3 About Dataset (GSE149689)
3.1 Data description
This dataset consists of single-cell RNA sequencing (scRNA-seq) profiles from peripheral blood mononuclear cells (PBMCs) of patients with severe influenza, patients with COVID-19 of varying severity, and healthy controls.
Hospitalized patients diagnosed with influenza A virus infection by a rapid antigen test of a nasopharyngeal swab were also enrolled from Asan Medical Center and Chungbuk National University Hospital between December 2015 and April 2016, prior to the emergence of COVID-19. Patients’ clinical features, laboratory findings, and chest radiographs were collected from their electronic medical records at each hospital.
| Topic | Description |
|---|---|
| Status | Public on Jul 06, 2020 |
| Accession | BioProject: PRJNA629752; GEO: GSE149689 |
| Title | Immunophenotyping of COVID-19 and Influenza Underscores the Association of Type I IFN Response in Severe COVID-19 |
| Organism | Homo sapiens |
| Experiment type | Expression profiling by high throughput sequencing |
| Summary |
Although most SARS-CoV-2-infected individuals experience mild 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-seq 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 hyper-inflammatory signatures across all types of cells among PBMCs, particularly upregulation of the TNF/IL-1beta-driven inflammatory response as compared to severe influenza. In classical monocytes from patients with severe COVID-19, type I IFN response co-existed with the TNF/IL-1beta-driven inflammation, and this was not seen in patients with milder COVID-19 infection. Based on this, we propose that the type I IFN response exacerbates inflammation in patients with severe COVID-19 infection. |
3.2 Experimental design
This study was conducted using single-cell RNA sequencing (scRNA-seq) on peripheral blood mononuclear cells (PBMCs) from three groups:
- 5 patients with severe influenza
- 11 patients with COVID-19 (with varying degrees of severity: severe and mild)
- 4 healthy controls (uninfected)
This design allowed for a direct comparison of immune responses between influenza and COVID-19, as well as the identification of features associated with progression to severe forms of COVID-19.
| Topic | Description |
|---|---|
| Cell types | PBMCs (Peripheral Blood Mononuclear Cells) |
| Chemistry | Chromium Single Cell 3’ |
| Platforms | 10x Genomics |
| Sequencer | Illumina NovaSeq 6000 |
| Genome used for alignment | GRCh38 / hg38 |
| Cell Ranger version | v3.0.2 was used for preprocessing and alignment. |