A new method for analysing disease transmission patterns is described in Nature Communications this week. Applying the algorithm to a subgroup of HIV gene sequences, scientists identify transmission clusters and link them to molecular and epidemiological data.

Understanding a phenomenon called partition of phylogenies — the evolution of a disease — can help to identify the determinants of virus transmission and disease transmission chains. Currently, no software is available for the automated analysis of large phylogenies. Mattia Prosperi and colleagues use a new search algorithm to identify transmission clusters within the phylogeny of HIV-1 gene sequences in a large Italian cohort. The method can characterise transmissions chains according to different clinical or demographic factors and could aid in the development of future screening and early intervention strategies for the disease.