Time-course single-cell and spatial transcriptomics of reovirus-induced myocarditis in neonatal mice

A significant fraction of sudden death in young adults is due to myocarditis, an inflammatory disease of the heart, most often caused by viral infection. Here we used single-cell and spatially resolved RNA sequencing (RNA-seq) to study the cellular and spatial heterogeneity of myocarditic processes in the hearts of reovirus-infected neonatal mice at multiple predetermined time points after initial infection at the primary site of infection. We further applied these technologies to study the innate response to reovirus infection in the intestine. In addition, we performed time-dependent single-cell RNA-seq (scRNA-seq) of cardiac tissues of mice infected with a reovirus point mutant that does not cause myocarditis. To establish viral tropism, we implemented molecular enrichment of non-polyadenylated viral transcripts that were otherwise poorly represented in the transcriptomes. Our measurements give insight into the cardiac cell-type specificity of innate immune responses, into the tropism of the virus in the intestine and the heart, into the transcriptional states of cell types involved in the production of inflammatory cytokines and the recruitment of circulating immune cells, and into the cell type specific gene expression in a spatial context. Overall, our data identify cellular interactions and cell-type specific host responses during reovirus-induced myocarditis. Overall design: Time-course single-cell and spatial transcriptomics of ileum and heart tissues from reovirus-infected neonatal mice