Severe long-COVID is driven by monocyte reprogramming and broad immune dysregulation linked to herpesvirus activation

Long-COVID (LC) continues to impose a significant burden on patients and society, yet its pathophysiology remains poorly understood. Here, we characterize the functional, transcriptomic, and epigenomic state of monocytes from 21 patients with severe LC (sLC) at a median of 3.4 years after primary infection, as well as the transcriptomic profiles of T and B-cells. Plasma proteomics revealed elevated chemokines and type-I interferon-associated proteins, alongside a reduction in circulating monocytes. Monocytes from sLC patients demonstrated markedly reduced cytokine secretion upon ex vivo LPS stimulation, a finding reproduced in an in vitro model of LC. ATAC-sequencing revealed an epigenomic state of immune dysfunction in monocytes, partially driven by a loss of AP-1 transcription factor binding motifs. Single-cell transcriptomics using STAMP across 113,000 peripheral blood mononuclear cells (PBMCs) confirmed the downregulation of activator protein 1 (AP-1) family members and pro-inflammatory signaling in monocytes, along with impaired antigen presentation, dysregulated viral signaling, and immunosuppressive gene upregulation. T and B-cells demonstrated similar immune dysfunction at the transcriptome level. Epigenomic and transcriptomic evidence of herpesvirus activity, combined with elevated HHV-6 IgG serology in sLC patients, points toward viral reactivation as a candidate mechanism underlying persistent immune dysfunction. Together, these findings suggest that sLC is characterized by a long-lived, infection-induced interferon-priming state that drives monocyte hyporesponsiveness through AP-1-mediated epigenetic reprogramming and implicate HHV-6 reactivation as a potential therapeutic target.