On Feb. 03rd, 2021, the Zhang Lab from Biomedical Pioneering Innovation Center (BIOPIC), in collaboration with researchers from more than 40 hospitals, universities, and research institutions, published a paper entitled “COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas” in  Cell , providing new insights and clues for revealing the pathogenesis and immune characteristics of COVID-19.

　　The outbreak of COVID-19 has brought disasters to the global society and economy. Since 2019, SARS-Cov-2 has infected more than 100 million people, causing over 2 million death. Hence, understanding the pathogenesis of the disease is of great significance to its diagnosis, treatment, prevention, and control. The wide application of single-cell transcriptome sequencing technology in various life science fields has illustrated many important biological discoveries. However, the application of this technology in the study of COVID19 has suffered from high cost, small sample size, insufficient statistical power, which leads to questionable conclusions.

　　Figure 1: Flowchart depicting the overall experimental design of this study

　　To tackle this problem, more than 40 hospitals, universities, and research institutions from more than ten provinces and cities of China formed Single Cell Consortium for COVID-19 in China (SC4), which aims to reveal the pathogenesis and immunological characteristics of COVID-19 through single-cell RNA-seq based on large COVID-19 cohort. After four months, SC4 obtained over 25T sequencing data for ~1.5 million single cells from a total of 284 samples (including sputum, BALF, BFMC, and PBMC) of 196 COVID-19 patients (including normal controls) (Fig. 1). The data was rapidly integrated and analyzed, shedding light on the mechanism of SARS-CoV-2 infection and the characteristics of the immune response at different stages of the disease.

　　The research highlighted that, in addition to the canonical host epithelial cells, the RNA sequence of SARS-CoV-2 was detected in various immune cells, including neutrophils, macrophages, plasma B cells, T cells, and natural killer cells. The expression of viral RNA exhibits features of subgenomic transcription, suggesting active transcription and duplication of the viral genome in the immune cells, implying SARS-CoV-2 infection. This finding may be an essential feature distinguishing SARS-CoV-2 from the SARS coronavirus. This finding was consistent with the strong interferon response in the SARS-CoV-2-positive cells and was confirmed by staining SARS-CoV-2 S-protein on tissue sections. Notably, ACE2, previously known as the receptor protein of SARS-CoV-2, is barely expressed in immune cells, suggesting other ways for SARS-CoV-2 to infect immune cells.

　　The further analysis illustrated that different epithelial cells have distinct responses after the SARS-CoV-2 infection. Ciliated epithelial cells tended to be denudated without causing any immune responses after infection. Squamous cells infected by SARS-CoV-2 tended to enhance their interaction with neutrophils and macrophages, presumably through the ANXA1-FPR1 and S100A8/9-TLR4 axes. Notably, ANXA1 and S100A8/9 were systematically upregulated in the immune cells in the peripheral blood of patients in critical condition, suggesting a systemic immune response storm mediating by ANXA1-FPR1 and S100A8/9-TLR4.　

　　This study also enables the analysis of the impact by the severity, the stage of disease, age, gender, and other technical factors on the composition of immune cells in the peripheral blood. Severe patients had a higher proportion of proliferating plasma B cells and T cells in the peripheral blood, but the overall T cell composition was significantly lower than that of mild patients, healthy controls, or convalescent patients. The elevated proliferating plasma B cells and T cells were significantly correlated with the severity of the disease, and the overall B cell level was related to the disease stage, i.e ., a higher B cell level occurred during the recovery period. Epidemiological studies revealed that age and sex are risk factors of COVID-19. This study suggested that age was mainly related to the decrease of neutrophils and naïve CD8⁺ T cells while sex was mainly associated with effector T cells. Age and sex not only affected the level of different immune cell types in peripheral blood but also affected the diversity of the B cell, or T cell receptor spectrum. Older patients had lower B cell or T cell spectrum diversity, which was even lower in males, which may be related to the overall immunity.

　　Although cytokine storm is in dispute in the pathogenesis of COVID-19, this study provides detailed data to illustrate the potential source of cytokines. Megakaryocytes and subtypes of monocytes expressed a high level of various cytokines, which was higher in patients in critical condition. Thus, these cells were presumed to be the source of potential cytokine storms. This hypothesis was further supported by the plasma-based cytokine detection experiments. The secreted cytokines also contribute to the cross-talk between peripheral blood and infected lesions in the lung, forming a complicated cytokine interaction network.

　　Figure 2: Research highlights of this study

　　This large single-cell RNA-seq study provided by SC4 not only provides new insights and clues for revealing the pathogenesis and immune characteristics of COVID-19 but also demonstrates the collaborative spirit of Chinese scientists in combating the pandemic.

　　Dr. Xianwen Ren, Dr. Jiesheng Li, Ph.D. candidate Fei Tang, and Ph.D. candidate Yu Yang are in the co-first author’s list of the paper. Prof. Zemin Zhang is one of the paper’s corresponding authors, together with 18 other senior investigators across the nation.