OutbreakIndividualMalariaVarGenes#

The OutbreakIndividualMalariaVarGenes intervention class is an individual-level intervention that enables infecting people with an exact set of antigens. This can be helpful when experimenting with the immune model, such as testing how a person’s immune system reacts if they are reinfected by the same parasite. To use this intervention, set the configuration parameters Malaria_Model to MALARIA_MECHINISTIC_MODEL and Malaria_Strain_Model to FALCIPARUM_FIXED_STRAIN.

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.

The table below describes all possible parameters with which this class can be configured. The JSON example that follows shows one potential configuration.

Parameter

Data type

Minimum

Maximum

Default

Description

Example

Ignore_Immunity

boolean

0

1

1

Individuals will be force-infected (with a specific strain) regardless of actual immunity level when set to true (1).

 
{
  "Intervention_Config": {
    "class": "OutbreakIndividualVarGenes",
    "Ignore_Immunity": 0
  }
}

Incubation_Period_Override

integer

-1

2.14E+09

-1

The incubation period, in days, that infected individuals will go through before becoming infectious. This value overrides the incubation period set in the configuration file. Set to -1 to honor the configuration parameter settings.

 
{
  "Incubation_Period_Override": 0
}

IRBC_Type

array of integers

0

10,000

[]

The array of PfEMP1 Major epitope variant values. Each value in the array must be less than or equal to the value for the configuration parameter Falciparum_PfEMP1_Variants. Note: The array must contain 50 values.

 
{
  "IRBC_Type": [
    2,
    75,
    148,
    221,
    294,
    367,
    440,
    513,
    586,
    659,
    732,
    805,
    878,
    951,
    24,
    97,
    170,
    243,
    316,
    389,
    462,
    535,
    608,
    681,
    754,
    827,
    900,
    973,
    46,
    119,
    192,
    265,
    338,
    411,
    484,
    557,
    630,
    703,
    776,
    849,
    922,
    995,
    68,
    141,
    214,
    287,
    360,
    433,
    506,
    579
  ]
}

Minor_Epitope_Type

array of integers

0

10,000

[]

The array of PfEMP1 Minor epitope variant values. There must be exactly 50 values. Min value = 0, MAX value = Falciparum_Nonspecific_Types * MINOR_EPITOPE_VARS_PER_SET(=5).

 
{
  "Minor_Epitope_Type": [
    2,
    0,
    3,
    3,
    1,
    2,
    3,
    3,
    0,
    1,
    3,
    2,
    1,
    3,
    0,
    1,
    1,
    2,
    4,
    0,
    1,
    1,
    0,
    4,
    0,
    1,
    1,
    4,
    4,
    0,
    2,
    0,
    4,
    1,
    2,
    1,
    1,
    0,
    1,
    3,
    3,
    1,
    2,
    4,
    2,
    4,
    4,
    3,
    2,
    4
  ]
}

MSP_Type

integer

0

1000

0

The Merozoite Surface Protein variant value of this infection. Min value = 0, MAX value = Falciparum_MSP_Variants.

 
{
  "MSP_Type": 2
}

{
    "Event_Coordinator_Config": {
        "class": "StandardInterventionDistributionEventCoordinator",
        "Number_Repetitions": 30,
        "Timesteps_Between_Repetitions": 150,
        "Target_Demographic": "Everyone",
        "Demographic_Coverage": 1.0,
        "Intervention_Config": {
            "class": "OutbreakIndividualMalariaVarGenes",
            "MSP_Type": 2,
            "IRBC_Type": [
                2, 75, 148, 221, 294, 367, 440, 513, 586, 659, 732, 805, 878, 951, 24, 97, 170,
                243, 316, 389, 462, 535, 608, 681, 754, 827, 900, 973, 46, 119, 192, 265, 338,
                411, 484, 557, 630, 703, 776, 849, 922, 995, 68, 141, 214, 287, 360, 433, 506, 579
            ],
            "Minor_Epitope_Type": [
                2, 0, 3, 3, 1, 2, 3, 3, 0, 1, 3, 2, 1, 3, 0, 1, 1, 2, 4, 0,
                1, 1, 0, 4, 0, 1, 1, 4, 4, 0, 2, 0, 4, 1, 2, 1, 1, 0, 1, 3, 3,
                1, 2, 4, 2, 4, 4, 3, 2, 4
            ]
        }
    }
}