Geospatial model of COVID-19 spreading and vaccination with event Gillespie algorithm

We have developed a mathematical model and stochastic numerical simulation for the transmission of COVID-19 and other similar infectious diseases that accounts for the geographic distribution of population density, detailed down to the level of location of individuals, and age-structured contact rates. Our analytical framework includes a surrogate model optimization process to rapidly fit the parameters of the model to the observed epidemic curves for cases, hospitalizations, and deaths. This toolkit (the model, the simulation code, and the optimizer) is a useful tool for policy makers and epidemic response teams, who can use it to forecast epidemic development scenarios in local settings (at the scale of cities to large countries) and design optimal response strategies. The simulation code also enables spatial visualization, where detailed views of epidemic scenarios are displayed directly on maps of population density. The model and simulation also include the vaccination process, which can be tailored to different levels of efficiency and efficacy of different vaccines. We used the developed framework to generate predictions for the spread of COVID-19 in the canton of Geneva, Switzerland, and validated them by comparing the calculated number of cases and recoveries with data from local seroprevalence studies.