How does new disease emerge, virulence evolve and drug resistance spread? The analysis of ongoing viral epidemics, especially SARS-CoV-2, HIV and influenza, unequivocally demonstrate the pace of pathogen evolution in real time. Such events can be tracked by population genomic analysis, which can also be applied to bacterial and parasite genomes to follow the emergence of drug resistance, or changes in host range and pathogenesis. Although the underlying selection pressures appear predictable, in reality the complex interactions of emergent host-pathogen relationships and their interactions in a diverse host population create considerable uncertainty, generating risks as diseases transmit between humans and animals. In this theme, we will identify the genetic changes that provide the early-warning signals for disease emergence or drug resistance and exploit evolutionary analysis and modelling approaches to help predict, and limit, their spread through populations. This article was published on 2025-03-12
