Probability of a major infection in a stochastic within-host model with multiple stages

Establishment or spread of a viral infection within healthy individuals depends on exposure to a viral source, either through virus particles or through cells that have been infected. We assume that a potential infection has reached the site of the healthy target cells and we apply stochastic within-host models and multitype branching processes to investigate whether a major infection becomes established. The model includes multiple latent and actively infected stages. It is shown that the probability of a major infection is generally more likely after the virus has entered the target cell and the cell is actively infected. In some cases, the probability of a major infection is less likely if the burst size of actively infected cells is small.