Disease progression

The following parameters determine the characteristics of tuberculosis progression, such as incubation, latency, activation, and whether progression is fast or slow.

Note

Parameters are case-sensitive. For Boolean parameters, set to 1 for true or 0 for false. Minimum, maximum, or default values of “NA” indicate that those values are not applicable for that parameter.

EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.

JSON format does not permit comments, but you can add “dummy” parameters to add contextual information to your files. Any keys that are not EMOD parameter names will be ignored by the model.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Acute_Duration_In_Months

float

0

5

2.9

The time since infection, in months, over which the Acute_Stage_Infectivity_Multiplier is applied to coital acts occurring in that time period.

 
{
    "Acute_Duration_In_Months": 2.9
}

AIDS_Duration_In_Months

float

7

12

9

The length of time, in months, prior to an AIDS-related death over which the AIDS_Stage_Infectivity_Multiplier is applied.

 
{
    "AIDS_Duration_In_Months": 8
}

CD4_Num_Steps

integer

1

2.15E+09

10

Number of time steps in CD4 forward vector for reactivation.

 
{
    "CD4_Num_Steps": 10
}

CD4_Strata_Activation

array of floats

1

2000

1

An array of CD4 count thresholds by which to stratify the population. Increased risk of TB activation for each stratum is set using TB_CD4_Activation_Vector.

 
{
    "CD4_Strata_Activation": [
        0,
        350,
        500,
        1000
    ],
    "TB_CD4_Activation_Vector": [
        0.01,
        0.01,
        0.02,
        0.02
    ]
}

CD4_Time_Step

float

1

3.40282e+38

365

The length of steps in the CD4 longitudinal tracker.

 
{
    "CD4_Time_Step": 730
}

TB_Active_Cure_Rate

float

0

1

0

The mean rate at which active symptomatic individuals progress to a cured (uninfected) state. This is an exponential rate.

In the absence of treatment, this rate is added to TB_Inactivation_Rate and TB_Active_Mortality_Rate to determine the total rate of the active smear-positive state, then the ratio of TB_Active_Cure_Rate to total rate determines the probability that an actively infected individual will go to a cured state after a mean duration of 1 / total rate.

 
{
    "TB_Active_Cure_Rate": 1e-09
}

TB_Active_Period_Distribution

enum

NA

NA

NOT_INITIALIZED

Distribution for duration of active disease. For both possible values, the mean is defined by total disease progression rate, which is the sum of TB_Active_Cure_Rate, TB_Inactivation_Rate, and TB_Active_Mortality_Rate corrected for smear status. By default, the progression rates are exponential. Possible values are:

GAUSSIAN_DURATION

Duration of the active period is defined by the mean and standard deviation (defined by TB_Active_Period_Std_Dev) of the Gaussian distribution. Negative values are truncated at zero.

EXPONENTIAL_DURATION

The active period is the mean of the exponential random draw.

 
{
    "TB_Active_Period_Distribution": "EXPONENTIAL_DURATION"
}

TB_Active_Period_Std_Dev

float

0

3.40E+38

1

The standard deviation for the distribution of the duration of active TB. Used when TB_Active_Period_Distribution is set to GAUSSIAN_DURATION.

 
{
    "TB_Active_Period_Std_Dev": 200
}

TB_Active_Presymptomatic_Infectivity_Multiplier

float

0

1

0.0274

The scale factor for Base_Infectivity to give the infectiousness of active presymptomatic individuals.

 
{
    "TB_Active_Presymptomatic_Infectivity_Multiplier": 0.19999999999999998
}

TB_CD4_Activation_Vector

array of floats

0

3.40E+38

1

The increased risk per time step of TB activation by CD4 strata defined in CD4_Strata_Activation.

 
{
    "CD4_Strata_Activation": [
        0,
        350,
        500,
        1000
    ],
    "TB_CD4_Activation_Vector": [
        0.01,
        0.01,
        0.02,
        0.02
    ]
}

TB_CD4_Primary_Progression

array of floats

1

3.40282e+38

1

The proportion (multiplier) increase in primary progression with by CD4.

 
{
    "TB_CD4_Primary_Progression": [
        2,
        2,
        2,
        1,
        1,
        1,
        1
    ]
}

TB_Enable_Exogenous

boolean

0

1

0

Controls whether or not exogenous reinfection of latent TB can occur.

 
{
    "TB_Enable_Exogenous": 1
}

TB_Extrapulmonary_Fraction_Adult

float

0

1

0

The fraction of active cases in adults (age 15 or over) that are extrapulmonary. The sum of this and TB_Smear_Positive_Fraction_Adult must be less than or equal to 1. Extrapulmonary individuals are considered non-infectious.

 
{
    "TB_Extrapulmonary_Fraction_Adult": 0.33
}

TB_Extrapulmonary_Fraction_Child

float

0

1

0

The fraction of active cases in children (under age 15) that are extrapulmonary. The sum of this and TB_Smear_Positive_Fraction_Child must be less than or equal to 1. Extrapulmonary individuals are considered non-infectious.

 
{
    "TB_Extrapulmonary_Fraction_Child": 0.33
}

TB_Extrapulmonary_Mortality_Multiplier

float

0

1

0.4

The scale factor for TB_Active_Mortality_Rate to give the mortality rate of active extrapulmonary individuals. In the absence of treatment, the product is added to TB_Active_Cure_Rate and TB_Inactivation_Rate to determine the total rate of the active extrapulmonary state, then the ratio of the aforementioned product to total rate determines the probability that an active extrapulmonary individual will die from TB disease after mean duration of 1 / total rate. Extrapulmonary individuals are considered non-infectious.

 
{
    "TB_Extrapulmonary_Mortality_Multiplier": 1
}

TB_Fast_Progressor_Fraction_Adult

float

0

1

1

The fraction of adults (age 15 or over) that are fast progressors.

 
{
    "TB_Fast_Progressor_Fraction_Adult": 0.5
}

TB_Fast_Progressor_Fraction_Child

float

0

1

1

The fraction of children (under age 15) that are fast progressors.

 
{
    "TB_Fast_Progressor_Fraction_Child": 0.5
}

TB_Fast_Progressor_Fraction_Type

enum

NA

NA

AGE

The characteristic, such as age or social determinates like poverty, by which to configure a fraction of the population as fast progressors. Currently the only supported value is “AGE”.

 
{
    "TB_Fast_Progressor_Fraction_Type": "AGE",
    "TB_Fast_Progressor_Fraction_Adult": 0.1,
    "TB_Fast_Progressor_Fraction_Child": 0.3
}

TB_Fast_Progressor_Rate

float

0

1

4.11E-05

The mean rate at which individuals who are fast progressors progress from a latently infected state to an active presymptomatic state. This rate is added to the TB_Latent_Cure_Rate to determine the total rate of the latently infected state, then the ratio of TB_Fast_Progressor_Rate to the total rate is calculated. This ratio determines the probability that a latently infected fast progressor will go to an active presymptomatic state after a mean duration of 1 / total rate.

 
{
    "TB_Fast_Progressor_Rate": 0.02
}

TB_Inactivation_Rate

float

0

1

0.00041096

The mean rate at which active symptomatic (smear-positive, smear-negative, and extrapulmonary) individuals progress to an inactivated (latently infected) state. This is an exponential rate.

In the absence of treatment, this rate is added to TB_Active_Cure_Rate and TB_Active_Mortality_Rate to determine the total rate of the active symptomatic state, then the ratio of TB_Active_Cure_Rate to total rate determines the probability that an active syptomatic individual will go to a latently infected state after a mean duration of 1 / total rate.

 
{
    "TB_Inactivation_Rate": 0.05
}

TB_Latent_Cure_Rate

float

0

1

0.0005479

The mean rate at which individuals progress from a latently infected state to a cured (uninfected) state. This rate is added to either the TB_Fast_Progressor_Rate or the TB_Slow_Progressor_Rate to determine the total rate of the latently infected state (depending on whether the individual is a fast progressor or slow progressor, respectively), then the ratio of TB_Latent_Cure_Rate to total rate is calculated. This ratio determines the probability that a latently infected individual will go to a cured state.

 
{
    "TB_Latent_Cure_Rate": 0.1
}

TB_Presymptomatic_Cure_Rate

float

0

1

0.0274

The mean rate at which active presymptomatic individuals progress to a cured (uninfected) state. This rate is added to TB_Presymptomatic_Rate to determine the total rate of the active presymptomatic state, then the ratio of TB_Presymptomatic_Cure_Rate to total rate is calculated. This ratio determines the probability that an active presymptomatic individual will go to a cured state after a mean duration of 1 / total rate.

 
{
    "TB_Presymptomatic_Cure_Rate": 0.05
}

TB_Presymptomatic_Rate

float

0

1

0.0274

The mean rate at which active presymptomatic individuals progress to an active symptomatic state. This rate is added to TB_Presymptomatic_Cure_Rate to determine the total rate of the active presymptomatic state, then the ratio of TB_Presymptomatic_Rate to total rate is calculated. This ratio determines the probability that an active presymptomatic individual will go to active symptomatic disease after a mean duration of 1 / total rate.

 
{
    "TB_Presymptomatic_Rate": 0.0333
}

TB_Relapsed_to_Active_Rate

float

0

1

4.11E-05

The mean rate at which relapsed individuals progress to an active symptomatic state.

 
{
    "TB_Relapsed_to_Active_Rate": 0.01
}

TB_Slow_Progressor_Rate

float

0

1

2.05E-06

The mean rate at which individuals who are slow progressors progress from a latently infected state to an active presymptomatic state. This rate is added to the TB_Latent_Cure_Rate to determine the total rate of the latently infected state, then the ratio of TB_Slow_Progressor_Rate to the total rate is calculated. This ratio determines the probability that a latently infected fast progressor will go to an active presymptomatic state after a mean duration of 1 / total rate.

 
{
    "TB_Slow_Progressor_Rate": 0.02
}

TB_Smear_Positive_Fraction_Adult

float

0

1

1

The fraction of active cases in adults (age 15 and over) that are smear-positive. The sum of TB_Smear_Positive_Fraction_Adult and TB_Extrapulmonary_Fraction_Adult must be less than or equal to 1. This sum plus the fraction of smear-negative adults is equal to 1.

 
{
    "TB_Smear_Positive_Fraction_Adult": 1
}

TB_Smear_Positive_Fraction_Child

float

0

1

1

The fraction of active cases in children (under age 15) that are smear-positive. The sum of TB_Smear_Positive_Fraction_Child and TB_Extrapulmonary_Fraction_Child must be less than or equal to 1. This sum plus the fraction of smear-negative children is equal to 1.

 
{
    "TB_Smear_Positive_Fraction_Child": 1
}