Self-inhibiting percolation and viral spreading in epithelial tissue
- Niels Bohr Institute, University of Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Denmark
- PandemiX Center, Department of Science and Environment, Roskilde University, Denmark
- High Meadows Environmental Institute, Princeton University, United States
Figures
Figure 1 with 2 supplements
Cell states during SARS-CoV-2 infection in human tracheal/bronchial epithelial cells.
(a) 6162 cells (Fiege et al., 2021) covering samples of mock-infected (0 h), 24 hpi (hours post-infection), and 48 hpi visualized with UMAP. (b) Average expression of representative viral genes, …
Figure 1—figure supplement 1
Expression of antiviral genes at different stages of early SARS-CoV-2 infection.
Once the infection has proceeded for 2 days, cells in the state express all the antiviral genes highly. The typical state can be identified from the 0 hr panels where some cells express low to …
Figure 1—figure supplement 2
Detected viral genes and expression of IFNs at different stages of early SARS-CoV-2 infection.
Once the infection has proceeded for 2 days, viral genes (cov.*) are detected at a high level in the cells. The IFN genes are mainly expressed in cells, amounting to 0.6% at 24hr and to 4.8% …
Figure 2 with 1 supplement
NOVAa model.
(a) The cell state transitions are included in the NOVAa model. The straight black arrows indicate transitions between cell states. The curved yellow arrows indicate the effects of IFNs on activating …
Figure 2—figure supplement 1
Stochastic conversion.
Average final-state cell fractions in a variant of the model with stochastic conversion, i.e. in which each conversion of a neighboring cell takes place with a probability . In this figure, . Note …
Figure 3 with 1 supplement
Cluster size distribution.
(a) The distribution of cluster sizes of infected cells () for different values of , simulated by starting with one infected cell in a 2D square lattice of linear extent . (b) The exponents …
Figure 3—figure supplement 1
Cell fractions within the different states over times, at a range of values (below the critical value ), for two interferon spreading radii, and .
Figure 4 with 2 supplements
Range of IFN.
(a) Typical cluster for an simulation at . (b) The dependence of with , approximately reproduced by a fit . For comparison, the OVA model as well as percolation has . In all cases, when …
Figure 4—figure supplement 1
We introduced the simplified OVA model, which does not include an N state, but rather gives each susceptible cell a probability of spontaneously converting to an antiviral state in each time step.
OVA Model: In each time step, updates are made. At each update, one of the sites is randomly selected. If this site is in the state, nothing happens. If the site is state then its …
Figure 4—figure supplement 2
Comparison of the Gaussian Model and the main NOVAa model at identical parameters.
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