Figure 3.

Distinct coevolutionary outcomes and patterns emerge at different combinations of initial antigen diversity and epitope conservation

(A) Phase diagram of three coevolution outcomes: Viral clearance (magenta), rebound (grey), and persistence (blue). At high initial Ag diversity (large σ_A), both clearance and rebound could happen in repeated simulations (each hybrid symbol indicating the proportion of occurrence among 100 runs).

(B and C) Population trajectories of Ags (B) and plasma cell (C) in three phases, shown with mean ± SD (shade) from 10 simulations in each case. Here and after, we measure time in units of GCR cycles; one GCR cycle corresponds to 6 to 12 hr in real time.

(D–I) Representative population trajectories and shape-space configurations of Ags (red) and plasma cell (blue) in each phase.

(D, G) Persistence; n_c=2, σ_A=0.5. (E, H) Rebound; n_c=3, σ_A=2. (F, I) Clearance; n_c=3, σ_A=1. Snapshots in a binding subspace of n_b=3 dimensions are taken at time points marked by black dots in (D–F). (G) and (H) illustrate Ag escape in a variable subspace; (I) demonstrates Ag clearance by bnAbs in a conserved subspace. For visual clarity, a random subset of 5% of plasma cell and 25% of Ags are shown. Shape-space coordinates are scaled by the radius R_f of the B cell founder hypersphere; black circles delineate the cross-sections of founder sphere with three orthogonal planes intersecting at the origin.