Data and code availability
Single cell RNA sequencing data generated for this study is available from Gene Expression Omnibus (GEO): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167747. The scripts used for pathway analyses (PROGENy and DoRothEA), ligand-receptor analysis, virus read detection (viral track), as well as the Fiji macro for fibrosis quantification in Masson’s trichrome staining are available on Zenodo: https://zenodo.org/record/5776147. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.