Gaussian process approximations for fast inference from infectious disease data

Estimating intervention effects on infectious disease control: The effect of community mobility reduction on Coronavirus spread

Understanding the effects of interventions, such as restrictions on community and large group gatherings, is critical to controlling the spread of COVID-19. Susceptible-Infectious-Recovered (SIR) models are traditionally used to forecast the infection rates but do not provide insights into the causal effects of interventions. We propose a spatiotemporal model that estimates the causal effect of changes in community mobility (intervention) on infection rates. Using an approximation to the SIR model and incorporating spatiotemporal dependence, the proposed model estimates a direct and indirect (spillover) effect of intervention. Under an interference and treatment ignorability assumption, this model is able to estimate causal intervention effects, and additionally allows for spatial interference between locations. Reductions in community mobility were measured by cell phone movement data. The results suggest that the reductions in mobility decrease Coronavirus cases 4 to 7 weeks after the intervention.

Efficient Bayesian inference of fully stochastic epidemiological models with applications to COVID-19

Epidemiological forecasts are beset by uncertainties about the underlying epidemiological processes, and the surveillance process through which data are acquired. We present a Bayesian inference methodology that quantifies these uncertainties, for epidemics that are modelled by (possibly) non-stationary, continuous-time, Markov population processes. The efficiency of the method derives from a functional central limit theorem approximation of the likelihood, valid for large populations. We demonstrate the methodology by analysing the early stages of the COVID-19 pandemic in the UK, based on age-structured data for the number of deaths. This includes maximum a posteriori estimates, Markov chain Monte Carlo sampling of the posterior, computation of the model evidence, and the determination of parameter sensitivities via the Fisher information matrix. Our methodology is implemented in PyRoss, an open-source platform for analysis of epidemiological compartment models.

An interactive tool to forecast US hospital needs in the coronavirus 2019 pandemic

OBJECTIVE

We developed an application (https://rush-covid19.herokuapp.com/) to aid US hospitals in planning their response to the ongoing Coronavirus Disease 2019 (COVID-19) pandemic.

MATERIALS AND METHODS

Our application forecasts hospital visits, admits, discharges, and needs for hospital beds, ventilators, and personal protective equipment by coupling COVID-19 predictions to models of time lags, patient carry-over, and length-of-stay. Users can choose from 7 COVID-19 models, customize 23 parameters, examine trends in testing and hospitalization, and download forecast data.

RESULTS

Our application accurately predicts the spread of COVID-19 across states and territories. Its hospital-level forecasts are in continuous use by our home institution and others.

DISCUSSION

Our application is versatile, easy-to-use, and can help hospitals plan their response to the changing dynamics of COVID-19, while providing a platform for deeper study.

CONCLUSION

Empowering healthcare responses to COVID-19 is as crucial as understanding the epidemiology of the disease. Our application will continue to evolve to meet this need.