Non-lytic Clearance of Influenza B Virus as a Host Defense Mechanism

Abstract

Influenza viruses cause acute respiratory disease, infecting 3-5 million people and causing 290-660,000 deaths annually. The vast majority of human disease is caused by influenza A and B viruses which first infect epithelial cells in the upper respiratory tract and then can spread to neighboring tissue depending on the severity of disease. Traditionally it’s been thought that tissue damage resulting from influenza disease was due to an entirely cytolytic viral infection, in which every infected cell was killed either through viral replication or immune-mediated mechanisms. Previous work from our lab and others have demonstrated, however, that cells are able to survive direct infection with apparently cytopathic viruses and that some cells can intrinsically clear the virus and persist in the host long-term. The work in this thesis focuses on the cellular response to influenza B virus infection, with an emphasis on the upper respiratory tract as the primary presentation of viral disease in seasonal influenza infections.Influenza B viruses (IBVs) are major contributors to total human influenza disease, responsible for ~1/3 of all infections. While it has historically been assumed that the viral biology and mechanisms of pathogenesis for all influenza viruses were highly similar, studies have shown that IBVs possess unique characteristics that affect how they interact with the host cell. Therefore, to determine if any cells can survive direct IBV infection, we generated a recombinant IBV capable of activating a host-cell reporter topermanently label all infected cells. In chapter one, using this system, we demonstrate that IBV infection leads to the formation of a survivor cell population in the proximal airways that are ciliated-like, but transcriptionally altered from uninfected ciliated cells in the same lung. This is the first report of cells surviving direct infection with influenza B virus and provides the basis for the work done in subsequent chapters of this thesis.In chapter two, we build on this work to demonstrate that transcriptionally altered survivor cells are phenotypically distinct from both actively infected and bystander ciliated cells. To further understand the contribution of these survivor cells to lung function during and following infection, we used depletion assays to test lung barrier function, leakiness and overall morbidity in animals with and without survivor cells. In this work we demonstrate that survivor cells are critical to maintain respiratory barrier function. These results highlight a host response pathway that preserves the epithelium to limit the severity of IBV disease.Lastly, we wanted to understand how influenza infection affects the heterogeneous upper respiratory tract tissue. Our studies demonstrated that both respiratory and olfactory epithelial cells were infected by IBV and demonstrated divergent antiviral profiles over the course of infection. As a result, the olfactory sensory neurons were able to non-lytically clear viral protein more rapidly than respiratory epithelial cells. This is, to our knowledge, the first report of infection and non-lytic clearance of a seasonal strain of IBV in the olfactory epithelium. Overall, these results demonstrate a heterogeneity in cell-intrinsic antiviral responses that contribute to differences in cellular outcomes of infection.