library_construction_protocol: Spleens were harvested from infected mice and cut into small pieces. These pieces were the exposed to a medium containing digestive enzymes (Dnase, Liberase) for 1h hour at 37°C shaking at 240rpm. The digested tissue was then macerated through a 100µm Nytex filter, washed with DMEM and erythrocyte lysis was performed using a hypotonic ACK medium. Lysis was stopped by adding DMEM containing 10% FCS. Cells were counted using a Neubauer counting chamber and a CD90.2 MACS enrichment (Miltneyi) was performed accoring to the manufacurteres instructions. Finally, cells were stained with flurorescently labelled antibodies against CD8a, CD45.1 and CD44 as well as a fixable live/dead dye. Single, live CD8a+CD45.1+ cells were sorted and subsequently used to prepare scRNA-Seq libraries Single-cell RNA libraries were prepared using the BD Rhapsody system (BD Biosciences). First, sample tags were added to individual cell samples (BD Ms Single Cell Sample multiplexing kit, protocol 23-21340(02)). Sample tags 5 to 8 were used for replicates 1 to 4, respectively. Next, single cells of the pooled samples were captured using the BD Rhapsody HT Xpress system and an 8-lane cartridge, followed by reverse transcription and cDNA amplification (BD Rhapsody cDNA kit, protocol 23-24252(01)). Sequencing libraries were constructed using the BD Rhapsody whole transcriptome analysis and TCR/BCR approach (BD Rhapsody Whole Transcriptome Analysis Amplification Kit, BD Rhapsody Mouse TCR/BCR Amplification Kit, protocol 23-24365(01)). QC of libraries was done with Bioanalyzer 2100 using the High Sensitivity DNA Kit (Agilent) and Qubit 2.0 fluorometer with the Qubit 1X dsDNA HS Assay-Kit (Invitrogen). Libraries were sequenced on a NovaSeq X Plus (Illumina) with paired-end 2x150bp reads.