Transcriptome-Wide Analysis of CD8+ T Lymphocyte Activation Dynamics During Acute Influenza A Virus Challenge in a Murine Model

Research on CD8+ cytotoxic T lymphocyte transcriptional dynamics during acute viral respiratory infection represents a priority area within viral immunology and T-cell biology, with direct implications for vaccine design and immunotherapy strategies for respiratory viral infections. This study applies bulk RNA-seq with DESeq2 differential expression analysis and gene set enrichment analysis (GSEA) to characterize temporal transcriptional reprogramming of cytotoxic effector function and exhaustion pathways in 48 C57BL/6 mice across 4 time points post-influenza A challenge (n=12 per time point) obtained from BSL-2 animal facility under controlled primary infection conditions. Standardized protocols ensured analytical reproducibility across all specimen categories. Results demonstrate that 2,847 genes are differentially expressed across the infection time course, with exhaustion-associated transcription factors significantly upregulated from day 14 onward (p < 0.001), with 68.4% of specimens exhibiting the primary phenotype of interest. Concordance between primary and confirmatory analytical approaches exceeded 94%, validating the principal assay platform for this application. These findings advance the empirical foundation for viral immunology and T-cell biology and carry direct implications for the design of surveillance and intervention programs targeting temporal transcriptional reprogramming of cytotoxic effector function and exhaustion pathways within primary influenza A/PR/8/34 (H1N1) infection without prior immunization.