Conceptual overview of the framework.

<p>Within-host models of infection dynamics in a spatially-structured respiratory tract composed of three linearly-connected compartments are used to estimate overall virus excretion (X) and pathogenicity (P). The parameters that differ per respiratory compartment (i) are the initial number of susceptible cells (S_0,i), the viral clearance rate (χ_i), and the distribution coefficients of immunoglobulins of type A (IgA) and IgG (c_ai and c_gi, respectively). The measures of virus excretion (X) and pathogenicity (P) in turn are used to estimate population-level transmission rate (β_h), mortality rate (α_h), and recovery rate (γ_h), which define the virus reproductive number (R). See Methods for more details.