A population genomic perspective on persistent viral infections: from within-host evolution to large-scale epidemiological dynamics

Viral infections and their associated diseases represent an eminent and worldwide threat to public health. Although viral pathologies are well described, it remains an enormous challenge to intervene with epidemic spread and disease development in the host. A better understanding of the link between diseases, epidemic processes and pathogen evolution, both within and among hosts, is essential in the struggle against viral infections. The goal of this project is to optimize experimental protocols and develop novel analytical methods that take advantage of the output of 454 sequencing results to better understand the dynamics of mutation and adaptation in chronic infection, focusing specifically on what happens to genomic viral diversity when the selective landscape is altered significantly, for example following transmission to a new host or following the initiation of drug treatment. We will exploit the depth of this information – both in terms of full-genome and quasispecies coverage - to comprehensively analyze the dynamics of immune escape and viral archiving.status: publishe