Immune cell profiling of patients with COVID-19 with mild, severe and prognosis states revealed by single-cell RNA sequencing

Objective: To construct single-cell transcription landscape of peripheral blood mononuclear cells (PBMCs) of patients with mild, severe and prognosis states of corona virus disease 2019 (COVID-19), and to analyze the relationship between disease progression and host immune response. Methods: Single-cell RNA sequence (scRNA-seq) data of healthy controls and for severe, mild, early recovery stage and later recovery stage PBMCs of patients with COVID-19 were obtained from public databases. After the cells were clustered according to the expression profile of each cell, the cell subtypes of each cluster were determined according to the known cell markers, and the proportion of each cell subtype was counted.The differentially expressed genes of each cell subtype were analyzed. Results: After quality control, the 115 334 PBMCs were classified into 22 cell subsets.Among them, CD14+ monocytes, inflammatory monocytes, naïve B cells and intermediate memory B cells significantly increased in PBMCs of severe patients.The proportion of proliferative CD8+ T/NK cells significantly increased in T cells of severe patients.XCL1+NK cells significantly decrease in PBMCs of severe patients.The proportion of cDC2 cells and pDC cells were significantly increased in PBMCs of recovery patients.With the remission and recovery of the disease, the proportion of NK cells in PBMCs increased gradually.The genes related to leukocyte activation and immune regulation were upregulated in both disease stage and recovery stage. Conclusion: The cell proportion and expression profile of PBMCs in patients with mild, severe and prognosis states of COVID-19 varied greatly. © 2022, Editorial Department of Fudan University Journal of Medical Sciences. All right reserved.

SARS-CoV-2 productively infects primary human immune system cells in vitro and in COVID-19 patients.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with a hyperinflammatory state and lymphocytopenia, a hallmark that appears as both signature and prognosis of disease severity outcome. Although cytokine storm and a sustained inflammatory state are commonly associated with immune cell depletion, it is still unclear whether direct SARS-CoV-2 infection of immune cells could also play a role in this scenario by harboring viral replication. We found that monocytes, as well as both B and T lymphocytes, were susceptible to SARS-CoV-2 infection in vitro, accumulating double-stranded RNA consistent with viral RNA replication and ultimately leading to expressive T cell apoptosis. In addition, flow cytometry and immunofluorescence analysis revealed that SARS-CoV-2 was frequently detected in monocytes and B lymphocytes from coronavirus disease 2019 (COVID-19) patients. The rates of SARS-CoV-2-infected monocytes in peripheral blood mononuclear cells from COVID-19 patients increased over time from symptom onset, with SARS-CoV-2-positive monocytes, B cells, and CD4+ T lymphocytes also detected in postmortem lung tissue. These results indicated that SARS-CoV-2 infection of blood-circulating leukocytes in COVID-19 patients might have important implications for disease pathogenesis and progression, immune dysfunction, and virus spread within the host.