Longitudinal single-cell transcriptomics of gamma herpesvirus infection in mouse lungs

Type-2 immunity is essential for tissue repair processes and is a common contributing factor in the development of fibrosis. We used single cell transcriptomics to comparatively analyze how type-1 and type-2 driven immunity unfolds over a time-course of 100 days in mouse lungs after infection with the murine gamma herpesvirus strain MHV68. In wild type (WT) mice, the virus is cleared within 28 days in an interferon-gamma (IFNγ) dependent manner. In contrast, the IFNγ knock out (IFNγR-/-) mice with MHV68 leads to an incomplete virus clearance, a type-2 bias of the immune response, and the development of irreversible pulmonary fibrosis within 100 days after virus infection. We infected WT (n=30) and IFNγR-/- (n=30) mice with the MHV-68 virus, harvested the lungs for scRNAseq at days 3/6/15/28/45 and 100 post infection, and sequenced a total of 70.000 single cells. Single cell analysis enabled us to derive an unprecedented resolution of the MHV-68 virus and its host transcriptomes at the same single cell level. This facilitates a deep insight into the differential response of infected versus uninfected cells and provides strict monitoring of the general course of the disease. We analyzed cell type specific responses to the virus and resolved gene expression kinetics for more than 30 individual cell types, revealing prominent type-1 and type-2 immune polarization patterns in WT and IFNγR-/- mice, respectively.