Quarantegan (@quarantegan.bsky.social)

Single-cell multi-omics show disruption of blood and airway T-cells in pulmonary long COVID | medRxiv Background: Approximately 10% of individuals who recover from COVID-19 experience residual respiratory symptoms impacting their quality of life, but the mechanisms behind pulmonary long COVID (PLC) are largely unknown. Objectives: We characterized airway and circulating immune cells in patients with and without PLC. Methods: Participants were recruited and allocated into two groups: 1) PLC, defined by a St. George's Respiratory Questionnaire (SGRQ) total score of >10 at least three months following an acute SARS-CoV-2 infection with self-reported new or worsening symptoms, and 2) controls, defined by SGRQ =<10 with or without a prior history of COVID. We performed research bronchoscopy and obtained bronchoalveolar lavage (BAL) in seven PLC patients and seven age- and sex-matched control subjects. Single-cell RNA sequencing (scRNAseq) was performed on the BAL cells. Peripheral blood mononuclear cells (PBMCs) were cryopreserved in 30 participants (17 PLC, 13 controls) for proteomic analysis. Serum was submitted for microarray detection of auto-IgG antibodies. Methods: We annotated 105,836 cells using scRNAseq and found that CD4+ T-cells were credibly increased in participants with PLC. scRNAseq also revealed up-regulation of anti-viral pathways including those related to interferon signaling in T-cells as well as antigen presenting cells. In PBMCs, T-cells expressing both CD4 and CD8 were elevated in PLC participants. Autoantibodies targeting genomic DNA, collagen II, and TIF-gamma were significantly increased in PLC patients. Conclusions: PLC is associated with dysregulation of T-cell mediated immunity, which may be related to autoimmunity. These cells represent potential novel therapeutic targets in patients suffering from PLC. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by the Canadian Institute of Health Research, Genome British Columbia and Mitacs. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee of University of British Columbia/Providence Health Care gave ethical approval for this work (H21-02149 and H19-02222) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors https://www.medrxiv.org/content/10.1101/2025.09.18.25336101v1