RNA-seq in imprinted vs naive Omicron-positive volunteers
Introduction: Transcriptome analysis using various methods offers insights into gene expression profiles during specific immune responses. In this study, we investigated the differences in gene expression and immune responses among infection-na?ve individuals, those previously infected with SARS-CoV-2, and those primarily immunized via vaccination.  Methods: We employed total RNA-seq to analyze differentially expressed genes (DEGs) during the acute phase of SARS-CoV-2 Omicron B.1.1.529 infection. Patient immune statuses were characterized, and virus strains were identified using specific PCR and melting curve analysis. Additionally, patient immune statuses were confirmed via serological testing.  Results: Individuals immunized primarily via vaccination exhibited distinct gene expression patterns compared to infection-na?ve and previously infected individuals. Contrary to expectations, vaccination primarily led to downregulation of DNA metabolism-related signaling pathways rather than upregulation of immune response pathways.  Discussion: Our findings highlight potential differences in physiological responses between natural infection and vaccination. Despite the preliminary nature of our results and the limitations of the study, such as the small sample size and unique study timing, our study provides valuable insights into transcriptomic responses to SARS-CoV-2 infection and vaccination. These results underscore the need for further investigation to validate and generalize these findings, thereby contributing to a better understanding of immune responses to SARS-CoV-2.