c Cell type UMAP representation of all merged samples. The same color palette was used throughout the study. Green, orange, blue, and red represent samples collected from healthy controls, asymptomatic, moderate, and severe patients, respectively. b Bar plot shows the log 10 transformed cell number of each sample for each subject at different time points. The days were recorded based on the time after symptom onset for moderate and severe patients and the first positive RT-PCR test for SARS-CoV-2 for asymptomatic patients. Single-cell RNA sequencing of peripheral blood cells from COVID-19 patients.Ī Timeline of blood sample collection in the 19 subjects (seven asymptomatic, eight moderate, one severe patient, and three healthy controls) and schematic outline of the study design. To explore characteristics that might lead to immunopathology in asymptomatic and moderate COVID-19, we performed scRNA-seq together with single-cell V(D)J sequencing using longitudinal PBMCs from 16 hospitalized COVID-19 patients and three healthy controls (HCs) to identify immunological profiles between distinct immune phenotype and disease severity. 18 Despite the clinical and immunological assessment of asymptomatic individuals, 19 transcriptome profiles of asymptomatic individuals are lacking, which might help us understand the nature of the asymptomatic COVID-19 disease. On the other hand, the contribution of asymptomatic individuals to the transmission of SARS-CoV-2 raises a significant public health concern. 9, 13– 17 Longitudinal immune responses of moderate and severe COVID-19 patients have been analyzed by flow cytometry, 10 while unbiased longitudinal single-cell transcriptome profiling is still missing. 3, 5– 12 Further, single-cell RNA sequencing (scRNA-seq) studies in peripheral blood mononuclear cells (PBMCs) or bronchoalveolar lavages of moderate and severe patients have revealed that moderate disease was associated with more protective T cell-dependent response, with exacerbated systemic inflammation and less effect T cells in severe disease.

Elevated pro-inflammatory cytokines (e.g., IL-1β, IL-6, and TNF-α) and inflammatory monocytes and neutrophils, and a sharp decrease in lymphocytes have also been reported in severe patients. In severe COVID-19 patients, hyper-inflammation responses referred to as cytokine storm 3, 4 and lymphopenia 5, 6 have been considered risk factors associated with the detrimental progression of COVID-19 patients. 2 Therefore, understanding the host immune response involved in the disease course is of supreme importance to developing effective therapies. 1 COVID-19 patient exhibit a broad spectrum of clinical manifestations, ranging from mild or even asymptomatic infection to severe disease or death. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19), has rapidly caused a worldwide pandemic with ever-increasing cases and COVID-19-related deaths. Our data provide evidence of different immune signatures to SARS-CoV-2 in asymptomatic infections. Moreover, asymptomatic patients have lower interferon-stimulated genes (ISGs) expression in general but large interpatient variability, whereas moderate patients showed various magnitude and temporal dynamics of the ISGs expression across multiple cell populations but lower than a patient with severe disease. They showed more robust TCR clonal expansion, especially in effector CD4 + T cells, but lack strong BCR clonal expansion compared to moderate patients. Asymptomatic patients displayed increased CD56 briCD16 − natural killer (NK) cells and upregulation of interferon-gamma in effector CD4 + and CD8 + T cells and NK cells. We performed single-cell transcriptome and T-cell/B-cell receptor (TCR/BCR) sequencing in 37 longitudinal collected peripheral blood mononuclear cell samples from asymptomatic, moderate, and severe patients with healthy controls. We sought to identify the distinction of immune response between asymptomatic and moderate patients. While some individuals infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present mild-to-severe disease, many SARS-CoV-2-infected individuals are asymptomatic.

Immune repertoire and disease