Immuno-proteomic profiling reveals abundant airway CD8 T cells and ongoing epithelial injury in prolonged post-COVID19 respiratory disease

Some patients hospitalized with acute COVID19 suffer respiratory symptoms that persist for many months. To characterize the local and systemic immune responses associated with this form of ‘Long COVID’, we delineated the immune and proteomic landscape in the airway and peripheral blood of normal volunteers and patients from 3 to 6 months after hospital discharge. The bronchoalveolar lavage (but not peripheral blood) proteome was abnormal in patients with post-COVID19 lung disease with significantly elevated concentration of proteins associated with apoptosis, tissue repair and epithelial injury. This correlated with an increase in cytotoxic lymphocytes (especially tissue resident CD8+ T cells), lactate dehydrogenase and albumin (biomarkers of cell death and barrier integrity). Follow-up of a subset of these patients greater than 1-year post-COVID19 indicated these abnormalities resolved over time. Collectively, these data indicate that COVID-19 results in a prolonged change to the airway immune landscape in those with persistent lung disease, with evidence of cell death and tissue repair linked to ongoing activation of cytotoxic T cells. Highlights ### Competing Interest Statement The authors have declared no competing interest. ### Clinical Trial NCT04459351 ### Funding Statement This work was supported by a Wellcome Trust Senior Fellowship 107059/Z/15/Z to C.M.L., a Rosetrees Seed Fund to P.L.M. and J.A.H. (A2172) and an Imperial College Healthcare NHS Trust BRC award to J.A.H. (RDF04). B.V. is funded by the Joint Research Committee on behalf of a joint collaboration between CW+ and Westminster Medical School Research Trust. K.B. is funded by an Asthma UK PhD Studentship as part of the Asthma UK centre in allergic mechanisms of asthma (AUK-BC-2015-01). R.J.S. is supported by a Wellcome Trust Senior Fellowship (209458/Z/17/Z). J.E.P. is supported by a UKRI COVID19 Rapid Response Rolling Call (MR/V027638/1), the Imperial College London Community Jameel and the Imperial President's Excellence Fund, and a UKRI Innovation Fellowship at Health Data Research UK (MR/S004068/2). ### 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: Post-COVID19 bronchoalveolar lavage fluid (BAL) was obtained from patients recruited to the PHENOTYPE study (NCT 04459351), an observational, longitudinal study recruiting patients at Chelsea and Westminster Hospital, London. 38 samples were collected from patients requiring sampling for clinical purposes. Ethical approval for the study was given by Yorkshire & The Humber - Sheffield Research Ethics Committee (IRAS 284497). Ethics for collection of samples from healthy volunteers was approved by the South Central Hampshire Research Ethics Committee (15/SC/0101). All patients provided informed written consent All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. 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 and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data will be made available for this study upon acceptance after peer review.