CD8+ T-cell exhaustion contributes to the progression of COVID-19
Lymphocytopenia, defined as a lymphocyte count of <1,500/mm3, was seen in symptomatic patients (35%) but was less frequently observed in asymptomatic (14%) and presymptomatic patients (17%). There were significant differences in lymphocyte percentages between asymptomatic and symptomatic patients (29.7% vs. 26.1%, P -value < 0.05, Fig. 5A). Moreover, we analyzed the expression levels of cytokines in symptomatic COVID-19 patients and found that the expression levels of interleukin 6 (IL-6), IL-10, and IL-17 in severely ill patients were significantly higher than those in non-severe patients (P <0.001, Fig. S3). In addition, those in the asymptomatic and presymptomatic groups had lower levels of IL-6 (median: 1.5 vs. 2 pg/ml,P -value=0.012, Table S2) than patients in the symptomatic group. These findings were consistent with previous reports (19, 20) and indicated that asymptomatic patients have a weaker immune response to SARS-CoV-2 infection than symptomatic patients and play an immune protective role without cytokine storms.
To investigate the association of lymphocyte function with COVID-19 severity, we further analyzed single-cell sequencing data obtained from lung lavage fluids. Compared with that in severe COVID-19 patients, the proportion of lymphocytes (mainly T lymphocytes) increased significantly in mild COVID-19 patients (Fig. 5B). The T-distribution stochastic neighbor embedding (t-SNE) plot showed that 11 main cell clusters were identified from COVID-19 patients (Fig. 5C and 5D). CD8+ T-cells were subclustered by the known markers of CD3D and CD8A (Fig. 5E). Furthermore, the inhibitory membrane receptors expressed by CD8+ T-cells, such as PDCD1 (PD1), CTLA4, and HAVCR2 (TIM3), were significantly upregulated in severe COVID-19 patients when compared with those in healthy people and mild COVID-19 patients (Fig. 5F). Surprisingly, the expression of interferon gamma (IFNγ) in severely ill patients was significantly higher than that in non-severely ill patients. To identify the specific inhibitor phenotype related to IFNγ, the co-expression of cytokines and inhibitory membrane receptors was further analyzed. This revealed that the LAG3+IFNγ+CD8+ T-cells (10.12% CD8+T-cells in mildly symptomatic COVID-19 patients and 25.83% CD8+T-cells in severely symptomatic COVID-19 patients) and CTLA4+IL10RA+CD8+ T-cells (4.42% CD8+T in mildly symptomatic COVID-19 patients and 13.88% CD8+T in severely symptomatic COVID-19 patients) might contribute to the T-cell exhaustion associated with the severe phenotype of COVID-19 in patients (Fig. 5G–J).