Single cells infected by influenza can produce hundreds to thousands of infectious new virions. These virions spread non-uniformly, producing wide variations in the viral load per cell that are concentrated around the initial site of infection. Differences in the amount of virus that infects a particular cell can influence whether or not that cell produces new virions of its own, or if it mounts an anti-viral response. Understanding how influenza virions spread is therefore critical to understanding how infection progresses and how the host responds. The central goal of this project is to understand how genetic and biophysical features of both virus and host contribute to the spatial structure of influenza virus cellular spread, and how differences in cellular spread shape the progression of infection and the resulting cellular responses. Our prior data demonstrate that genetic and biophysical features of influenza control the way that the virus spreads at the cellular level. These features are strongly linked to three viral proteins in particular: HA, NA, and M1. The receptor-binding protein HA mediates virus attachment to naïve cells, while the receptor-destroying protein NA facilitates virus release and dissemination. The matrix protein M1 controls the shape of the virus particle and the distribution of HA and NA on the virion surface. Collectively, these proteins control the biophysical characteristics of virus particles and shape the way that virions spread throughout the host. We hypothesize that genetic mechanisms acting through these proteins, together with host factors involved in mucociliary clearance, determine the spatial pattern of viral spread and the frequency of cellular co-infection, thereby shaping the progression of disease. We will test this hypothesis through two specific aims. In Aim 1, we will use high- resolution imaging to track the spread of virions and viral infection, and we will determine how this depends on natural variations in HA, NA, and M1. Through these experiments, we will identify how these proteins collectively influence the degree of cellular co-infection that occurs during multi-cycle virus replication. In Aim 2, we will investigate how host factors involved in mucociliary clearance contribute to cellular spread of IAV, and we will determine the collective impact of viral and host factors that alter the frequency of co-infection on key infection outcomes in differentiated human airway cells. The expected outcome of this project is an improved understanding of how influenza virus surface and structural proteins contribute to intracellular aspects of viral replication by tuning the degree of co-infection that occurs during multi-cycle growth. Insights from this work will inform basic understanding of how influenza viruses navigate the host environment and will identify host and viral factors that contribute to the disparate outcomes of infection that are sometimes observed. This proposal will also introduce new tools and methodologies for investigating the spatial organization and dynamics of influenza virus infection.

The proposed research seeks to understand how genetic and biophysical features of influenza viruses contribute to the spread of virions within infected hosts. Viral spread is central to the medical outcomes of influenza virus infection. It is expected that by understanding how this process works, how it differs between genetically-distinct viruses, and how it impacts the progression of infection, it will become possible to identify new strategies for preventing and controlling influenza.