A. Scheme of the infection and immunization processes. N_S: susceptible (non-infected) cells. N_E: infected cells in eclipse phase. N_P: virion-producing cells. N_D: cells killed by the virus. N_R: immunized cells (blue). W-infected cells: red. D-infected cells: green. An eclipse phase between viral sensing (N_ε) and IFN secretion (N_π) is also considered. The relative speed of infection and IFN production can vary. Hence, D-infected cells can be in four possible stages (N_Eε, N_Pε, N_Eπ, N_Pπ). k_v: virion infectivity (infection rate). k_R: IFN immunization rate. τ_EP: viral eclipse half time. τ_επ: half time between infection and IFN secretion. τ_PD: half time between virion production and cell death. Hence, τ_PD +τ_EP is the total duration of the infection cycle. r_v(W) and r_v(D): virion production rates for W and D, respectively. K = r_vτ_PD is thus the number of virions produced per infected cell. δ_V: virion degradation/outflow rate. r_β: IFN production rate of immunized cells. δ_β: IFN degradation/outflow rate. Values for each parameter are provided in Table 1. In this model, post-infection IFN effects are not allowed. S2 Fig shows a model with IFN-induced apoptosis. B. Fitness partition according to direct and indirect (neighborhood) components. For the W virus in a W neighborhood, f_W|W = 0. The term c is the direct fitness effect of being an IFN-suppressor (c > 0: IFN suppression is costly; c < 0: IFN suppression is beneficial). For a D virus in an W neighborhood, f_D|W = c. The term b is the indirect benefit of being in an IFN-suppressive (W) neighborhood, independent of direct effects. The derivation of the overall relative fitness of each variant (f_W and f_D) is shown in the text. r_W quantifies how strongly W viruses are influenced by neighbors of the same type, and analogously for r_D. The term r measures the spatial segregation between W and D in terms of infection and immunity. Three possible scenarios are shown (red: W-infected cells, green: D-infected, light blue: IFN-immunized cells). Left: full segregation (r = 1). Center: partial segregation (0 < r < 1). Right: complete mixing (r = 0).

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