Clinical applications of pathogen phylogenies

•Phylogenetic methods are not being used to their potential in clinical studies.•Recent advances can link pathogen genetics to infection outcomes.•These developments can determine internal infection spread, and detecting CTL escape mutations.•A more thorough use of these tools will aid infections disease research.

Innovative sequencing techniques now allow the routine access of whole genomes of pathogens, generating vast amounts of data. Phylogenetic trees are a common method for synthesizing this information. Unfortunately, these trees are often seen only as a visual support to guide researchers, thus neglecting the value of employing phylogenetic techniques to perform hypothesis testing on clinical questions. These include investigating how a pathogen spreads within a patient, or whether the infection severity (often measured by virus load) is controlled by viral genetics. Advances in methodology mean the time is ripe for combining phylogenies with clinical data to better understand and fight infectious diseases.