Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection.

Viral infection outcomes are governed by the complex and dynamic interplay between the infecting virus population and the host response. It is increasingly clear that both viral and host cell populations are highly heterogeneous, but little is known about how this heterogeneity influences infection dynamics or viral pathogenicity. To dissect the interactions between influenza A virus (IAV) and host cell heterogeneity, we examined the combined host and viral transcriptomes of thousands of individual cells, each infected with a single IAV virion. We observed complex patterns of viral gene expression and the existence of multiple distinct host transcriptional responses to infection at the single cell level. We show that human H1N1 and H3N2 strains differ significantly in patterns of both viral and host anti-viral gene transcriptional heterogeneity at the single cell level. Our analyses also reveal that semi-infectious particles that fail to express the viral NS can play a dominant role in triggering the innate anti-viral response to infection. Altogether, these data reveal how patterns of viral population heterogeneity can serve as a major determinant of antiviral gene activation. Author summary: The combination of the enormous diversity of viral populations, underlying heterogeneity within host cells, and random chance mean that no two infected cells look exactly the same. The role that single cell heterogeneity plays in determining infection outcomes remains very poorly understood. Here, we describe an approach that allowed us to quantify both viral and host gene expression in thousands of influenza A virus infected cells. We observed an enormous degree of heterogeneity in both viral and host gene expression between individual infected cells. We found that virions that fail to express the viral NS gene can be major drivers of host antiviral immune activation. Comparison of antiviral gene expression patterns between H1N1 and H3N2 infection revealed surprising differences in single cell patterns of innate immune activation. Altogether, these studies identify patterns of single cell heterogeneity in both host and viral gene expression as a significant driver of infection outcomes. [ABSTRACT FROM AUTHOR]