The paper presents a model of virus mutations and evolution of epidemics in a system of interacting individuals, where the intensity of the pathology, described by a real discrete positive variable, is heterogeneously distributed, and the virus is in competition with the immune system or therapeutical actions. The model is developed within the framework of the Kinetic Theory of Active Particles. The paper also presents a qualitative analysis developed to study the well-posedness of the mathematical problem associated to the general framework. Finally, simulations show the ability of the model to predict some interesting emerging phenomena, such as the mutation to a subsequent virus stage, the heterogeneous evolution of the pathology with the co-presence of individual carriers of the virus at different levels of progression, and the presence of oscillating time phases with either virus prevalence or immune system control.