Prerequisites: This module assumes knowledge of the material from Module 2: Mathematical Models of Infectious Diseases, though not necessarily from taking that module. Programming exercises will be conducted in Python; some familiarity would be helpful, but not required.

This module provides an introduction to modeling antigenically diverse pathogen populations. Complementary epidemiological and evolutionary approaches will be covered.

The first part of the course will introduce multistrain compartmental models and potential mechanisms of competition. These simple models will be contrasted with models with more complex assumptions (e.g., multiple forms of immunity and spatial structure). We will review how to statistically investigate multistrain models with longitudinal data from individuals and time series data from populations.

The second part of the course will show how, using the coalescent as a neutral expectation, evolutionary pressures can be quantified using sequence data. We will detail bioinformatic methods to build phylogenies, quantify selective pressures and estimate pathogen population structure. Methods to measure pathogen phenotypic similarity and antigenic evolution, such as antigenic cartography, will be introduced.