RT Journal Article SR Electronic T1 Cell-to-cell variation in defective virus expression and effects on host responses during influenza virus infection JF bioRxiv FD Cold Spring Harbor Laboratory SP 487785 DO 10.1101/487785 A1 Chang Wang A1 Christian V. Forst A1 Tsui-wen Chou A1 Adam Geber A1 Minghui Wang A1 Wissam Hamou A1 Melissa Smith A1 Robert Sebra A1 Bin Zhang A1 Bin Zhou A1 Elodie Ghedin YR 2018 UL http://biorxiv.org/content/early/2018/12/10/487785.abstract AB Virus and host factors contribute to cell-to-cell variation in viral infections and determine the outcome of the overall infection. However, the extent of the variability at the single cell level and how it impacts virus-host interactions at a systems level are not well understood. To characterize the dynamics of viral transcription and host responses, we used single-cell RNA sequencing to quantify at multiple time points the host and viral transcriptomes of human A549 cells and primary bronchial epithelial cells infected with influenza A virus. We observed substantial variability of viral transcription between cells, including the accumulation of defective viral genomes (DVGs) that impact viral replication. We show a correlation between DVGs and viral-induced variation of the host transcriptional program and an association between differential induction of innate immune response genes and attenuated viral transcription in subpopulations of cells. These observations at the single cell level improve our understanding of the complex virus-host interplay during influenza infection.AUTHOR SUMMARY Defective influenza virus particles, which are products of error-prone viral replication, carry incomplete versions of the genome and can interfere with the replication of competent viruses. These defective genomes are thought to modulate disease severity and pathogenicity of the influenza infection. Different defective viral genomes can have different interfering abilities, and introduce another source of variation across a heterogeneous cell population. Evaluating the impact of defective virus genomes on host cell responses cannot be fully resolved at the population level, requiring single cell transcriptional profiling. Here we characterized virus and host transcriptomes in influenza-infected cells, including that of defective viruses that arise during influenza A virus infection. We profiled single cell transcriptional landscapes over the course of the infection and established an association between defective virus transcription and host responses. We identified dominant defective viral genome species and validated their interfering and immunostimulatory functions in vitro. This study demonstrates the intricate effects of defective viral genomes on host transcriptional responses and highlights the importance of capturing host-virus interactions at the single-cell level.