The largest magnitude differences between uninfected and productively infected cells were observed in the jejunum, with >2-fold increases in BAX, CTLA4, ICOS, IFIT3, IL2RG, IL6R, LAT, OAS2, OASL, PRKACB, TNF, and USP18. The considerable heterogeneity in host gene expression across animals, tissue type, and cell infection status indicates that viral expression occurs in a wide range of distinct subsets of CD4 T cells–making selective targeting of infected cells, necessary for cure modalities, a much greater hurdle. Here, PRKACB is linked to infection.