Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing

COVID-19, caused by SARS-CoV-2, has recently affected over 1,200,000 people and killed more than 60,000. The key immune cell subsets change and their states during the course of COVID-19 remain unclear. Researchers at the National Center for Liver Cancer, Shanghai sought to comprehensively characterize the transcriptional changes in peripheral blood mononuclear cells during the recovery stage of COVID-19 by single-cell RNA sequencing technique.

It was found that T cells decreased remarkably, whereas monocytes increased in patients in the early recovery stage (ERS) of COVID-19. There was an increased ratio of classical CD14++ monocytes with high inflammatory gene expression as well as a greater abundance of CD14++IL1β+ monocytes in the ERS. CD4+ T cells and CD8+ T cells decreased significantly and expressed high levels of inflammatory genes in the ERS. Among the B cells, the plasma cells increased remarkably, whereas the naïve B cells decreased. Several novel B cell-receptor (BCR) changes were identified, such as IGHV3-23 and IGHV3-7, and isotypes (IGHV3-15, IGHV3-30, and IGKV3-11) previously used for virus vaccine development were confirmed. The strongest pairing frequencies, IGHV3-23-IGHJ4, indicated a monoclonal state associated with SARS-CoV-2 specificity, which had not been reported yet. Furthermore, integrated analysis predicted that IL-1β and M-CSF may be novel candidate target genes for inflammatory storm and that TNFSF13, IL-18, IL-2, and IL-4 may be beneficial for the recovery of COVID-19 patients.

Study design and analysis of single immune cell profiling in COVID-19 patients

a Schematics of the experimental design for single-cell RNA (sc-RNA) sequencing. Peripheral blood mononuclear cells (PBMCs) were collected from COVID-19 patients and healthy controls (HCs) and then processed via sc-RNA, sc-BCR, and sc-TCR sequencing using the 10x-Based Genomics platform. b The heatmaps show differentially expressed genes (DEGs) upregulated in myeloid cells, NK and T cells, B cells, and other clusters of PBMCs. c t-distributed stochastic neighbor embedding (t-SNE) plot showing myeloid cells (red), NK and T cells (blue), B cells (green), and other clusters (gray) of PBMCs identified using integrated and classification analysis. d t-SNE projection of canonical markers, including CD14, CD1C, and FCGR3A for myeloid cells; CD3E, CD4, CD8A, and NCAM1 for NK and T cells; and CD19 for B cells as indicated in the legend.

This study provides the first evidence of an inflammatory immune signature in the ERS, suggesting COVID-19 patients are still vulnerable after hospital discharge. Identification of novel BCR signaling may lead to the development of vaccines and antibodies for the treatment of COVID-19.