The dynamics of the spread of epidemics, such as the recent outbreak of the SARS-CoV-2 virus, is highly nonlinear and therefore difficult to predict. As time evolves in the present pandemic, it appears more and more clearly that a clustered dynamics is a key element of the description. This means that the disease rapidly evolves within spatially localized networks, that diffuse and eventually create new clusters. We improve upon the simplest possible compartmental model, the SIR model, by adding an additional compartment associated with the clustered individuals.