A heating, ventilation, or air conditioning (HVAC) system for one or more building zones includes airside HVAC equipment operable to provide clean air to the one or more building zones and a controller. The controller is configured to obtain a dynamic temperature model and a dynamic infectious quanta model for the one or more building zones, determine an infection probability, and generate control decisions for the airside HVAC equipment using the dynamic temperature model, the dynamic infectious quanta model, and the infection probability.