Novel insights on unraveling dynamics of transmission clusters in outbreaks using phylogeny-based methods

Molecular data analysis is invaluable in understanding the overall behavior of a rapidly spreading virus population when epidemiological surveillance is problematic. It is also particularly beneficial in describing subgroups within the population, often identified as clades within a phylogenetic tree that represent individuals connected via direct transmission or transmission via differing risk factors in viral spread. However, transmission patterns or viral dynamics within these smaller groups should not be expected to exhibit homogeneous behavior over time. As such, standard phylogenetic approaches that identify clusters based on summary statistics would not be expected to capture dynamic clusters of transmission. We, therefore, sought to evaluate the performance of existing and adapted phylogeny-based cluster identification tools on simulated transmission clusters exhibiting dynamic transmission behavior over time. Despite the complementarity of the tools, we provide strong evidence that novel cluster identification methods are needed for reliable detection of epidemiologically linked individuals, particularly those exhibiting changing transmission dynamics during dynamic outbreak scenarios.