In the last decades, new network theories and epidemiological evidences have substantially advanced our knowledge about how acute respiratory infections spread in the human population. Temporal and multi-layer networks provide a paradigmatic example. These frameworks allow for clearly describing the heterogeneous connectivity features driving transmission, e.g. different connectivity by settings (household, workplace, school, etc.), and occasional vs. recurrent encounters. However, intrinsic properties of individuals and pathogens, besides individuals’ connectivity are central in shaping the dynamics of transmission. For instance, individuals may be heterogeneous in their susceptibility and their probability to develop a severe form of infection. On the other hand, heterogeneous pathogens and pathogen strains alter the dynamics and burden of an epidemic and are among the drivers of pathogen emergence events. These levels of complexity mutually affect each other which makes it difficult to disentangle their relative role on the epidemic unfolding and the effect of interventions. During the talk I will tackle this issue, presenting recent theoretical and applied works. I will review some studies on the COVID-19 pandemic and discuss the implications of multi-strain/multi-pathogen interaction for the emergence of new pathogens and their co-existence.