This module provides an introduction to infectious diseases, immunology and modeling on the level of the individual host. Using influenza, SARS-CoV-2, TB, and other pathogens as examples, this module introduces basic immunological concepts and explains how to use mathematical models to study within-host infection dynamics.

We focus on simple compartmental deterministic models. We discuss how those models can be used to analyze the dynamics of pathogens and the immune response, and how to model intervention strategies, such as vaccines and drug treatments. Hands-on exercises using the R programming language are included, using the DSAIRM R package (https://ahgroup.github.io/DSAIRM/).