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
}
|
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:
|
{
"Parasite_Switch_Type": "RATE_PER_PARASITE_7VARS"
}
|