Differential rates of influenza A virus infection between avian and mammalian cells. Influenza A virus strain:A/Guinea Fowl/Hong Kong/WF10/99 (H9N2)

The the ability to genetically recombine provides influenza A virus a mechanism by which to generate novel viruses. IAV has a segmented RNA genome. This segmentation is important for viral evolution and emergence because it allows genetic diversification through reassortment of co-infecting IAV genomes. Our work on IAV reassortment over the past five years has raised exciting new questions about the fundamental biology of IAV and the strategies that have evolved to ensure both viral proliferation and viral adaptive potential. In particular, our data indicate that a large majority of IAV genomes within infected cells are incomplete, comprising fewer than eight gene segments. This observation led us to ask: What underlying mechanisms give rise to incomplete genomes? Here, we propose to quantify incomplete genome levels of IAV by examining viral gene expression in single cells infected with single viruses. We will use multiple viral strains and multiple host cell types to support related research efforts aimed at identifying viral and host factors that play a role in rendering IAV genomes incomplete.