We use an activity-based transport model to simulate the progression of a virus at the regional scale. We analyse several scenarios corresponding to distinct situations and describing how small initial clusters of infected agents expand and reach a pandemic level. We evaluate the effectiveness of some public restrictions and compare the number of infections with respect to the base-case scenario, where no restrictions are in place. We consider the wearing of masks in public transport and/or in some activities (work, leisure and shopping) and the implementation of a lockdown. Our analysis shows that education, including the primary level, is one of the major activities where infections occur. We find that the wearing of masks in transportation only does not yield important impacts. The lockdown is efficient in containing the spread of the virus but, at the same time, significantly increases the length of the wave (factor of two). This is because the number of agents who are susceptible to be infected remains high. Our analysis uses the murdasp tool specifically designed to process the output of transport models and performs the simulation of the pandemic.