SIMCoV

SIMCoV simulates the spatial-temporal dynamics of SARS-CoV-2 infection within the human lung to analyze virus spread and immune interactions at cellular resolution.

Key Features:

• Scalability: Simulates hundreds of millions of lung cells, including respiratory epithelial cells and T cells, enabling large-scale cellular-resolution analysis.
• Spatial-Temporal Dynamics: Represents the spatial distribution of infections and demonstrates how dispersed viral sites can lead to increased viral loads.
• Immune Response Simulation: Models the timing and strength of T cell responses and their effects on viral persistence, oscillations, and control.
• Branching Airway Structure Representation: Explicitly models the lung's branching airway structure, yielding viral spread dynamics faster than a 2D layer but slower than a well-mixed model.

Scientific Applications:

• Understanding Viral Load Variability: Examines how variation in initial infection site distribution and immune response parameters can produce diverse viral load trajectories among patients.
• Insights into Immune Response Timing: Evaluates how different timings and magnitudes of T cell responses influence disease progression and viral control.
• Enhanced In Vivo Study Complements: Provides a computational framework to complement in vivo studies by exploring spatial infection scenarios that are difficult to measure experimentally.

Methodology:

SIMCoV uses a spatially explicit computational model that explicitly represents the lung's branching airway structure to simulate interactions among viral particles, respiratory epithelial cells, and T cells at scales of hundreds of millions of cells.