Table 1 Studies reporting T cell analysis in patients with COVID-19
Donor cohort | Sample origin | Profiling technology used | Major conclusions for αβT cells | Refs |
|---|---|---|---|---|
3 healthy, 3 mild/moderate disease, 6 severe disease | Bronchoalveolar lavage fluid | 10x Genomics scRNA-seq, 10× Genomics scTCR-seq | Greater clonal expansion of T cells in moderate disease than severe disease; T cells in moderate disease have stronger signatures of tissue residency | |
8 moderate disease, 11 severe disease | Nasopharyngeal and bronchial samples | 10x Genomics scRNA-seq | Fewer CTLs in severe disease than moderate disease; hyperactivation of CTLs in the respiratory tract, with a signature of interacting with epithelial cells and other immune cell types | |
5 healthy, 5Â early-recovered, 5Â late-recovered | PBMCs | 10x Genomics scRNA-seq, 10x Genomics scTCR-seq | Greater clonal expansion of T cells in late-recovered than in early-recovered patients; fewer CD8+ T cells but greater cytotoxic signatures in early-recovered than in late-recovered patients | |
6 healthy, 3Â non-ventilated, 4Â with ARDS | PBMCs | Seq-Well scRNA-seq | Heterogeneity of immune responses, including of interferon-stimulated genes; no transcriptional signature of exhaustion; features of T cell hyperactivation in some of the patients with ARDS | |
3 healthy, 6 mild/moderate disease, 4 severe disease | PBMCs | 10x Genomics scRNA-seq, flow cytometry | Strong T cell lymphopenia in severe disease with potential systemic adaptive immune dysregulation; altered T cell differentiation and a hyperactivation stage in severe disease; thymosin α1 can expand the memory-like T cell population and prevent T cell hyperactivation | 25 (Preprint) |
15 healthy, 79 COVID-19 (15 with ARDS), 26 influenza (7 with ARDS) | PBMCs | 10x Genomics scRNA-seq (3 influenza and 4 COVID-19), flow cytometry | Similar total and activated T cell counts for influenza and COVID-19 groups; higher IFNα-responding and IFNγ-responding signatures in the severe influenza groups than in the COVID-19 groups | 40 (Preprint) |
28 with ARDS, 26 non-ARDS, other infection controls | PBMCs | Flow cytometry | Stronger T cell lymphopenia in more severe COVID-19; lower CD4+ T cell counts in COVID-19 (n = 17) than in influenza (H1N1; n = 4) | |
12 healthy, 7Â recovered, 7Â moderate disease, 27 severe disease | PBMCs | High-dimensional flow cytometry | Stronger T cell lymphopenia in more severe disease; heterogeneity of T cell responses related to activation and cytotoxicity signatures; T cells express more markers of terminal differentiation or exhaustion in severe disease | |
60 healthy, 36 recovered, 125 hospitalized patients (NIH ordinal score 2–5) | PBMCs | High-dimensional flow cytometry | Stronger T cell lymphopenia in severe disease, with a bias towards CD8+ T cells; heterogeneity of T cell responses based on high-dimensional immune profiling, with three potential immune subtypes; T cells more activated but also express more markers of terminal differentiation and exhaustion in patients with COVID-19 than in individuals who are healthy or who recovered | |
40 healthy, 522 with varying disease severity | PBMCs | Flow cytometry | Stronger T cell lymphopenia in ICU patients, elderly patients and severe disease, for both CD4+ and CD8+ T cells; IL-6, IL-10 and TNF levels negatively correlate with lymphocyte count; T cells express higher levels of PD1 and TIM3 in ICU patients than in non-ICU individuals | |
55 healthy, 6Â mild disease, 26Â moderate disease, 31 severe disease | PBMCs | High-dimensional flow cytometry | Stronger T cell lymphopenia in severe disease; increased number of hyperactivated proliferating CD4+ and CD8+ T cells in severe disease; increased markers of terminal differentiation or exhaustion in severe disease compared with milder disease | 11 (Preprint) |
10 moderate disease, 11 severe disease | PBMCs | Flow cytometry | Higher lymphocyte counts in moderate disease than in severe disease, for both CD4+ and CD8+ T cells; more IFNγ-producing T cells in moderate disease than severe disease | |
20 healthy, 30 with varying disease severity | PBMCs | Flow cytometry | T cell lymphopenia in patients compared with healthy controls, with an increased ratio of CD4+ T cells to CD8+ T cells; increased proportion of terminally differentiated or senescent CD8+ T cells in patients, with a reduced proportion of IFNγ-producing cells; tocilizumab improves lymphocyte counts (n = 5) | |
30 healthy, 55 mild disease, 13 severe disease | PBMCs | Flow cytometry | Stronger T cell lymphopenia in severe disease than in mild disease or healthy controls, with recovery of T cell numbers in convalescent individuals; reduced levels of multiple cytokines in CD8+ T cells in disease groups, with higher levels of NKG2A expression than healthy controls | |
6 healthy, 10 mild disease, 6 severe disease | PBMCs | Flow cytometry | Increased cytotoxicity but decreased cytokine secretion of T cells, particularly CD8+ T cells, in severe disease compared with mild disease; CD8+ T cells in severe disease express more inhibitory receptors | |
Case report, multiple time points | PBMCs | Flow cytometry | ICOS+PD1+ circulating TFH cells increase during recovery; activated CD4+ and CD8+ T cells peak at day 9 post disease onset and decline after recovery | |
20 healthy, 20Â convalescent, other common cold coronaviruses | PBMCs | Flow cytometry | CD4+ and CD8+ T cells from convalescent patients respond to SARS-CoV-2 epitopes, including S, M and N proteins and other ORFs; T cell reactivity to SARS-CoV-2 also detected in non-exposed donors, with potential cross-reactivity to other common cold coronaviruses | |
14 convalescent | PBMCs | Flow cytometry | CD4+ and CD8+ T cells from convalescent patients respond to SARS-CoV-2 epitopes | |
16 healthy, 28Â recovered from mild disease, 14Â recovered from severe disease | PBMCs | Flow cytometry | T cells from convalescent patients with mild or severe disease respond to SARS-CoV-2 epitopes; convalescent patients with mild disease have a better memory CD8+ T cell response than convalescent patients with severe disease | 31 (Preprint) |
8 healthy, 8 with varying disease severity | PBMCs | Flow cytometry | T cell lymphopenia in COVID-19 compared with healthy controls, with an increase of T cell activation phenotypes; SARS-CoV-2-specific T cells mainly produce TH1-type cytokines | |
10 healthy, 21Â non-ICU, 12 in ICU | PBMCs | Flow cytometry | CD4+ T cells in ICU patients produce more GM-CSF and IL-6 than non-ICU individuals and healthy controls | |
245 healthy, 19 mild disease, 41 severe disease | PBMCs | Flow cytometry | Stronger T cell lymphopenia in severe disease compared with mild disease and healthy controls; IL-6 levels negatively correlate with lymphocyte count; patients who respond to treatment recover lymphocyte numbers | |
15 male and 29 female healthy, 17 male and 21 female with COVID-19 | PBMCs | High-dimensional flow cytometry | Male and female patients have T cell lymphopenia; female patients have more T cell activation than male patients; male patients with severe disease have greater reduction of T cell activation and loss of IFNγ-producers than those with stable disease | 60 (Preprint) |
