Infections and Disease

Daily Transmission Cycle

The core of the model is a daily loop that captures people's movement between different locations and the transmission of SARS-CoV-2 in these locations between infectious and susceptible individuals. Because transmission is modeled independently in different locations, we have the ability to incorporate different location-based interventions such as school or workplace closures (see Synthetic Population — Locations for more information.

Simulation of Infection

Incorporated in our ABM is a representation of SARS-CoV-2 infection that follows an SEIRD model:

Susceptible ( S )

Most people are initially susceptible to infection, also known as serologically naive. For more information on how introductions in the model are handled, see Model Minutia — Introductions.

Exposed ( E )

When an infectious and susceptible individuals co-localize, transmission events can occur. When a susceptible individual becomes exposed, the full fate of this exposure event is calculated. That is, upon exposure, it will be known if this individual will be infected, and if so, the time-scale for the progression of that infection (i.e., the severity and timing of symptoms, if hospitalization is required, and if the infection will be fatal). For more details, see Model Minutia — Infection.

Infected/Infectious ( I )

Upon exposure, the timing and severity of an infection will be known. Infections can be asymptomatic (I_A) or can progress to three different levels of symptomatic severity: mild (I_M), severe (I_S), and critical (I_C). To reach a specific level of severity, an infection will progress through all previous levels (e.g., a critical infection must progress through mild and severe stages first). Individuals with severe and critical infections are eligible for hospitalization, and only those with critical infections may receive ICU care (see Synthetic Population — Locations for more details on hospitals).

Recovered ( R )

This category captures those individuals who had non-fatal infections and thus have natural immunity. Similarly, individuals who are vaccinated can be thought of as recovered and having artificial immunity (or a combination of natural and artificial immunity in the case that an individual was vaccinated after natural infection).

However, we do not consider that natural infections are completely immunizing and we model realistic vaccine efficacies (see Model Implementation — Vaccination for more details). Thus, people in the recovered category can transition back into the susceptible category but with some immunity from their natural infection and/or vaccination.

Dead ( D )

Although the time of death for a fatal infection is known at the time of exposure, an individual will not be considered dead until that calculated time of death. This allows that individual to participate in transmission opportunities and occupy hospital/ICU beds (if applicable). To be a fatal case, one's infection must progress through all three categories of symptom severity (mild, severe, and critical).