GSE116031
Non-lytic clearance of influenza B virus from infected cells [scRNA-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. To ensure that we were studying ciliated cells with markers that were maintained during viral infection in vivo, we performed single-cell transcriptional profiling on infected and surviving ciliated cell populations. We digested mouse lungs and sorted cells using tdTomato as a marker of infection. We sorted cell populations from the lungs of animals mock infected with PBS (Mock) and during active infection (2 DPI). The resulting data revealed that the marker CD24 is consistently expressed on ciliated cells before and during viral infection. Overall design: Analysis of RNA from lung epithelial cells  from Mock and 2 days after influenza virus infection.