Table 1.
Characteristics of COVID-19 studies used to derive signatures for COVID-19 risk profiling on tuberculosis datasets
| Study | Tissue | Sequencing platform | Cohort | Severity | Eligible signatures | Signature type |
|---|---|---|---|---|---|---|
| Wilk et al., (2020) | PBMCs | Seq-Well | 7 patients hospitalized with confirmed COVID-19 (all male, aged 20-80 + yrs.), 6 healthy controls | 3 COVID-19 patients were on ventilation and diagnosed with ARDS; 4 were less severely ill patients. Samples collected 2-16 days following symptom onset | 4 | Monocytes, NK cells, “activated granulocytes”, and interferon sensitivity genes |
| Huang et al., (2020) | PBMCs | 10X Chromium | 8 active disease patients, 2 cured patients, 3 healthy controls, and non-COVID-19 patients | Active disease patients: 1 critical case, 1 severe case, 6 moderate cases. Non-COVID-19 patients: 1 case of influenza A, 1 case of acute pharyngitis, and 1 case of cerebral infarction | 1 | Interferon |
| Wen et al., (2020) | PBMCs | 10X Chromium | 10 recovering patients (5 male, 5 female, aged 40-70 years), plus healthy controls | 5 early-recovery stage (ERS) and 5 late-recovery stage (LRS) patients, classified by days between blood sampling date and negative qPCR | 5 | Monocytes, NK cells, CD4 T cells, CD8 T cells, B cells |
| Liao et al., (2020) | BALF | 10X Chromium | 6 COVID-19 patients (5 male, 1 female, median age: 49.5), 8 previously reported healthy lung controls | 3 severe, 3 mild | 6 | Macrophages (G1–G4), CD8 T cells |
| Xiong et al., (2020) | BALF and PBMCs | MGISEQ-2000 | 3 COVID-19 patients and 3 healthy controls | No severity information provided | 2 | PBMC and cytokine |
| Hadjadj et al., (2020) | Whole blood | nanoString nCounter | 50 COVID-19 patients with a spectrum of disease severity | 15 mild/moderate, 17 severe, and 18 critical | 5 | Interferon sensitivity genes, whole blood, mild/moderate, severe, critical |
| Wei et al., (2020) | PBMCs | 10X Chromium | 4 COVID-19 patients | Patients sampled before, during, and after ICU care | 4 | Inactivated monocytes, classical monocytes, T cells, B cells |
| Silvin et al., (2020) | Whole blood | 10X Chromium | 3 COVID-19 patients and 3 healthy controls | 1 mild, 2 severe patients sampled at day 0 and day 10 | 3 | Monocytes, neutrophils, whole blood |
| Arunachalam et al., (2020) | PBMCs | 10X Chromium | 7 COVID-19 patients and 5 healthy controls | No severity information provided for scRNA-seq samples | 5 | PBMC, moderate, severe, intensive care unit, blood transcriptional module |
| Dunning et al., (2018) | Whole blood | Illumina GenomeStudio | 131 influenza patients, 155 healthy controls | Not applicable | 1 | Whole blood |
ARDS, acute respiratory distress syndrome. BALF, bronchoalveolar lavage fluid; ICU, intensive care unit. NK, natural killer. PBMC, peripheral blood mononuclear cells. scRNA-seq, single cell RNA sequencing. See also Figures S1, S2, and S3 and Table S1.