design: Nucleic acids were extracted using the MagNA Pure 96 DNA and Viral NA Small Volume kit (https://lifescience.roche.com). Viral RNA load was quantified using a previously described RT-qPCR assay (1). The library was prepared using the KAPA RNA HyperPrep kit (https://sequencing.roche.com), and sequencing was performed on a MiniSeq high-output reagent kit (150 cycles paired-end) (https://www.illumina.com/). The reads were then mapped to the Venezuelan Equine Encephalitis Virus (VEEV) subtype ID reference sequence (GenBank accession number NC_001449) using Geneious (2023.2.1).