Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of interconnected temporal, organizational and spatial scales, which even within a single pathogen often span hours to months, cellular to ecosystem levels, and local to pandemic spread. Some pathogens are directly transmitted between individuals of a single species, while others circulate among multiple hosts, need arthropod vectors, or can survive in environmental reservoirs. Many factors, including increasing antimicrobial resistance, increased human connectivity, and dynamic human behavior, raise prevention and control from formerly national to international issues. In the face of this complexity, mathematical models offer essential tools for synthesizing information to understand epidemiological patterns, and for developing the quantitative evidence base for decision-making in global health.

Summary A wide variety of phenomena of geographical spread can be described in terms of a mechanism of “growth” (e.g. birth, infection) and a “contact distribution” which describes how the locations of the individual(s) involved in a migratory move, or infection at a distance, are spatially related. I shall survey work on such models, beginning with an examination of the relations between stochastic and deterministic models; it emerges that both linear and nonlinear deterministic models have close connections with the less interesting “linear” (exponential growth) stochastic models. More realistic models must be nonlinear as well as stochastic; some results are now available for such models. As in the linear case, these deal mainly with asymptotic behaviour. Simulations reveal that nonlinear stochastic processes have a richer spectrum of non‐asymptotic behaviour than linear models, though in some circumstances the simpler models may provide an adequate approximation. Thus theoretical study of the short‐term behaviour of such processes may be difficult, but should prove rewarding. The other main outstanding problems are those of inference for such models, especially the estimation of contact distributions.

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HighlightsSpatial models will become more important as geolocated data become the norm for infectious disease.Network models can be thought of as a unifying framework within which metapopulation models and individual-based models are contained.Work is needed on threshold parameters for spatial models, partly because they often do not produce exponential growth.Accurately predicting the impact of interventions requires models to be constructed with the appropriate resolution.

Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute ‘Models for an exit strategy’ workshop (11–15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.

The analysis of infectious disease data presents challenges arising from the dependence in the data and the fact that only part of the transmission process is observable. These dif®culties are usually overcome by making simplifying assumptions. The paper explores the use of Markov chain Monte Carlo (MCMC) methods for the analysis of infectious disease data, with the hope that they will permit analyses to be made under more realistic assumptions. Two important kinds of data sets are considered, containing temporal and non-temporal information, from outbreaks of measles and in¯uenza. Stochastic epidemic models are used to describe the processes that generate the data. MCMC methods are then employed to perform inference in a Bayesian context for the model parameters. The MCMC methods used include standard algorithms, such as the Metropolis±Hastings algorithm and the Gibbs sampler, as well as a new method that involves likelihood approximation. It is found that standard algorithms perform well in some situations but can exhibit serious convergence dif®culties in others. The inferences that we obtain are in broad agreement with estimates obtained by other methods where they are available. However, we can also provide inferences for parameters which have not been reported in previous analyses.