Long-term longitudinal analysis of peripheral blood transcriptome in COVID-19 patients

We performed the longitudinal peripheral blood transcriptome profiling after diagnosis in five patients, and found that patients' blood transcriptomes undergo dramatic and consistent changes in early recovery stage (ERS). Meanwhile, the blood transcriptome did not fully return to the healthy state even after more than one month of recovery. We also realized that differential expressed genes (DEGs) are enriched in biological processes of antigen processing and related processes, and promoter regions of these genes enrich key transcription factors (TFs) involved in T cell differentiation and activation. We further provided potential mechanisms underlying these orchestrated processes, by revealing these specific TFs mediated gene co-expression network. Overall design: Examination between recovery stage and healthy control. Differential gene expression analysis was performed using DESeq2 (Love et al., 2014). Genes that displayed ±1 log2FC (FDR <0.01) between ERS or LRS and healthy control samples were considered as significantly differentially expressed.