Compensatory mutations during viral replication can result in the generation of escape mutants from immune recognition or in the emergence of transmissible drug resistant viruses. We discuss the interplay between host-immune responses and the evolution of drug resistance viral mutations in the context of influenza infection. We develop a basic modelling framework to illustrate the effects of timing in start of antiviral treatment and the efficacy of drugs in viral inhibition in the absence/presence of pre-existing immunity.