# Transcriptomic insights into the immune dynamics of wild-type mice challenged with SARS-CoV-2 Beta variant

## TL;DR

This study explores how wild-type mice respond to SARS-CoV-2 Beta variant infection by analyzing gene activity in their lungs.

## Contribution

It is the first transcriptomic analysis of wild-type mice infected with a clinical SARS-CoV-2 isolate.

## Key findings

- 285 and 46 differentially expressed genes were identified at 3 and 6 days post-infection.
- Key pathways like apoptosis and cytokine response were upregulated in infected lungs.
- Hub genes and inflammatory mediators such as IL-6 and CCL2 were significantly increased.

## Abstract

Mice are useful small animal models to study the pathogenesis of SARS-CoV-2 infection. As the ancestral SARS-CoV-2 strains did not utilize murine Ace2 as a receptor, wild-type mice were not susceptible to the SARS-CoV-2 infection. Infection of human ACE2-expressing transgenic mice with SARS-CoV-2 induces fatal encephalitis, which is not commonly observed in humans. We and others have previously demonstrated the ability of the SARS-CoV-2 Beta variant to productively infect wild-type mice. Herein, we employed RNA-seq to investigate the transcriptomic landscapes in the lungs after the infection of wild-type mice with SARS-CoV-2 Beta variant.

We intranasally infected 6-week-old wild-type C57BL/6J mice with the SARS-CoV-2 (B.1.351 strain) and collected lungs at 3- and 6-days post-infection for RNA-sequencing. We used the Limma-Voom package to identify differentially expressed genes (DEGs) and the fgsea package for pathway enrichment analysis. We used Cytoscape to identify hub genes and gene networks. Lastly, we employed RT-qPCR and multiplex assay to validate the RNA-seq data.

Using a cutoff of an adjusted p-value below 0.05 and an absolute log2 fold change value greater than 0.75, we identified 285 DEGs on day 3 and 46 DEGs on day 6. The canonical pathways analysis showed that several key pathways such as apoptosis and cytokine response were upregulated in the infected lungs. Protein-protein interaction analyses identified innovative target genes such as Kif11, Ccna2, and Aurkb. We also identified the top 10 hub genes that included Prc1, Ube2c, Ccnb2, Ncapg, Aurkb, Cep55, Mki67, Dlgap5, Ccna2, and Kif11. RT-qPCR analysis for Tnfa, Il6, Ccl2, and Ccl3 further validated the RNA-seq analysis. Consistent with gene expression results, we detected significantly increased protein levels of various inflammatory mediators such as IL-6, CCL2, CXCL2, and CXCL10 in the infected lungs.

This is the first transcriptomic analysis of the lungs of wild-type mice infected with a clinical isolate of SARS-CoV-2. Our findings provide a further understanding of the pathogenic events that occur in this mouse model of SARS-CoV-2 infection.

The online version contains supplementary material available at 10.1186/s42826-025-00264-4.