Prerequisites: This module assumes knowledge of the material in Module 1: Probability and Statistical Inference, though not necessarily from taking that module (common probability distributions, maximum likelihood estimation). All programming will be in R; we provide a tutorial to be completed before the module for any students new to R.

In this era of genomic epidemiology there have been high hopes that sequencing will reveal who infected whom in a way that is not accessible with standard epidemiological investigations. To this end, several methods have been developed, drawing upon techniques from phylogenetics, Bayesian statistical inference, and probability, among others. This course will describe some of these methods, and compare and contrast their assumptions and data requirements. Students will learn to use several of them to reconstruct transmission – who infected whom – in densely sampled outbreaks with the help of pathogen sequence data.