Here we urge the adoption of a new paradigm for the design and interpretation of intervention trials in infectious diseases, particularly in emerging infectious disease, that more accurately reflects the dynamics of the transmission process. Interventions in infectious diseases can have indirect effects on those not receiving the intervention as well as direct effects on those receiving the intervention. Combinations of interventions can have complex interactions at the population level. These often cannot be adequately addressed with standard study designs and analytic methods. Simulations can help to accurately represent transmission dynamics in an increasingly complex world which is critical for proper trial design and interpretation. Some ethical aspects of a trial can also be quantified using simulations. After a trial has been conducted, simulations can be used to explore possible explanations for the observed effects. A great deal is to be gained through a multidisciplinary approach that builds collaborations among experts in infectious disease dynamics, epidemiology, statistical science, economics, simulation methods and the conduct of clinical trials.Keywords: clinical trial design, infectious diseases, simulations, vaccine Designing intervention trials in infectious diseases poses many challenges. First, in many infectious diseases, interventions can have indirect effects on individuals not receiving the intervention as well as on those receiving the intervention. Such indirect effects, sometimes called spillover effects, may affect estimation of the direct effects and are also of public health significance themselves. Second, because transmission is a nonlinear and stochastic process, outcomes in different arms of an intervention trial may be more variable than expected in a population where each individual's outcome is statistically independent of those of other individuals. Third, heterogeneity from different sources, such as host susceptibility, pathogen variability, and exposure heterogeneity, can complicate study design. Fourth, the effects of a combination of interventions in a trial, such as vaccination and behavioral intervention, may be difficult to predict at the design phase.Other factors, including logistical complexities and ethical considerations can add to these challenges. After a trial has been conducted, interpreting unexpected trial results can be difficult.Recently, investigators have used computer simulation to assist in the design, analysis and interpretation of randomized trials of infectious disease prevention measures to address these challenges. Here we describe these challenges in more detail and illustrate ways in which simulation can help to conduct better trials and to improve understanding of trial results. We conclude by advocating that for many infectious disease prevention trials, simulating the trial with the underlying transmission dynamics is an efficient way to . CC-BY-ND 4.0 International license peer-reviewed) is the author/funder. It is made available u...