Single-cell virus sequence of influenza infections that trigger innate immunity

The outcome of viral infection is extremely heterogeneous at the cellular level, and infected cells only sometimes activate innate immunity. Here we assess how the genetic variation inherent in viral populations contributes to this heterogeneity. We do this by developing a new approach to determine both the cellular transcriptome and full-length sequences of all viral genes in single influenza-infected cells. Infections that activate an innate-immune response in single cells are associated with viral defects that include amino-acid mutations, internal deletions, and failure to express key genes. However, immune activation remains stochastic in cells infected by virions with these defects, and sometimes occurs even in cells infected by virions that express unmutated copies of all genes. Our work shows that the genetic variation present in influenza virus populations substantially contributes to but does not fully explain the heterogeneity in infection outcome and immune activation in single infected cells. Overall design: Combined single-cell transcriptomics and viral genome sequencing of influenza infected cells. A549 cells with an IFN reporter were infected with the A/WSN/1933 strain of influenza virus, and enriched for IFN+ cells. Then single-cell transcriptomics was performed on a 10X Chromium (v2 reagents) and viral mRNA was enriched for full-length PacBio sequencing.