Fig 1.

Longitudinal study of viral transcript abundance and nonsynonymous (Ns) mutations in brain following intranasal infection with VEEV TC-83. Twenty, 5- to 6-week-old mice were humanely sacrificed at 1, 3, 5, 6, or 7 dpi (n = 4/day) for brain sections were dissected for RNA-Seq as described in the Materials and Methods. The number of VEEV TC-83 transcripts per million or TPM (A) and the number of Ns mutations (B) are presented for each day for each of the eight areas of the brain. To identify Ns, variant calling was performed such that each variant had a minimum coverage of 100, a count of 50, and a frequency of 1%. (C) The number of Ns mutations discovered from all samples are presented in the context of the structural and nonstructural genes of the genome. CBX, cerebellum; dpi, days post-infection; HIP, hippocampus; MOB, main olfactory bulb; MTX, motor cortex; PIR, piriform cortex; STR, striatum; THA, thalamus.