The transitions and their corresponding rates in the Markov chain part of the within-host model in Fig 1.

The symbol represents an indicator function, which is equal to 1 if A is true, and 0 otherwise. Variables not directly involved in the corresponding reaction are not shown in the transition, since they remain constant during the event. The continuous variables for the amounts of PA (units ng) in the lymph nodes and blood compartments do not undergo discrete transitions in the same way as the other variables listed here but instead follow the ODEs in Eq (4).