Systems Immunology of Long Covid: Insights from the STOP-PASC Clinical Trial

BackgroundPost Acute Sequelae of COVID-19 (PASC), also referred to as Long COVID, is an infection-associated chronic syndrome with heterogenous symptom profiles that occurs in a subset of people following SARS-CoV-2 infection. Despite proposed viral persistence mechanisms, no therapeutic benefit was observed in two randomized placebo-controlled trials of nirmatrelvir/ritonavir (NMV/r) in adults with Long COVID, including the Selective Trial of Paxlovid for PASC (STOP-PASC) and PAX LC. This systems immunology analysis aimed to characterize immune profiles of participants during clinical trial intervention, identify biomarkers associated with patient-reported outcomes, and investigate potential mechanisms underlying Long COVID. MethodsWe performed comprehensive immunological profiling of 152 STOP-PASC trial participants using plasma proteomics (Olink(R) Explore HT 5400 panel), autoantigen arrays, viral serology, and microclot assays at baseline, day 15, and week 10. We assessed associations between immune features and patient-reported outcomes. We also conducted meta-analysis of nine independent Long COVID proteomics cohorts (n=590 total samples) to identify conserved inflammatory signatures. ResultsNMV/r treatment at day 15 compared with baseline induced transient changes in plasma proteins that normalized by week 10, primarily impacting myeloid cell/monocyte, lysosome, and complement activation pathways. Cardiovascular symptoms were negatively associated with SARS-CoV-2 antibody levels at baseline. No widespread differences in autoantibody profiles, Epstein-Barr virus (EBV) reactivation, or microclotting were observed between STOP-PASC Long COVID participants, pre-pandemic controls, and individuals without Long COVID. Meta-analysis of publicly available Olink(R) data from Long COVID cohorts identified a conserved 60-protein Long COVID Signature (LCS) score revealing multi-compartment immune activation involving monocyte, neutrophil, and T/NK cell modules. ConclusionsThese findings advance our understanding of Long COVID immunology and may help direct future proteomic biomarker endpoints for Long COVID clinical trials.