The primary goal is to model how prior T-cell immunity (from infections and vaccinations) affects the dynamics of infection and transmission following exposure to drifted and shifted influenza strains using a multi-scale modeling approach. Animal and human studies showed that T cells can provide strain-transcending protection, resulting in more rapid viral clearance, decreased immunopathology, and improved clinical outcomes, and thus the improvement of strategies to induce protective levels of influenza-specific T cells are of critical importance. We estimate waning of T cell immunity in a mouse model, and how it affects the protection to new strains of influenza. We also explore how the antigenic distance from prior immunity for the live-attenuated influenza vaccine affects generation of optimal protective immunity. Mice studies will inform how to better interpret the limited information about immunity waning available in human studies. Using multi-scale modeling approach we explore how waning of immunity affects the influenza epidemic size and severity. The knowledge gained form this study will help guide future vaccination efforts against influenza viruses to better generate broadly protective T cell immunity within individuals and across the population.