The use of the local branching index for characterizing transmission in genomic epidemiological datasets

Music City Center 

Relating genomic data to transmission patterns is an ongoing challenge. In many practical applications, researchers focus on clustering: how many of the sequences in a dataset are "clustered with" any other sequence? Clustering is interpreted as a sign of recent transmission. However, clustering is a very simple measure. It depends on the clustering threshold, is a binary variable, and it typically does not account for much evolutionary complexity. Here, we explore how well the local branching index (LBI) can capture patterns of transmission. LBI is a measure of the rate of branching in a phylogenetic tree that is specific to each tip. Tips with very rapid nearby branching are likely to be clustered, as their sequence is likely close to other sequences. LBI can therefore be seen as a continuous variable that should contain some of the same information as clustering. We use simulations and analysis of simulated phylogenetic trees to explore the relationships among LBI, transmission patterns, and sampling.

Infectious diseases

Phylogenetic tree