Understanding evasion of cell intrinsic innate immunity in viral populations with high rates of replicative failure

Cell intrinsic innate immunity is a barrier that all viral pathogens must overcome or otherwise subvert in order to successfully complete their infectious lifecycle. Collectively, these pathways detect non-self or danger associated molecules, and, in response, produce signaling proteins called interferons that induce both local and systemic anti-pathogen responses. These responses ultimately drive the clearance of most acute infections, although they also lead to much of the observed pathology. Most, if not all, viral pathogens encode antagonists of these pathways; frequently at the level of interferon production. One such pathogen, human influenza A virus, is so successful that only around 0.5% of infected cells successfully detect viral infection at early timepoints. Nevertheless, that small fraction of responders is crucial to the course of disease—individuals with defects in interferon pathways are often at extremely high risk of complications or death following infection by respiratory viruses, including influenza. Paradoxically, while most viral populations maintain stringent suppression of host detection, they replicate with relatively low fidelity. For influenza, only about 10% of viral particles can successfully complete the viral lifecycle. The rest of the particles are capable of entering cells and exposing potential innate immune ligands, but nevertheless fail at some step to produce infectious progeny. Regardless, the vast majority of virions, even those which cannot complete the viral lifecycle, still go undetected. What mechanisms, then, allow viral populations to remain undetected by host cells despite failing so frequently at replication? As a starting point to this ambitious line of inquiry, we are focusing on several discrete mechanisms in influenza A virus for which we already possess either preliminary data or the capacity to readily procure such data: 1) How the structure of the segmented genome of influenza A virus influences the range of potential immunostimulatory failure 2) How the multifunctionality of influenza’s predominant innate immune antagonist, NS1, influences rates of viral detection, and 3) How polymerase error rate may be subject to innate immune pressure. To address these questions my group will use a combination of variant analysis, deep mutational scanning, and more classical molecular virology. By profiling the challenges viral populations must overcome to evade innate immunity, and the mechanisms by which they do so, it is our hope to better inform models of viral evolution and potentially even identify novel therapeutic routes exploiting those challenges. viral Critically, our approaches have already identified key components of the viral lifecycle that are subject to surveillance, and have identified viral variants with desirable properties as potential vaccine candidates or oncolytic therapeutics.