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Mathematical modelling of (re)emerging infectious respiratory diseases among humans poses multiple challenges for modellers, which can arise as a result of limited data and surveillance, uncertainty in the natural history of the disease, as well as public health and individual responses to outbreaks. Here, we propose a COVID-19-inspired health state diagram (HSD) to serve as a foundational framework for conceptualising the modelling process for (re)emerging respiratory diseases, and public health responses, in the early stages of their emergence. The HSD aims to serve as a starting point for reflection on the structure and parameterisation of a transmission model to assess the impact of the (re)emerging disease and the capacity of public health interventions to control transmission. We also explore the adaptability of the HSD to different (re)emerging diseases using the characteristics of three respiratory diseases of historical public health importance. We outline key questions to contemplate when applying and adapting this HSD to (re)emerging infectious diseases and provide reflections on adapting the framework for public health-related interventions., (© 2024. Crown.)

Background: The COVID-19 pandemic underlined the need for pandemic planning but also brought into focus the use of mathematical modelling to support public health decisions. The types of models needed (compartment, agent-based, importation) are described. Best practices regarding biological realism (including the need for multidisciplinary expert advisors to modellers), model complexity, consideration of uncertainty and communications to decision-makers and the public are outlined., Methods: A narrative review was developed from the experiences of COVID-19 by members of the Public Health Agency of Canada External Modelling Network for Infectious Diseases (PHAC EMN-ID), a national community of practice on mathematical modelling of infectious diseases for public health., Results: Modelling can best support pandemic preparedness in two ways: 1) by modelling to support decisions on resource needs for likely future pandemics by estimating numbers of infections, hospitalized cases and cases needing intensive care, associated with epidemics of "hypothetical-yet-plausible" pandemic pathogens in Canada; and 2) by having ready-to-go modelling methods that can be readily adapted to the features of an emerging pandemic pathogen and used for long-range forecasting of the epidemic in Canada, as well as to explore scenarios to support public health decisions on the use of interventions., Conclusion: There is a need for modelling expertise within public health organizations in Canada, linked to modellers in academia in a community of practice, within which relationships built outside of times of crisis can be applied to enhance modelling during public health emergencies. Key challenges to modelling for pandemic preparedness include the availability of linked public health, hospital and genomic data in Canada.

Background: Commercial air travel can result in global dispersal of infectious diseases. During the coronavirus disease 2019 (COVID-19) pandemic, many countries implemented border measures, including restrictions on air travel, to reduce the importation risk of COVID-19. In the context of inbound air travel to Canada, this study aimed to: 1) characterize travel trends before and during the pandemic, and 2) statistically assess the association between travel volumes and travel restrictions during the pandemic., Methods: Monthly commercial air travel volume data from March 2017 to February 2023 were obtained from the International Air Transport Association (IATA). National and airport-level travel trends to Canada were characterized by inbound travel volumes, the number of countries contributing travellers and the ranking of the top ten countries contributing travellers across the study period, by six year-length subperiod groupings (three pre-pandemic and three pandemic). Using seasonal autoregressive integrated moving average (SARIMA) models, interrupted time series (ITS) analyses assessed the association between major travel restrictions and travel volumes by including variables to represent changes to the level and slope of the time series., Results: The pre-pandemic inbound travel volume increased by 3% to 7% between consecutive subperiods, with three seasonal peaks (July-August, December-January, March). At the onset of the pandemic, travel volume decreased by 90%, with the number of contributing countries declining from approximately 200 to 140, followed by a slow recovery in volume and seasonality. A disruption in the ranking of countries that contributed travellers was also noticeable during the pandemic. Results from the ITS analysis aligned with the timing of travel restrictions as follows: implementation in March 2020 coincided with a sharp reduction in volumes, while the easing of major restrictions, starting with the authorization of fully vaccinated travellers from the United States to enter Canada in August 2021, coincided with an increase in the slope of travel volumes. Descriptive and statistical results suggest a near-return of pre-pandemic travel patterns by the end of the study period., Conclusion: Study results suggest resilience in commercial air travel into Canada. Although the COVID-19 pandemic led to a disruption in travel trends, easing of travel restrictions appeared to enable pre-pandemic trends to re-emerge. Understanding trends in air travel volumes, as demonstrated here, can provide information that supports preparedness and response regarding importation risk of infectious pathogens., Competing Interests: Competing interests The authors declare no competing interests.

Background: Estimating rates of disease importation by travellers is a key activity to assess both the risk to a country from an infectious disease emerging elsewhere in the world and the effectiveness of border measures. We describe a model used to estimate the number of travellers infected with SARS-CoV-2 into Canadian airports in 2021, and assess the impact of pre-departure testing requirements on importation risk., Methods: A mathematical model estimated the number of essential and non-essential air travellers infected with SARS-CoV-2, with the latter requiring a negative pre-departure test result. The number of travellers arriving infected (i.e. imported cases) depended on air travel volumes, SARS-CoV-2 exposure risk in the departure country, prior infection or vaccine acquired immunity, and, for non-essential travellers, screening from pre-departure molecular testing. Importation risk was estimated weekly from July to November 2021 as the number of imported cases and percent positivity (PP; i.e. imported cases normalised by travel volume). The impact of pre-departure testing was assessed by comparing three scenarios: baseline (pre-departure testing of all non-essential travellers; most probable importation risk given the pre-departure testing requirements), counterfactual scenario 1 (no pre-departure testing of fully vaccinated non-essential travellers), and counterfactual scenario 2 (no pre-departure testing of non-essential travellers)., Results: In the baseline scenario, weekly imported cases and PP varied over time, ranging from 145 to 539 cases and 0.15 to 0.28%, respectively. Most cases arrived from the USA, Mexico, the United Kingdom, and France. While modelling suggested that essential travellers had a higher weekly PP (0.37 - 0.65%) than non-essential travellers (0.12 - 0.24%), they contributed fewer weekly cases (62 - 154) than non-essential travellers (84 - 398 per week) given their lower travel volume. Pre-departure testing was estimated to reduce imported cases by one third (counterfactual scenario 1) to one half (counterfactual scenario 2)., Conclusions: The model results highlighted the weekly variation in importation by traveller group (e.g., reason for travel and country of departure) and enabled a framework for measuring the impact of pre-departure testing requirements. Quantifying the contributors of importation risk through mathematical simulation can support the design of appropriate public health policy on border measures., (© 2024. Crown.)

This study illustrates what may have happened, in terms of coronavirus disease 2019 (COVID-19) infections, hospitalizations and deaths in Canada, had public health measures not been used to control the COVID-19 epidemic, and had restrictions been lifted with low levels of vaccination, or no vaccination, of the Canadian population. The timeline of the epidemic in Canada, and the public health interventions used to control the epidemic, are reviewed. Comparisons against outcomes in other countries and counterfactual modelling illustrate the relative success of control of the epidemic in Canada. Together, these observations show that without the use of restrictive measures and without high levels of vaccination, Canada could have experienced substantially higher numbers of infections and hospitalizations and almost a million deaths., Competing Interests: Competing interest: None., (Public Health Agency of Canada, 2022.)

Public health measures applied exclusively within vulnerable populations have been suggested as an alternative to community-wide interventions to mitigate SARS-CoV-2 transmission. With the population demography and healthcare capacity of Canada as an example, a stochastic age-stratified agent-based model was used to explore the progression of the COVID-19 epidemic under three intervention scenarios (infection-preventing vaccination, illness-preventing vaccination and shielding) in individuals above three age thresholds (greater than or equal to 45, 55 and 65 years) while lifting shutdowns and physical distancing in the community. Compared with a scenario with sustained community-wide measures, all age-stratified intervention scenarios resulted in a substantial epidemic resurgence, with hospital and ICU bed usage exceeding healthcare capacities even at the lowest age threshold. Individuals under the age threshold were severely impacted by the implementation of all age-stratified interventions, with large numbers of avoidable deaths. Among all explored scenarios, shielding older individuals led to the most detrimental outcomes (hospitalizations, ICU admissions and mortality) for all ages, including the targeted population. This study suggests that, in the absence of community-wide measures, implementing interventions exclusively within vulnerable age groups could result in unmanageable levels of infections, with serious outcomes within the population. Caution is therefore warranted regarding early relaxation of community-wide restrictions., (© 2021 The Authors.)

Australia, home to the iconic dingo, is currently free from canine rabies. However northern Australia, including Indigenous communities with large free-roaming domestic dog populations, is at increased risk of rabies incursion from nearby Indonesia. We developed a novel agent-based stochastic spatial rabies spread model to evaluate the potential spread of rabies within the dingo population of the Northern Peninsula Area (NPA) region of northern Australia. The model incorporated spatio-temporal features specific to this host-environment system, including landscape heterogeneity, demographic fluctuations, dispersal movements and dingo ecological parameters-such as home range size and density-derived from NPA field studies. Rabies spread between dingo packs in nearly 60% of simulations. In such situations rabies would affect a median of 22 dingoes (approximately 14% of the population; 2.5-97.5 percentiles: 2-101 dingoes) within the study area which covered 1,131 km2, and spread 0.52 km/week for 191 days. Larger outbreaks occurred in scenarios in which an incursion was introduced during the dry season (vs. wet season), and close to communities (vs. areas with high risk of interaction between dingoes and hunting community dogs). Sensitivity analyses revealed that home range size and duration of infectious clinical period contributed most to the variance of outputs. Although conditions in the NPA would most likely not support a sustained propagation of the disease in the dingo population, due to the predicted number of infected dingoes following a rabies incursion and the proximity of Indigenous communities to dingo habitat, we conclude that the risk for human transmission could be substantial., Competing Interests: The authors have declared that no competing interests exist.

Australia is currently free of canine rabies. Spatio-ecological knowledge about dingoes in northern Australia is currently a gap that impedes the application of disease spread models and our understanding of the potential transmission of rabies, in the event of an incursion. We therefore conducted a one-year camera trap survey to monitor a dingo population in equatorial northern Australia. The population is contiguous with remote Indigenous communities containing free-roaming dogs, which potentially interact with dingoes. Based on the camera trap data, we derived dingo density and home range size estimates using maximum-likelihood, spatially explicit, mark-resight models, described dingo movements and evaluated spatial correlation and temporal overlap in activities between dingoes and community dogs. Dingo density estimates varied from 0.135 animals/km 2 (95% CI = 0.127-0.144) during the dry season to 0.147 animals/km 2 (95% CI = 0.135-0.159) during the wet season. The 95% bivariate Normal home range sizes were highly variable throughout the year (7.95-29.40 km 2 ). Spatial use and daily activity patterns of dingoes and free-roaming community dogs, grouped over ~3 month periods, showed substantial temporal activity overlap and spatial correlation, highlighting the potential risk of disease transmission at the wild-domestic interface in an area of biosecurity risk in equatorial northern Australia. Our results have utility for improving preparedness against a potential rabies incursion.

Background: Dingoes and wild-living dogs in Australia, which include feral domestic dogs and dingo-dog hybrids, play a role as reservoirs of disease. In the case of an exotic disease incursion-such as rabies-these reservoirs could be a threat to the health of humans, domestic animals and other wildlife in Australia. Disease spread models are needed to explore this impact and develop mitigation strategies for responding to an incursion. Our study aim was to describe relevant information from the literature, using a scoping review, on specific topics related to dingo and wild-living dog ecology and biology (topics of interest) in Australia to inform parameterisation of disease spread modelling and identify major research gaps. Methods: A broad electronic search was conducted in five bibliographic databases and grey literature. Two levels of screening and two levels of data extraction were each performed independently by two reviewers. Data extracted included topics of interest investigated, type of population sampled, the presence of lethal control, type of environment, years of collection and GPS coordinates of study sites. Results: From 1666 records captured, the screening process yielded 229 individual studies published between 1862 and 2016. The most frequently reported topics of interest in studies were index of abundance ( n = 93) and diet ( n = 68). Among the three key parameters in disease spread modelling (i.e., density, contacts and home range), data on density and contacts were identified as major research gaps in the literature due to the small number of recent studies on these topics and the scarcity of quantitative estimates. The research reviewed was mostly located around central Australia and the east coast, including a few studies on density, contacts and home range. Data from these regions could potentially be used to inform parameterisation for disease spread modelling of dingoes and wild-living dogs. However, the number of studies is limited in equatorial and tropical climate zones of northern Australia, which is a high-risk area for a rabies incursion. Conclusions: Research in northern regions of Australia, especially to generate data regarding density, contacts and home ranges, should be prioritised for future research on dingoes and wild-living dogs.

Lyme disease is emerging in Canada due to geographic range expansion of the tick vector Ixodes scapularis Say. Recent areas of emergence include parts of the southeastern Canadian Prairie region. We developed a map of potential risk areas for future I. scapularis establishment in the Canadian Prairie Provinces. Six I. scapularis risk algorithms were developed using different formulations of three indices for environmental suitability: temperature using annual cumulative degree-days > 0 °C (DD > 0 °C; obtained from Moderate Resolution Imaging Spectroradiometer satellite data as an index of conditions that allow I. scapularis to complete its life cycle), habitat as a combined geolayer of forest cover and agricultural land use, and rainfall. The relative performance of these risk algorithms was assessed using receiver-operating characteristic (ROC) area under the curve (AUC) analysis with data on presence-absence of I. scapularis obtained from recent field surveillance in the Prairie Provinces accumulated from a number of sources. The ROC AUC values for the risk algorithms were significantly different (P < 0.01). The algorithm with six categories of DD > 0 °C, habitat as a simple dichotomous variable of presence or absence of forest, and normalized rainfall had the highest AUC of 0.74, representing "fair to good" performance of the risk algorithm. This algorithm had good (>80%) sensitivity in predicting positive I. scapularis surveillance sites, but low (50%) specificity as expected in this region where not all environmentally suitable habitats are expected to be occupied. Further prospective studies are needed to validate and perhaps improve the risk algorithm., (© Crown copyright 2017.)

In Canada, Francisella tularensis , the zoonotic bacterial agent of tularemia, affects mostly snowshoe hares ( Lepus americanus ), muskrats ( Ondatra zibethicus ), and beavers ( Castor canadensis ). Despite numerous studies, the ecologic cycle and natural reservoirs of F. tularensis are not clearly defined. We conducted a cross-sectional study to estimate the prevalence of F. tularensis in snowshoe hares, muskrats, and coyotes ( Canis latrans ) in four regions of Québec, Canada, and to describe the risk of infection in relation to host and environmental characteristics at three spatial scales. Between October 2012 and April 2013, trappers captured 345 snowshoe hares, 411 muskrats, and 385 coyotes. Blood samples were tested by microagglutination tests, and DNA extracts of liver, kidney, lung, and spleen of snowshoe hares and muskrats were tested by real-time PCR to detect past and active infection to F. tularensis , respectively. Individual host characteristics, including body condition, age, and sex, were evaluated as risk factors of infection, along with ecologic characteristics of the location of capture extracted from geographic databases. Prevalences of antibody to F. tularensis and 95% confidence intervals were 2.9% (1.4-5.1%) in coyotes, 0.6% (0.1-2.1%) in hares, and 0% (0.0-0.9%) in muskrats. Francisella tularensis DNA was not detected by real-time PCR in the pools of four organs from muskrats and hares, but F. tularensis type AI was detected during testing of the individual organs of two antibody-positive hares. Exact logistic regression analyses showed that age was a significant predictor of antibody detection in coyotes, as were the proportion of forest and the proportion of area considered as suitable habitat for hares in the environment around the location of capture of the coyotes. Our results suggest a terrestrial cycle of F. tularensis in the regions studied.

Feral pigeons (Columbia livia) can harbor a range of zoonotic pathogens. A transversal study was undertaken to estimate the prevalence of feral pigeons infected by various pathogens in public areas in Montreal, Quebec. Cloacal swabs from captured birds were cultured for Salmonella spp. and Campylobacter spp. and tested by real-time polymerase chain reaction (RT-PCR) for the detection of Coxiella burnetii. An oropharyngeal swab was also submitted to real-time reverse-transcription polymerase chain reaction (RRT-PCR) for the detection of Newcastle disease virus. Among the 187 pigeons tested from 10 public areas, 9.1% (95% CI: 3.0 to 15.2) were positive for Campylobacter spp. with all strains identified as Campylobacter jejuni. The Campylobacter status of birds was not associated with individual characteristics of birds, with the exception of body score. None of the pigeons tested positive for the other pathogens. Direct or indirect contacts with feral pigeons may constitute a potential risk for Campylobacter infection in humans.

Tick-borne diseases are a growing public health concern as their incidence and range have increased in recent decades. Lyme disease is an emerging infectious disease in Canada due to northward expansion of the geographic range of Ixodes scapularis, the principal tick vector for the Lyme disease agent Borrelia burgdorferi, into central and eastern Canada. In this study the geographical distributions of Ixodid ticks, including I. scapularis, and environmental factors associated with their occurrence were investigated in New Brunswick, Canada, where few I. scapularis populations have been found to date. Density of host-seeking ticks was evaluated by drag sampling of woodland habitats in a total of 159 sites. Ixodes scapularis ticks (n = 5) were found on four sites, Ixodes muris (n = 1) on one site and Haemaphysalis leporispalustris (n = 243) on 41 sites. One of four adult I. scapularis ticks collected was PCR-positive for B. burgdorferi. No environmental variables were significantly associated with the presence of I. scapularis although comparisons with surveillance data in neighbouring provinces (Québec and Nova Scotia) suggested that temperature conditions may be too cold for I. scapularis (< 2800 annual degree days above 0°C [DD > 0°C]) across much of New Brunswick. In contrast, the presence of H. leporispalustris, which is a competent vector of tularaemia, was significantly (P < 0.05) associated with specific ranges of mean DD > 0°C, mean annual precipitation, percentage of clay in site soil, elevation and season in a multivariable logistic regression model. With the exception of some localized areas, temperature conditions and deer density may be too low for the establishment of I. scapularis and Lyme disease risk areas in New Brunswick, while environmental conditions were suitable for H. leporispalustris at many sites. These findings indicate differing ecological niches for two tick species of public health significance.