Transmission of typhoid occurs via two routes in EMOD: contact and environmental. The contact route is the fundamental method of transmission from the GENERIC_SIM, and represents person-to- person transmission. The environmental route is a secondary pathway inherited from the ENVIRONMENTAL_SIM, and represents environmental contagions, such as sewage, waterways, etc.). Each route functions independently, such that individuals in the model can be exposed to contagion via each route (and each route can have different levels of contagions). Further, within each route, contagion levels can be independently attenuated or amplified.
Infectious individuals (e.g. those in the prepatent, subclinical, and chronic stages of typhoid) shed contagion into both the contact and environmental routes at the same rate. Rates of shedding vary by disease stage using stage-specific configuration parameters (see Configuration parameters for more information).
The amount of contagion in the overall contagion pool decays, and the decay rate is route-specific. Contagion in the contact route is 100% per timestep (1 day in the typhoid model), while the environmental route decays exponentially over each timestep, and is defined by the configuration parameter Node_Contagion_Decay_Rate.
Within a timestep, individuals are independently exposed through both the environment and contact transmission routes. The probability of infection is determined by a poisson draw with rate parameters determined through the configuration parameters Typhoid_Contact_Exposure_Rate and Typhoid_Environmental_Exposure_Rate. It is important to note that the exposures aren’t completely independent: since exposure occurs through one route before the other each time, if the first has a high contagion population (or rate), exposure will skew to that transmission route. Superinfection does not occur: once an individual becomes infected, they do not get an additional infection via the other route.