In the EMOD STI model, disease transmission can occur via two routes: sexual transmission or vertical transmission (e.g. mother-to-child). The probability of transmission is calculated for each discordant coital act and each childbirth.
Unlike the relationship parameters (see Relationships and contact networks), parameters that govern transmission are found in the configuration file (see Configuration parameters for a complete list of configuration parameters). Parameters used to interrupt transmission will be found in the campaign file (see Campaign parameters for a complete list of campaign events and their parameters).
Sexual transmission occurs between disease-discordant individuals that are paired in a relationship. Transmission occurs via coital acts, so the probability of transmission will vary by relationship type (see Relationships and contact networks for information on relationship type, formation, and coital frequencies). In addition, there are numerous configurable factors that can influence the transmission rate.
Base infectivity and its multipliers¶
Sexual transmission is configured through a base rate of infectivity, which is the transmission rate per total coital acts. See Infectivity and transmission parameters for more information. This base rate can be modified through various multipliers and scalars, such that transmission rates can vary by:
Age and gender. The rate of male-to-female heterosexual transmission can be configured to be different than the rate of female-to-male heterosexual transmission. This gender bias in transmission can also be varied according to the age of the female partner. Both the gender and age multipliers on transmission are configured through a pair of matched arrays in the config.json file (Male_to_Female_Relative_Infectivity_Ages and Male_to_Female_Relative_Infectivity_Multipliers). Note that the lengths of both arrays must be equal, so each multiplier has a corresponding age. To remove age dependence, put just one value in each array. When multiple values are provided, the multiplier on the probability of transmission is linearly interpolated between the specified ages. Ages do not have to be integer values, and ages younger than the youngest specified age are assigned the value for the youngest specified age. Likewise, ages older than the oldest specified age are assigned the value for the oldest specified age.
Individuals. The transmission rate can also be configured to be heterogeneous among individuals, with a multiplier on infectiousness sampled from a log normal scale. The multiplier is assigned to each individual at birth, and will be applied to every infection in that individual’s lifetime.
STI co-infection. While the EMOD STI model does not support simultaneous transmission of more than one sexually transmitted infection, it does support the inclusion of non-transmitting co-infections that increase infectiousness and susceptibility for the transmission of the primary disease being modeled. Co-infection multipliers are set in the configuration file, while seeding or clearing co-infections is accomplished by using campaign interventions.
Condom usage. Unlike the above multipliers, condom usage configures a blocking effect on transmission, such that the parameter represents the proportion of reduction in transmission. Each relationship type can have an independent probability of condom usage, which changes over time (recall that relationship types are configured in the demographics file; see Relationships and contact networks for more information). The transmission blocking properties of condoms are then set in the config.json file. This blocking probability will be applied to condom use across all relationship types. Finally, it should be noted that condoms may also be distributed through a campaign intervention. For more information, see STIBarrier.
Note that in addition to configuration parameters, there are campaign interventions that will also impact the transmission rate. For example, voluntary male medical circumcision, the use of vaccines, and the use of treatments, can be distributed to individuals to lower the transmission rate. For more information, see Individual-level interventions.
The EMOD STI model supports vertical transmission of STIs via mother-to-child transmission (MTCT). The model links the STI status of specific mothers with exposure to specific children, and does this through the simulation of individual pregnancies. While overall fertility rates and birth rates are configured in the demographics file, the transmission parameters governing MTCT are configured in the configuration file.
To implement MTCT, maternal transmission must be enabled. This will allow infectious mothers to transmit to their children. Additionally, there are parameters that can modify the transmission probability. Finally, in order to simulate individual pregnancies, the Birth_Rate_Dependence parameter must be set to INDIVIDUAL_PREGNANCIES_BY_AGE_AND_YEAR. For more information on these parameters, see Population dynamics.