Text S1: Supporting Information for The Timing and Targeting of Treatment in In- fluenza Pandemics Influences the Emergence of Resistance in Structured Populations

ODE Model Equations Our deterministic SIR model extends a framework presented by Lipsitch et al. (2008) [1]. We have five classes of individuals: susceptible (S), infectious and untreated (Iu), infectious and treated (It), infectious with a resistant strain (Ir) or recovered (R). Let γu, γt and γr be the recovery rate for untreated, treated and resistant infections, respectively and let c be the probability of a sensitive infection evolving de novo resistance to treatment. Let βu, βt, and βr be the transmission parameters for untreated sensitive, treated sensitive, and resistant virus respectively. As in [1], treatment reduces the infectiousness but not the duration of infection. Let ρ be the fraction of drug-sensitive infections that receive treatment. The governing differential equations are then: