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. We 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.Our 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.

COVID-19, caused by SARS-CoV-2, has recently affected over 300,000 people and killed more than 10,000. The manner in which the key immune cell subsets change and their states during the course of COVID-19 remain unclear. Here, we applied single-cell technology to comprehensively characterize transcriptional changes in peripheral blood mononuclear cells during the recovery stage of COVID-19. Compared with healthy controls, in patients in the early recovery stage (ERS) of COVID-19, T cells decreased remarkably, whereas monocytes increased. A detailed analysis of the monocytes revealed that there was an increased ratio of classical CD14 ++ monocytes with high inflammatory gene expression as well as a greater abundance of CD14 ++ IL1B + monocytes in the ERS. CD4 + 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. Our study identified several novel B cell-receptor (BCR) changes, such as IGHV3-23 and IGHV3-7, and confirmed isotypes (IGHV3-15, IGHV3-30, and IGKV3-11) previously used for virus vaccine development. The strongest pairing frequencies, IGHV3-23-IGHJ4, indicated a monoclonal state associated with SARS-CoV-2 specificity. 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. Our study provides the first evidence of an inflammatory immune signature in the ERS, suggesting that COVID-19 patients are still vulnerable after hospital discharge. Our identification of novel BCR signaling may lead to the development of vaccines and antibodies for the treatment of COVID-19. Software and AlgorithmsPrism 8 https://www.graphpad.com/scientificsoftware/ prism/ Cell Ranger 3.1.0 https://support.10xgenomics.com Loupe Browser 4.0.0 https://support.10xgenomics.com Loupe V(D)J Browser 3.0.0 https://support.10xgenomics.com R 3.6.1 https://www.r-project.org/ Seurat V3 [37] https://satijalab.org/ Monocle3 [38] https://cole-trapnell-lab.github.io/monocle3 GO analysis [39] https://www.metascape.org Patients 10 COVID-19 patients diagnosed with by real-time fluorescent RT-PCR were collected in the Wuhan Hankou Hospital China. Patients were divided into early-recovery stage (ERS) group and late-recovery stage (LRS) group according to the days from first negative nucleic acid transfer date to blood sampling date. We defined the RES group of five cases as the date of nucleic acid turningnegative to blood sampling is less than seven days and LRS group of five cases as is more than fourteen days. The 10 patients consisted of five males and five females and ranged from ages 40 to 70 years old, with a median of 50 years old. The demographic characteristics of these patients are provided in Fig. S1. A written informed consent was regularly obtained from all patients. The study was approved by the Ethics Committee of Wuhan Hankou Hospital, ...

Highlights d We single-cell RNA-sequenced 56,771 endothelial cells (ECs) from human, mouse, and cultured lung tumor models d Tip ECs were resolved into migratory and basementmembrane remodeling phenotypes d Capillary and venous ECs expressed immunoregulatory gene signatures d Integrated analysis identified collagen modification as an angiogenic pathway

Highlights d Single-cell RNA-seq reveals EC heterogeneity in choroidal neovascularization d ECs display metabolic transcriptome heterogeneity in the cell cycle and quiescence d Data integration with a genome-scale metabolic model identifies angiogenic targets d SQLE and ALDH18A1 are validated as metabolic angiogenic candidates

In the original article, the surname of co-author Wouter Everaerts was spelled incorrectly as "Everaert." It appears correctly in this Correction, and the error has been corrected online.