GSE115952
Non-lytic clearance of influenza B virus from infected cells [RNA-seq]
Influenza B virus (IBV) is an acute respiratory pathogen that induces phenotypic alterations to the lung epithelium, such as the denudation of the respiratory cilium, during and after IBV infection.  It has been assumed that these epithelial changes are non-adaptive, and simply the result of cellular death following lytic virus infection. However, previous reports have shown that not all infected cells are killed after viral infection; some cells can completely clear viral RNA and protein and persist in the host long-term.  In this study, we utilized a novel recombinant virus in combination with a Cre recombinase-responsive transgenic mouse model to demonstrate that IBV infection leads to the formation of a population of survivor ciliated cells in the proximal airways of infected mice. We then performed transcriptional profiling on infected and surviving ciliated cell populations to determine how surviving viral infection affected these cells. To specifically profile ciliated cells, we digested mouse lungs and sorted cells based on their expression of CD24 with tdTomato as a marker of infection.  We sorted cell populations from the lungs of animals mock infected with PBS (Mock), during active infection (2 DPI), and matched ciliated cell populations at 14 days post-infection that had either experienced direct viral infection (14 DPI Survivor Cell) or those that had never been infected (14 DPI). The resulting data indicate that after surviving infection and clearing the virus, survivor ciliated cells undergo significant transcriptional reprogramming. Overall design: Analysis of RNA from lung ciliated cells  at various timepoints after influenza virus infection, 4 samples collected in duplicate on 2 lanes for a total of 16 samples.