Mathematical modelling for pandemic preparedness in Canada: Learning from COVID-19.

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.

Is SARS-CoV-2 elimination or mitigation best? Regional and disease characteristics determine the recommended strategy.

Public health responses to the COVID-19 pandemic varied across the world. Some countries (e.g.

Canada's provincial COVID-19 pandemic modelling efforts: A review of mathematical models and their impacts on the responses.

Setting: Mathematical modelling played an important role in the public health response to COVID-19 in Canada. Variability in epidemic trajectories, modelling approaches, and data infrastructure across provinces provides a unique opportunity to understand the factors that shaped modelling strategies.

Intervention: Provinces implemented stringent pandemic interventions to mitigate SARS-CoV-2 transmission, considering evidence from epidemic models.

Extensive SARS-CoV-2 testing reveals BA.1/BA.2 asymptomatic rates and underreporting in school children.

Background: Case underreporting during the coronavirus disease 2019 (COVID-19) pandemic has been a major challenge to the planning and evaluation of public health responses. School children were often considered a less vulnerable population and underreporting rates may have been particularly high. In January 2022, the Canadian province of Newfoundland and Labrador (NL) was experiencing an Omicron variant outbreak (BA.

Resource and seasonality drive interspecific variability in simulations from a dynamic energy budget model.

Animals show a vast array of phenotypic traits in time and space. Such variation patterns have traditionally been described as ecogeographical rules; for example, the tendency of size and clutch size to increase with latitude (Bergmann's and Lack's rules, respectively). Despite considerable research into these variation patterns and their consequences for biodiversity and conservation, the processes behind trait variation remain controversial.

Pandemic modelling for regions implementing an elimination strategy.

During the COVID-19 pandemic, some countries, such as Australia, China, Iceland, New Zealand, Thailand, and Vietnam successfully implemented an elimination strategy, enacting strict border control and periods of lockdowns to end community transmission. Atlantic Canada and Canada's territories implemented similar policies, and reported long periods with no community cases. In Newfoundland and Labrador (NL), Nova Scotia, and Prince Edward Island a median of 80% or more of daily reported cases were travel-related from July 1, 2020 to May 31, 2021.

Parasite-induced shifts in host movement may explain the transient coexistence of high- and low-pathogenic disease strains.

Many parasites induce decreased host movement, known as lethargy, which can impact disease spread and the evolution of virulence. Mathematical models have investigated virulence evolution when parasites cause host death, but disease-induced decreased host movement has received relatively less attention. Here, we consider a model where, due to the within-host parasite replication rate, an infected host can become lethargic and shift from a moving to a resting state, where it can die.

Downsizing of COVID-19 contact tracing in highly immune populations.

Contact tracing is a key component of successful management of COVID-19. Contacts of infected individuals are asked to quarantine, which can significantly slow down (or prevent) community spread. Contact tracing is particularly effective when infections are detected quickly, when contacts are traced with high probability, when the initial number of cases is low, and when social distancing and border restrictions are in place.

Modelling the impact of travel restrictions on COVID-19 cases in Newfoundland and Labrador.

In many jurisdictions, public health authorities have implemented travel restrictions to reduce coronavirus disease 2019 (COVID-19) spread. Policies that restrict travel within countries have been implemented, but the impact of these restrictions is not well known. On 4 May 2020, Newfoundland and Labrador (NL) implemented travel restrictions such that non-residents required exemptions to enter the province.

Skewed temperature dependence affects range and abundance in a warming world.

Population growth metrics such as R are usually asymmetric functions of temperature, with cold-skewed curves arising when the positive effects of a temperature increase outweigh the negative effects, and warm-skewed curves arising in the opposite case. Classically, cold-skewed curves are interpreted as more beneficial to a species under climate warming, because cold-skewness implies increased population growth over a larger proportion of the species's fundamental thermal niche than warm-skewness. However, inference based on the shape of the fitness curve alone, and without considering the synergistic effects of net reproduction, density and dispersal, may yield an incomplete understanding of climate change impacts.

Regional climate affects salmon lice dynamics, stage structure and management.

Regional variation in climate can generate differences in population dynamics and stage structure. Where regional differences exist, the best approach to pest management may be region-specific. Salmon lice are a stage-structured marine copepod that parasitizes salmonids at aquaculture sites worldwide, and have fecundity, development and mortality rates that depend on temperature and salinity.

Host allometry influences the evolution of parasite host-generalism: theory and meta-analysis.

Parasites vary widely in the diversity of hosts they infect: some parasite species are specialists-infecting just a single host species, while others are generalists, capable of infecting many. Understanding the factors that drive parasite host-generalism is of basic biological interest, but also directly relevant to predicting disease emergence in new host species, identifying parasites that are likely to have unidentified additional hosts, and assessing transmission risk. Here, we use mathematical models to investigate how variation in host body size and environmental temperature affect the evolution of parasite host-generalism.

Mechanistic movement models to understand epidemic spread.

An overlooked aspect of disease ecology is considering how and why animals come into contact with one and other resulting in disease transmission. Mathematical models of disease spread frequently assume mass-action transmission, justified by stating that susceptible and infectious hosts mix readily, and foregoing any detailed description of host movement. Numerous recent studies have recorded, analysed and modelled animal movement.

Benefits and unintended consequences of antimicrobial de-escalation: Implications for stewardship programs.

Sequential antimicrobial de-escalation aims to minimize resistance to high-value broad-spectrum empiric antimicrobials by switching to alternative drugs when testing confirms susceptibility. Though widely practiced, the effects de-escalation are not well understood. Definitions of interventions and outcomes differ among studies.

How to measure the impacts of antibiotic resistance and antibiotic development on empiric therapy: new composite indices.

Objectives: We aimed to construct widely useable summary measures of the net impact of antibiotic resistance on empiric therapy. Summary measures are needed to communicate the importance of resistance, plan and evaluate interventions, and direct policy and investment.

Design, Setting And Participants: As an example, we retrospectively summarised the 2011 cumulative antibiogram from a Toronto academic intensive care unit.

A model for sea lice (Lepeophtheirus salmonis) dynamics in a seasonally changing environment.

Sea lice (Lepeophtheirus salmonis) are a significant source of monetary losses on salmon farms. Sea lice exhibit temperature-dependent development rates and salinity-dependent mortality, but to date no deterministic models have incorporated these seasonally varying factors. To understand how environmental variation and life history characteristics affect sea lice abundance, we derive a delay differential equation model and parameterize the model with environmental data from British Columbia and southern Newfoundland.

Determinants of the Final Size and Case Rate of Nosocomial Outbreaks.

Different nosocomial pathogen species have varying infectivity and durations of infectiousness, while the transmission route determines the contact rate between pathogens and susceptible patients. To determine if the pathogen species and transmission route affects the size and spread of outbreaks, we perform a meta-analysis that examines data from 933 outbreaks of hospital-acquired infection representing 14 pathogen species and 8 transmission routes. We find that the mean number of cases in an outbreak is best predicted by the pathogen species and the mean number of cases per day is best predicted by the species-transmission route combination.

Immune evasion and the evolution of molecular mimicry in parasites.

Parasites that are molecular mimics express proteins which resemble host proteins. This resemblance facilitates immune evasion because the immune molecules with the specificity to react with the parasite also cross-react with the host's own proteins, and these lymphocytes are rare. Given this advantage, why are not most parasites molecular mimics? Here we explore potential factors that can select against molecular mimicry in parasites and thereby limit its occurrence.

Mechanistic models for the spatial spread of species under climate change.

Global climate change is a major threat to biodiversity. The most common methods for predicting the response of biodiversity to changing climate do not explicitly incorporate fundamental evolutionary and ecological processes that determine species responses to changing climate, such as reproduction, dispersal, and adaptation. We provide an overview of an emerging mechanistic spatial theory of species range shifts under climate change.

Linking antimicrobial prescribing to antimicrobial resistance in the ICU: before and after an antimicrobial stewardship program.

Antimicrobials are an effective treatment for many types of infections, but their overuse promotes the spread of resistant microorganisms that defy conventional treatments and complicate patient care. In 2009, an antimicrobial stewardship program was implemented at Mount Sinai Hospital (MSH, Toronto, Canada). Components of this program were to alter the fraction of patients prescribed antimicrobials, to shorten the average duration of treatment, and to alter the types of antimicrobials prescribed.

Next-generation tools for evolutionary invasion analyses.

Evolutionary invasion analysis is a powerful technique for modelling in evolutionary biology. The general approach is to derive an expression for the growth rate of a mutant allele encoding some novel phenotype, and then to use this expression to predict long-term evolutionary outcomes. Mathematically, such 'invasion fitness' expressions are most often derived using standard linear stability analyses from dynamical systems theory.

GPS measurement error gives rise to spurious 180 degree turning angles and strong directional biases in animal movement data.

Background: Movement data are frequently collected using Global Positioning System (GPS) receivers, but recorded GPS locations are subject to errors. While past studies have suggested methods to improve location accuracy, mechanistic movement models utilize distributions of turning angles and directional biases and these data present a new challenge in recognizing and reducing the effect of measurement error.

Methods: I collected locations from a stationary GPS collar, analyzed a probabilistic model and used Monte Carlo simulations to understand how measurement error affects measured turning angles and directional biases.

A spatially explicit model for an Allee effect: why wolves recolonize so slowly in Greater Yellowstone.

A reduced probability of finding mates at low densities is a frequently hypothesized mechanism for a component Allee effect. At low densities dispersers are less likely to find mates and establish new breeding units. However, many mathematical models for an Allee effect do not make a distinction between breeding group establishment and subsequent population growth.