MANTIS

MANTIS simulates multilocus models of pathogen evolution to analyze host-pathogen dynamics and competition among pathogen genetic variants driven by cross-protective immune responses.

Key Features:

• Simulation Capabilities: Simulates epidemiological time-series data based on the strain theory of host-pathogen interactions and multilocus competition among pathogen variants.
• Integration with R: Implemented as an R package to execute simulations and analyses within the R environment.
• C/C++ Backend: Implements an ordinary-differential-equations system in C/C++ coupled with a Runge-Kutta solver for numerical integration.
• Visualization and Exportation: Provides functions for plotting time-series data and exporting simulation results.

Scientific Applications:

• Pathogen evolution under immune pressure: Analyzing how host immunity and cross-protection shape evolutionary dynamics among strains.
• Vaccine development: Exploring effects of immune-mediated competition on strain prevalence relevant to vaccine design.
• Disease management strategies: Evaluating immune-driven dynamics to inform control and intervention strategies.
• Prediction of pathogen adaptation: Assessing trajectories of strain emergence and adaptation under varied immunological scenarios.

Methodology:

Implemented in R with a C/C++ ordinary-differential-equations system numerically integrated using a Runge-Kutta solver; simulations follow the strain theory framework modeling competition among pathogen variants via cross-protective immune responses to generate epidemiological time-series.