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, 685445Michael WZ LiMichael Li is Senior Scientist in the Public Health Risk Science Division (PHRS) of the Public Health Agency of Canada (PHAC) and a Research Associate at the South African Centre for Epidemiological Modelling and Analysis (SACEMA).10019D3ABAB, 701020CANMOD – PublicationsPublications by CANMOD Members144B5ACA0, 701037MfPH – Publications144B5ACA0, 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

[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.

[medRxiv, 20 December 2024]

Background: Canadian notifiable disease surveillance provides data on the incidence of communicable diseases, dating back to the late 19th century. The Public Health Agency of Canada offers summaries of these data (from 1924–2022) through an online portal. These summaries provide historical context for Canadian health researchers, but lack information on intra-annual and inter-provincial patterns. Sub-annual and sub-national data can be found in published documents, or requested from archives of government agencies, but are only available in typewritten or handwritten hard copies. We digitized and collated these data sources to create a resource for epidemiology and public health.

Methods: We manually entered data from scans of hard copies into spreadsheets resembling the originals, facilitating accurate transcription through easier cross-checking. We developed open-source pipelines to harmonize these spreadsheets into CSV files that blend data across sources.

Results: We assembled and processed 1,631,380 incidence values from 1903–2021. Focusing on sub-annual and sub-national data and removing redundancy yielded 934,009 weekly, monthly, or quarterly incidence values broken down by province/territory, containing 139 diseases. We give two examples of sub-annual and sub-national patterns: strong annual cycles of poliomyelitis that peaked simultaneously across provinces, and spatially heterogeneous resurgence of whooping cough in the 1990s.

Interpretation: Canada’s history of infectious disease surveillance has produced a detailed record of sub-annual and sub-national disease incidence patterns that remains largely unexplored. This important record is now available as the Canadian Disease Incidence Dataset (CANDID), hosted on a publicly accessible website along with the pipelines used to create it and scans of the original sources.

R package version 0.1.0

Github: https://github.com/can...