Viral heterogeneity
Influenza virus populations are highly heterogeneous at multiple levels. In addition to physical and sequence diversity, individual virions vary greatly in the specific viral genes they encode, with most virions lacking the full set of viral genes needed for replication. The mechanisms that give rise to the enormous amount of genomic heterogeneity within viral populations, and more importantly the consequences for viral replication, transmission, and pathogenesis, remain unknown.
Virus-virus interactions and cooperativity
Most influenza virions can’t replicate on their own because they are missing essential genes. While this seems like it would be a big problem for the virus, incomplete virions can complement each other through cellular co-infection, collectively encoding a productive infection. We and others have shown that cellular co-infection is common and serves as an important determinant of viral replication efficiency, one that influenza (and other viruses) may have evolved to depend upon. Further, cellular co-infection likely plays a large role in governing the evolutionary dynamics of viral populations.
We want to understand how the prevalence of cellular co-infection influences viral replication and evolutionary dynamics as well as the host response to infection. We are especially focused on identifying the specific host and viral factors that influence patterns of cellular co-infection, as well as using theoretical approaches to model the effects of co-infection on viral replication and evolution.
Cellular heterogeneity in innate immune function
We and others have shown that the induction of critical innate immune factors such as interferon is surprisingly rare and highly stochastic at the single cell level during viral infection. The inherent stochasticity of cellular responsiveness to infection is largely ignored in efforts to dissect models of viral pathogenesis, which often conceptualize the host anti-viral response as a series of deterministic pathways and signaling cascades.
Why are so few cells capable of mounting an IFN response? This question represents a fundamental knowledge gap in our understanding of host defense and infection biology and raises broader questions about how phenotypic heterogeneity is regulated within cellular populations. we are using an array of single cell and computational approaches to define the central role that cellular heterogeneity and stochastic processes play in initiating the innate immune response, identify key regulators of cellular heterogeneity in innate immune function, and explore the potential benefits of stochastic circuitry in host defense.
Viral evolutionary constraints
The persistence of influenza virus (as well as many other viruses) within the human population depends upon the ability of the virus to continually evolve to evade adaptive immune memory elicited by prior infection. Unfortunately, we still know very little about the fundamental rules that govern the antigenic evolution of influenza viruses, a limitation that has hobbled efforts to develop next-generation “universal” influenza vaccines that elicit responses that the virus cannot escape from.
We are working to define the specific constraints that govern the process of antigenic evolution. We are especially interested in understanding how interactions between the viral genome segments and constraints imposed by specific host environments influence the specific evolutionary pathways taken by viral populations.
Spatial dynamics of infection and immunity
Viral populations are often highly spatially structured within a host; however, the determinants and consequences of viral spatial distribution during infection have not been explored. Further, the spatial structure of the innate antiviral response in vivo is also poorly understood. We are using tissue clearing and 3D light sheet microscopy to identify the determinants that influence the spatial distributions of virus and host immune factors and combine these data with mathematical models to define how spatial dynamics of viral replication and innate immune activation influence infection outcomes
Infection dynamics in humans
With the exception of SARS-CoV-2, we lack data on (a) the dynamics of viral replication and shedding in humans, (b) the dynamics of the immune response during acute infection, and (c) how these dynamics may differ between different viruses. To address these questions, we have established the FLUdetect study at the University of Illinois with the support of NIH and Flu Lab. The FLUdetect study uses frequent screening to identify community acquired respiratory infections during the early stages of infection. We then capture daily samples generate a high resolution of viral shedding and immune dynamics over the course of infection. These data will hopefully identify new immune correlates of viral transmission risk that can guide next generation vaccine design.