Single-cell RNA sequencing reveals the diversity of the immunological landscape in response to murine coronavirus infection of the central nervous system

Intracranial (i.c.) infection of susceptible C57BL/6 mice with a neurotropic JHM strain mouse hepatitis virus (a member of the Coronaviridae family) results in acute encephalomyelitis and viral persistence associated with an immune-mediated demyelinating disease. The present study was undertaken to better understand the molecular pathways evoked during innate and adaptive immune responses as well as the chronic demyelinating stage of disease in response to JHMV infection of the central nervous system (CNS). Using single cell RNA sequencing analysis (scRNAseq) on flow-sorted CD45-positive cells (CD45+) enriched from brains and spinal cords of experimental mice, we demonstrate the heterogeneity of the immune response as determined by unique molecular signatures and pathways involved in effective anti-viral host defense. Furthermore, we identify potential genes involved in contributing to demyelination as well as remyelination being expressed by both microglia and macrophages. Collectively, these findings emphasize the diversity of the immune response and molecular networks at defined stages following viral infection of the CNS. Adult (5-6 week old) C57BL/6 mice were intracranially (i.c.) infected with 1,500 plaque forming units (PFU) of JHMV and CD45-positive (CD45+) cells were flow sorted from the brains of JHMV-infected mice at days 3 and 7 post-infection (p.i.) and spinal cords at day 21 p.i. as well as the brains of infected mice. FACS sorted CD45+ cells then underwent single-cell RNA-sequencing analysis