Figure 2.

Schematic of the epithelial grid, four cell states, and infectious virion fates. (A) A discretization of the cell simulation region described in Fig. 1, with cells classified as either uninfectable (white) or infectable by a SARS-CoV-2 virion. Infectable cells are in one of three states: uninfected (blue), infected and in eclipse phase (yellow), or infected and shedding (red). (B) Individual virions (labeled vj) are placed into a generation, either shed by an infected cell (v1, v2, and v3) or by deposition onto the air-mucus interface (v4 and v5). Virions diffuse, advect, and potentially encounter epithelial cells, until reaching their ultimate fate in the generation of deposition, including: 1) infect an already infected cell (v1 and v4); 2) infect an uninfected cell (v2); 3) exit the generation in the mucus escalator (v3); or 4) exit the generation in the PCL (v5). Virion v1 is shed from the infected cell at position (a), diffuses to an infected cell at position (b), where it encounters but does not re-infect the infected cell, then diffuses to an uninfected cell at position (c), where it encounters but does not infect the uninfected cell, before finally diffusing to an infected cell at position (d), with a successful infection event. Virion v2 is shed at (a), diffuses to the PCL-mucus interface at (e), where the predominant driver of motion is the advective mucosal flow, then re-enters the PCL at (f), where it diffuses until a successful infection event with the uninfected cell at (g). Virion v3 is shed into the PCL at (a) and diffuses throughout the PCL until reaching the PCL-mucus interface at (h), before being carried by the mucosal flow out of the generation at (i). Virion v4 is deposited at the air-mucus interface at position (j), where its motion is predominantly in the direction of the mucus flow, until it crosses into the PCL at (k), then diffuses until reaching the uninfectable cell at (l), where it is reflected back into PCL and diffuses until successfully infecting an already infected cell at position (m). Virion v5 is deposited at the air-mucus interface at position (n), where its motion is dominated by the advective flow in the mucus, until it crosses into the PCL at position (o), at which point it diffuses until exiting the generation at position (p).