Introduction of New Strains and External Populations

The "External" Population

The Scenarios Mechanistic Model introduces new variants into the studied population through the use of an external infected population. This group of infectious individuals is not a part of any compartment tracked by the model but is instead a part of a time varying external population meant to symbolize travel from neighboring regions. Because this is a mechanistic model, random chance extinction dynamics do not impact the long-term dynamics of the new strain in the population.

The external population compartment mimics the shape of the infectious compartment, but individuals do not recover into other tracked compartments. The external compartment varies only on time, with pulses of infectious individuals appearing and disappearing in the compartment depending on a user defined mean introduction date. The user has the following control over introduction dynamics and the external population as a whole:

Introduction Times:

Pulses are defined by a normal distribution, with a mean centered around the user defined introduction date (INTRODUCTION_TIMES), and a user defined standard deviation (INTRODUCTION_SCALE) to dictate how quickly or slowly external individuals mix with the tracked population. The sizes of these pulses (INTRODUCTION_PERCENTAGE) are relative to the population of each age bin selected.

Pulses are defined by normal distributions to keep the external infectious population continuously differentiable.

Introduction Age Groups:

Users are able to define what age bin to classify external populations into (INTRODUCTION_AGE_MASK). Different age strata of externally introduced populations have impacts on interactions with tracked susceptible groups, since this model implements hetero genius mixing of age groups in the contact matrix.

If modeling business travelers, then it is best to set the introduced age groups to those in the working population etc.

Example:

if a user specifies 5% introduction percentage, a total of 5% of each selected introduction age bin will be mixed in with tracked infectious individuals in exposing tracked susceptible populations. This pulse will be centered around the specified mean introduction time, with a standard deviation of 7 days on either side.