SEEDY

SEEDY simulates within-host mutation accumulation and individual-level transmission dynamics to model pathogen evolutionary and epidemiological dynamics during infectious disease outbreaks.

Key Features:

• Implementation: Provided as an R package for simulation of pathogen evolutionary and epidemiological processes.
• Stochastic Simulation Models: Implements stochastic models that simulate the accumulation of mutations within hosts and individual-level disease transmission dynamics.
• Customizable Parameters: Allows specification of transmission bottleneck size, within-host effective population size, and population mixing rates.
• Genetic Distance Distribution Analysis: Computes theoretical pairwise genetic distance distributions to assess the likelihood of person-to-person transmission from genomic data.
• Transmission Route Assessment: Enables assessment of potential transmission routes and reconstruction of transmission chains from outbreak genomic data.

Scientific Applications:

• Outbreak investigation: Simulating pathogen dynamics to test hypotheses about transmission patterns and evolutionary processes during infectious disease outbreaks.
• Transmission likelihood assessment: Evaluating person-to-person transmission likelihoods using pairwise genetic distance distributions derived from genomic data.
• Transmission chain reconstruction: Reconstructing and assessing potential transmission routes from pathogen genomes collected during outbreaks.
• Parameter sensitivity analysis: Exploring how transmission bottleneck size, within-host effective population size, and population mixing rates influence observed genomic variation.

Methodology:

Performs stochastic simulations of within-host mutation accumulation and individual-level transmission dynamics using user-specified epidemiological and evolutionary parameters and computes theoretical pairwise genetic distance distributions.