ScenarioTransmission

Levels of Transmission

OpenMalaria simulations of malaria transmission require specification of:

• The level and seasonality of exposure (measured by the Entomological Inoculation Rate, EIR) to malaria at the start of the simulation

• The model for malaria transmission from humans to mosquitoes

• The dynamics of malaria parasite cycle within humans and also the model for transmission from mosquitoes to humans (the entomological model).

• The entomological model. There are two different variants of the entomological model:

  • The "Non-vector" variant does not consider mosquito dynamics and hence does not allow the user to modify the vectorial capacity. It is appropriate for modeling situations where interventions (such as chemotherapy or vaccines that only act on humans) and is described in: Smith et al, 2006.. Specification of this variant is described [below](ScenarioTransmission#specifying-the-nonvector model-variant)

  • The "Vector" variant comprises discrete-time population models that simulate how many mosquitoes belong in each of several categories at each time. The models assume that the infectious (sporozoite positive) mosquitoes act to distribute infections at random to the human population (with human exposure proportionate to availability). Entomological interventions modify the vectorial capacity and require the "vector" transmission model variant. The simulations that include non-periodic changes in the vectorial capacity use a seasonally forced version of the difference equation model for vector dynamics of Chitnis et al (2008)Journal of Biological Dynamics Vol. 2, No. 3, July 2008, 259–285, further described in Chitnis et al (2010) American Journal of Tropical Medicine and Hygiene Vol. 83, No. 2, 230--240.

  The vector transmission model is required for modeling interventions that have effects on mosquitoes, and hence change the vectorial capacity. In addition to the specification of transmission described below additional XML parameters for specifying this sub-model are described here.

The default use of both the "non-Vector" and "Vector" model variants follows the original Ross-Macdonald model in assuming that intervention-induced reductions in adult mosquitoes do not affect the numbers of emerging females, (which depend on local carrying-capacity of the breeding sites). OpenMalaria also supports an extension of the "Vector" model variant that incorporates a full-life cycle model that can capture effects of adulticiding on emergence, described here.

Specifying the nonVector model variant

The "non vector" model assumes a fixed seasonal vectorial capacity, and either forces infection rates (EIR) or makes EIR dependent on human infectiousness to vectors while forcing vectorial capacity. Initial exposure of humans to infectious mosquito bites is input and any intervention effects on transmission to the mosquito translate into proportionate effects on transmission back to the human. This model is valid when the only interventions are ones that do not affect the vectorial capacity (e.g. vaccines or chemotherapeutic interventions). When vector control interventions are applied, the "Vector" model must be used.

The nonVector element primarily consists of a list of daily EIR (Entomological Inoculation Rate) parameters (EIRDaily elements) specifying the annual EIR (thus 365 values are expected) (see example above). Assuming the first value is the EIR for January 1st, time 0 corresponds to the beginning of the year (since this is the only input affecting seasonality it can be rotated as desired).

Values in this list are averaged per timestep to calculate the EIR per timestep of the year for the pre-intervention equilibrium state. Where data for more than one year are provided, the data is assumed to wrap into the next year and all values for the same timestep of the year are averaged.

nonVector also has an eipDuration attribute: the extrinsic incubation period (sporozoite development time, in days), which determines the delay before changes in human infectiousness affect the EIR (in dynamic mode only), and an annualEIR element, which is an optional number. If this is provided, the EIR description is scaled such that the total number of infectious bites per adult is this number.

An example of the entomology element, for the non-vector model variant is thus as follows:

<entomology mode="4" name="a name">
  <nonVector eipDuration="10">
    <EIRDaily origin="monthly">0.0738</EIRDaily>
    <EIRDaily origin="monthly">0.0738</EIRDaily>
    <EIRDaily origin="monthly">0.0738</EIRDaily>
    <EIRDaily origin="monthly">0.0738</EIRDaily>
    <EIRDaily origin="monthly">0.0738</EIRDaily>
    <EIRDaily origin="monthly">0.0738</EIRDaily>
    ...
  </nonVector>
</entomology>

Attributes of the entomology element also include the name which is simply a text string giving a user-friendly name for the transmission Setting.

Note that prior to schema 24, the vector model used EIR in units of infectious bites per person per time-period, averaged across the population, while the non-vector model used units of infectious bites per adult per time-period. From schema version 24 both use units of infectious bites per adult per day/timestep/month/year. (The difference being that children receive fewer bites than adults.)

Change EIR

The changeEIR intervention can be used to override the default transmission settings with the non-vector transmission model (but not with the 'vector' model). It is used to simulate the impact of an intervention package with known impact on EIR, either on public health outcomes, or on as a factor modifying the impacts of interventions that can be simulated with the non-vector transmission model. It can be used, for example, to switch to EIR settings recorded during a trial, while retaining the main transmission description for the warm-up and pre-trial periods of the simulation. This intervention updates the transmission model with an entirely new description. It is described like:

<interventions>
  <changeEIR name="name of new transmission settings">
    <timedDeployment eipDuration="10" time="0">
        <EIRDaily origin="interpolate">0.00219</EIRDaily>
        <EIRDaily origin="interpolate">0.00210</EIRDaily>
        <EIRDaily origin="interpolate">0.00202</EIRDaily>
        ...
      </timedDeployment>
  </changeEIR>
  ...
</interventions>

The new EIR is always matched to the whole intervention period, thus must contain enough entries to cover from the beginning of the intervention period to the end, even if not deployed at time 0 or replaced before the end of the simulation. Values are, however, only used from the time of deployment (with some values potentially going unused).

Any number of timedDeployment elements may be used, each of which specifies a time of deployment (in timesteps) and has the same type of content as the nonVector element used to describe the initial transmission.

Deploying a changeEIR intervention changes the transmission mode parameter to static (human infectiousness to mosquitoes has no further effect on EIR).