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Joshua Looker

Publications and source records attributed to Joshua Looker.

2 recordsLinked to original sources

Early warning signals of non-critical transitions from linearised time-varying dynamics with applications to epidemic systems

In the wake of the SARS-CoV-2 pandemic, there has been heightened interest from applied mathematicians in infectious disease modelling. Modelling efforts often focus on predicting whether diseases are likely to be eliminated or, instead, (re-)emerge, especially as a result of control measures.This tipping point between elimination and infection waves has been successfully anticipated in the literature through the use of early warning signals and such signals often rely on the theory of critical slowing down. Recent developments have shown that these signals (increases in fluctuation variance and return time) can emerge from the system geometry in the case of non-normal dynamics rather than a change in asymptotic stability. We show how such dynamical behaviour occurs in the fluctuations from the mean-field in general stochastic systems. Using the susceptible-infectious-recovered model as an example application, we analyse how critical-like behaviour can be exploited to anticipate infection waves in the absence of an equilibrium bifurcation.

q-bio.PE

Modelling Immunity in Agent-based Models

Vaccination policies play a central role in public health interventions and models are often used to assess the effectiveness of these policies. Many vaccines are leaky, in which case the observed vaccine effectiveness depends on the force of infection. Within models, the immunity parameters required for agent-based models to achieve observed vaccine effectiveness values are further influenced by model features such as its transmission algorithm, contact network structure, and approach to simulating vaccination. We present a method for determining parameters in agent-based models such that a set of target immunity values is achieved. We construct a dataset of desired population-level immunity values against various disease outcomes considering both vaccination and prior infection from COVID-19. This dataset incorporates immunological data, data collection methodologies, immunity models, and biological insights. We then describe how we choose minimal parameters for continuous waning immunity curves that result in those target values being realized in simulations. We use simulations of the household secondary attack rates to establish a relationship between the protection per infection attempt and overall immunity, thus accounting for the dependence of protection from acquisition on model features and the force of infection.

q-bio.PE