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Watson LM, Plank MJ, Armstrong BA, Chapman JR, Hewitt J, Morris H, Orsi A, Bunce M, Donnelly CA, Steyn N. Jointly estimating epidemiological dynamics of Covid-19 from case and wastewater data in Aotearoa New Zealand. COMMUNICATIONS MEDICINE 2024; 4:143. [PMID: 39009723 PMCID: PMC11250817 DOI: 10.1038/s43856-024-00570-3] [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: 08/22/2023] [Accepted: 07/04/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Timely and informed public health responses to infectious diseases such as COVID-19 necessitate reliable information about infection dynamics. The case ascertainment rate (CAR), the proportion of infections that are reported as cases, is typically much less than one and varies with testing practices and behaviours, making reported cases unreliable as the sole source of data. The concentration of viral RNA in wastewater samples provides an alternate measure of infection prevalence that is not affected by clinical testing, healthcare-seeking behaviour or access to care. METHODS We construct a state-space model with observed data of levels of SARS-CoV-2 in wastewater and reported case incidence and estimate the hidden states of the effective reproduction number, R, and CAR using sequential Monte Carlo methods. RESULTS We analyse data from 1 January 2022 to 31 March 2023 from Aotearoa New Zealand. Our model estimates that R peaks at 2.76 (95% CrI 2.20, 3.83) around 18 February 2022 and the CAR peaks around 12 March 2022. We calculate that New Zealand's second Omicron wave in July 2022 is similar in size to the first, despite fewer reported cases. We estimate that the CAR in the BA.5 Omicron wave in July 2022 is approximately 50% lower than in the BA.1/BA.2 Omicron wave in March 2022. CONCLUSIONS Estimating R, CAR, and cumulative number of infections provides useful information for planning public health responses and understanding the state of immunity in the population. This model is a useful disease surveillance tool, improving situational awareness of infectious disease dynamics in real-time.
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Affiliation(s)
- Leighton M Watson
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand.
| | - Michael J Plank
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | | | - Joanne R Chapman
- Institute of Environmental Science and Research Ltd, Porirua, New Zealand
| | - Joanne Hewitt
- Institute of Environmental Science and Research Ltd, Porirua, New Zealand
| | - Helen Morris
- Institute of Environmental Science and Research Ltd, Porirua, New Zealand
| | - Alvaro Orsi
- Institute of Environmental Science and Research Ltd, Porirua, New Zealand
| | - Michael Bunce
- Institute of Environmental Science and Research Ltd, Porirua, New Zealand
| | - Christl A Donnelly
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
| | - Nicholas Steyn
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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2
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Acheampong E, Husain AA, Dudani H, Nayak AR, Nag A, Meena E, Shrivastava SK, McClure P, Tarr AW, Crooks C, Lade R, Gomes RL, Singer A, Kumar S, Bhatnagar T, Arora S, Kashyap RS, Monaghan TM. Population infection estimation from wastewater surveillance for SARS-CoV-2 in Nagpur, India during the second pandemic wave. PLoS One 2024; 19:e0303529. [PMID: 38809825 PMCID: PMC11135679 DOI: 10.1371/journal.pone.0303529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool for predicting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease outbreaks in high-income countries (HICs) with centralized sewage infrastructure. However, few studies have applied WBE alongside epidemic disease modelling to estimate the prevalence of SARS-CoV-2 in low-resource settings. This study aimed to explore the feasibility of collecting untreated wastewater samples from rural and urban catchment areas of Nagpur district, to detect and quantify SARS-CoV-2 using real-time qPCR, to compare geographic differences in viral loads, and to integrate the wastewater data into a modified Susceptible-Exposed-Infectious-Confirmed Positives-Recovered (SEIPR) model. Of the 983 wastewater samples analyzed for SARS-CoV-2 RNA, we detected significantly higher sample positivity rates, 43.7% (95% confidence interval (CI) 40.1, 47.4) and 30.4% (95% CI 24.66, 36.66), and higher viral loads for the urban compared with rural samples, respectively. The Basic reproductive number, R0, positively correlated with population density and negatively correlated with humidity, a proxy for rainfall and dilution of waste in the sewers. The SEIPR model estimated the rate of unreported coronavirus disease 2019 (COVID-19) cases at the start of the wave as 13.97 [95% CI (10.17, 17.0)] times that of confirmed cases, representing a material difference in cases and healthcare resource burden. Wastewater surveillance might prove to be a more reliable way to prepare for surges in COVID-19 cases during future waves for authorities.
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Affiliation(s)
- Edward Acheampong
- Department of Statistics and Actuarial Science, University of Ghana, Legon, Accra, Ghana
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Aliabbas A. Husain
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Hemanshi Dudani
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Amit R. Nayak
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Aditi Nag
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Ekta Meena
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Sandeep K. Shrivastava
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Patrick McClure
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Alexander W. Tarr
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Colin Crooks
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | | | - Rachel L. Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Andrew Singer
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Saravana Kumar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Tarun Bhatnagar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Sudipti Arora
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Rajpal Singh Kashyap
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Tanya M. Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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3
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Li L, Haak L, Carine M, Pagilla KR. Temporal assessment of SARS-CoV-2 detection in wastewater and its epidemiological implications in COVID-19 case dynamics. Heliyon 2024; 10:e29462. [PMID: 38638959 PMCID: PMC11024598 DOI: 10.1016/j.heliyon.2024.e29462] [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: 01/04/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
This research evaluated the relationship between daily new Coronavirus Disease 2019 (COVID-19) cases and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) concentrations in wastewater, followed by effects of differential SARS-CoV-2 shedding loads across various COVID-19 outbreaks. Linear regression analyses were utilized to examine the lead time of the SARS-CoV-2 signal in wastewater relative to new COVID-19 clinical cases. During the Delta wave, no lead time was evident, highlighting limited predictive capability of wastewater monitoring during this phase. However, significant lead times were observed during the Omicron wave, potentially attributed to testing capacity overload and subsequent case reporting delays or changes in shedding patterns. During the Post-Omicron wave (Febuary 23 to May 19, 2022), no lead time was discernible, whereas following the lifting of the COVID-19 state of emergency (May 30, 2022 to May 30, 2023), the correlation coefficient increased and demonstrated the potential of wastewater surveillance as an early warning system. Subsequently, we explored the virus shedding in wastewater through feces, operationalized as the ratio of SARS-CoV-2 concentrations to daily new COVID-19 cases. This ratio varied significantly across the Delta, Omicron, other variants and post-state-emergency phases, with the Kruskal-Wallis H test confirming a significant difference in medians across these stages (P < 0.0001). Despite its promise, wastewater surveillance of COVID-19 disease prevalence presents several challenges, including virus shedding variability, data interpretation complexity, the impact of environmental factors on viral degradation, and the lack of standardized testing procedures. Overall, our findings offer insights into the correlation between COVID-19 cases and wastewater viral concentrations, potential variation in SARS-CoV-2 shedding in wastewater across different pandemic phases, and underscore the promise and limitations of wastewater surveillance as an early warning system for disease prevalence trends.
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Affiliation(s)
- Lin Li
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV, 89557, USA
| | - Laura Haak
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV, 89557, USA
| | - Madeline Carine
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV, 89557, USA
| | - Krishna R. Pagilla
- Department of Civil and Environmental Engineering, University of Nevada Reno, Reno, NV, 89557, USA
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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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5
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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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6
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Amato E, Hyllestad S, Heradstveit P, Langlete P, Moen LV, Rohringer A, Pires J, Baz Lomba JA, Bragstad K, Feruglio SL, Aavitsland P, Madslien EH. Evaluation of the pilot wastewater surveillance for SARS-CoV-2 in Norway, June 2022 - March 2023. BMC Public Health 2023; 23:1714. [PMID: 37667223 PMCID: PMC10476384 DOI: 10.1186/s12889-023-16627-2] [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: 05/02/2023] [Accepted: 08/26/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND During the COVID-19 pandemic, wastewater-based surveillance gained great international interest as an additional tool to monitor SARS-CoV-2. In autumn 2021, the Norwegian Institute of Public Health decided to pilot a national wastewater surveillance (WWS) system for SARS-CoV-2 and its variants between June 2022 and March 2023. We evaluated the system to assess if it met its objectives and its attribute-based performance. METHODS We adapted the available guidelines for evaluation of surveillance systems. The evaluation was carried out as a descriptive analysis and consisted of the following three steps: (i) description of the WWS system, (ii) identification of users and stakeholders, and (iii) analysis of the system's attributes and performance including sensitivity, specificity, timeliness, usefulness, representativeness, simplicity, flexibility, stability, and communication. Cross-correlation analysis was performed to assess the system's ability to provide early warning signal of new wave of infections. RESULTS The pilot WWS system was a national surveillance system using existing wastewater infrastructures from the largest Norwegian municipalities. We found that the system was sensitive, timely, useful, representative, simple, flexible, acceptable, and stable to follow the general trend of infection. Preliminary results indicate that the system could provide an early signal of changes in variant distribution. However, challenges may arise with: (i) specificity due to temporary fluctuations of RNA levels in wastewater, (ii) representativeness when downscaling, and (iii) flexibility and acceptability when upscaling the system due to limited resources and/or capacity. CONCLUSIONS Our results showed that the pilot WWS system met most of its surveillance objectives. The system was able to provide an early warning signal of 1-2 weeks, and the system was useful to monitor infections at population level and complement routine surveillance when individual testing activity was low. However, temporary fluctuations of WWS values need to be carefully interpreted. To improve quality and efficiency, we recommend to standardise and validate methods for assessing trends of new waves of infection and variants, evaluate the WWS system using a longer operational period particularly for new variants, and conduct prevalence studies in the population to calibrate the system and improve data interpretation.
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Affiliation(s)
- Ettore Amato
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway.
| | - Susanne Hyllestad
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Petter Heradstveit
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Petter Langlete
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Line Victoria Moen
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Andreas Rohringer
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - João Pires
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
- Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), ECDC Fellowship Programme, Stockholm, Sweden
| | - Jose Antonio Baz Lomba
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Karoline Bragstad
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri Laura Feruglio
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Preben Aavitsland
- Norwegian Institute of Public Health, Oslo, Norway
- Pandemic Centre, University of Bergen, Bergen, Norway
| | - Elisabeth Henie Madslien
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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McManus O, Christiansen LE, Nauta M, Krogsgaard LW, Bahrenscheer NS, von Kappelgaard L, Christiansen T, Hansen M, Hansen NC, Kähler J, Rasmussen A, Richter SR, Rasmussen LD, Franck KT, Ethelberg S. Predicting COVID-19 Incidence Using Wastewater Surveillance Data, Denmark, October 2021-June 2022. Emerg Infect Dis 2023; 29:1589-1597. [PMID: 37486168 PMCID: PMC10370843 DOI: 10.3201/eid2908.221634] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
Analysis of wastewater is used in many settings for surveillance of SARS-CoV-2, but it remains unclear how well wastewater testing results reflect incidence. Denmark has had an extensive wastewater analysis system that conducts 3 weekly tests in ≈200 sites and has 85% population coverage; the country also offers free SARS-CoV-2 PCR tests to all residents. Using time series analysis for modeling, we found that wastewater data, combined with information on circulating variants and the number of human tests performed, closely fitted the incidence curve of persons testing positive. The results were consistent at a regional level and among a subpopulation of frequently tested healthcare personnel. We used wastewater analysis data to estimate incidence after testing was reduced to a minimum after March 2022. These results imply that data from a large-scale wastewater surveillance system can serve as a good proxy for COVID-19 incidence and for epidemic control.
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Phan T, Brozak S, Pell B, Ciupe SM, Ke R, Ribeiro RM, Gitter A, Mena KD, Perelson AS, Kuang Y, Wu F. Prolonged viral shedding from noninfectious individuals confounds wastewater-based epidemiology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.08.23291144. [PMID: 37333173 PMCID: PMC10274979 DOI: 10.1101/2023.06.08.23291144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Wastewater surveillance has been widely used to track and estimate SARS-CoV-2 incidence. While both infectious and recovered individuals shed virus into wastewater, epidemiological inferences using wastewater often only consider the viral contribution from the former group. Yet, the persistent shedding in the latter group could confound wastewater-based epidemiological inference, especially during the late stage of an outbreak when the recovered population outnumbers the infectious population. To determine the impact of recovered individuals' viral shedding on the utility of wastewater surveillance, we develop a quantitative framework that incorporates population-level viral shedding dynamics, measured viral RNA in wastewater, and an epidemic dynamic model. We find that the viral shedding from the recovered population can become higher than the infectious population after the transmission peak, which leads to a decrease in the correlation between wastewater viral RNA and case report data. Furthermore, the inclusion of recovered individuals' viral shedding into the model predicts earlier transmission dynamics and slower decreasing trends in wastewater viral RNA. The prolonged viral shedding also induces a potential delay in the detection of new variants due to the time needed to generate enough new cases for a significant viral signal in an environment dominated by virus shed by the recovered population. This effect is most prominent toward the end of an outbreak and is greatly affected by both the recovered individuals' shedding rate and shedding duration. Our results suggest that the inclusion of viral shedding from non-infectious recovered individuals into wastewater surveillance research is important for precision epidemiology.
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Affiliation(s)
- Tin Phan
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Samantha Brozak
- School of Mathematical and Statistical Sciences, Arizona State University, AZ 85281, USA
| | - Bruce Pell
- Department of Mathematics and Computer Science, Lawrence Technological University, MI 48075, USA
| | - Stanca M. Ciupe
- Department of Mathematics, Virginia Tech, Blacksburg, VA 24060, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
| | - Anna Gitter
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Texas Epidemic Public Health Institute, TX, USA
| | - Kristina D. Mena
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Texas Epidemic Public Health Institute, TX, USA
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87544, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, AZ 85281, USA
| | - Fuqing Wu
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Texas Epidemic Public Health Institute, TX, USA
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