50 % of pipe lengths exhibited a full flow state; (3) When the lockdown was in place during a hot summer day, sewage overflow phenomena were observed in 4.6 % and 9.6 % of manholes, respectively, with per capita daily drainage equivalent reaching 40-50 %. These findings hold significant implications for the proactive planning and operational management of water industry infrastructure during major emergencies.
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Affiliation(s)
- Jinjun Zhou
- Faculty of architecture, civil and transportation engineering, Beijing University of Technology, Beijing 100124, China
| | - Yali Pang
- Faculty of architecture, civil and transportation engineering, Beijing University of Technology, Beijing 100124, China
| | - Hao Wang
- Faculty of architecture, civil and transportation engineering, Beijing University of Technology, Beijing 100124, China.
| | - Wentao Li
- Faculty of architecture, civil and transportation engineering, Beijing University of Technology, Beijing 100124, China
| | - Jiahong Liu
- China Institute of Water Resources and Hydropower Research State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 100038, China
| | - Zhuoran Luo
- School of Water Resources and Hydropower Engineering, North China Electric Power University, Beijing 102206, China
| | - Weiwei Shao
- China Institute of Water Resources and Hydropower Research State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 100038, China
| | - Haijia Zhang
- Faculty of architecture, civil and transportation engineering, Beijing University of Technology, Beijing 100124, China
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Torabi F, Li G, Mole C, Nicholson G, Rowlingson B, Smith CR, Jersakova R, Diggle PJ, Blangiardo M. Wastewater-based surveillance models for COVID-19: A focused review on spatio-temporal models. Heliyon 2023; 9:e21734. [PMID: 38053867 PMCID: PMC10694161 DOI: 10.1016/j.heliyon.2023.e21734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 12/07/2023] Open
Abstract
The evident shedding of the SARS-CoV-2 RNA particles from infected individuals into the wastewater opened up a tantalizing array of possibilities for prediction of COVID-19 prevalence prior to symptomatic case identification through community testing. Many countries have therefore explored the use of wastewater metrics as a surveillance tool, replacing traditional direct measurement of prevalence with cost-effective approaches based on SARS-CoV-2 RNA concentrations in wastewater samples. Two important aspects in building prediction models are: time over which the prediction occurs and space for which the predicted case numbers is shown. In this review, our main focus was on finding mathematical models which take into the account both the time-varying and spatial nature of wastewater-based metrics into account. We used six main characteristics as our assessment criteria: i) modelling approach; ii) temporal coverage; iii) spatial coverage; iv) sample size; v) wastewater sampling method; and vi) covariates included in the modelling. The majority of studies in the early phases of the pandemic recognized the temporal association of SARS-CoV-2 RNA concentration level in wastewater with the number of COVID-19 cases, ignoring their spatial context. We examined 15 studies up to April 2023, focusing on models considering both temporal and spatial aspects of wastewater metrics. Most early studies correlated temporal SARS-CoV-2 RNA levels with COVID-19 cases but overlooked spatial factors. Linear regression and SEIR models were commonly used (n = 10, 66.6 % of studies), along with machine learning (n = 1, 6.6 %) and Bayesian approaches (n = 1, 6.6 %) in some cases. Three studies employed spatio-temporal modelling approach (n = 3, 20.0 %). We conclude that the development, validation and calibration of further spatio-temporally explicit models should be done in parallel with the advancement of wastewater metrics before the potential of wastewater as a surveillance tool can be fully realised.
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Affiliation(s)
- Fatemeh Torabi
- Turing-RSS Health Data Lab, London, UK
- Population Data Science HDRUK-Wales, Medical School, Swansea University, Wales, UK
| | - Guangquan Li
- Turing-RSS Health Data Lab, London, UK
- Applied Statistics Research Group, Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Callum Mole
- Turing-RSS Health Data Lab, London, UK
- The Alan Turing Institute, London, UK
| | - George Nicholson
- Turing-RSS Health Data Lab, London, UK
- University of Oxford, Oxford, UK
| | - Barry Rowlingson
- Turing-RSS Health Data Lab, London, UK
- CHICAS, Lancaster Medical School, Lancaster University, England, UK
| | | | - Radka Jersakova
- Turing-RSS Health Data Lab, London, UK
- The Alan Turing Institute, London, UK
| | - Peter J. Diggle
- Turing-RSS Health Data Lab, London, UK
- CHICAS, Lancaster Medical School, Lancaster University, England, UK
| | - Marta Blangiardo
- Turing-RSS Health Data Lab, London, UK
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College, London, UK
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Alamin M, Hara-Yamamura H, Hata A, Zhao B, Ihara M, Tanaka H, Watanabe T, Honda R. Reduction of SARS-CoV-2 by biological nutrient removal and disinfection processes in full-scale wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165097. [PMID: 37356766 PMCID: PMC10290167 DOI: 10.1016/j.scitotenv.2023.165097] [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: 04/19/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 06/27/2023]
Abstract
Detection of SARS-CoV-2 RNA in wastewater poses people's concerns regarding the potential risk in water bodies receiving wastewater treatment effluent, despite the infectious risk of SARS-CoV-2 in wastewater being speculated to be low. Unlike well-studied nonenveloped viruses, SARS-CoV-2 in wastewater is present abundantly in both solid and liquid fractions of wastewater. Reduction of SARS-CoV-2 in past studies were likely underestimated, as SARS-CoV-2 in influent wastewater were quantified in either solid or liquid fraction only. The objectives of this study were (i) to clarify the reduction in SARS-CoV-2 RNA during biological nutrient removal and disinfection processes in full-scale WWTPs, considering the SARS-CoV-2 present in both solid and liquid fractions of wastewater, and (ii) to evaluate applicability of pepper mild mottle virus (PMMoV) as a performance indicator for reduction of SARS-CoV-2 in WWTPs. Accordingly, large amount of SARS-CoV-2 RNA were partitioned in the solid fraction of influent wastewater for composite sampling than grab sampling. When SARS-CoV-2 RNA in the both solid and liquid fractions were considered, log reduction values (LRVs) of SARS-CoV-2 during step-feed multistage biological nitrogen removal (SM-BNR) and enhanced biological phosphorus removal (EBPR) processes ranged between>2.1-4.4 log and did not differ significantly from those in conventional activated sludge (CAS). The LRVs of SARS-CoV-2 RNA in disinfection processes by ozonation and chlorination did not differ significantly. PMMoV is a promising performance indicator to secure reduction of SARS-CoV-2 in WWTPs, because of its higher persistence in wastewater treatment processes and abundance at a detectable concentration even in the final effluent after disinfection.
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Affiliation(s)
- Md Alamin
- Graduate School of Natural Science and Technology, Kanazawa University, Japan
| | | | - Akihiko Hata
- Department of Environmental and Civil Engineering, Toyama Prefectural University, Japan
| | - Bo Zhao
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Japan; College of Environment, Hohai University, Nanjing 210098, China
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Japan; Faculty of Agriculture and Marine Science, Kochi University, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Japan
| | | | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Japan; Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Japan.
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Di DYW, Li B, Jeon MK, Yan T. Comparing solid-based concentration methods for rapid and efficient recovery of SARS-CoV-2 for wastewater surveillance. J Virol Methods 2023; 320:114790. [PMID: 37558056 DOI: 10.1016/j.jviromet.2023.114790] [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: 05/01/2023] [Revised: 07/26/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
As wastewater-based surveillance of SARS-CoV-2 attracts interest globally, there is a need to evaluate and identify rapid and efficient methods for concentrating enveloped viruses in wastewater. When comparing five precipitation/flocculation-based concentration methods (including aluminum hydroxide adsorption-precipitation, AHAP; zinc acetate precipitation, ZAP; skimmed milk flocculation, SMF; FeCl3 precipitation, FCP; and direct centrifugation, DC), AHAP was found to be the most efficient method in terms of seeded BCoV recovery (50.2 %). Based on the BCoV recovery efficiency and turnaround time, the AHAP and DC methods were selected and tested on five additional wastewater samples containing both seeded BCoV and indigenous wastewater SARS-CoV-2 RNA. The BCoV recovery (DC: average=30.1 %, sx =14.7 %; AHAP: average=33.0 %, sx =14.2 %) and SARS-CoV-2 based on the N2 gene assay (DC: average=3.6 ×103 gene copies or GC/mL, sx =1.9 × 103 GC/mL; AHAP: average=3.0 ×103 GC/mL, sx =2.0 ×103 GC/mL) of both methods were not significantly different in solid fraction (p = 0.89). This study showed significant higher BCoV recovery and SARS-CoV-2 viral RNA in wastewater solid fraction (p = 0.006) than liquid fraction. Our result suggests that the solid fraction of wastewater samples is more suitable for recovering enveloped viruses from wastewater, and the DC and AHAP methods equally provide suitably rapid, cost-effective, and significantly higher recovery of SARS-CoV-2 viral RNA in wastewater samples.
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Affiliation(s)
- Doris Yoong Wen Di
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Bo Li
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Min Ki Jeon
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Tao Yan
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA; Water Resources Research Center, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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de Araújo Rolo C, Machado BAS, Dos Santos MC, Dos Santos RF, Fonseca MS, Hodel KVS, Silva JR, Nunes DDG, Dos Santos Almeida E, de Andrade JB. Long-term monitoring of COVID-19 prevalence in raw and treated wastewater in Salvador, the largest capital of the Brazilian Northeast. Sci Rep 2023; 13:15238. [PMID: 37709804 PMCID: PMC10502096 DOI: 10.1038/s41598-023-41060-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023] Open
Abstract
Wastewater-based epidemiology (WBE) becomes an interesting epidemiological approach to monitoring the prevalence of SARS-CoV-2 broadly and non-invasively. Herein, we employ for the first time WBE, associated or not with the PEG 8000 precipitation method, for the detection of SARS-CoV-2 in samples of raw or treated wastewater from 22 municipal wastewater treatment stations (WWTPs) located in Salvador, the fourth most populous city in Brazil. Our results demonstrate the success of the application of WBE for detecting SARS-CoV-2 in both types of evaluated samples, regardless of the usage of PEG 8000 concentration procedure. Further, an increase in SARS-CoV-2 positivity rate was observed in samples collected in months that presented the highest number of confirmed COVID-19 cases (May/2021, June/2021 and January/2022). While PEG 8000 concentration step was found to significantly increase the positivity rate in treated wastewater samples (p < 0.005), a strong positive correlation (r: 0.84; p < 0.002) between non-concentrated raw wastewater samples with the number of new cases of COVID-19 (April/2021-February/2022) was observed. In general, the present results reinforce the efficiency of WBE approach to monitoring the presence of SARS-CoV-2 in either low- or high-capacity WWTPs. The successful usage of WBE even in raw wastewater samples makes it an interesting low-cost tool for epidemiological surveillance.
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Affiliation(s)
- Carolina de Araújo Rolo
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Bruna Aparecida Souza Machado
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, 41650-010, Brazil
| | - Matheus Carmo Dos Santos
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Rosângela Fernandes Dos Santos
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Maísa Santos Fonseca
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Katharine Valéria Saraiva Hodel
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Jéssica Rebouças Silva
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Danielle Devequi Gomes Nunes
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Edna Dos Santos Almeida
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, 41650-010, Brazil
| | - Jailson Bittencourt de Andrade
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil.
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, 41650-010, Brazil.
- Centro Interdisciplinar de Energia e Ambiente - CIEnAm, Federal University of Bahia, Salvador, 40170-115, Brazil.
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Ruan Y, Huang T, Zhou W, Zhu J, Liang Q, Zhong L, Tang X, Liu L, Chen S, Xie Y. The lead time and geographical variations of Baidu Search Index in the early warning of COVID-19. Sci Rep 2023; 13:14705. [PMID: 37679512 PMCID: PMC10484897 DOI: 10.1038/s41598-023-41939-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023] Open
Abstract
Internet search data was a useful tool in the pre-warning of COVID-19. However, the lead time and indicators may change over time and space with the new variants appear and massive nucleic acid testing. Since Omicron appeared in late 2021, we collected the daily number of cases and Baidu Search Index (BSI) of seven search terms from 1 January to 30 April, 2022 in 12 provinces/prefectures to explore the variation in China. Two search peaks of "COVID-19 epidemic", "Novel Coronavirus" and "COVID-19" can be observed. One in January, which showed 3 days lead time in Henan and Tianjin. Another on early March, which occurred 0-28 days ahead of the local epidemic but the lead time had spatial variation. It was 4 weeks in Shanghai, 2 weeks in Henan and 5-8 days in Jilin Province, Jilin and Changchun Prefecture. But it was only 1-3 days in Tianjin, Quanzhou Prefecture, Fujian Province and 0 day in Shenzhen, Shandong Province, Qingdao and Yanbian Prefecture. The BSI was high correlated (rs:0.70-0.93) to the number of cases with consistent epidemiological change trend. The lead time of BSI had spatial and temporal variation and was close related to the strength of nucleic acid testing. The case detection ability should be strengthened when perceiving BSI increase.
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Affiliation(s)
- Yuhua Ruan
- State Key Laboratory of Infectious Disease Prevention and Control (SKLID), National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Tengda Huang
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Wanwan Zhou
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Jinhui Zhu
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Qiuyu Liang
- Department of Health Management, The People's Hospital of Guangxi Zhuang Autonomous Region & Research Center of Health Management, Guangxi Academy of Medical Sciences, Nanning, China
| | - Lixian Zhong
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Xiaofen Tang
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Lu Liu
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Shiwen Chen
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Yihong Xie
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China.
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, China.
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Kuhn KG, Shukla R, Mannell M, Graves GM, Miller AC, Vogel J, Malloy K, Deshpande G, Florea G, Shelton K, Jeffries E, De León KB, Stevenson B. Using Wastewater Surveillance to Monitor Gastrointestinal Pathogen Infections in the State of Oklahoma. Microorganisms 2023; 11:2193. [PMID: 37764037 PMCID: PMC10536226 DOI: 10.3390/microorganisms11092193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
During the COVID-19 pandemic, wastewater surveillance was widely used to monitor temporal and geographical infection trends. Using this as a foundation, a statewide program for routine wastewater monitoring of gastrointestinal pathogens was established in Oklahoma. The results from 18 months of surveillance showed that wastewater concentrations of Salmonella, Campylobacter, and norovirus exhibit similar seasonal patterns to those observed in reported human cases (F = 4-29, p < 0.05) and that wastewater can serve as an early warning tool for increases in cases, offering between one- and two-weeks lead time. Approximately one third of outbreak alerts in wastewater correlated in time with confirmed outbreaks of Salmonella or Campylobacter and our results further indicated that several outbreaks are likely to go undetected through the traditional surveillance approach currently in place. Better understanding of the true distribution and burden of gastrointestinal infections ultimately facilitates better disease prevention and control and reduces the overall socioeconomic and healthcare related impact of these pathogens. In this respect, wastewater represents a unique opportunity for monitoring infections in real-time, without the need for individual human testing. With increasing demands for sustainable and low-cost disease surveillance, the usefulness of wastewater as a long-term method for tracking infectious disease transmission is likely to become even more pronounced.
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Affiliation(s)
- Katrin Gaardbo Kuhn
- Department of Biostatistics & Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (K.M.); (G.D.)
| | - Rishabh Shukla
- School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, OK 73019, USA; (R.S.); (G.M.G.); (A.C.M.); (J.V.); (G.F.)
| | - Mike Mannell
- Acute Diseases Division, Oklahoma State Department of Health, Oklahoma City, OK 73102, USA;
| | - Grant M. Graves
- School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, OK 73019, USA; (R.S.); (G.M.G.); (A.C.M.); (J.V.); (G.F.)
| | - A. Caitlin Miller
- School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, OK 73019, USA; (R.S.); (G.M.G.); (A.C.M.); (J.V.); (G.F.)
| | - Jason Vogel
- School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, OK 73019, USA; (R.S.); (G.M.G.); (A.C.M.); (J.V.); (G.F.)
| | - Kimberly Malloy
- Department of Biostatistics & Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (K.M.); (G.D.)
| | - Gargi Deshpande
- Department of Biostatistics & Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (K.M.); (G.D.)
| | - Gabriel Florea
- School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, OK 73019, USA; (R.S.); (G.M.G.); (A.C.M.); (J.V.); (G.F.)
- Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kristen Shelton
- School of Biological Sciences, University of Oklahoma, Norman, OK 73019, USA; (K.S.); (E.J.); (K.B.D.L.)
| | - Erin Jeffries
- School of Biological Sciences, University of Oklahoma, Norman, OK 73019, USA; (K.S.); (E.J.); (K.B.D.L.)
| | - Kara B. De León
- School of Biological Sciences, University of Oklahoma, Norman, OK 73019, USA; (K.S.); (E.J.); (K.B.D.L.)
| | - Bradley Stevenson
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL 60208, USA;
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Arts PJ, Kelly JD, Midgley CM, Anglin K, Lu S, Abedi GR, Andino R, Bakker KM, Banman B, Boehm AB, Briggs-Hagen M, Brouwer AF, Davidson MC, Eisenberg MC, Garcia-Knight M, Knight S, Peluso MJ, Pineda-Ramirez J, Diaz Sanchez R, Saydah S, Tassetto M, Martin JN, Wigginton KR. Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage. mSphere 2023; 8:e0013223. [PMID: 37338211 PMCID: PMC10506459 DOI: 10.1128/msphere.00132-23] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/03/2023] [Indexed: 06/21/2023] Open
Abstract
Wastewater-based epidemiology (WBE) emerged during the coronavirus disease 2019 (COVID-19) pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden. The lack of high-resolution fecal shedding data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) limits our ability to link WBE measurements to disease burden. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as for the commonly used fecal indicators pepper mild mottle virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. The shedding trajectories from 48 SARS-CoV-2-infected individuals suggest a highly individualized, dynamic course of SARS-CoV-2 RNA fecal shedding. Of the individuals that provided at least three stool samples spanning more than 14 days, 77% had one or more samples that tested positive for SARS-CoV-2 RNA. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall. CrAssphage DNA was detected in at least one sample from 80% (38/48) of individuals and was detected in 48% (179/371) of all samples. The geometric mean concentrations of PMMoV and crAssphage in stool across all individuals were 8.7 × 104 and 1.4 × 104 gene copies/milligram-dry weight, respectively, and crAssphage shedding was more consistent for individuals than PMMoV shedding. These results provide us with a missing link needed to connect laboratory WBE results with mechanistic models, and this will aid in more accurate estimates of COVID-19 burden in sewersheds. Additionally, the PMMoV and crAssphage data are critical for evaluating their utility as fecal strength normalizing measures and for source-tracking applications. IMPORTANCE This research represents a critical step in the advancement of wastewater monitoring for public health. To date, mechanistic materials balance modeling of wastewater-based epidemiology has relied on SARS-CoV-2 fecal shedding estimates from small-scale clinical reports or meta-analyses of research using a wide range of analytical methodologies. Additionally, previous SARS-CoV-2 fecal shedding data have not contained sufficient methodological information for building accurate materials balance models. Like SARS-CoV-2, fecal shedding of PMMoV and crAssphage has been understudied to date. The data presented here provide externally valid and longitudinal fecal shedding data for SARS-CoV-2, PMMoV, and crAssphage which can be directly applied to WBE models and ultimately increase the utility of WBE.
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Affiliation(s)
- Peter J. Arts
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
- Division of Hospital Medicine, UCSF, San Francisco, California, USA
- F.I. Proctor Foundation, University of California, San Francisco, California, USA
| | - Claire M. Midgley
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Khamal Anglin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Glen R. Abedi
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Raul Andino
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
| | - Kevin M. Bakker
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Bryon Banman
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandria B. Boehm
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California, USA
| | - Melissa Briggs-Hagen
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrew F. Brouwer
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marisa C. Eisenberg
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Sterling Knight
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael J. Peluso
- Division of HIV, Infectious Disease, and Global Medicine, UCSF, San Francisco, California, USA
| | - Jesus Pineda-Ramirez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Ruth Diaz Sanchez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
- Institute for Global Health Sciences, University of California, San Francisco, California, USA
| | - Sharon Saydah
- National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Krista R. Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
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Rioux MD, Guillemette F, Lemarchand K, Doiron K, Lemay JF, Maere T, Dolcé P, Quessy P, Abonnenc N, Vanrolleghem PA, Frigon D. Wastewater-based epidemiology: the crucial role of viral shedding dynamics in small communities. Front Public Health 2023; 11:1141837. [PMID: 37601171 PMCID: PMC10433918 DOI: 10.3389/fpubh.2023.1141837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/30/2023] [Indexed: 08/22/2023] Open
Abstract
Background Wastewater surveillance (WWS) of pathogens is a rapidly evolving field owing to the 2019 coronavirus disease pandemic, which brought about a paradigm shift in public health authorities for the management of pathogen outbreaks. However, the interpretation of WWS in terms of clinical cases remains a challenge, particularly in small communities where large variations in pathogen concentrations are routinely observed without a clear relation to clinical incident cases. Methods Results are presented for WWS from six municipalities in the eastern part of Canada during the spring of 2021. We developed a numerical model based on viral kinetics reduction functions to consider both prevalent and incident cases to interpret the WWS data in light of the reported clinical cases in the six surveyed communities. Results The use of the proposed numerical model with a viral kinetics reduction function drastically increased the interpretability of the WWS data in terms of the clinical cases reported for the surveyed community. In line with our working hypothesis, the effects of viral kinetics reduction modeling were more important in small communities than in larger communities. In all but one of the community cases (where it had no effect), the use of the proposed numerical model led to a change from a +1.5% (for the larger urban center, Quebec City) to a +48.8% increase in the case of a smaller community (Drummondville). Conclusion Consideration of prevalent and incident cases through the proposed numerical model increases the correlation between clinical cases and WWS data. This is particularly the case in small communities. Because the proposed model is based on a biological mechanism, we believe it is an inherent part of any wastewater system and, hence, that it should be used in any WWS analysis where the aim is to relate WWS measurement to clinical cases.
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Affiliation(s)
- Marc-Denis Rioux
- Department of Mathematics and Engineering, Université du Québec à Rimouski, Quebec, QC, Canada
| | - François Guillemette
- Department of Environmental Science, Université du Québec à Trois-Rivière, Quebec, QC, Canada
| | - Karine Lemarchand
- Institut des Sciences de la Mer, Université du Québec à Rimouski, Quebec, QC, Canada
| | - Kim Doiron
- Northern Institute for Research in Environment and Occupational Health and Safety, Quebec, QC, Canada
| | - Jean-François Lemay
- Centre National en Électrochimie et Technologies Environnementales, Cegep of Shawinigan, Quebec, QC, Canada
| | - Thomas Maere
- modelEAU, Département de génie civil et de génie des eaux, Université Laval, Quebec, QC, Canada
| | - Patrick Dolcé
- Centre Intégré de Santé et de services sociaux du Bas-Saint-Laurent, Quebec, QC, Canada
| | - Patrik Quessy
- Centre National en Électrochimie et Technologies Environnementales, Cegep of Shawinigan, Quebec, QC, Canada
| | - Nanouk Abonnenc
- Centre National en Électrochimie et Technologies Environnementales, Cegep of Shawinigan, Quebec, QC, Canada
| | - Peter A. Vanrolleghem
- modelEAU, Département de génie civil et de génie des eaux, Université Laval, Quebec, QC, Canada
| | - Dominic Frigon
- Department of Civil Engineering, McGill University, Quebec, QC, Canada
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Keshaviah A, Huff I, Hu XC, Guidry V, Christensen A, Berkowitz S, Reckling S, Noble RT, Clerkin T, Blackwood D, McLellan SL, Roguet A, Musse I. Separating signal from noise in wastewater data: An algorithm to identify community-level COVID-19 surges in real time. Proc Natl Acad Sci U S A 2023; 120:e2216021120. [PMID: 37490532 PMCID: PMC10401018 DOI: 10.1073/pnas.2216021120] [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: 10/07/2022] [Accepted: 06/11/2023] [Indexed: 07/27/2023] Open
Abstract
Wastewater monitoring has provided health officials with early warnings for new COVID-19 outbreaks, but to date, no approach has been validated to distinguish signal (sustained surges) from noise (background variability) in wastewater data to alert officials to the need for heightened public health response. We analyzed 62 wk of data from 19 sites participating in the North Carolina Wastewater Monitoring Network to characterize wastewater metrics around the Delta and Omicron surges. We found that wastewater data identified outbreaks 4 to 5 d before case data (reported on the earlier of the symptom start date or test collection date), on average. At most sites, correlations between wastewater and case data were similar regardless of how wastewater concentrations were normalized and whether calculated with county-level or sewershed-level cases, suggesting that officials may not need to geospatially align case data with sewershed boundaries to gain insights into disease transmission. Although wastewater trend lines captured clear differences in the Delta versus Omicron surge trajectories, no single wastewater metric (detectability, percent change, or flow-population normalized viral concentrations) reliably signaled when these surges started. After iteratively examining different combinations of these three metrics, we developed the Covid-SURGE (Signaling Unprecedented Rises in Groupwide Exposure) algorithm, which identifies unprecedented signals in the wastewater data. With a true positive rate of 82%, a false positive rate of 7%, and strong performance during both surges and in small and large sites, our algorithm provides public health officials with an automated way to flag community-level COVID-19 surges in real time.
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Affiliation(s)
| | - Ian Huff
- Mathematica, Inc., Princeton, NJ08543
| | | | - Virginia Guidry
- North Carolina Department of Health and Human Services, Division of Public Health, Raleigh, NC27609
| | - Ariel Christensen
- North Carolina Department of Health and Human Services, Division of Public Health, Raleigh, NC27609
| | - Steven Berkowitz
- North Carolina Department of Health and Human Services, Division of Public Health, Raleigh, NC27609
| | - Stacie Reckling
- North Carolina Department of Health and Human Services, Division of Public Health, Raleigh, NC27609
| | - Rachel T. Noble
- Institute of Marine Sciences, University of North Carolina-Chapel Hill, Morehead City, NC28557
| | - Thomas Clerkin
- Institute of Marine Sciences, University of North Carolina-Chapel Hill, Morehead City, NC28557
| | - Denene Blackwood
- Institute of Marine Sciences, University of North Carolina-Chapel Hill, Morehead City, NC28557
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI53204
| | - Adélaïde Roguet
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI53204
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47
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Wannigama DL, Amarasiri M, Hongsing P, Hurst C, Modchang C, Chadsuthi S, Anupong S, Phattharapornjaroen P, Rad S. M. AH, Fernandez S, Huang AT, Vatanaprasan P, Jay DJ, Saethang T, Luk-in S, Storer RJ, Ounjai P, Devanga Ragupathi NK, Kanthawee P, Sano D, Furukawa T, Sei K, Leelahavanichkul A, Kanjanabuch T, Hirankarn N, Higgins PG, Kicic A, Singer AC, Chatsuwan T, Trowsdale S, Abe S, McLellan AD, Ishikawa H. COVID-19 monitoring with sparse sampling of sewered and non-sewered wastewater in urban and rural communities. iScience 2023; 26:107019. [PMID: 37351501 PMCID: PMC10250052 DOI: 10.1016/j.isci.2023.107019] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/31/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Equitable SARS-CoV-2 surveillance in low-resource communities lacking centralized sewers is critical as wastewater-based epidemiology (WBE) progresses. However, large-scale studies on SARS-CoV-2 detection in wastewater from low-and middle-income countries is limited because of economic and technical reasons. In this study, wastewater samples were collected twice a month from 186 urban and rural subdistricts in nine provinces of Thailand mostly having decentralized and non-sewered sanitation infrastructure and analyzed for SARS-CoV-2 RNA variants using allele-specific RT-qPCR. Wastewater SARS-CoV-2 RNA concentration was used to estimate the real-time incidence and time-varying effective reproduction number (Re). Results showed an increase in SARS-CoV-2 RNA concentrations in wastewater from urban and rural areas 14-20 days earlier than infected individuals were officially reported. It also showed that community/food markets were "hot spots" for infected people. This approach offers an opportunity for early detection of transmission surges, allowing preparedness and potentially mitigating significant outbreaks at both spatial and temporal scales.
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Affiliation(s)
- Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- 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
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Biofilms and Antimicrobial Resistance Consortium of ODA receiving countries, The University of Sheffield, Sheffield, UK
- Pathogen Hunter’s Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Mohan Amarasiri
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - 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
| | - 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
| | - Sudarat Chadsuthi
- Department of Physics, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Suparinthon Anupong
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - 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
| | | | - Dylan John Jay
- Pathogen Hunter’s Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - 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
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Phitsanuruk Kanthawee
- Public Health major, School of Health Science, Mae Fah Luang University, Chiang Rai, 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, Kitasato, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - Kazunari Sei
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - Asada Leelahavanichkul
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- 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
| | - Nattiya Hirankarn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - 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
| | - Alexander D. McLellan
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago 9010, New Zealand
| | - Hitoshi Ishikawa
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata 990-2212, Japan
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Hayase S, Katayama YA, Hatta T, Iwamoto R, Kuroita T, Ando Y, Okuda T, Kitajima M, Natsume T, Masago Y. Near full-automation of COPMAN using a LabDroid enables high-throughput and sensitive detection of SARS-CoV-2 RNA in wastewater as a leading indicator. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163454. [PMID: 37061063 PMCID: PMC10098305 DOI: 10.1016/j.scitotenv.2023.163454] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 06/01/2023]
Abstract
Wastewater-based epidemiology (WBE) is a promising tool to efficiently monitor COVID-19 prevalence in a community. For WBE community surveillance, automation of the viral RNA detection process is ideal. In the present study, we achieved near full-automation of a previously established method, COPMAN (COagulation and Proteolysis method using MAgnetic beads for detection of Nucleic acids in wastewater), which was then applied to detect SARS-CoV-2 in wastewater for half a year. The automation line employed the Maholo LabDroid and an automated-pipetting device to achieve a high-throughput sample-processing capability of 576 samples per week. SARS-CoV-2 RNA was quantified with the automated COPMAN using samples collected from two wastewater treatment plants in the Sagami River basin in Japan between 1 November 2021 and 24 May 2022, when the numbers of daily reported COVID-19 cases ranged from 0 to 130.3 per 100,000 inhabitants. The automated COPMAN detected SARS-CoV-2 RNA from 81 out of 132 samples at concentrations of up to 2.8 × 105 copies/L. These concentrations showed direct correlations with subsequently reported clinical cases (5-13 days later), as determined by Pearson's and Spearman's cross-correlation analyses. To compare the results, we also conducted testing with the EPISENS-S (Efficient and Practical virus Identification System with ENhanced Sensitivity for Solids, Ando et al., 2022), a previously reported detection method. SARS-CoV-2 RNA detected with EPISENS-S correlated with clinical cases only when using Spearman's method. Our automated COPMAN was shown to be an efficient method for timely and large-scale monitoring of viral RNA, making WBE more feasible for community surveillance.
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Affiliation(s)
- Shin Hayase
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Yuka Adachi Katayama
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Tomohisa Hatta
- Robotic Biology Institute, Inc., 2-5-10, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ryo Iwamoto
- AdvanSentinel Inc., 3-1-8 Doshomachi, Chuo-ku, Osaka 541-0045, Japan
| | - Tomohiro Kuroita
- AdvanSentinel Inc., 3-1-8 Doshomachi, Chuo-ku, Osaka 541-0045, Japan
| | - Yoshinori Ando
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Tomohiko Okuda
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Tohru Natsume
- Robotic Biology Institute, Inc., 2-5-10, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yusaku Masago
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.
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49
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Ashraf MA, Nawaz M, Asif A, Ali MA, Mehmood A, Aziz MW, Shabbir MZ, Mukhtar N, Shabbir MAB, Raza S, Yaqub T. Temporal study of wastewater surveillance from September 2020 to March 2021: an estimation of COVID-19 patients in Lahore, Pakistan. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:80855-80862. [PMID: 37308626 DOI: 10.1007/s11356-023-28041-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/29/2023] [Indexed: 06/14/2023]
Abstract
The first aim of study was to quantify the viral load in the wastewater samples by RT-qPCR testing in Lahore population to estimate the number of patients affected and predict the next resurgence of COVID-19 wave in the city. The second aim of the study was to determine the hotspot areas of Lahore which remained positive more often for virus with high viral load. In this study, n = 420 sewage samples were collected on an average of two weeks intervals from 30 different sewage water disposal stations (14 sampling events) from Sept 2020 to March 2021. RNA was extracted and quantified by RT-qPCR without concentrating the virus in samples. Number of positive disposal sites (7-93%), viral load from sewage samples (100.296 to 103.034), and estimated patients (660-17,030) ranged from low to high according to the surge and restrain of 2nd and 3rd COVID-19 waves in the country. The viral load and estimated patients were reported high in January 2021 and March 2021 which were similar to the peak of 2nd and 3rd waves in Pakistan. Site 18 (Niaz Baig village DS) showed the highest viral load among all sites. Findings of the present study helped to estimate the number of patients and track the resurgence in COVID-19 waves in Lahore particularly, and in Punjab generally. Furthermore, it emphasizes the role of wastewater-based epidemiology to help policymakers strengthen the quarantine measures along with immunization to overcome enteric viral diseases. Local and national stake holders should work in collaboration to improve the environmental hygiene to control the disease.
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Affiliation(s)
- Muhammad Adnan Ashraf
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Nawaz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Ali Asif
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Asad Ali
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Adnan Mehmood
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Waqar Aziz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Muhammad Zubair Shabbir
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Nadia Mukhtar
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | | | - Sohail Raza
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
| | - Tahir Yaqub
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan
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50
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Gupta P, Liao S, Ezekiel M, Novak N, Rossi A, LaCross N, Oakeson K, Rohrwasser A. Wastewater Genomic Surveillance Captures Early Detection of Omicron in Utah. Microbiol Spectr 2023; 11:e0039123. [PMID: 37154725 PMCID: PMC10269515 DOI: 10.1128/spectrum.00391-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
Wastewater-based epidemiology has emerged as a powerful public health tool to trace new outbreaks, detect trends in infection, and provide an early warning of COVID-19 community spread. Here, we investigated the spread of SARS-CoV-2 infections across Utah by characterizing lineages and mutations detected in wastewater samples. We sequenced over 1,200 samples from 32 sewersheds collected between November 2021 and March 2022. Wastewater sequencing confirmed the presence of Omicron (B.1.1.529) in Utah in samples collected on November 19, 2021, up to 10 days before its corresponding detection via clinical sequencing. Analysis of diversity of SARS-CoV-2 lineages revealed Delta as the most frequently detected lineage during November 2021 (67.71%), but it started declining in December 2021 with the onset of Omicron (B.1.1529) and its sublineage BA.1 (6.79%). The proportion of Omicron increased to ~58% by January 4, 2022, and completely displaced Delta by February 7, 2022. Wastewater genomic surveillance revealed the presence of Omicron sublineage BA.3, a lineage that was not identified from Utah's clinical surveillance. Interestingly, several Omicron-defining mutations began to appear in early November 2021 and increased in prevalence across sewersheds from December to January, aligning with the surge in clinical cases. Our study highlights the importance of tracking epidemiologically relevant mutations in detecting emerging lineages in the early stages of an outbreak. Wastewater genomic epidemiology provides an unbiased representation of community-wide infection dynamics and is an excellent complementary tool to SARS-CoV-2 clinical surveillance, with the potential of guiding public health action and policy decisions. IMPORTANCE SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has had a significant impact on public health. Global emergence of novel SARS-CoV-2 variants, shift to at-home tests, and reduction in clinical tests demonstrate the need for a reliable and effective surveillance strategy to contain COVID-19 spread. Monitoring of SARS-CoV-2 viruses in wastewater is an effective way to trace new outbreaks, establish baseline levels of infection, and complement clinical surveillance efforts. Wastewater genomic surveillance, in particular, can provide valuable insights into the evolution and spread of SARS-CoV-2 variants. We characterized the diversity of SARS-CoV-2 mutations and lineages using whole-genome sequencing to trace the introduction of lineage B.1.1.519 (Omicron) in Utah. Our data showed that Omicron appeared in Utah on November 19, 2021, up to 10 days prior to its detection in patient samples, indicating that wastewater surveillance provides an early warning signal. Our findings are important from a public health perspective as timely identification of communities with high COVID-19 transmission could help guide public health interventions.
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Affiliation(s)
- Pooja Gupta
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Stefan Liao
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Maleea Ezekiel
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Nicolle Novak
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Alessandro Rossi
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Nathan LaCross
- Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Kelly Oakeson
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Andreas Rohrwasser
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
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