Toward a quantitative understanding of viral phylogeography

Phylogeographic approaches help uncover the imprint that spatial epidemiological processes leave in the genomes of fast evolving viruses. Recent Bayesian inference methods that consider phylogenetic diffusion of discretely and continuously distributed traits offer a unique opportunity to explore genotypic and phenotypic evolution in greater detail. To provide a taste of the recent advances in viral diffusion approaches, we highlight key findings arising at the intrahost, local and global epidemiological scales. We also outline future areas of research and discuss how these may contribute to a quantitative understanding of the phylodynamics of RNA viruses.

► Phylogeographic analyses allow testing and quantifying viral spatial dynamics at diverse scales. ► Statistical methods reconstruct the spread of viral lineages in discrete or continuous space. ► These approaches can be used to study how viruses explore different hosts or phenotypes over time. ► Phylogeographic analyses can identify predictors of viral emergence and spread.