Benchmarking of viruses detection from single-cell RNA sequencing data

We developed a new computational pipeline called Viral-Track that can detect the viruses in a single-cell RNA sequencing sample. To validate this tool, we benchmarked it on several mouse models of infection, including lymph node infection by the Lymphocytic choriomeningitis virus (LCMV) and the Vesicular Stomatitis Virus (VSV). We also used a GFP expressing LCMV strain to infect a mouse and then sequenced the infected (GFP+) cells. Overall design: Tissue from LCMV or VSV infected mouse are collected 24h (Lymph Node) or 72h (Spleen) after infection. For spleen samples, an LCMV-GFP virus is used and GFP+ cells are sorted sequenced. For Lymph Node samples, Cd45+ non B/T cells are sorted and sequenced