Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19
Jeong Seok Lee, Seongwan Park, Hye Won Jeong, Jin Young Ahn, Seong Jin Choi, Hoyoung Lee, Baekgyu Choi, Su Kyung Nam, Moa Sa, Ji-Soo Kwon, Su Jin Jeong, Heung Kyu Lee, Sung Ho Park, Su-Hyung Park, Jun Yong Choi, Sung-Han Kim, Inkyung Jung, Eui-Cheol Shin
Abstract
Although most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–infected individuals experience mild coronavirus disease 2019 (COVID-19), some patients suffer from severe COVID-19, which is accompanied by acute respiratory distress syndrome and systemic inflammation. To identify factors driving severe progression of COVID-19, we performed single-cell RNA sequencing using peripheral blood mononuclear cells (PBMCs) obtained from healthy donors, patients with mild or severe COVID-19, and patients with severe influenza. Patients with COVID-19 exhibited hyperinflammatory signatures across all types of cells among PBMCs, particularly up-regulation of the tumor necrosis factor/interleukin-1β (TNF/IL-1β)–driven inflammatory response as compared with severe influenza. In classical monocytes from patients with severe COVID-19, type I interferon (IFN) response coexisted with the TNF/IL-1β–driven inflammation, and this was not seen in patients with milder COVID-19. We documented type I IFN–driven inflammatory features in patients with severe influenza as well. On the basis of this, we propose that the type I IFN response plays a pivotal role in exacerbating inflammation in severe COVID-19.
Datasets
1. Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19
Metadata
Sample ID
Disease group
Comorbidity
Hospital day
WBC per microL
Neutrophil per microL (%)
Lymphocyte per microL (%)
Monocyte prt microL (%)
C-reactive protein (mg per dL)
Chest X-ray
Treatment
Respiratory rate (BPM)
O2 saturation
O2 supplement
Temperature
Systolic BP
Heart rate (BPM)
Consciousness
NEWS score
Severity
Celltype
tissue_ontology_term_id
assay_ontology_term_id
disease_ontology_term_id
cell_type_ontology_term_id
self_reported_ethnicity_ontology_term_id
development_stage_ontology_term_id
sex_ontology_term_id
organism_ontology_term_id
donor_id
suspension_type
tissue_type
cell_type
assay
disease
organism
sex
tissue
self_reported_ethnicity
development_stage
severe influenza10519 cells severe COVID-1910296 cells mild COVID-19 (asymptomatic)4425 cells not applicable17590 cells hypertension, rheumatoid arthritis4895 cells history of tuberculous pleuritis4584 cells diabetes mellitus, dyslipidemia4526 cells hypothyroidism, dyslipidemia4425 cells hypertension, asthma, atrial fibrillation3375 cells kidney transplantation status due to ESRD, atrial fibrillation, stroke, hypertension, diabetes, history of pulmonary tuberculosis2601 cells stroke, diabetes1331 cells liver cirrhosis with chronic hepatitis B, history of splenectomy1040 cells lymphoma, hypertension, asthma, prostate cancer652 cells not applicable17590 cells not applicable17590 cells not applicable17590 cells not applicable17590 cells not applicable17590 cells not applicable17590 cells not applicable17590 cells peribronchial opacity in both lungs, pleural effusion4895 cells unchanged extent of consolidation and GGO in both lungs3239 cells total collapse LLL, pleural effusion, pericardial effusion2601 cells diffuse increased lung opacity and multifocal consolidation1873 cells multifocal patchy opacities in both lungs1502 cells no gross change of consolidation and GGO in both lungs1345 cells multifocal consolidations in both lungs1112 cells interstitial marking in both lungs1040 cells peribronchial infiltration in BLL, pleural effusion, cardiomegaly652 cells not applicable17590 cells lopinavir and ritonavir, ceftriaxone4999 cells lopinavir and ritonavir, hydroxychloroquine4526 cells lopinavir and ritonavir, hydroxychloroquine, nafamostat4464 cells ciclesonide inhalor3978 cells lopinavir and ritonavir, linezolid, cefepime, vancomycin, meropenem, colistin, tigecycline, anidulafungin, hydrocortisone1502 cells lopinavir and ritonavir1345 cells lopinavir and ritonavir, levofloxacin398 cells not applicable17590 cells not applicable28109 cells not applicable28109 cells not applicable28109 cells not applicable28109 cells not applicable28109 cells not applicable28109 cells not applicable28109 cells not applicable28109 cells mild (asymptomatic)4425 cells classical Monocyte18465 cells CD8, non-EM-like6651 cells CD4, non-EM-like2380 cells nonclassical Monocyte1919 cells intermediate Monocyte704 cells UBERON:000017859572 cells HsapDv:000015712918 cells NCBITaxon:960659572 cells classical monocyte18465 cells natural killer cell9369 cells CD8-positive, alpha-beta T cell6651 cells IgG-negative class switched memory B cell4345 cells effector CD4-positive, alpha-beta T cell3517 cells effector CD8-positive, alpha-beta T cell3242 cells CD4-positive helper T cell2380 cells IgG memory B cell2048 cells non-classical monocyte1919 cells intermediate monocyte704 cells 63-year-old human stage12918 cells 67-year-old human stage5602 cells 82-year-old human stage4999 cells 68-year-old human stage4895 cells 54-year-old human stage4646 cells 61-year-old human stage4584 cells 38-year-old human stage4526 cells 62-year-old human stage4425 cells 46-year-old human stage3978 cells 73-year-old human stage3375 cells 70-year-old human stage2601 cells 75-year-old human stage1331 cells 56-year-old human stage1040 cells 78-year-old human stage652 cells Analyze this study
Source data
https://cellxgene.cziscience.com/collections/4f889ffc-d4bc-4748-905b-8eb9db47a2ed
Alias names
GSE149689, E-GEOD-149689, PMID32651212, PMC7402635
Cite this study
Lee, J.S., Park, S., Jeong, H.W., Ahn, J.Y., Choi, S.J., Lee, H., Choi, B., Nam, S.K., Sa, M., Kwon, J.S. and Jeong, S.J., 2020. Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19. Science immunology, 5(49), p.eabd1554. https://doi.org/10.1126/sciimmunol.abd1554
