Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients

Dysfunctional immune response in the COVID-19 patients is a recurrent theme impacting symptoms and mortality, yet the detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 205 COVID-19 patients and controls to create a comprehensive immune landscape. Lymphopenia and active T and B cell responses were found to coexist and associated with age, sex and their interactions with COVID-19. Diverse epithelial and immune cell types were observed to be virus-positive and showed dramatic transcriptomic changes. Elevation of ANXA1 and S100A9 in virus-positive squamous epithelial cells may enable the initiation of neutrophil and macrophage responses via the ANXA1-FPR1 and S100A8/9-TLR4 axes. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis and designing effective therapeutic strategies for COVID-19. HIGHLIGHTSO_LILarge-scale scRNA-seq analysis depicts the immune landscape of COVID-19 C_LIO_LILymphopenia and active T and B cell responses coexist and are shaped by age and sex C_LIO_LISARS-CoV-2 infects diverse epithelial and immune cells, inducing distinct responses C_LIO_LICytokine storms with systemic S100A8/A9 are associated with COVID-19 severity C_LI

The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing

Understanding the mechanism that leads to immune dysfunction induced by SARS-CoV2 virus is crucial to develop treatment for severe COVID-19. Here, using single cell RNA-seq, we characterized the peripheral blood mononuclear cells (PBMC) from uninfected controls and COVID-19 patients, and cells in paired broncho-alveolar lavage fluid (BALF). We found a close association of decreased dendritic cells (DC) and increased monocytes resembling myeloid-derived suppressor cells (MDSC) which correlated with lymphopenia and inflammation in the blood of severe COVID-19 patients. Those MDSC-like monocytes were immune-paralyzed. In contrast, monocyte-macrophages in BALFs of COVID-19 patients produced massive amounts of cytokines and chemokines, but secreted little interferons. The frequencies of peripheral T cells and NK cells were significantly decreased in severe COVID-19 patients, especially for innate-like T and various CD8+ T cell subsets, compared to health controls. In contrast, the proportions of various activated CD4+ T cell subsets, including Th1, Th2 and Th17-like cells were increased and more clonally expanded in severe COVID-19 patients. Patients peripheral T cells showed no sign of exhaustion or augmented cell death, whereas T cells in BALFs produced higher levels of IFNG, TNF, CCL4 and CCL5 etc. Paired TCR tracking indicated abundant recruitment of peripheral T cells to the patients lung. Together, this study comprehensively depicts how the immune cell landscape is perturbed in severe COVID-19.

Potent human neutralizing antibodies elicited by SARS-CoV-2 infection

The pandemic caused by emerging coronavirus SARS-CoV-2 presents a serious global public health emergency in urgent need of prophylactic and therapeutic interventions. SARS-CoV-2 cellular entry depends on binding between the viral Spike protein receptor-binding domain (RBD) and the angiotensin converting enzyme 2 (ACE2) target cell receptor. Here, we report on the isolation and characterization of 206 RBD-specific monoclonal antibodies (mAbs) derived from single B cells of eight SARS-CoV-2 infected individuals. These mAbs come from diverse families of antibody heavy and light chains without apparent enrichment for particular families in the repertoire. In samples from one patient selected for further analyses, we found coexistence of germline and germline divergent clones. Both clone types demonstrated impressive binding and neutralizing activity against pseudovirus and live SARS-CoV-2. However, the antibody neutralizing potency is determined by competition with ACE2 receptor for RBD binding. Surprisingly, none of the SARS-CoV-2 antibodies nor the infected plasma cross-reacted with RBDs from either SARS-CoV or MERS-CoV although substantial plasma cross-reactivity to the trimeric Spike proteins from SARS-CoV and MERS-CoV was found. These results suggest that antibody response to RBDs is viral species-specific while that cross-recognition target regions outside the RBD. The specificity and neutralizing characteristics of this plasma cross-reactivity requires further investigation. Nevertheless, the diverse and potent neutralizing antibodies identified here are promising candidates for prophylactic and therapeutic SARS-CoV-2 interventions.

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

The new coronavirus (2019-nCoV) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by 2019-nCov to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. 2019-nCoV may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.

The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing

The novel coronavirus SARS-CoV-2, etiological agent of recently named Coronavirus infected disease (COVID-19) by WHO, has caused more than 2, 000 deaths worldwide since its emergency in Wuhan City, Hubei province, China, in December, 2019. The symptoms of COVID-19 varied from modest, mild to acute respiratory distress syndrome (ARDS), and the latter of which is generally associated with deregulated immune cytokine production; however, we currently know little as to the interplay between the extent of clinical symptoms and the compositions of lung immune microenvironment. Here, we comprehensively characterized the lung immune microenvironment with the bronchoalveolar lavage fluid (BALF) from 3 severe and 3 mild COVID-19 patients and 8 previously reported healthy lung controls through single-cell RNA sequence (scRNA-seq) combined with TCR-seq. Our data shows that monocyte-derived FCN1+ macrophages, whereas notFABP4+ alveolar macrophages that represent a predominant macrophage subset in BALF from patients with mild diseases, overwhelm in the severely damaged lungs from patients with ARDS. These cells are highly inflammatory and enormous chemokine producers implicated in cytokine storm. Furthermore, the formation of tissue resident, highly expanded clonal CD8+ T cells in the lung microenvironment of mild symptom patients suggests a robust adaptive immune response connected to a better control of COVID-19. This study first reported the cellular atlas of lung bronchoalveolar immune microenvironment in COVID-19 patients at the single-cell resolution, and unveiled the potential immune mechanisms underlying disease progression and protection in COVID-19. HighlightsO_LIImmune microenvironment of SARS-CoV-2-infected lungs revealed by scRNA/TCR seq C_LIO_LIIncreased inflammatory FCN1+ macrophages are replacing FABP4+ macrophages in the BALF from severe COVID-19 patients C_LIO_LIHighly expanded and functional competent tissue resident clonal CD8+ T cells in mild COVID-19 patients C_LI

Erratum to: Irreversible phenotypic perturbation and functional impairment of B cells during HIV-1 infection / 医学前沿

The original version of this article unfortunately contained a mistake. One of the authors of this article has been misspelled. Xiaoyang Zhang should be Xiaoyan Zhang. The update is also provided here.

Polymorphisms in p.S267F of SLC10A1 gene is associated with clinical outcomes of HBV infection / 中华临床感染病杂志

Objective To investigate the association of restriction fragment length polymorphisms (RFLP) in p.S267F of SLC10A1 gene with clinical outcomes of hepatitis B virus (HBV) infection. Methods Clinical data of 1 268 patients with HBV infections admitted in Public Health Clinical Center Affiliated to Fudan University during July 2014 and February 2015 were collected.Polymerase chain reaction-restriction fragment length polymorphism ( PCR-RFLP) method was used to genotype the p .S267F of SLC10A1 gene in all patients, and the potential association between variants in p .S267F of SLC10A1 gene and the clinical outcomes of HBV infection was analyzed .Results Among 1 268 patients with HBV infections, 1 226 were of genotype CC, and 42 were of genotype CT, so the variation rate in p.S267F was 3.31%(42/1 268).Compared with patients with genotype CC , patients with genotype CT had a higher incidence of acute HBV infections (13.6%vs.28.6%,χ2 =19.819, P<0.05) and a lower incidence of HBV-related liver cirrhosis or hepatocellular carcinoma (13.9% vs.4.8%, χ2 =18.945, P <0.05). Conclusion RFLP in p.S267F of SLC10A1 gene may be associated with chronicity and aggravation of HBV infection, and genotype CT is possibly a protective factor .

Expression of CD127 and its association with apoptosis of CD8 + T lymphocytes in patients with chronic HIV-1 infection / 中华临床感染病杂志

Objective To investigate the expression of CD127 (interleukin-7 receptor α, IL-7Rα)and its association with apoptosis of CD8 + T lymphocytes in patients with chronic HIV-1 infection. Methods The expression of CD127 on T lymphocytes and spontaneous apoptosis of CD8+ T lymphocytes were measured by flow cytometry in peripheral blood from 24 patients with chronic HIV-1 infections and 12 healthy subjects. The associations of CD127 expression with CD4 +T lymphocytes counts, HIV RNA loads and cell apoptosis were analyzed. Mann-Whitney U test was performed to compare between the groups, and Spearman test was used for correlation analysis. Results The expression of CD127 on CD8 + T lymphocytes was significantly down-regulated in HIV-1 infected subjects (Z = -4.796, P ＜ 0. 01 ), which was positively correlated with CD4 + T lymphocytes (r = 0.817, P ＜ 0.01 ) and negatively correlated with HIV RNA load and CD8+T lymphocytes apoptosis (r= -0.442 and -0.688,P＜0.05 and ＜0.01). Conclusion CD127 down-regulation may play an important role in the descended ability of receiving survival signals and ascended apoptosis of CD8 + T lymphocytes during chronic HIV-1 infection, which indicates that IL-7 might be a novel strategy in treatment of HIV infection.