Fig. 3

Changes in brain transcriptome following SHIV dissemination in the CNS. A Kinetics of plasma (red) and CSF (green) viral loads following intravenous infection with. SHIV.C.CH505. CSF vRNA correlates with Plasma vRNA (r = 0.96, p < 0.001; two-tailed Spearman correlation). B vRNA and vDNA copies in various brain regions, dura mater, deep cervical lymph nodes, and PBMCs. Correlation of vDNA with vRNA from all brain regions sampled (r = 0.82, p < 0.001; two-tailed Spearman correlation). Bottom graph shows ratio of CSF glucose and albumin (in mg/dL) during acute viremia. C Cluster dendrogram showing modules of significantly co-expressed genes associated with SHIV infection indicated by color (pink [393 genes] royal blue [30 genes], turquoise [1466 genes], blue [1411 genes]). D Expression levels of module eigengene based on SHIV infection status (+ infected, −uninfected) in the pre-frontal cortex white matter (PFCw), superior temporal sulcus (STS), caudate nucleus, and hippocampus (Left). Significantly enriched biological process gene ontology (GO) terms in SHIV-specific gene co-expression modules (Right). D Box plots indicate quartiles. P values determined by Fisher’s exact test. A, B Symbols indicate individual animals. A Data points in correlation plot indicate samples collected from individual animals (referenced by shape) and collection timepoint (weeks 1–4). B Data points in correlation plot indicate samples collected from individual animals and tissues (Brain regions, Dura mater, deep cervical lymph nodes, and PBMCs).