library_construction_protocol: Infected cells from culture and mice were sorted into 500 µL of 40% CCS complete media, which was further diluted in PBS (up to 1 mL total volume) after sorting. After centrifugation and resuspension in 1x PBS (calcium and magnesium free) containing 0.04% weight/volume BSA (400 µg/mL), cells were loaded onto a chromium chip for encapsulation via the 10x Genomics platform. 10x Chromium Single Cell 3' Library v3 chemistry was used and manufacturer's instructions were followed for cDNA amplification and library construction. The NextSeq 500/550 High Output Kit v2.5 (75 cycles) was used to obtain paired-end reads from an Illumina NextSeq 500 sequencer.