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Chen Z, Bancej C, Lee L, Champredon D. Publisher Correction: Antigenic drift and epidemiological severity of seasonal influenza in Canada. Sci Rep 2024; 14:2952. [PMID: 38316957 PMCID: PMC10844617 DOI: 10.1038/s41598-024-53476-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Affiliation(s)
- Zishu Chen
- National Microbiology Laboratory, Public Health Risk Sciences Division, Public Health Agency of Canada, Guelph, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Christina Bancej
- Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Disease, Public Health Agency of Canada, Ottawa, ON, Canada
| | - Liza Lee
- Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Disease, Public Health Agency of Canada, Ottawa, ON, Canada
| | - David Champredon
- National Microbiology Laboratory, Public Health Risk Sciences Division, Public Health Agency of Canada, Guelph, ON, Canada.
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Champredon D, Becker D, Peterson SW, Mejia E, Hizon N, Schertzer A, Djebli M, Oloye FF, Xie Y, Asadi M, Cantin J, Pu X, Osunla CA, Brinkmann M, McPhedran KN, Servos MR, Giesy JP, Mangat C. Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data. BMC Infect Dis 2024; 24:139. [PMID: 38287244 PMCID: PMC10823614 DOI: 10.1186/s12879-024-08997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND The spread of SARS-CoV-2 has been studied at unprecedented levels worldwide. In jurisdictions where molecular analysis was performed on large scales, the emergence and competition of numerous SARS-CoV-2lineages have been observed in near real-time. Lineage identification, traditionally performed from clinical samples, can also be determined by sampling wastewater from sewersheds serving populations of interest. Variants of concern (VOCs) and SARS-CoV-2 lineages associated with increased transmissibility and/or severity are of particular interest. METHOD Here, we consider clinical and wastewater data sources to assess the emergence and spread of VOCs in Canada retrospectively. RESULTS We show that, overall, wastewater-based VOC identification provides similar insights to the surveillance based on clinical samples. Based on clinical data, we observed synchrony in VOC introduction as well as similar emergence speeds across most Canadian provinces despite the large geographical size of the country and differences in provincial public health measures. CONCLUSION In particular, it took approximately four months for VOC Alpha and Delta to contribute to half of the incidence. In contrast, VOC Omicron achieved the same contribution in less than one month. This study provides significant benchmarks to enhance planning for future VOCs, and to some extent for future pandemics caused by other pathogens, by quantifying the rate of SARS-CoV-2 VOCs invasion in Canada.
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Affiliation(s)
- David Champredon
- Public Health Agency of Canada, National Microbiology Laboratory, Public Health Risk Sciences Division, Guelph, ON, Canada.
| | - Devan Becker
- Public Health Agency of Canada, National Microbiology Laboratory, Public Health Risk Sciences Division, Guelph, ON, Canada
| | - Shelley W Peterson
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
| | - Edgard Mejia
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
| | - Nikho Hizon
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
| | - Andrea Schertzer
- Public Health Agency of Canada, Centre for Immunization and Respiratory Infectious Diseases, Ottawa, ON, Canada
| | - Mohamed Djebli
- Public Health Agency of Canada, Centre for Immunization and Respiratory Infectious Diseases, Ottawa, ON, Canada
| | - Femi F Oloye
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Chemistry, Division of Physical and Computational Sciences, University of Pittsburgh at Bradford, Bradford, United States.
| | - Yuwei Xie
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Xia Pu
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Charles A Osunla
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
| | - Markus Brinkmann
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
- Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - John P Giesy
- Toxicology Program, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Environmental Sciences, Baylor University, Waco, TX, USA.
- Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Chand Mangat
- Public Health Agency of Canada, National Microbiology Laboratory, One Health Division, Winnipeg, MB, Canada
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Champredon D, Vanrolleghem PA. Editorial: Wastewater-based epidemiological surveillance of respiratory pathogens. Front Public Health 2023; 11:1328452. [PMID: 38045979 PMCID: PMC10690582 DOI: 10.3389/fpubh.2023.1328452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023] Open
Affiliation(s)
| | - Peter A. Vanrolleghem
- Department of Civil Engineering and Water Engineering, modelEAU – Université Laval, Québec, QC, Canada
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4
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Asadi M, Oloye FF, Xie Y, Cantin J, Challis JK, McPhedran KN, Yusuf W, Champredon D, Xia P, De Lange C, El-Baroudy S, Servos MR, Jones PD, Giesy JP, Brinkmann M. A wastewater-based risk index for SARS-CoV-2 infections among three cities on the Canadian Prairie. Sci Total Environ 2023; 876:162800. [PMID: 36914129 PMCID: PMC10008033 DOI: 10.1016/j.scitotenv.2023.162800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/01/2023]
Abstract
Wastewater surveillance (WWS) is useful to better understand the spreading of coronavirus disease 2019 (COVID-19) in communities, which can help design and implement suitable mitigation measures. The main objective of this study was to develop the Wastewater Viral Load Risk Index (WWVLRI) for three Saskatchewan cities to offer a simple metric to interpret WWS. The index was developed by considering relationships between reproduction number, clinical data, daily per capita concentrations of virus particles in wastewater, and weekly viral load change rate. Trends of daily per capita concentrations of SARS-CoV-2 in wastewater for Saskatoon, Prince Albert, and North Battleford were similar during the pandemic, suggesting that per capita viral load can be useful to quantitatively compare wastewater signals among cities and develop an effective and comprehensible WWVLRI. The effective reproduction number (Rt) and the daily per capita efficiency adjusted viral load thresholds of 85 × 106 and 200 × 106 N2 gene counts (gc)/population day (pd) were determined. These values with rates of change were used to categorize the potential for COVID-19 outbreaks and subsequent declines. The weekly average was considered 'low risk' when the per capita viral load was 85 × 106 N2 gc/pd. A 'medium risk' occurs when the per capita copies were between 85 × 106 and 200 × 106 N2 gc/pd. with a rate of change <100 %. The start of an outbreak is indicated by a 'medium-high' risk classification when the week-over-week rate of change was >100 %, and the absolute magnitude of concentrations of viral particles was >85 × 106 N2 gc/pd. Lastly, a 'high risk' occurs when the viral load exceeds 200 × 106 N2 gc/pd. This methodology provides a valuable resource for decision-makers and health authorities, specifically given the limitation of COVID-19 surveillance based on clinical data.
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Affiliation(s)
- Mohsen Asadi
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Femi F Oloye
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jenna Cantin
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Kerry N McPhedran
- Department of Civil, Geological and Environmental Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Warsame Yusuf
- Public Health Risk Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - David Champredon
- Public Health Risk Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Pu Xia
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Chantel De Lange
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Seba El-Baroudy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Integrative Biology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada.
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5
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Becker D, Champredon D, Chato C, Gugan G, Poon A. SUP: a probabilistic framework to propagate genome sequence uncertainty, with applications. NAR Genom Bioinform 2023; 5:lqad038. [PMID: 37101658 PMCID: PMC10124968 DOI: 10.1093/nargab/lqad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 02/15/2023] [Accepted: 04/06/2023] [Indexed: 04/28/2023] Open
Abstract
Genetic sequencing is subject to many different types of errors, but most analyses treat the resultant sequences as if they are known without error. Next generation sequencing methods rely on significantly larger numbers of reads than previous sequencing methods in exchange for a loss of accuracy in each individual read. Still, the coverage of such machines is imperfect and leaves uncertainty in many of the base calls. In this work, we demonstrate that the uncertainty in sequencing techniques will affect downstream analysis and propose a straightforward method to propagate the uncertainty. Our method (which we have dubbed Sequence Uncertainty Propagation, or SUP) uses a probabilistic matrix representation of individual sequences which incorporates base quality scores as a measure of uncertainty that naturally lead to resampling and replication as a framework for uncertainty propagation. With the matrix representation, resampling possible base calls according to quality scores provides a bootstrap- or prior distribution-like first step towards genetic analysis. Analyses based on these re-sampled sequences will include a more complete evaluation of the error involved in such analyses. We demonstrate our resampling method on SARS-CoV-2 data. The resampling procedures add a linear computational cost to the analyses, but the large impact on the variance in downstream estimates makes it clear that ignoring this uncertainty may lead to overly confident conclusions. We show that SARS-CoV-2 lineage designations via Pangolin are much less certain than the bootstrap support reported by Pangolin would imply and the clock rate estimates for SARS-CoV-2 are much more variable than reported.
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Affiliation(s)
- Devan Becker
- To whom correspondence should be addressed. Tel: +1 519 884 1970 (Ext 2464);
| | | | - Connor Chato
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Gopi Gugan
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Art Poon
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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Joung MJ, Mangat CS, Mejia EM, Nagasawa A, Nichani A, Perez-Iratxeta C, Peterson SW, Champredon D. Coupling wastewater-based epidemiological surveillance and modelling of SARS-COV-2/COVID-19: Practical applications at the Public Health Agency of Canada. Can Commun Dis Rep 2023; 49:166-174. [PMID: 38404704 PMCID: PMC10890812 DOI: 10.14745/ccdr.v49i05a01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Wastewater-based surveillance (WBS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) offers a complementary tool for clinical surveillance to detect and monitor coronavirus disease 2019 (COVID-19). Since both symptomatic and asymptomatic individuals infected with SARS-CoV-2 can shed the virus through the fecal route, WBS has the potential to measure community prevalence of COVID-19 without restrictions from healthcare-seeking behaviours and clinical testing capacity. During the Omicron wave, the limited capacity of clinical testing to identify COVID-19 cases in many jurisdictions highlighted the utility of WBS to estimate disease prevalence and inform public health strategies; however, there is a plethora of in-sewage, environmental and laboratory factors that can influence WBS outcomes. The implementation of WBS, therefore, requires a comprehensive framework to outline a pipeline that accounts for these complex and nuanced factors. This article reviews the framework of the national WBS conducted at the Public Health Agency of Canada to present WBS methods used in Canada to track and monitor SARS-CoV-2. In particular, we focus on five Canadian cities-Vancouver, Edmonton, Toronto, Montréal and Halifax-whose wastewater signals are analyzed by a mathematical model to provide case forecasts and reproduction number estimates. The goal of this work is to share our insights on approaches to implement WBS. Importantly, the national WBS system has implications beyond COVID-19, as a similar framework can be applied to monitor other infectious disease pathogens or antimicrobial resistance in the community.
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Affiliation(s)
- Meong Jin Joung
- National Microbiology Laboratory, Public Health Risk Sciences Division, Public Health Agency of Canada, Guelph, ON
- Dalla Lana School of Public Health, University of Toronto. Toronto, ON
| | - Chand S Mangat
- National Microbiology Laboratory, Wastewater Surveillance Unit, Public Health Agency of Canada, Winnipeg, MB
| | - Edgard M Mejia
- National Microbiology Laboratory, Wastewater Surveillance Unit, Public Health Agency of Canada, Winnipeg, MB
| | - Audra Nagasawa
- Statistics Canada, Centre for Direct Health Measures, Ottawa, ON
| | - Anil Nichani
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON
| | | | - Shelley W Peterson
- National Microbiology Laboratory, Wastewater Surveillance Unit, Public Health Agency of Canada, Winnipeg, MB
| | - David Champredon
- National Microbiology Laboratory, Public Health Risk Sciences Division, Public Health Agency of Canada, Guelph, ON
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7
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Rees EE, Avery BP, Carabin H, Carson CA, Champredon D, de Montigny S, Dougherty B, Nasri BR, Ogden NH. Effectiveness of non-pharmaceutical interventions to reduce SARS-CoV-2 transmission in Canada and their association with COVID-19 hospitalization rates. Can Commun Dis Rep 2022; 48:438-448. [PMID: 38162959 PMCID: PMC10756332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Background Non-pharmaceutical interventions (NPIs) aim to reduce the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections mostly by limiting contacts between people where virus transmission can occur. However, NPIs limit social interactions and have negative impacts on economic, physical, mental and social well-being. It is, therefore, important to assess the impact of NPIs on reducing the number of coronavirus disease 2019 (COVID-19) cases and hospitalizations to justify their use. Methods Dynamic regression models accounting for autocorrelation in time series data were used with data from six Canadian provinces (British Columbia, Alberta, Saskatchewan, Manitoba, Ontario, Québec) to assess 1) the effect of NPIs (measured using a stringency index) on SARS-CoV-2 transmission (measured by the effective reproduction number), and 2) the effect of the number of hospitalized COVID-19 patients on the stringency index. Results Increasing stringency index was associated with a statistically significant decrease in the transmission of SARS-CoV-2 in Alberta, Saskatchewan, Manitoba, Ontario and Québec. The effect of stringency on transmission was time-lagged in all of these provinces except for Ontario. In all provinces except for Saskatchewan, increasing hospitalization rates were associated with a statistically significant increase in the stringency index. The effect of hospitalization on stringency was time-lagged. Conclusion These results suggest that NPIs have been effective in Canadian provinces, and that their implementation has been, in part, a response to increasing hospitalization rates of COVID-19 patients.
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Affiliation(s)
- Erin E Rees
- Public Health Risk Sciences Division, National Microbiology Laboratory (PHRSD), Public Health Agency of Canada, Saint-Hyacinthe, QC and Guelph, ON
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC
- Centre de recherche en santé publique (CReSP), Université de Montréal, Montréal, QC
| | - Brent P Avery
- Food-borne Disease and Antimicrobial Resistance Surveillance Division, Centre for Food-borne and Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON
| | - Hélène Carabin
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC
- Centre de recherche en santé publique (CReSP), Université de Montréal, Montréal, QC
- Faculty of Veterinary Medicine, Université de Montréal, Montréal, QC
| | - Carolee A Carson
- Food-borne Disease and Antimicrobial Resistance Surveillance Division, Centre for Food-borne and Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON
| | - David Champredon
- Public Health Risk Sciences Division, National Microbiology Laboratory (PHRSD), Public Health Agency of Canada, Saint-Hyacinthe, QC and Guelph, ON
| | - Simon de Montigny
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC
- School of Public Health, Université de Montréal, Montréal, QC
- Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, QC
| | - Brendan Dougherty
- Food-borne Disease and Antimicrobial Resistance Surveillance Division, Centre for Food-borne and Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON
| | - Bouchra R Nasri
- Centre de recherche en santé publique (CReSP), Université de Montréal, Montréal, QC
- School of Public Health, Université de Montréal, Montréal, QC
| | - Nicholas H Ogden
- Public Health Risk Sciences Division, National Microbiology Laboratory (PHRSD), Public Health Agency of Canada, Saint-Hyacinthe, QC and Guelph, ON
- Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC
- Centre de recherche en santé publique (CReSP), Université de Montréal, Montréal, QC
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Hua N, Corsten M, Bello A, Bhatt M, Milwid R, Champredon D, Turgeon P, Zemek R, Dawson L, Mitsakakis N, Webster R, Caulley L, Angel JB, Bastien N, Poliquin G, Johnson-Obaseki S. Salivary testing for SARS-CoV-2 in the pediatric population: a diagnostic accuracy study. CMAJ Open 2022; 10:E981-E987. [PMID: 36347561 PMCID: PMC9648623 DOI: 10.9778/cmajo.20210279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Accurate and timely testing for SARS-CoV-2 in the pediatric population is crucial to control the COVID-19 pandemic; saliva testing has been proposed as a less invasive alternative to nasopharyngeal swabs. We sought to compare the detection of SARS-CoV-2 using saliva versus nasopharyngeal swab in the pediatric population, and to determine the optimum time of testing for SARS-CoV-2 using saliva. METHODS We conducted a longitudinal diagnostic study in Ottawa, Canada, from Jan. 19 to Mar. 26, 2021. Children aged 3-17 years were eligible if they exhibited symptoms of COVID-19, had been identified as a high-risk or close contact to someone confirmed positive for SARS-CoV-2 or had travelled outside Canada in the previous 14 days. Participants provided both nasopharyngeal swab and saliva samples. Saliva was collected using a self-collection kit (DNA Genotek, OM-505) or a sponge-based kit (DNA Genotek, ORE-100) if they could not provide a saliva sample into a tube. RESULTS Among 1580 paired nasopharyngeal and saliva tests, 60 paired samples were positive for SARS-CoV-2. Forty-four (73.3%) were concordant-positive results and 16 (26.6%) were discordant, among which 8 were positive only on nasopharyngeal swab and 8 were positive only on saliva testing. The sensitivity of saliva was 84.6% (95% confidence interval 71.9%-93.1%). INTERPRETATION Salivary testing for SARS-CoV-2 in the pediatric population is less invasive and shows similar detection of SARS-CoV-2 to nasopharyngeal swabs. It may therefore provide a feasible alternative for diagnosis of SARS-CoV-2 infection in children.
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Affiliation(s)
- Nadia Hua
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Martin Corsten
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Alexander Bello
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Maala Bhatt
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Rachael Milwid
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - David Champredon
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Patricia Turgeon
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Roger Zemek
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Lauren Dawson
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Nicholas Mitsakakis
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Richard Webster
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Lisa Caulley
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Jonathan B Angel
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Nathalie Bastien
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Guillaume Poliquin
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man
| | - Stephanie Johnson-Obaseki
- Department of Otolaryngology - Head and Neck Surgery (Hua, Caulley, Johnson-Obaseki), University of Ottawa, Ottawa, Ont.; Division of Otolaryngology - Head and Neck Surgery (Corsten), Dalhousie University, Halifax, NS; National Microbiology Laboratory (Bello, Bastien, Poliquin), Public Health Agency of Canada, Winnipeg, Man.; Department of Pediatrics and Emergency Medicine (Bhatt, Zemek), Children's Hospital of Eastern Ontario; Division of Pediatric Emergency Research (Bhatt, Zemek, Dawson, Mitsakakis, Webster), Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ont.; National Microbiology Laboratory (Milwid, Turgeon), Public Health Agency of Canada, Saint-Hyacinthe, Que.; National Microbiology Laboratory (Champredon), Public Health Agency of Canada, Guelph, Ont.; Division of Infectious Diseases (Angel), University of Ottawa, Ottawa, Ont.; Chronic Disease Program (Angel), Ottawa Hospital Research Institute, Ottawa, Ont.; Department of Pediatrics and Child Health (Poliquin), University of Manitoba, Winnipeg, Man.
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9
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Chen Z, Bancej C, Lee L, Champredon D. Antigenic drift and epidemiological severity of seasonal influenza in Canada. Sci Rep 2022; 12:15625. [PMID: 36115880 PMCID: PMC9482630 DOI: 10.1038/s41598-022-19996-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/07/2022] [Indexed: 12/05/2022] Open
Abstract
Seasonal influenza epidemics circulate globally every year with varying levels of severity. One of the major drivers of this seasonal variation is thought to be the antigenic drift of influenza viruses, resulting from the accumulation of mutations in viral surface proteins. In this study, we aimed to investigate the association between the genetic drift of seasonal influenza viruses (A/H1N1, A/H3N2 and B) and the epidemiological severity of seasonal epidemics within a Canadian context. We obtained hemagglutinin protein sequences collected in Canada between the 2006/2007 and 2019/2020 flu seasons from GISAID and calculated Hamming distances in a sequence-based approach to estimating inter-seasonal antigenic differences. We also gathered epidemiological data on cases, hospitalizations and deaths from national surveillance systems and other official sources, as well as vaccine effectiveness estimates to address potential effect modification. These aggregate measures of disease severity were integrated into a single seasonal severity index. We performed linear regressions of our severity index with respect to the inter-seasonal antigenic distances, controlling for vaccine effectiveness. We did not find any evidence of a statistical relationship between antigenic distance and seasonal influenza severity in Canada. Future studies may need to account for additional factors, such as co-circulation of other respiratory pathogens, population imprinting, cohort effects and environmental parameters, which may drive seasonal influenza severity.
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Affiliation(s)
- Zishu Chen
- National Microbiology Laboratory, Public Health Risk Sciences Division, Public Health Agency of Canada, Guelph, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Christina Bancej
- Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Disease, Public Health Agency of Canada, Ottawa, ON, Canada
| | - Liza Lee
- Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Disease, Public Health Agency of Canada, Ottawa, ON, Canada
| | - David Champredon
- National Microbiology Laboratory, Public Health Risk Sciences Division, Public Health Agency of Canada, Guelph, ON, Canada.
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10
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Nourbakhsh S, Fazil A, Li M, Mangat CS, Peterson SW, Daigle J, Langner S, Shurgold J, D’Aoust P, Delatolla R, Mercier E, Pang X, Lee BE, Stuart R, Wijayasri S, Champredon D. A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities. Epidemics 2022; 39:100560. [PMID: 35462206 PMCID: PMC8993419 DOI: 10.1016/j.epidem.2022.100560] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/07/2022] [Accepted: 04/03/2022] [Indexed: 02/03/2023] Open
Abstract
The COVID-19 pandemic has stimulated wastewater-based surveillance, allowing public health to track the epidemic by monitoring the concentration of the genetic fingerprints of SARS-CoV-2 shed in wastewater by infected individuals. Wastewater-based surveillance for COVID-19 is still in its infancy. In particular, the quantitative link between clinical cases observed through traditional surveillance and the signals from viral concentrations in wastewater is still developing and hampers interpretation of the data and actionable public-health decisions. We present a modelling framework that includes both SARS-CoV-2 transmission at the population level and the fate of SARS-CoV-2 RNA particles in the sewage system after faecal shedding by infected persons in the population. Using our mechanistic representation of the combined clinical/wastewater system, we perform exploratory simulations to quantify the effect of surveillance effectiveness, public-health interventions and vaccination on the discordance between clinical and wastewater signals. We also apply our model to surveillance data from three Canadian cities to provide wastewater-informed estimates for the actual prevalence, the effective reproduction number and incidence forecasts. We find that wastewater-based surveillance, paired with this model, can complement clinical surveillance by supporting the estimation of key epidemiological metrics and hence better triangulate the state of an epidemic using this alternative data source.
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Affiliation(s)
- Shokoofeh Nourbakhsh
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Aamir Fazil
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Michael Li
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Chand S. Mangat
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Shelley W. Peterson
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jade Daigle
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Stacie Langner
- One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jayson Shurgold
- Antimicrobial Resistance Division, Infectious Diseases Prevention and Control Branch, Public Health Agency of Canada, Ottawa, ON, Canada
| | - Patrick D’Aoust
- University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
| | - Robert Delatolla
- University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
| | - Elizabeth Mercier
- University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
| | - Xiaoli Pang
- Public Health Laboratory, Alberta Precision Laboratory, Edmonton, AB, Canada,Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Bonita E. Lee
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | | | - Shinthuja Wijayasri
- Toronto Public Health, Toronto, ON, Canada,Canadian Field Epidemiology Program, Emergency Management, Public Health Agency of Canada, Canada
| | - David Champredon
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada,Corresponding author
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11
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Champredon D, Bancej C, Lee L, Buckrell S. Implications of the unexpected persistence of human rhinovirus/enterovirus during the COVID-19 pandemic in Canada. Influenza Other Respir Viruses 2021; 16:190-192. [PMID: 34747155 PMCID: PMC8652650 DOI: 10.1111/irv.12930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 11/30/2022] Open
Abstract
Stringent public health measures imposed across Canada to control the COVID-19 pandemic have nearly suppressed most seasonal respiratory viruses, with the notable exception of human rhinovirus/enterovirus (hRV/EV). Thanks to this unexpected persistence, we highlight that hRV/EV could serve as a sentinel for levels of contact rate in populations to inform on the efficiency, or the need of, public health measures to control the subsequent COVID-19 epidemic, but also for future epidemics from other seasonal or emerging respiratory pathogens.
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Affiliation(s)
- David Champredon
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Christina Bancej
- Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Disease, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Liza Lee
- Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Disease, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Steven Buckrell
- Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Disease, Public Health Agency of Canada, Ottawa, Ontario, Canada
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12
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Champredon D, Fazil A, Ogden NH. Simple mathematical modelling approaches to assessing the transmission risk of SARS-CoV-2 at gatherings. Can Commun Dis Rep 2021; 47:184-194. [PMID: 34035664 PMCID: PMC8127697 DOI: 10.14745/ccdr.v47i04a02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Gatherings may contribute significantly to the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For this reason, public health interventions have sought to constrain unrepeated or recurrent gatherings to curb the coronavirus disease 2019 (COVID-19) pandemic. Unfortunately, the range of different types of gatherings hinders specific guidance from setting limiting parameters (e.g. total size, number of cohorts, the extent of physical distancing). METHODS We used a generic modelling framework, based on fundamental probability principles, to derive simple formulas to assess introduction and transmission risks associated with gatherings, as well as the potential efficiency of some testing strategies to mitigate these risks. RESULTS Introduction risk can be broadly assessed with the population prevalence and the size of the gathering, while transmission risk at a gathering is mainly driven by the gathering size. For recurrent gatherings, the cohort structure does not have a significant impact on transmission between cohorts. Testing strategies can mitigate risk, but frequency of testing and test performance are factors in finding a balance between detection and false positives. CONCLUSION The generality of the modelling framework used here helps to disentangle the various factors affecting transmission risk at gatherings and may be useful for public health decision-making.
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Affiliation(s)
- David Champredon
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON
| | - Aamir Fazil
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON
| | - Nicholas H Ogden
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, St.-Hyacinthe, QC and Guelph, ON
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13
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Papst I, Li M, Champredon D, Bolker BM, Dushoff J, D Earn DJ. Age-dependence of healthcare interventions for COVID-19 in Ontario, Canada. BMC Public Health 2021; 21:706. [PMID: 33845807 PMCID: PMC8040357 DOI: 10.1186/s12889-021-10611-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/08/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Patient age is one of the most salient clinical indicators of risk from COVID-19. Age-specific distributions of known SARS-CoV-2 infections and COVID-19-related deaths are available for many regions. Less attention has been given to the age distributions of serious medical interventions administered to COVID-19 patients, which could reveal sources of potential pressure on the healthcare system should SARS-CoV-2 prevalence increase, and could inform mass vaccination strategies. The aim of this study is to quantify the relationship between COVID-19 patient age and serious outcomes of the disease, beyond fatalities alone. METHODS We analysed 277,555 known SARS-CoV-2 infection records for Ontario, Canada, from 23 January 2020 to 16 February 2021 and estimated the age distributions of hospitalizations, Intensive Care Unit admissions, intubations, and ventilations. We quantified the probability of hospitalization given known SARS-CoV-2 infection, and of survival given COVID-19-related hospitalization. RESULTS The distribution of hospitalizations peaks with a wide plateau covering ages 60-90, whereas deaths are concentrated in ages 80+. The estimated probability of hospitalization given known infection reaches a maximum of 27.8% at age 80 (95% CI 26.0%-29.7%). The probability of survival given hospitalization is nearly 100% for adults younger than 40, but declines substantially after this age; for example, a hospitalized 54-year-old patient has a 91.7% chance of surviving COVID-19 (95% CI 88.3%-94.4%). CONCLUSIONS Our study demonstrates a significant need for hospitalization in middle-aged individuals and young seniors. This need is not captured by the distribution of deaths, which is heavily concentrated in very old ages. The probability of survival given hospitalization for COVID-19 is lower than is generally perceived for patients over 40. If acute care capacity is exceeded due to an increase in COVID-19 prevalence, the distribution of deaths could expand toward younger ages. These results suggest that vaccine programs should aim to prevent infection not only in old seniors, but also in young seniors and middle-aged individuals, to protect them from serious illness and to limit stress on the healthcare system.
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Affiliation(s)
- Irena Papst
- Center for Applied Mathematics, Cornell University, Ithaca, USA.
| | - Michael Li
- Department of Biology, McMaster University, Hamilton, Canada
- South African Centre for Epidemiological Modelling and Analysis, University of Stellenbosch, Stellenbosch, South Africa
| | - David Champredon
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Benjamin M Bolker
- Department of Biology, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- Department of Mathematics & Statistics, McMaster University, Hamilton, Canada
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, Canada
- South African Centre for Epidemiological Modelling and Analysis, University of Stellenbosch, Stellenbosch, South Africa
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - David J D Earn
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- Department of Mathematics & Statistics, McMaster University, Hamilton, Canada
- Department of Mathematics, University of Toronto, Toronto, Canada
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14
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Abdollahi E, Champredon D, Langley JM, Galvani AP, Moghadas SM. Estimations du taux de létalité de la COVID-19 au Canada et aux États-Unis sur une période donnée. CMAJ 2020; 192:E1482-E1486. [PMID: 33199459 PMCID: PMC7682996 DOI: 10.1503/cmaj.200711-f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2020] [Indexed: 11/01/2022] Open
Abstract
CONTEXTE: Les estimations du taux de létalité de la maladie à coronavirus 2019 (COVID-19) varient grandement selon les populations. L’objectif était d’estimer et de comparer ce taux pour le Canada et les États-Unis en tenant compte de 2 sources de biais potentiel du taux brut. MÉTHODES: Pour ce faire, nous sommes partis du nombre quotidien de cas confirmés et de décès au Canada et aux États-Unis pour la période du 31 janvier au 22 avril 2020. Nous y avons appliqué une méthode statistique qui réduit au minimum les biais du taux de létalité brut de 2 façons : en intégrant la durée de survie, soit le délai entre le début de la maladie et le décès, et en considérant que moins de 50 % des cas de COVID-19 sont confirmés (intervalle de confiance à 95 % 10 %–50 %). RÉSULTATS: À partir du nombre de cas confirmés au Canada, nous avons évalué le taux brut en date en 22 avril 2020 à 4,9 %, et le taux ajusté à 5,5 % (intervalle de crédibilité [ICr] 4,9 %–6,4 %). En appliquant divers taux de cas confirmés inférieurs à 50 %, nous avons obtenu un taux ajusté de 1,6 % (ICr 0,7 %–3,1 %). Pour les États-Unis, le taux brut en date du 20 avril 2020 était de 5,4 %, et le taux ajusté, de 6,1 % (ICr 5,4 %–6,9 %). Combiné à des taux de cas confirmés inférieurs à 50 %, le taux ajusté est passé à 1,78 % (ICr 0,8 %–3,6 %). INTERPRÉTATION: Nos estimations montrent que si le taux de cas confirmés est de moins de 50 %, le taux de létalité ajusté de la COVID-19 est vraisemblablement inférieur à 2 % au Canada. Aux États-Unis, les estimations sont plus élevées, mais le taux ajusté reste sous la barre des 2 %. Si le taux de cas confirmés était connu, nous pourrions mieux évaluer la virulence du coronavirus du syndrome respiratoire aigu sévère 2 et la charge associée.
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Affiliation(s)
- Elaheh Abdollahi
- Agent-Based Modelling Laboratory (Abdollahi, Moghadas), Université York, Toronto, Ont.; Département de pathologie et de médecine de laboratoire (Champredon), Université Western, London, Ont.; Centre canadien de vaccinologie (Langley), Université Dalhousie, Centre de soins de santé IWK et Régie de la santé de la Nouvelle-Écosse (Langley), Halifax, N.-É.; Center for Infectious Disease Modeling and Analysis ( Galvani), École de santé publique de Yale, New Haven (Connecticut)
| | - David Champredon
- Agent-Based Modelling Laboratory (Abdollahi, Moghadas), Université York, Toronto, Ont.; Département de pathologie et de médecine de laboratoire (Champredon), Université Western, London, Ont.; Centre canadien de vaccinologie (Langley), Université Dalhousie, Centre de soins de santé IWK et Régie de la santé de la Nouvelle-Écosse (Langley), Halifax, N.-É.; Center for Infectious Disease Modeling and Analysis ( Galvani), École de santé publique de Yale, New Haven (Connecticut)
| | - Joanne M Langley
- Agent-Based Modelling Laboratory (Abdollahi, Moghadas), Université York, Toronto, Ont.; Département de pathologie et de médecine de laboratoire (Champredon), Université Western, London, Ont.; Centre canadien de vaccinologie (Langley), Université Dalhousie, Centre de soins de santé IWK et Régie de la santé de la Nouvelle-Écosse (Langley), Halifax, N.-É.; Center for Infectious Disease Modeling and Analysis ( Galvani), École de santé publique de Yale, New Haven (Connecticut).
| | - Alison P Galvani
- Agent-Based Modelling Laboratory (Abdollahi, Moghadas), Université York, Toronto, Ont.; Département de pathologie et de médecine de laboratoire (Champredon), Université Western, London, Ont.; Centre canadien de vaccinologie (Langley), Université Dalhousie, Centre de soins de santé IWK et Régie de la santé de la Nouvelle-Écosse (Langley), Halifax, N.-É.; Center for Infectious Disease Modeling and Analysis ( Galvani), École de santé publique de Yale, New Haven (Connecticut)
| | - Seyed M Moghadas
- Agent-Based Modelling Laboratory (Abdollahi, Moghadas), Université York, Toronto, Ont.; Département de pathologie et de médecine de laboratoire (Champredon), Université Western, London, Ont.; Centre canadien de vaccinologie (Langley), Université Dalhousie, Centre de soins de santé IWK et Régie de la santé de la Nouvelle-Écosse (Langley), Halifax, N.-É.; Center for Infectious Disease Modeling and Analysis ( Galvani), École de santé publique de Yale, New Haven (Connecticut)
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15
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Park SW, Bolker BM, Champredon D, Earn DJD, Li M, Weitz JS, Grenfell BT, Dushoff J. Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak. J R Soc Interface 2020; 17:20200144. [PMID: 32693748 PMCID: PMC7423425 DOI: 10.1098/rsif.2020.0144] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A novel coronavirus (SARS-CoV-2) emerged as a global threat in December 2019. As the epidemic progresses, disease modellers continue to focus on estimating the basic reproductive number [Formula: see text]-the average number of secondary cases caused by a primary case in an otherwise susceptible population. The modelling approaches and resulting estimates of [Formula: see text] during the beginning of the outbreak vary widely, despite relying on similar data sources. Here, we present a statistical framework for comparing and combining different estimates of [Formula: see text] across a wide range of models by decomposing the basic reproductive number into three key quantities: the exponential growth rate, the mean generation interval and the generation-interval dispersion. We apply our framework to early estimates of [Formula: see text] for the SARS-CoV-2 outbreak, showing that many [Formula: see text] estimates are overly confident. Our results emphasize the importance of propagating uncertainties in all components of [Formula: see text], including the shape of the generation-interval distribution, in efforts to estimate [Formula: see text] at the outset of an epidemic.
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Affiliation(s)
- Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton, NJ, USA
| | - Benjamin M Bolker
- Department of Biology, McMaster University, Hamilton, Ontario, Canada.,Department of Mathematics and Statistics, McMaster University, Hamilton, Ontario, Canada.,M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - David Champredon
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - David J D Earn
- Department of Mathematics and Statistics, McMaster University, Hamilton, Ontario, Canada.,M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Michael Li
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton, NJ, USA.,Princeton School of Public and International Affairs, Princeton, NJ, USA.,Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, Ontario, Canada.,Department of Mathematics and Statistics, McMaster University, Hamilton, Ontario, Canada.,M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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16
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Park SW, Bolker BM, Champredon D, Earn DJD, Li M, Weitz JS, Grenfell BT, Dushoff J. Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak. J R Soc Interface 2020. [PMID: 32693748 DOI: 10.1101/2020.01.30.20019877] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
A novel coronavirus (SARS-CoV-2) emerged as a global threat in December 2019. As the epidemic progresses, disease modellers continue to focus on estimating the basic reproductive number [Formula: see text]-the average number of secondary cases caused by a primary case in an otherwise susceptible population. The modelling approaches and resulting estimates of [Formula: see text] during the beginning of the outbreak vary widely, despite relying on similar data sources. Here, we present a statistical framework for comparing and combining different estimates of [Formula: see text] across a wide range of models by decomposing the basic reproductive number into three key quantities: the exponential growth rate, the mean generation interval and the generation-interval dispersion. We apply our framework to early estimates of [Formula: see text] for the SARS-CoV-2 outbreak, showing that many [Formula: see text] estimates are overly confident. Our results emphasize the importance of propagating uncertainties in all components of [Formula: see text], including the shape of the generation-interval distribution, in efforts to estimate [Formula: see text] at the outset of an epidemic.
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Affiliation(s)
- Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton, NJ, USA
| | - Benjamin M Bolker
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Department of Mathematics and Statistics, McMaster University, Hamilton, Ontario, Canada
- M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - David Champredon
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - David J D Earn
- Department of Mathematics and Statistics, McMaster University, Hamilton, Ontario, Canada
- M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Michael Li
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton, NJ, USA
- Princeton School of Public and International Affairs, Princeton, NJ, USA
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Department of Mathematics and Statistics, McMaster University, Hamilton, Ontario, Canada
- M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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17
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Abstract
Generation intervals, defined as the time between when an individual is infected and when that individual infects another person, link two key quantities that describe an epidemic: the initial reproductive number, Rinitial, and the initial rate of exponential growth, r. Generation intervals can be measured through contact tracing by identifying who infected whom. We study how realized intervals differ from ‘intrinsic’ intervals that describe individual-level infectiousness and identify both spatial and temporal effects, including truncating (due to observation time), and the effects of susceptible depletion at various spatial scales. Early in an epidemic, we expect the variation in the realized generation intervals to be mainly driven by truncation and by the population structure near the source of disease spread; we predict that correcting realized intervals for the effect of temporal truncation but not for spatial effects will provide the initial forward generation-interval distribution, which is spatially informed and correctly links r and Rinitial. We develop and test statistical methods for temporal corrections of generation intervals, and confirm our prediction using individual-based simulations on an empirical network.
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Affiliation(s)
- Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Department of Mathematics and Statistics, McMaster University, Hamilton, ON, Canada
| | - David Champredon
- Department of Biology, McMaster University, Hamilton, ON, Canada.,Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON, Canada
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
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18
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Abdollahi E, Champredon D, Langley JM, Galvani AP, Moghadas SM. Temporal estimates of case-fatality rate for COVID-19 outbreaks in Canada and the United States. CMAJ 2020; 192:E666-E670. [PMID: 32444481 PMCID: PMC7828851 DOI: 10.1503/cmaj.200711] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Estimates of the case-fatality rate (CFR) associated with coronavirus disease 2019 (COVID-19) vary widely in different population settings. We sought to estimate and compare the COVID-19 CFR in Canada and the United States while adjusting for 2 potential biases in crude CFR. METHODS We used the daily incidence of confirmed COVID-19 cases and deaths in Canada and the US from Jan. 31 to Apr. 22, 2020. We applied a statistical method to minimize bias in the crude CFR by accounting for the survival interval as the lag time between disease onset and death, while considering reporting rates of COVID-19 cases less than 50% (95% confidence interval 10%-50%). RESULTS Using data for confirmed cases in Canada, we estimated the crude CFR to be 4.9% on Apr. 22, 2020, and the adjusted CFR to be 5.5% (credible interval [CrI] 4.9%-6.4%). After we accounted for various reporting rates less than 50%, the adjusted CFR was estimated at 1.6% (CrI 0.7%-3.1%). The US crude CFR was estimated to be 5.4% on Apr. 20, 2020, with an adjusted CFR of 6.1% (CrI 5.4%-6.9%). With reporting rates of less than 50%, the adjusted CFR for the US was 1.78 (CrI 0.8%-3.6%). INTERPRETATION Our estimates suggest that, if the reporting rate is less than 50%, the adjusted CFR of COVID-19 in Canada is likely to be less than 2%. The CFR estimates for the US were higher than those for Canada, but the adjusted CFR still remained below 2%. Quantification of case reporting can provide a more accurate measure of the virulence and disease burden of severe acute respiratory syndrome coronavirus 2.
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Affiliation(s)
- Elaheh Abdollahi
- Agent-Based Modelling Laboratory (Abdollahi, Moghadas), York University, Toronto, Ont.; Department of Pathology and Laboratory Medicine (Champredon), Western University, London, Ont.; Canadian Center for Vaccinology (Langley), Dalhousie University, IWK Health Centre and Nova Scotia Health Authority (Langley), Halifax, NS; Center for Infectious Disease Modeling and Analysis ( Galvani), Yale School of Public Health, New Haven, Conn
| | - David Champredon
- Agent-Based Modelling Laboratory (Abdollahi, Moghadas), York University, Toronto, Ont.; Department of Pathology and Laboratory Medicine (Champredon), Western University, London, Ont.; Canadian Center for Vaccinology (Langley), Dalhousie University, IWK Health Centre and Nova Scotia Health Authority (Langley), Halifax, NS; Center for Infectious Disease Modeling and Analysis ( Galvani), Yale School of Public Health, New Haven, Conn
| | - Joanne M Langley
- Agent-Based Modelling Laboratory (Abdollahi, Moghadas), York University, Toronto, Ont.; Department of Pathology and Laboratory Medicine (Champredon), Western University, London, Ont.; Canadian Center for Vaccinology (Langley), Dalhousie University, IWK Health Centre and Nova Scotia Health Authority (Langley), Halifax, NS; Center for Infectious Disease Modeling and Analysis ( Galvani), Yale School of Public Health, New Haven, Conn.
| | - Alison P Galvani
- Agent-Based Modelling Laboratory (Abdollahi, Moghadas), York University, Toronto, Ont.; Department of Pathology and Laboratory Medicine (Champredon), Western University, London, Ont.; Canadian Center for Vaccinology (Langley), Dalhousie University, IWK Health Centre and Nova Scotia Health Authority (Langley), Halifax, NS; Center for Infectious Disease Modeling and Analysis ( Galvani), Yale School of Public Health, New Haven, Conn
| | - Seyed M Moghadas
- Agent-Based Modelling Laboratory (Abdollahi, Moghadas), York University, Toronto, Ont.; Department of Pathology and Laboratory Medicine (Champredon), Western University, London, Ont.; Canadian Center for Vaccinology (Langley), Dalhousie University, IWK Health Centre and Nova Scotia Health Authority (Langley), Halifax, NS; Center for Infectious Disease Modeling and Analysis ( Galvani), Yale School of Public Health, New Haven, Conn
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19
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Champredon D, Shoukat A, Moghadas SM. Effectiveness and cost-effectiveness of a Clostridium difficile vaccine candidate in a hospital setting. Vaccine 2020; 38:2585-2591. [PMID: 32014268 DOI: 10.1016/j.vaccine.2020.01.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/18/2020] [Accepted: 01/23/2020] [Indexed: 11/27/2022]
Abstract
Toxoid vaccines against Clostridium difficile infections (CDI) appear promising in reducing the risk of developing toxin-mediated symptoms. We sought to evaluate the effectiveness and cost-effectiveness of a vaccine candidate in a hospital setting. We developed an agent-based simulation model of nosocomial CDI in a 300-bed hospital. Targeting high-risk patients for vaccination, we estimated the reduction of symptomatic CDI. Using the net reduction of CDI-associated isolation days, we evaluated the vaccine's cost-effectiveness from a healthcare provider perspective over a 2-year period with an average monthly incidence of 5 cases per 10,000 patient-days pre-vaccination. Assuming a vaccine efficacy in the range 60-90%, vaccinating 40% of high-risk patients pre-admission reduced symptomatic CDI by 16.6% (95% CI: 15.2, 17.9). When the vaccine coverage increased to 80%, the reduction of symptomatic CDI was 34.6% (95% CI: 33.7, 35.9). For a willingness to pay (WTP) of CDN$1000 (corresponding to the average costs of case isolation per day), vaccine was cost-effective for vaccination costs per individual (VCPI) up to CDN$111 in the scenario of 40% vaccine coverage. With the same WTP, vaccine was cost-effective for VCPI up to CDN$121 when the vaccine coverage increased to 80%. A significant portion (~80%) of hospital colonization is caused by environmental transmission of C. difficile, which markedly reduced the effectiveness of vaccine below its assumed efficacy. However, due to the number of CDI-associated isolation days averted, vaccination of high-risk patients can be cost-effective depending on the WTP and the VCPI.
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Affiliation(s)
- David Champredon
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario N6A 3K7, Canada; Agent-Based Modelling Laboratory, York University, Toronto, Ontario M3J 1P3, Canada
| | - Affan Shoukat
- Center for Infectious Disease Modelling and Analysis, Yale University, New Haven, CT 06510, USA; Agent-Based Modelling Laboratory, York University, Toronto, Ontario M3J 1P3, Canada
| | - Seyed M Moghadas
- Agent-Based Modelling Laboratory, York University, Toronto, Ontario M3J 1P3, Canada.
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20
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Champredon D, Zhang K, Smieja M, Moghadas SM. Clostridium difficile intervention timelines for diagnosis, isolation, and treatment. Am J Infect Control 2019; 47:1370-1374. [PMID: 31182236 DOI: 10.1016/j.ajic.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 02/02/2023]
Abstract
BACKGROUND Developing timelines of nosocomial Clostridium difficile infection (CDI) is critical to improving control and preventive measures. The objective of this study was to provide data-driven estimates of CDI timelines of diagnosis, isolation, and treatment in a hospital setting. METHODS We obtained data for all CDI inpatients with symptoms onset occurring between January 1, 2013, and December 30, 2017, from St Joseph's Healthcare in Hamilton, Canada. We analyzed full empirical distributions of timelines associated with the diagnosis, isolation, and treatment of CDI. RESULTS A total of 683 inpatients with CDI symptoms were recorded, of which 243 cases were identified as health care-associated infection (HAI). The mean time intervals between the onset of CDI symptoms after admission and the release of laboratory results were 1.2 days and 1.9 days for the HAI and community-associated infection (CAI) patient groups, respectively. The mean time intervals from symptoms onset to the start of isolation were 1.5 days and 2.6 days for the corresponding patient groups. The initiation of treatment within 2 days of symptoms onset reduced the duration of first isolation (P value < .0001); however, the type of initial antibiotic used for CDI treatment was not associated with the duration of isolation. CONCLUSIONS Estimated timelines did not differ (P values > .6) between HAI and CAI patient groups with symptoms onset after admission. These estimates are useful for evaluating the effectiveness of CDI interventions.
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21
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Park SW, Champredon D, Weitz JS, Dushoff J. A practical generation-interval-based approach to inferring the strength of epidemics from their speed. Epidemics 2019; 27:12-18. [PMID: 30799184 DOI: 10.1016/j.epidem.2018.12.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 12/18/2018] [Accepted: 12/28/2018] [Indexed: 11/16/2022] Open
Abstract
Infectious disease outbreaks are often characterized by the reproduction number R and exponential rate of growth r. R provides information about outbreak control and predicted final size, but estimating R is difficult, while r can often be estimated directly from incidence data. These quantities are linked by the generation interval - the time between when an individual is infected by an infector, and when that infector was infected. It is often infeasible to obtain the exact shape of a generation-interval distribution, and to understand how this shape affects estimates of R. We show that estimating generation interval mean and variance provides insight into the relationship between R and r. We use examples based on Ebola, rabies and measles to explore approximations based on gamma-distributed generation intervals, and find that use of these simple approximations are often sufficient to capture the r-R relationship and provide robust estimates of R.
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Affiliation(s)
- Sang Woo Park
- Department of Mathematics & Statistics, McMaster University, Hamilton, Ontario, Canada
| | - David Champredon
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; Department of Mathematics & Statistics, Agent-Based Modelling Laboratory, York University, Toronto, Ontario, Canada
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States; School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, Ontario, Canada.
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22
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Champredon D, Najafi M, Laskowski M, Chit A, Moghadas SM. Individual movements and contact patterns in a Canadian long-term care facility. AIMS Public Health 2018; 5:111-121. [PMID: 30094274 PMCID: PMC6079054 DOI: 10.3934/publichealth.2018.2.111] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/07/2018] [Indexed: 11/18/2022] Open
Abstract
Contact networks of individuals in healthcare facilities are poorly understood, largely due to the lack of spatio-temporal movement data. A better understanding of such networks of interactions can help improve disease control strategies for nosocomial outbreaks. We sought to determine the spatio-temporal patterns of interactions between individuals using movement data collected in the largest veterans long-term care facility in Canada. We processed close-range contact data generated by the exchange of ultra-low-power radio signals, in a prescribed proximity, between wireless sensors worn by the participants over a two-week period. Statistical analyses of contact and movement data were conducted. We found a clear dichotomy in the contact network and movement patterns between residents and healthcare workers (HCWs) in this facility. Overall, residents tend to have significantly more distinct contacts with the mean of 17.3 (s.d. 3.6) contacts, versus 3.5 (s.d. 2.3) for HCWs (p-value < 10-12), for a longer duration of time (with mean contact duration of 8 minutes for resident-resident pair versus 4.6 minutes for HCW-resident pair) while being less mobile than HCWs. Analysis of movement data and clustering coefficient of the hourly aggregated network indicates that the contact network is loosely connected (mean clustering coefficient: 0.25, interquartile range 0-0.40), while being highly structured. Our findings bring quantitative insights regarding the contact network and movements in a long-term care facility, which are highly relevant to infer direct human-to-human and indirect (i.e., via the environment) disease transmission processes. This data-driven quantification is essential for validating disease dynamic models, as well as decision analytic methods to inform control strategies for nosocomial infections.
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Affiliation(s)
- David Champredon
- Agent-Based Modelling Laboratory, York University, Toronto, ON M3J 1P3, Canada
| | - Mehdi Najafi
- Department of Mechanical & Industrial Engineering, Faculty of Applied Science & Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Marek Laskowski
- Agent-Based Modelling Laboratory, York University, Toronto, ON M3J 1P3, Canada.,Schulich School of Business, York University, Toronto, Ontario, Canada M3J1P3, Canada
| | - Ayman Chit
- Sanofi Pasteur, Swiftwater, PA, USA, and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Seyed M Moghadas
- Agent-Based Modelling Laboratory, York University, Toronto, ON M3J 1P3, Canada
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23
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Bellan SE, Champredon D, Dushoff J, Meyers LA. Couple serostatus patterns in sub-Saharan Africa illuminate the relative roles of transmission rates and sexual network characteristics in HIV epidemiology. Sci Rep 2018; 8:6675. [PMID: 29703941 PMCID: PMC5923291 DOI: 10.1038/s41598-018-24249-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/19/2018] [Indexed: 11/21/2022] Open
Abstract
HIV prevalence has surpassed 30% in some African countries while peaking at less than 1% in others. The extent to which this variation is driven by biological factors influencing the HIV transmission rate or by variation in sexual network characteristics remains widely debated. Here, we leverage couple serostatus patterns to address this question. HIV prevalence is strongly correlated with couple serostatus patterns across the continent; in particular, high prevalence countries tend to have a lower ratio of serodiscordancy to concordant positivity. To investigate the drivers of this continental pattern, we fit an HIV transmission model to Demographic and Health Survey data from 45,041 cohabiting couples in 25 countries. In doing so, we estimated country-specific HIV transmission rates and sexual network characteristics reflective of pre-couple and extra-couple sexual contact patterns. We found that variation in the transmission rate could parsimoniously explain between-country variation in both couple serostatus patterns and prevalence. In contrast, between-country variation in pre-couple or extra-couple sexual contact rates could not explain the observed patterns. Sensitivity analyses suggest that future work should examine the robustness of this result to between-country variation in how heterogeneous infection risk is within a country, or to assortativity, i.e. the extent to which individuals at higher risk are likely to partner with each other.
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Affiliation(s)
- Steven E Bellan
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia, United States of America.
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America.
| | - David Champredon
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Lauren Ancel Meyers
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
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24
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Champredon D, Laskowski M, Charland N, Moghadas SM. Assessing the benefits of early pandemic influenza vaccine availability: a case study for Ontario, Canada. Sci Rep 2018; 8:6492. [PMID: 29691450 PMCID: PMC5915538 DOI: 10.1038/s41598-018-24764-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/06/2018] [Indexed: 01/25/2023] Open
Abstract
New vaccine production technologies can significantly shorten the timelines for availability of a strain-specific vaccine in the event of an influenza pandemic. We sought to evaluate the potential benefits of early vaccination in reducing the clinical attack rate (CAR), taking into account the timing and speed of vaccination roll-out. Various scenarios corresponding to the transmissibility of a pandemic strain and vaccine prioritization strategies were simulated using an agent-based model of disease spread in Ontario, the largest Canadian province. We found that the relative reduction of the CAR reached 60% (90%CI: 44-100%) in a best-case scenario, in which the pandemic strain was moderately transmissible, vaccination started 4 weeks before the first imported case, the vaccine administration rate was 4 times higher than its average for seasonal influenza, and the vaccine efficacy was up to 90%. But the relative reductions in the CAR decreased significantly when the vaccination campaign was delayed or the administration rate reduced. In urban settings with similar characteristics to our population study, early availability and high rates of vaccine administration has the potential to substantially reduce the number of influenza cases. Low rates of vaccine administration or uptake can potentially offset the benefits of early vaccination.
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Affiliation(s)
- David Champredon
- Agent-Based Modelling Laboratory, York University, Toronto, M3J 1P3, Ontario, Canada.
| | - Marek Laskowski
- Agent-Based Modelling Laboratory, York University, Toronto, M3J 1P3, Ontario, Canada
| | - Nathalie Charland
- Medicago Inc., 1020 Route de l'Eglise, Quebec, G1V 3V9, Quebec, Canada
| | - Seyed M Moghadas
- Agent-Based Modelling Laboratory, York University, Toronto, M3J 1P3, Ontario, Canada
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25
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Santillana M, Tuite A, Nasserie T, Fine P, Champredon D, Chindelevitch L, Dushoff J, Fisman D. Relatedness of the incidence decay with exponential adjustment (IDEA) model, "Farr's law" and SIR compartmental difference equation models. Infect Dis Model 2018; 3:1-12. [PMID: 30839910 PMCID: PMC6326218 DOI: 10.1016/j.idm.2018.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/02/2018] [Indexed: 01/14/2023] Open
Abstract
Mathematical models are often regarded as recent innovations in the description and analysis of infectious disease outbreaks and epidemics, but simple mathematical expressions have been in use for projection of epidemic trajectories for more than a century. We recently introduced a single equation model (the incidence decay with exponential adjustment, or IDEA model) that can be used for short-term epidemiological forecasting. In the mid-19th century, Dr. William Farr made the observation that epidemic events rise and fall in a roughly symmetrical pattern that can be approximated by a bell-shaped curve. He noticed that this time-evolution behavior could be captured by a single mathematical formula ("Farr's law") that could be used for epidemic forecasting. We show here that the IDEA model follows Farr's law, and show that for intuitive assumptions, Farr's Law can be derived from the IDEA model. Moreover, we show that both mathematical approaches, Farr's Law and the IDEA model, resemble solutions of a susceptible-infectious-removed (SIR) compartmental differential-equation model in an asymptotic limit, where the changes of disease transmission respond to control measures, and not only to the depletion of susceptible individuals. This suggests that the concept of the reproduction number ( R 0 ) was implicitly captured in Farr's (pre-microbial era) work, and also suggests that control of epidemics, whether via behavior change or intervention, is as integral to the natural history of epidemics as is the dynamics of disease transmission.
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Affiliation(s)
- Mauricio Santillana
- Computation Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Bonton, MA, USA
| | - Ashleigh Tuite
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,BlueDot, Toronto, Ontario, Canada
| | - Tahmina Nasserie
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,BlueDot, Toronto, Ontario, Canada
| | - Paul Fine
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - David Champredon
- Agent-Based Modelling Laboratory, York University, Toronto, Ontario, Canada.,Department of Theoretical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Leonid Chindelevitch
- School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jonathan Dushoff
- Department of Theoretical Biology, McMaster University, Hamilton, Ontario, Canada
| | - David Fisman
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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Qasim A, Turcotte M, de Souza RJ, Samaan MC, Champredon D, Dushoff J, Speakman JR, Meyre D. On the origin of obesity: identifying the biological, environmental and cultural drivers of genetic risk among human populations. Obes Rev 2018; 19:121-149. [PMID: 29144594 DOI: 10.1111/obr.12625] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/28/2017] [Accepted: 09/08/2017] [Indexed: 12/12/2022]
Abstract
Genetic predisposition to obesity presents a paradox: how do genetic variants with a detrimental impact on human health persist through evolutionary time? Numerous hypotheses, such as the thrifty genotype hypothesis, attempt to explain this phenomenon yet fail to provide a justification for the modern obesity epidemic. In this critical review, we appraise existing theories explaining the evolutionary origins of obesity and explore novel biological and sociocultural agents of evolutionary change to help explain the modern-day distribution of obesity-predisposing variants. Genetic drift, acting as a form of 'blind justice,' may randomly affect allele frequencies across generations while gene pleiotropy and adaptations to diverse environments may explain the rise and subsequent selection of obesity risk alleles. As an adaptive response, epigenetic regulation of gene expression may impact the manifestation of genetic predisposition to obesity. Finally, exposure to malnutrition and disease epidemics in the wake of oppressive social systems, culturally mediated notions of attractiveness and desirability, and diverse mating systems may play a role in shaping the human genome. As an important first step towards the identification of important drivers of obesity gene evolution, this review may inform empirical research focused on testing evolutionary theories by way of population genetics and mathematical modelling.
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Affiliation(s)
- A Qasim
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - M Turcotte
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - R J de Souza
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - M C Samaan
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Department of Pediatrics, McMaster University, Hamilton, ON, Canada.,Division of Pediatric Endocrinology, McMaster Children's Hospital, Hamilton, ON, Canada
| | - D Champredon
- Department of Biology, McMaster University, Hamilton, ON, Canada.,Agent-Based Modelling Laboratory, York University, Toronto, ON, Canada
| | - J Dushoff
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - J R Speakman
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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Champredon D, Li M, Bolker BM, Dushoff J. Two approaches to forecast Ebola synthetic epidemics. Epidemics 2017; 22:36-42. [PMID: 28325495 DOI: 10.1016/j.epidem.2017.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 12/21/2016] [Accepted: 02/17/2017] [Indexed: 10/20/2022] Open
Abstract
We use two modelling approaches to forecast synthetic Ebola epidemics in the context of the RAPIDD Ebola Forecasting Challenge. The first approach is a standard stochastic compartmental model that aims to forecast incidence, hospitalization and deaths among both the general population and health care workers. The second is a model based on the renewal equation with latent variables that forecasts incidence in the whole population only. We describe fitting and forecasting procedures for each model and discuss their advantages and drawbacks. We did not find that one model was consistently better in forecasting than the other.
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Affiliation(s)
- David Champredon
- McMaster University, Hamilton, Ontario, Canada; York University, Toronto, Ontario, Canada.
| | - Michael Li
- McMaster University, Hamilton, Ontario, Canada
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Abstract
The generation interval is the interval between the time when an individual is infected by an infector and the time when this infector was infected. Its distribution underpins estimates of the reproductive number and hence informs public health strategies. Empirical generation-interval distributions are often derived from contact-tracing data. But linking observed generation intervals to the underlying generation interval required for modelling purposes is surprisingly not straightforward, and misspecifications can lead to incorrect estimates of the reproductive number, with the potential to misguide interventions to stop or slow an epidemic. Here, we clarify the theoretical framework for three conceptually different generation-interval distributions: the 'intrinsic' one typically used in mathematical models and the 'forward' and 'backward' ones typically observed from contact-tracing data, looking, respectively, forward or backward in time. We explain how the relationship between these distributions changes as an epidemic progresses and discuss how empirical generation-interval data can be used to correctly inform mathematical models.
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Affiliation(s)
- David Champredon
- School of Computational Science and Engineering, McMaster University, Hamilton, Canada L8S 4L8
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, Canada L8S 4L8
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Champredon D, Earn DJD. Understanding apparently non-exponential outbreaks Comment on "Mathematical models to characterize early epidemic growth: A review" by Gerardo Chowell et al. Phys Life Rev 2016; 18:105-108. [PMID: 27575513 DOI: 10.1016/j.plrev.2016.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 08/23/2016] [Indexed: 10/21/2022]
Affiliation(s)
- David Champredon
- Agent-Based Modelling Laboratory, York University, Toronto, Ontario, M3J 1P3, Canada.
| | - David J D Earn
- Department of Mathematics & Statistics, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.
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Bellan SE, Pulliam JRC, Pearson CAB, Champredon D, Fox SJ, Skrip L, Galvani AP, Gambhir M, Lopman BA, Porco TC, Meyers LA, Dushoff J. Statistical power and validity of Ebola vaccine trials in Sierra Leone: a simulation study of trial design and analysis. Lancet Infect Dis 2015; 15:703-10. [PMID: 25886798 DOI: 10.1016/s1473-3099(15)70139-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Safe and effective vaccines could help to end the ongoing Ebola virus disease epidemic in parts of west Africa, and mitigate future outbreaks of the virus. We assess the statistical validity and power of randomised controlled trial (RCT) and stepped-wedge cluster trial (SWCT) designs in Sierra Leone, where the incidence of Ebola virus disease is spatiotemporally heterogeneous, and is decreasing rapidly. METHODS We projected district-level Ebola virus disease incidence for the next 6 months, using a stochastic model fitted to data from Sierra Leone. We then simulated RCT and SWCT designs in trial populations comprising geographically distinct clusters at high risk, taking into account realistic logistical constraints, and both individual-level and cluster-level variations in risk. We assessed false-positive rates and power for parametric and non-parametric analyses of simulated trial data, across a range of vaccine efficacies and trial start dates. FINDINGS For an SWCT, regional variation in Ebola virus disease incidence trends produced increased false-positive rates (up to 0·15 at α=0·05) under standard statistical models, but not when analysed by a permutation test, whereas analyses of RCTs remained statistically valid under all models. With the assumption of a 6-month trial starting on Feb 18, 2015, we estimate the power to detect a 90% effective vaccine to be between 49% and 89% for an RCT, and between 6% and 26% for an SWCT, depending on the Ebola virus disease incidence within the trial population. We estimate that a 1-month delay in trial initiation will reduce the power of the RCT by 20% and that of the SWCT by 49%. INTERPRETATION Spatiotemporal variation in infection risk undermines the statistical power of the SWCT. This variation also undercuts the SWCT's expected ethical advantages over the RCT, because an RCT, but not an SWCT, can prioritise vaccination of high-risk clusters. FUNDING US National Institutes of Health, US National Science Foundation, and Canadian Institutes of Health Research.
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Affiliation(s)
- Steven E Bellan
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA.
| | - Juliet R C Pulliam
- Department of Biology, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Carl A B Pearson
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - David Champredon
- School of Computational Science and Engineering, McMaster University, Hamilton, ON, Canada
| | - Spencer J Fox
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Laura Skrip
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Alison P Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, Yale University, New Haven, CT, USA; Department of Ecology and Evolution, Yale University, New Haven, CT, USA
| | - Manoj Gambhir
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia; Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; IHRC Inc, Atlanta, GA, USA
| | - Ben A Lopman
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Travis C Porco
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA; Department of Ophthalmology, University of California, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA; The Santa Fe Institute, Santa Fe, NM, USA
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Champredon D, Bellan S, Dushoff J. HIV sexual transmission is predominantly driven by single individuals rather than discordant couples: a model-based approach. PLoS One 2013; 8:e82906. [PMID: 24376602 PMCID: PMC3869741 DOI: 10.1371/journal.pone.0082906] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/07/2013] [Indexed: 12/03/2022] Open
Abstract
Understanding the relative contribution to HIV transmission from different social groups is important for public-health policy. Information about the importance of stable serodiscordant couples (when one partner is infected but not the other) relative to contacts outside of stable partnerships in spreading disease can aid in designing and targeting interventions. However, the overall importance of within-couple transmission, and the determinants and correlates of this importance, are not well understood. Here, we explore how mechanistic factors – like partnership dynamics and rates of extra-couple transmission – affect various routes of transmission, using a compartmental model with parameters based on estimates from Sub-Saharan Africa. Under our assumptions, when sampling model parameters within a realistic range, we find that infection of uncoupled individuals is usually the predominant route (median 0.62, 2.5%–97.5% quantiles: 0.26–0.88), while transmission within discordant couples is usually important, but rarely represents the majority of transmissions (median 0.33, 2.5%–97.5% quantiles: 0.10–0.67). We find a strong correlation between long-term HIV prevalence and the contact rate of uncoupled individuals, implying that this rate may be a key driver of HIV prevalence. For a given level of prevalence, we find a negative correlation between the proportion of discordant couples and the within-couple transmission rate, indicating that low discordance in a population may reflect a relatively high rate of within-couple transmission. Transmission within or outside couples and among uncoupled individuals are all likely to be important in sustaining heterosexual HIV transmission in Sub-Saharan Africa. Hence, intervention policies should be broadly targeted when practical.
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Affiliation(s)
- David Champredon
- School of Computational Science and Engineering, McMaster University, Hamilton, Canada
- * E-mail:
| | - Steve Bellan
- Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, Texas, United States of America
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