Abstract
Post-Acute Sequelae of COVID-19 (PASC), or "long COVID," describes persistent symptoms following recovery from SARS-CoV-2 infection. Early identification of circulating biomarkers predictive of PASC is critical for prognosis and therapeutic development yet remains poorly defined. To address this gap, we conducted a longitudinal, multi-omics analysis of blood samples from COVID-19 patients (n = 75), stratified by acute disease severity and PASC status. We integrated targeted multiplex assays, untargeted proteomics (LC-MS), and whole blood flow cytometry to define immune and vascular signatures associated with PASC. We found that individuals who went on to develop PASC exhibited a distinct phenotypic signature between 1 and 35 days post-infection, such as significantly elevated plasma Factor-IX, Tissue factor, and tPA, which reflected hyperactivation of immunothrombotic pathways. Similarly, pathway enrichment analysis revealed ongoing neutrophil degranulation, platelet activation, and extracellular matrix remodeling-indicating unresolved inflammation and immunothrombosis which persisted beyond 77 days post-symptom onset. Unlike prior studies using single biomarkers or limited timepoints, our study offers a comprehensive longitudinal analysis combining proteomic and cellular data to define a durable immune-vascular signature specific to PASC. This integrative approach reveals insights into PASC pathogenesis and highlights candidate biomarkers with potential utility in early risk stratification. Our findings underscore the critical role of chronic immune and endothelial dysfunction in long COVID and point toward actionable targets for intervention. This investigation links biorepository human samples with clinical symptoms and lays the foundation for precision diagnostics and therapeutic strategies aimed at improving long-term outcomes in COVID-19 survivors (NCT04603677).