Neurobiological Alterations Induced by SARS-CoV-2: Insights from Variant-Specific Host Gene Expression Patterns in hACE2-Expressing Mice

Since the onset of the COVID-19 pandemic, various severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants have emerged. Although the primary site of SARS-CoV-2 infection is the lungs, it can also affect the brain and induce neurological symptoms. However, the specific effects of different variants on the brain remain unclear. In this study, a whole-transcriptome analysis was conducted using the brain tissues of K18-hACE2 mice infected with the ancestral B.1 (Wuhan) variant and with major SARS-CoV-2 variants of concern, including B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta) and B.1.529 (Omicron). After sequencing, differential gene expression, gene ontology (GO) and genome pathway enrichment analyses were performed. An Immune Cell Abundance Identifier (ImmuCellAI) was used to identify the abundance of different cell populations. Additionally, RT-qPCR was used to validate the RNA-seq data. The viral load and hierarchical clustering analyses divided the samples into two different clusters with notable differences in gene expression at day 6 post-infection for all variants compared to the control group. GO and the Kyoto Encyclopedia of genes and genomes enrichment analyses revealed similar patterns of pathway enrichment for different variants. ImmuCellAI revealed the changes in immune cell populations, including the decrease in CD4⁺ T and B cell proportions and the increase in CD8⁺ T and dendritic cell proportions. A co-expression network analysis revealed that some genes, such as STAT1, interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α), were dysregulated in all variants. A RT-qPCR analysis for IL-6, CXCL10 and IRF7 further validated the RNA-seq analysis. In conclusion, this study provides, for the first time, an extensive transcriptome analysis of a K18-hACE2 mouse brain after infection with major SARS-CoV-2 variants.