Cell-to-cell variation in defective virus expression and effect on host response during influenza virus infection

Virus and host factors contribute to cell-to-cell variation in viral infection 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. Overall design: Dataset consists of 12 single-cell RNA-seq datasets generated from 10X Genomics Chromium 3' platform with v2 chemistry, 20 conventional bulk RNA-seq datasets generated with NEBNext Ultra II RNA library prep kit and poly(A) mRNA magnetic isolation module, and one viral genome sequencing dataset generated from multi-segment reverse-transcription PCR (M-RT-PCR) products followed by library preparation with Nextera DNA library prep kit.