The entire injection site was removed at 24 hpi from adult and weanling mice (mock and infected) and frozen at -80C. RNA was extracted using TRIzol reagent as described above for RT-qPCR. RNA was further purified using QIAamp Viral RNA kit (Qiagen).  Approximately 1 g of each extracted RNA was processed to generate sequencing libraries using TruSeq Stranded mRNA Reference Guide, October 2017, (Illumina, Inc.) and were barcoded using combinatory dual (CD) indexes. All finished libraries had an average fragment length of 300 base pairs as measured on a Bioanalyzer DNA1000 chip (Agilent, Inc.). The samples were quantitated and pooled in equimolar amounts using KAPA Library Quantification kit (Roche, Inc.) with measurement on a CFX96 Touch Real-Time PCR Detection System (BioRad, Inc.) Sequencing was performed using a NextSeq 550 instrument and High-Output v2.5 SBS chemistry (Illumina) for 75 cycles plus an additional 8 cycles to read the index, in each direction for a total of 166 cycles.