Single-cell profiling of innate and adaptive immune dysregulation in Long COVID

The COVID-19 pandemic has infected more than 778 million people worldwide. Roughly 7% of these patients progress to Long COVID (LC), suffering from persistent symptoms and cognitive impairment well past the acute stage. As the mechanisms of LC remain elusive, we utilized single-cell profiling (SCP) on 156,478 peripheral blood mononuclear cells (PBMCs) from 20 LC patients and 18 recovered controls (RC) to characterize the disease-associated immune dysregulation. Comparative analysis of LC and RC profiles revealed cellular heterogeneity along with differential abundances across B, T, and myeloid cell compartments. The focused analysis on the B-cell compartment showed that naïve B cells in the LC exhibit elevated IL4R expression and BCR signaling, indicative of sustained antigen exposure and aberrant chronic activation. Concurrently, monocytes adopted heightened interferon signaling and enhanced migratory states, culminating into impaired myeloid differentiation. Furthermore, the T-cell compartment exhibited a functional dichotomy, maintaining sustained quiescence in the central memory compartment while displaying chronic exhaustion within effector memory populations. This dysregulation of effector immunity extended to the NK compartment, where terminally differentiated cells exhibited increased cytotoxicity yet compromised regulatory function, potentially contributing to poor viral clearance. Cellular communication analysis further supports this NK cell dysfunction that is likely driven by galectin and prostaglandin signaling involving monocytes and B cells. We stratified LC patients into mild and severe groups based on symptom and cognitive severity, identifying a distinct immune signature where severe disease is linked to chronic AP-1-mediated inflammation in NK cells and CD14+ monocytes. In contrast, patients with mild symptoms retain functionally competent NK cells with significantly lower exhaustion and apoptosis scores. Collectively, these insights into persistent immune remodeling provide a crucial framework for future biomarker discovery and the development of targeted therapeutic strategies.