Comprehensive mapping of the signaling events evoked by SARS-CoV-2 variants delta and omicron in human astrocytes

COVID-19 causes a wide range of complications in the central nervous system, including encephalitis and other neurological symptoms such as memory problems, psychological disorders, depression, and anxiety. We present comprehensive data on the changes in gene expression levels in astrocytes infected with the Delta or Omicron variants of SARS-CoV-2. In RNA-seq data, we found 346 genes that were significantly evoked (197 up- and 149 down-regulated) in astrocytes challenged with the Omicron variant, compared to 341 evoked genes (215 up- and 126 down-regulated) in the Delta variant. A surprisingly large number of genes were exclusively evoked by Delta (82 up- and 48 downregulated) and Omicron variants (65 up and 60 downregulated). Numerous pathways, including those pertaining to the neuronal system, metabolism, response to viral infection, signal transduction, cytokine signaling, and homeostasis, were dysregulated in infected astrocytes. In this report we have dissected major pathways that are related to pathogen recognition, integrity of the BBB and glia limitans, and neurological disorders that could lead to neurological symptoms listed above. Our findings also reveal dysregulation of a large number of non-coding RNAs. The data presented here may help us better understand the role of astrocytes in the neurological disorders seen in COVID-19 patients.