Fig. 5

HSV-1 in the brain of an individual. a Detection of an individual (sample ID: X4EP) with severe HSV-1 infection. Each dot indicates the normalized read count of HSV-1 in each individual (n = 32). Note that HSV-1 reads were undetectable in 515 individuals. b HSV-1 transcript abundance across tissues in the individual (sample ID: X4EP). The normalized read counts of HSV-1 are shown. Only the brain was subdivided into each region. BA, Brodmann’s area. c Proportion of HSV-1 reads in the total assigned reads. The percentages in the respective brain regions of the individual (sample ID: X4EP) are shown. d Anatomical distribution of HSV-1 transcripts in the brain. The normalized expression levels of HSV-1 in the respective brain regions of the individual (sample ID: X4EP) are shown as a brain-shaped heatmap. The regions without RNA-Seq data are shown in gray. e Differential gene expression in the brain. DESeq2 was used for feature selection of genes toward downstream analyses. The heatmap contains 1242 DEGs (X4EP sample versus other samples) that were detected in any of the four brain regions (amygdala, hypothalamus, hippocampus, and anterior cingulate cortex). The DEGs were classified into three clusters: cluster 1 (blue), cluster 2 (red), and cluster 3 (orange), mainly consisting of commonly downregulated genes, commonly upregulated genes, and the genes upregulated specifically in the amygdala, respectively. f GO enrichment analysis of the three gene clusters. The terms with statistical significance (FDR < 0.05) are shown