Using artificial intelligence tools to automate data extraction for living evidence syntheses.

Living evidence synthesis (LES) involves repeatedly updating a systematic review or meta-analysis at regular intervals to incorporate new evidence into the summary results. It requires a considerable amount of human time investment in the article search, collection, and data extraction phases. Tools exist to automate the retrieval of relevant journal articles, but pulling data out of those articles is currently still a manual process.

Uncertainty in COVID-19 transmission could undermine our ability to predict long COVID.

As SARS-CoV-2 has transitioned from a novel pandemic-causing pathogen into an established seasonal respiratory virus, focus has shifted to post-acute sequelae of COVID-19 (PASC, colloquially 'long COVID'). We use compartmental mathematical models simulating emergence of new variants to help identify key sources of uncertainty in PASC trajectories. Some parameters (such as the duration and equilibrium prevalence of infection, as well as the fraction of infections that develop PASC) matter more than others (such as the duration of immunity and secondary vaccine efficacy against PASC).

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.

Fitting Epidemic Models to Data: A Tutorial in Memory of Fred Brauer.

Fred Brauer was an eminent mathematician who studied dynamical systems, especially differential equations. He made many contributions to mathematical epidemiology, a field that is strongly connected to data, but he always chose to avoid data analysis. Nevertheless, he recognized that fitting models to data is usually necessary when attempting to apply infectious disease transmission models to real public health problems.

The probability of epidemic burnout in the stochastic SIR model with vital dynamics.

We present an approach to computing the probability of epidemic "burnout," i.e., the probability that a newly emergent pathogen will go extinct after a major epidemic.

Modelling the impacts of male alternative reproductive tactics on population dynamics.

Observations of male alternative reproductive tactics (ARTs) in a variety of species have stimulated the development of mathematical models that can account for the evolution and stable coexistence of multiple male phenotypes. However, little attention has been given to the population dynamic consequences of ARTs. We present a population model that takes account of the existence of two male ARTs (guarders and sneakers), assuming that tactic frequencies are environmentally determined and tactic reproductive success depends on the densities of both types.

Protocol for a living evidence synthesis on variants of concern and COVID-19 vaccine effectiveness.

Background: It is evident that COVID-19 will remain a public health concern in the coming years, largely driven by variants of concern (VOC). It is critical to continuously monitor vaccine effectiveness as new variants emerge and new vaccines and/or boosters are developed. Systematic surveillance of the scientific evidence base is necessary to inform public health action and identify key uncertainties.

Testing and Isolation Efficacy: Insights from a Simple Epidemic Model.

Testing individuals for pathogens can affect the spread of epidemics. Understanding how individual-level processes of sampling and reporting test results can affect community- or population-level spread is a dynamical modeling question. The effect of testing processes on epidemic dynamics depends on factors underlying implementation, particularly testing intensity and on whom testing is focused.

Face masking and COVID-19: potential effects of variolation on transmission dynamics.

Face masks do not completely prevent transmission of respiratory infections, but masked individuals are likely to inhale fewer infectious particles. If smaller infectious doses tend to yield milder infections, yet ultimately induce similar levels of immunity, then masking could reduce the prevalence of severe disease even if the total number of infections is unaffected. It has been suggested that this effect of masking is analogous to the pre-vaccination practice of variolation for smallpox, whereby susceptible individuals were intentionally infected with small doses of live virus (and often acquired immunity without severe disease).

From science to politics: COVID-19 information fatigue on YouTube.

Objective: The COVID-19 pandemic is the first pandemic where social media platforms relayed information on a large scale, enabling an "infodemic" of conflicting information which undermined the global response to the pandemic. Understanding how the information circulated and evolved on social media platforms is essential for planning future public health campaigns. This study investigated what types of themes about COVID-19 were most viewed on YouTube during the first 8 months of the pandemic, and how COVID-19 themes progressed over this period.

Modelling song popularity as a contagious process.

Popular songs are often said to be 'contagious', 'infectious' or 'viral'. We find that download count time series for many popular songs resemble infectious disease epidemic curves. This paper suggests infectious disease transmission models could help clarify mechanisms that contribute to the 'spread' of song preferences and how these mechanisms underlie song popularity.

Adjuvanted trivalent influenza vaccine versus quadrivalent inactivated influenza vaccine in Hutterite Children: A randomized clinical trial.

Background: Children play an important role in the transmission of influenza. The best choice of vaccine to achieve both direct and indirect protection is uncertain. The objective of the study was to test whether vaccinating children with MF59 adjuvanted trivalent influenza vaccine (aTIV) can reduce influenza in children and their extended households compared to inactivated quadrivalent vaccine (QIV).

On inferring evolutionary stability in finite populations using infinite population models.

Models of evolution by natural selection often make the simplifying assumption that populations are infinitely large. In this infinite population limit, rare mutations that are selected against always go extinct, whereas in finite populations they can persist and even reach fixation. Nevertheless, for mutations of arbitrarily small phenotypic effect, it is widely believed that in sufficiently large populations, if selection opposes the invasion of rare mutants, then it also opposes their fixation.

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic.

One year into the global COVID-19 pandemic, the focus of attention has shifted to the emergence and spread of SARS-CoV-2 variants of concern (VOCs). After nearly a year of the pandemic with little evolutionary change affecting human health, several variants have now been shown to have substantial detrimental effects on transmission and severity of the virus. Public health officials, medical practitioners, scientists, and the broader community have since been scrambling to understand what these variants mean for diagnosis, treatment, and the control of the pandemic through nonpharmaceutical interventions and vaccines.

Transient disease dynamics across ecological scales.

Unlabelled: Analyses of transient dynamics are critical to understanding infectious disease transmission and persistence. Identifying and predicting transients across scales, from within-host to community-level patterns, plays an important role in combating ongoing epidemics and mitigating the risk of future outbreaks. Moreover, greater emphases on non-asymptotic processes will enable timely evaluations of wildlife and human diseases and lead to improved surveillance efforts, preventive responses, and intervention strategies.

Age-dependence of healthcare interventions for COVID-19 in Ontario, Canada.

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.

Forward-looking serial intervals correctly link epidemic growth to reproduction numbers.

The reproduction number R and the growth rate r are critical epidemiological quantities. They are linked by generation intervals, the time between infection and onward transmission. Because generation intervals are difficult to observe, epidemiologists often substitute serial intervals, the time between symptom onset in successive links in a transmission chain.

Patterns of smallpox mortality in London, England, over three centuries.

Smallpox is unique among infectious diseases in the degree to which it devastated human populations, its long history of control interventions, and the fact that it has been successfully eradicated. Mortality from smallpox in London, England was carefully documented, weekly, for nearly 300 years, providing a rare and valuable source for the study of ecology and evolution of infectious disease. We describe and analyze smallpox mortality in London from 1664 to 1930.

Estimating epidemic coupling between populations from the time to invasion.

Identifying the mechanisms by which diseases spread among populations is important for understanding and forecasting patterns of epidemics and pandemics. Estimating transmission coupling among populations is challenging because transmission events are difficult to observe in practice, and connectivity among populations is often obscured by local disease dynamics. We consider the common situation in which an epidemic is seeded in one population and later spreads to a second population.

Acceleration of plague outbreaks in the second pandemic.

Historical records reveal the temporal patterns of a sequence of plague epidemics in London, United Kingdom, from the 14th to 17th centuries. Analysis of these records shows that later epidemics spread significantly faster ("accelerated"). Between the Black Death of 1348 and the later epidemics that culminated with the Great Plague of 1665, we estimate that the epidemic growth rate increased fourfold.

Fast estimation of time-varying infectious disease transmission rates.

Compartmental epidemic models have been used extensively to study the historical spread of infectious diseases and to inform strategies for future control. A critical parameter of any such model is the transmission rate. Temporal variation in the transmission rate has a profound influence on disease spread.

Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak.

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.