Chemical Organization Theory (COT) has been successfully applied to analyze complex reaction networks where species interact and new species can emerge. The COT has been studied in detail yet to analyze high dimensional systems dynamics with respect to time that is equivalent to Ordinary Differential Equations (ODEs). Spatial effects such as diffusion and boundary conditions have been considered not yet. This study sheds light on the importance of extending COT to be able to analyze Reaction-diffusion systems (RDS) by first retracing the earlier application of COT to an ODE model of HIV dynamics. Then a reaction-diffusion model of HIV dynamics will be analyzed by extending COT to spatial aspects.