Spatial structure of influenza A infections in a guinea pig model using barcoded viruses

The upper and lower respiratory tracts are distinct environments for influenza A virus (IAV) replication, and the spatiotemporal dynamics of infection are not well understood. We inoculated guinea pigs were infected with two different barcoded influenza viruses (A/TX/50/2012 (H3N2) A/CA/07/2009 (H1N1)) through multiple routes of exposure. The barcoded virus enabled high-resolution tracking of dispersal through amplicon sequencing of RNA extracted from swabs and tissue samples.