Fig. 2. Synoptic medium-term immune landscapes and infection burden.

The immune and infection class colors are the same as in Fig. 1A. Each panel shows the following: (Top) Illustrative time series of the fraction of the population vaccinated with one or two doses [see (56)]. (Middle) The fraction of total and severe infections [see (57)]. (Bottom) Area plots of the fraction of the population that makes up each immune class (S_P, R, S_S, V₁, V₂, $S_{S_1}$, $S_{S_2}$) or infection class (I_P, I_S, I_V, $I_{S_1}$, $I_{S_2}$) from just before the introduction of vaccination until 5 years after onset of the pandemic. In all plots, the maximum rate of administration of the first vaccine dose is taken to be ν₀ = 2%, and the vaccine is introduced at t_vax = 48 weeks. We take ${ϵ}_{V_1}=0.1$ and ${ϵ}_{V_2}=0.05$, in keeping with data from clinical trials (3). The fraction of severe cases for primary infections, secondary infections, infection after vaccination, and infection after waned two-dose immunity are taken to be $x_{\mathrm{sev},p}=0.14$, $x_{\mathrm{sev},s}=0.07$, $x_{\mathrm{sev},V}=0.14$, and $x_{\mathrm{sev},2}=0$, respectively. The transmission rates and periods of NPI adoption are defined in the materials and methods. The leftmost column corresponds to a one-dose vaccine strategy (ω = 0), followed by interdose spacings of 24 weeks, 12 weeks, and 4 weeks (rightmost column). (A) An overall more pessimistic natural and vaccinal immunity scenario, with ϵ = ϵ₂ = 0.7 and 1/δ = 1/ρ₂ = 1 year. For a less effective one-dose vaccine (top section), we take ϵ₁ = 0.9 and 1/ρ₁ = 0.25 years, and the fraction of severe cases associated with infection after waned one-dose immunity is $x_{\mathrm{sev},1}=0.14$. For an effective one-dose vaccine (bottom section), we take ϵ₁ = 0.7 and 1/ρ₁ = 1 year, and the fraction of severe cases associated with infection after waned one-dose immunity is $x_{\mathrm{sev},1}=0$. (B) An overall more optimistic natural and vaccinal immunity scenario, with ϵ = ϵ₂ = 0.5 and 1/δ = 1/ρ₂ = 2 years. For a less effective one-dose vaccine (top section), we take ϵ₁ = 0.9 and 1/ρ₁ = 0.5 years, and the fraction of severe cases associated with infection after waned one-dose immunity is $x_{\mathrm{sev},1}=0.14$. For an effective one-dose vaccine (bottom section), we take ϵ₁ = 0.5 and 1/ρ₁ = 2 years, and the fraction of severe cases associated with infection after waned one-dose immunity is $x_{\mathrm{sev},1}=0$.