408. Single-cell Sequencing Identifies Variability in Host Response Among Different Genera of Influenza Viruses

Abstract

BackgroundSeroprevalence and surveillance studies indicate that influenza C virus (ICV) infection is common among humans, and initial exposure occurs early in life. ICV often causes milder disease than influenza A and B viruses, but the mechanisms underlying differences in pathogenicity remain poorly understood.MethodsTo compare early events of infection in natural target sites, we cultured primary human tracheal/bronchial epithelial cells under air-liquid interface conditions to allow differentiation. We-infected these cells with human strains of influenza A, B or C virus. Cells were infected at low MOI (0.1) to ensure populations of directly infected cells and uninfected neighboring cells. To compare the early immune response and cell tropism among these viruses, we performed single-cell RNA sequencing of mock- and influenza-infected cells. In parallel, we infected cells pretreated with interferon to mimic later rounds of infection after an early immune response is initiated.ResultsInfection of primary cells by all three viruses was confirmed by RT-qPCR of bulk cell lysates. As expected, prior exposure to interferon β results resulted in reduced levels of viral transcripts. At the single-cell level, we identified expression of genes associated with specific cell types, including basal, ciliated and secretory cells. We also identified expression of interferon stimulated genes, but these genes were not homogeneously expressed among all cell subpopulations and varied among cultures infected with different influenza viruses. We also found different patterns in gene expression in cells previously exposed to interferon, suggesting that host environment varies over subsequent rounds of infection.ConclusionSingle-cell sequencing is an important tool for studying the host response to influenza infection in complex cellular environments such as the respiratory tract, in which cells vary in their susceptibility to infection and antiviral response. Further analysis will characterize differences among directly infected vs. neighboring cells and correlate responses with pathogenicity.Disclosures All authors: No reported disclosures.