HIV model scenarios¶
The EMOD HIV model is explained in detail in HIV model overview. While the various components that comprise the model are explained with examples, it may be more useful to learn the model through hands-on implementation. The following sections will introduce sets of example files that illustrate how the HIV model works on particular topics. All files are available in the downloadable EMODScenarios folder and, in addition to the explanations below, each scenario will have a more detailed README file to cover relevant information. Within the EMODScenarios > Scenarios > HIV folder is an Excel worksheet titled “Weibull.xlsx,” which can be used to explore how Weibull parameters influence the shape of the distribution. Note that Weibull parameters are used often in the HIV model, so it will be useful to to understand the factors governing their shape.
Because all disease-specific EMOD simulation types are based on the generic model, the Generic model scenarios are helpful in learning the basics of modeling with EMOD, even if you intend to use one of the disease-specific simulation types.
For more information on the software architecture and inheritance, see Overview of EMOD software.
To use a contact network as the basis for disease transmission, the Simulation_Type should be set to STI_SIM. This simulation type does not include any HIV-specific biology, which will be included in later tutorials.
In the EMODScenarios > Scenarios > HIV > Relationship_networks folder, you will find sets of files to run simulations modeling contact networks. These simulations do not include disease outbreaks or subsequent transmission, but will demonstrate how to configure relationship networks beginning with eligibility for pair formation, preference for particular partner ages, relationship types and durations, concurrency in relationships, and coital frequency and dilution.
HIV parameters are added to the STI relationship networks when the Simulation_Type is set to HIV_SIM. Specifically, this adds transmission rates, mortality rates, and the evolution of biomarkers such as CD4 count specific to HIV-infected individuals. These factors impact the survival of HIV+ individuals according to their age, disease state, co-infection status, and use of antiretroviral therapy (ART) or other interventions.
In the EMODScenarios > Scenarios > HIV > HIVBiology folder you will find files to run an HIV simulation. In the README file, you will find instructions on how to configure baseline HIV transmission, how to change survival time for children and adults, how CD4 count and WHO stage progress, and how to configure heterogeneity in CD4 count.
HIV can be transmitted via two routes: sexually through a relationship network, or vertically by mother-to-child transmission. In EMOD, to initially seed a population with disease, you must use the campaign interventions Outbreak or OutbreakIndividual (see Outbreak or OutbreakIndividual for more information). These two campaign intervention classes work by “distributing” HIV to the configured population. After the initial seeding, transmission can occur via the sexual or vertical routes.
In the EMODScenarios > Scenarios > HIV > Transmission folder you will find files to run an HIV simulation. In the README file, you will find instructions on how to configure sexual transmission, vertical transmission, and how to initiate co-infections.
For detailed configuration instructions and example exercises to try, see the README in the Transmission folder.
Health care is critical for individuals with HIV. In EMOD, a system of health care can be created by using multiple interventions. Interventions can be linked to create a network of actions and results, where the outcome of one intervention can initiate the start of the next. This creates a cascade of care, where individuals enter the system due to a positive diagnostic test, and then move through the healthcare system created, with options for follow-up tests, and treatment options. Some individuals will exit the care system (e.g. “lost to follow up”), and in some cases, individuals that exit the care system may re-initiate care and return.
In the EMODScenarios > Scenarios > HIV > Health_care folder, you will find files to run simulations with a configured cascade of care. In the README file, you will be provided with instructions for working with cascades of care.
Care systems can range from simple diagnostics to a series of complex interventions, and the files within this section highlight these important aspects. Several interventions involved with care are highlighted, namely:
Voluntary male medical circumcision (VMMC)
Prevention of mother-to-child transmission (PMTCT)
Antiretroviral treatment (ART)
Steps in the care process, such as testing, staging, linking to care, treatment eligibility, and how to prevent individuals from entering care cascades multiple times.