Lifting barriers towards obtaining actionable public health information from pathogen genomes: model advancement, performance evaluation and application to respiratory syncytial virus types A and B

Molecular epidemiology approaches can glean epidemiological information from pathogen genomes, and have grown into an important instrument across infectious disease research. Harnessing these methods for actionable information to public health -an important goal in e.g. HIV research- requires the ability to obtain timely and unbiased information on key epidemic processes such as migration. The adoption of model-based phylogenetic inference of how pathogens migrate between sub-populations for informing public health policy is hampered by the inability of structured coalescentbased approaches to analyse the nowadays common large and complex data sets, and by reservations about the performance of a computationally more efficient and highly popular phylogeographic method. To address this critical topic, we aim to advance and thoroughly investigate the latter method's ability to accurately test hypotheses. Through this project we will also gain fundamental insights into the circulation dynamics of respiratory syncitial virus (RSV) types A and B, the leading causes of acute lower respiratory infections in infants worldwide, by making use of their first comprehensive global multi-annual full-genome sample. As part of this effort, a continual epidemic tracking of RSV A and B will be implemented to monitor key aspects of their genetic diversity and spread.