Parasite dynamics

The following parameters determine the dynamics of the Plasmodium falciparum parasite life cycle, including dynamics within the host and human population. For more information, see Malaria infection and immune model.

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

Base_Gametocyte_Fraction_Male

double

NA

NA

0.2

Fraction of gametocytes that are male.

 
{
    "Base_Gametocyte_Fraction_Male": 0.25
}

Base_Gametocyte_Mosquito_Survival_Rate

float

0

1

0.01

Average fraction of gametocytes in a blood meal that are successful in infecting the mosquito in the absence of other modulating effects, such as fever.

 
{
    "Base_Gametocyte_Mosquito_Survival_Rate": 0.015
}

Base_Gametocyte_Production_Rate

double

NA

NA

0.02

The fraction of infected red blood cells (IRBCs) producing gametocytes.

 
{
    "Base_Gametocyte_Mosquito_Survival_Rate": 0.01
}

Base_Sporozoite_Survival_Fraction

float

0

1

0.25

The fraction of sporozoites that survive to infect a hepatocyte in the absence of anti-CSP protection.

 
{
    "Base_Sporozoite_Survival_Fraction": 0.25
}

Cytokine_Gametocyte_Inactivation

float

0

1

0.02

The strength of inflammatory response inactivation of gametocytes.

 
{
    "Cytokine_Gametocyte_Inactivation": 0.0167
}

Enable_Sexual_Combination

boolean

0

1

0

Controls whether or not male and female gametocytes undergo sexual combination. Set to true (1) to allow for sexual combination; set to false (0) for transmission of each strain only.

Note

This parameter is currently not in use.

 
{
    "Enable_Sexual_Combination": 0
}

Gametocyte_Stage_Survival_Rate

double

0

1

1

The rate of gametocyte survival from one development stage to the next in the absence of drugs or inflammatory immune response.

 
{
    "Gametocyte_Stage_Survival_Rate": 0.8
}

Mean_Sporozoites_Per_Bite

float

0

1000

11

The mean number of sporozoites per infectious mosquito bite.

 
{
    "Mean_Sporozoites_Per_Bite": 11
}

Merozoites_Per_Hepatocyte

double

NA

NA

15000

The number of IRBCs caused by a single infected hepatocyte at the start of infection.

 
{
    "Merozoites_Per_Hepatocyte": 15000
}

Merozoites_Per_Schizont

double

NA

NA

16

The number of merozoites released by a single infected schizont after each asexual cycle. The number of resulting IRBC’s depends on the RBC availability and merozoite-specific immunity.

 
{
    "Merozoites_Per_Schizont": 16
}

Number_Of_Asexual_Cycles_Without_Gametocytes

integer

0

500

1

The number of asexual reproduction cycles that do not produce gametocytes. All later cycles will produce gametocytes according to Base_Gametocyte_Production_Rate.

 
{
    "Number_Of_Asexual_Cycles_Without_Gametocytes": 1
}

Parasite_Mortality_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) ).

This parameter configures the inverse width relative to threshold value of mortality turn-on around threshold for parasite density.

 
{
    "Parasite_Mortality_Inverse_Width": 100
}

Parasite_Mortality_Threshold

double

NA

NA

2000000

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the parasite-density mortality threshold for a simulation.

 
{
    "Parasite_Mortality_Threshold": 3000000
}

Parasite_Severe_Inverse_Width

float

0.1

1000000

10

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures the inverse width relative to threshold value of severe disease turn-on around threshold for parasite density.

 
{
    "Parasite_Severe_Inverse_Width": 48.66825295
}

Parasite_Severe_Threshold

float

0

3.40E+38

1000000

The probability of having severe or fatal malaria is calculated according to three causes: anemia, fever as a pro-inflammatory correlate of cerebral malaria, and total parasite density. The probability associated with each factor is configured with two parameters of a sigmoidal function:

probability = 1.0 / ( 1.0 + exp( (threshold-variable) / (threshold/invwidth) ) )

This parameter configures parasite density threshold level that results in severe disease.

 
{
    "Parasite_Severe_Threshold": 253871
}

Parasite_Smear_Sensitivity

float

0.0001

100

0.1

The number of microliters of blood tested to find single parasites in a traditional smear (corresponds to inverse parasites/microliters sensitivity).

 
{
    "Parasite_Smear_Sensitivity": 0.1
}

Parasite_Switch_Type

enum

NA

NA

CONSTANT_SWITCH_RATE_2VARS

The parasite switch type for erythrocyte surface antigens. Possible values are:

CONSTANT_SWITCH_RATE_2VARS

Introduction of new variants has a fixed probability which does not depend on the level of parasitemia.

RATE_PER_PARASITE_7VARS

Each IRBC has a fixed rate of switching to each of seven possible variants.

RATE_PER_PARASITE_5VARS_DECAYING

Each IRBC has a rate of switching to several possible variants, and the rate decreases with distance from the original variant.

 
{
    "Parasite_Switch_Type": "RATE_PER_PARASITE_7VARS"
}