Single-cell proteomic analysis of peripheral blood mononuclear cells in patients with pulmonary long COVID

An estimated 15% of patients are expected to continue to exhibit respiratory symptoms after their SARS-CoV-2 infection. The mechanisms behind these symptoms remain unknown. We recruited twenty-three patients (65% female) who were on average 406 ± 251 days post-COVID-19. The cohort consists of primarily mild (non-hospitalized) patients (87%), with an average age of 43 ± 15 years. Nine of these patients had self-reported dyspnea, which we defined as pulmonary long COVID (PLC). The remaining 14 patients recovered without persistent dyspnea. We performed a 38-panel cytometry by time-of-flight on the peripheral blood mononuclear cells of this cohort. Quality control was performed using FloJo. Further analysis, was done using the CyCombine, CATALYST, and FlowSom packages in R. Our final annotation uncovered 17 different cell clusters. In PLC patients, double-positive T-cells (DPTs) were significantly increased (Wilcoxon p<0.05), indicating that T-cell development or differentiation may be altered in these patients. Though DPTs are known to be increased in females, there was no significant difference in the proportion of DPTs between males and females in our cohort. PLC stem cells had increased expression of CD304 and CD200R (Wilcoxon p<0.05). CD304 is as a co-receptor for SARS-CoV-2, while CD200R is a limiter of pro-inflammatory activity. These findings indicate that the immune landscape in PLC patients is altered, compared to those who recover without residual pulmonary symptoms.