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CitationsAdd new citationList by: CiterankMap Link[2] Evaluating undercounts in epidemics: response to Maruotti et al. 2022
Author: Michael Li, Jonathan Dushoff, David J. D. Earn, Benjamin M. Bolker
Publication date: 22 September 2022
Publication info: arXiv:2209.11334 [q-bio.PE]
Cited by: David Price 12:15 PM 25 November 2023 GMT
Citerank: (6) 679758Benjamin BolkerI’m a professor in the departments of Mathematics & Statistics and of Biology at McMaster University, and currently Director of the School of Computational Science and Engineering and Acting Associate Chair (Graduate) for Mathematics.10019D3ABAB, 679776David EarnProfessor of Mathematics and Faculty of Science Research Chair in Mathematical Epidemiology at McMaster University.10019D3ABAB, 679814Jonathan DushoffProfessor in the Department Of Biology at McMaster University.10019D3ABAB, 701020CANMOD – PublicationsPublications by CANMOD Members144B5ACA0, 701037MfPH – Publications144B5ACA0, 715667mpox859FDEF6
URL:
DOI: https://doi.org/10.48550/arXiv.2209.11334
| | Excerpt / Summary [arXiv, 22 September 2022]
Maruotti et al. 2022 used a mark-recapture approach to estimate bounds on the true number of monkeypox infections in various countries. These approaches are fundamentally flawed; it is impossible to estimate undercounting based solely on a single stream of reported cases. Simulations based on a Richards curve for cumulative incidence show that, for reasonable epidemic parameters, the proposed methods estimate bounds on the ascertainment ratio of ≈0.2−0.5 roughly independently of the true ascertainment ratio. These methods should not be used. |
Link[3] The need for linked genomic surveillance of SARS-CoV-2
Author: Caroline Colijn, David JD Earn, Jonathan Dushoff, Nicholas H Ogden, Michael Li, Natalie Knox, Gary Van Domselaar, Kristyn Franklin, Gordon Jolly, Sarah P Otto
Publication date: 6 April 2022
Publication info: Can Commun Dis Rep. 2022 Apr 6; 48(4): 131–139, PMCID: PMC9017802PMID: 35480703
Cited by: David Price 10:39 PM 29 November 2023 GMT
Citerank: (11) 679761Caroline ColijnDr. Caroline Colijn works at the interface of mathematics, evolution, infection and public health, and leads the MAGPIE research group. She joined SFU's Mathematics Department in 2018 as a Canada 150 Research Chair in Mathematics for Infection, Evolution and Public Health. She has broad interests in applications of mathematics to questions in evolution and public health, and was a founding member of Imperial College London's Centre for the Mathematics of Precision Healthcare.10019D3ABAB, 679814Jonathan DushoffProfessor in the Department Of Biology at McMaster University.10019D3ABAB, 679875Sarah OttoProfessor in Zoology. Theoretical biologist, Canada Research Chair in Theoretical and Experimental Evolution, and Killam Professor at the University of British Columbia.10019D3ABAB, 701020CANMOD – PublicationsPublications by CANMOD Members144B5ACA0, 701023GenomicsWhile virus genomes can describe the global context of introductions and origins of local clusters of cases, CANMOD will focus on building methods for characterizing and modelling local transmission once it is established, and for surveillance for viral determinants of increased fitness and of enhanced risk of spillover, virulence and transmission.859FDEF6, 701037MfPH – Publications144B5ACA0, 704045Covid-19859FDEF6, 707634Gary Van DomselaarDr. Gary Van Domselaar, PhD (University of Alberta, 2003) is the Chief of the Bioinformatics Laboratory at the National Microbiology Laboratory in Winnipeg Canada, and Adjunct Professor in the Department of Medical Microbiology at the University of Manitoba.10019D3ABAB, 708734Genomics859FDEF6, 715277Covid-19Covid-19 » Relevance » Genomics10000FFFACD, 715329Nick OgdenNicholas Ogden is a senior research scientist and Director of the Public Health Risk Sciences Division within the National Microbiology Laboratory at the Public Health Agency of Canada.10019D3ABAB URL:
DOI: https://doi.org/10.14745/ccdr.v48i04a03
| | Excerpt / Summary [Canada Communicable Disease Report, 6 April 2022]
Genomic surveillance during the coronavirus disease 2019 (COVID-19) pandemic has been key to the timely identification of virus variants with important public health consequences, such as variants that can transmit among and cause severe disease in both vaccinated or recovered individuals. The rapid emergence of the Omicron variant highlighted the speed with which the extent of a threat must be assessed. Rapid sequencing and public health institutions’ openness to sharing sequence data internationally give an unprecedented opportunity to do this; however, assessing the epidemiological and clinical properties of any new variant remains challenging. Here we highlight a “band of four” key data sources that can help to detect viral variants that threaten COVID-19 management: 1) genetic (virus sequence) data; 2) epidemiological and geographic data; 3) clinical and demographic data; and 4) immunization data. We emphasize the benefits that can be achieved by linking data from these sources and by combining data from these sources with virus sequence data. The considerable challenges of making genomic data available and linked with virus and patient attributes must be balanced against major consequences of not doing so, especially if new variants of concern emerge and spread without timely detection and action. |
Link[4] A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities
Author: Shokoofeh Nourbakhsh, Aamir Fazil, Michael Li, Chand S. Mangat, Shelley W. Peterson, Jade Daigle, Stacie Langner, Jayson Shurgold, Patrick D’Aoust, Robert Delatolla, Elizabeth Mercier, Xiaoli Pang, Bonita E. Lee, Rebecca Stuart, Shinthuja Wijayasri, David Champredon
Publication date: 21 April 2022
Publication info: Epidemics, Volume 39, June 2022, 100560, ISSN 1755-4365,
Cited by: David Price 11:07 PM 29 November 2023 GMT
Citerank: (5) 701037MfPH – Publications144B5ACA0, 704022Surveillance859FDEF6, 704045Covid-19859FDEF6, 708744Wastewater-based surveillance (WBS) 859FDEF6, 715283David ChampredonDr. David Champredon is a senior scientist at the Public Health Agency of Canada. His work focuses on modelling the spread of infectious diseases at the population level, especially respiratory and sexually transmitted infections. During the past two years, he supported the modelling efforts to respond to the COVID-19 pandemic, particularly wastewater-based modelling.10019D3ABAB
URL:
DOI: https://doi.org/10.1016/j.epidem.2022.100560
| | Excerpt / Summary [Epidemics, 21 April 2022]
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. |
Link[5] Exploring the dynamics of the 2022 mpox outbreak in Canada
Author: Rachael M. Milwid, Michael Li, Aamir Fazil, Mathieu Maheu-Giroux, Carla M. Doyle, Yiqing Xia, Joseph Cox, Daniel Grace, Milada Dvorakova, Steven C. Walker, Sharmistha Mishra, Nicholas H. Ogden
Publication date: 6 December 2023
Publication info: Journal of Medical Virology, Volume 95, Issue 12 e29256
Cited by: David Price 8:27 PM 6 December 2023 GMT
Citerank: (9) 679844Mathieu Maheu-GirouxCanada Research Chair (Tier 2) in Population Health Modeling and Associate Professor, McGill University.10019D3ABAB, 679880Sharmistha MishraSharmistha Mishra is an infectious disease physician and mathematical modeler and holds a Tier 2 Canadian Research Chair in Mathematical Modeling and Program Science.10019D3ABAB, 685203McMasterPandemicCompartmental epidemic models for forecasting and analysis of infectious disease pandemics: contributions from Ben Bolker, Jonathan Dushoff, David Earn, Weiguang Guan, Morgan Kain, Michael Li, Irena Papst, Steve Walker (in alphabetical order).122C78CB7, 701020CANMOD – PublicationsPublications by CANMOD Members144B5ACA0, 701037MfPH – Publications144B5ACA0, 715290Steve WalkerSteve is the CANMOD Director of Data Science and a postdoctoral fellow in the Department of Mathematics and Statistics at McMaster University.10019D3ABAB, 715291macpan2McMasterPandemic was developed to provide forecasts and insights to Canadian public health agencies throughout the COVID-19 pandemic. The goal of this macpan2 project is to re-imagine McMasterPandemic, building it from the ground up with architectural and technological decisions that address the many lessons that we learned from COVID-19 about software.122C78CB7, 715329Nick OgdenNicholas Ogden is a senior research scientist and Director of the Public Health Risk Sciences Division within the National Microbiology Laboratory at the Public Health Agency of Canada.10019D3ABAB, 715667mpox859FDEF6 URL:
DOI: https://doi.org/10.1002/jmv.29256
| | Excerpt / Summary [Journal of Medical Virology, 6 December 2023]
The 2022 mpox outbreak predominantly impacted gay, bisexual, and other men who have sex with men (gbMSM). Two models were developed to support situational awareness and management decisions in Canada. A compartmental model characterized epidemic drivers at national/provincial levels, while an agent-based model (ABM) assessed municipal-level impacts of vaccination. The models were parameterized and calibrated using empirical case and vaccination data between 2022 and 2023. The compartmental model explored: (1) the epidemic trajectory through community transmission, (2) the potential for transmission among non-gbMSM, and (3) impacts of vaccination and the proportion of gbMSM contributing to disease transmission. The ABM incorporated sexual-contact data and modeled: (1) effects of vaccine uptake on disease dynamics, and (2) impacts of case importation on outbreak resurgence. The calibrated, compartmental model followed the trajectory of the epidemic, which peaked in July 2022, and died out in December 2022. Most cases occurred among gbMSM, and epidemic trajectories were not consistent with sustained transmission among non-gbMSM. The ABM suggested that unprioritized vaccination strategies could increase the outbreak size by 47%, and that consistent importation (≥5 cases per 10 000) is necessary for outbreak resurgence. These models can inform time-sensitive situational awareness and policy decisions for similar future outbreaks. |
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