VGsim

VGsim simulates viral genealogies on a world scale to model pandemic dynamics and the molecular evolution of viruses such as SARS-CoV-2.

Key Features:

• Scalability and Efficiency: Simulates world-scale scenarios involving millions of samples (e.g., >5.5 million SARS-CoV-2 sequences as of November 2021) to support large-scale genomic analyses.
• Two-Phase Simulation Process: Performs a forward run using a hierarchical Gillespie algorithm to generate chains of population-level events and a backward, coalescent-like run to construct tree genealogies of samples conditioned on those events.
• Complex Population Modeling: Models detailed population structure including epistasis and immunity escape to capture complex evolutionary and epidemiological dynamics.

Scientific Applications:

• Pandemic Spread Analysis: Uses simulated genealogies to investigate temporal and spatial dynamics of pandemic spread.
• Molecular Evolution Studies: Enables analysis of molecular evolutionary processes, including natural selection, to identify variants with altered transmissibility or immune evasion.

Methodology:

Simulations use a forward run with a hierarchical Gillespie algorithm to generate population-level events and a backward, coalescent-like run to construct tree genealogies conditioned on those events.