EpiLink: a simulation-based compatibility model for genomic transmission clustering in infectious disease surveillance

EpiLink is a new method for identifying recently linked cases of infectious diseases based on pathogen genome sequence analysis. The method operates without fixed genetic thresholds and estimates whether two cases are compatible with recent transmission. EpiLink simulates plausible recent transmission scenarios while accounting for uncertainty in infection timing, testing delays, and mutation accumulation. The method was tested on synthetic and empirical data from the SARS-CoV-2 epidemic in Boston in 2020. Two EpiLink variants exist - one with deterministic mutation accumulation and another with a stochastic approach using Poisson distribution. Although logistic regression trained on labelled transmission data achieved better results, EpiLink achieved comparable clustering accuracy. In the Boston data, EpiLink successfully identified clusters associated with documented outbreaks at conferences and skilled nursing facilities.