Antibody Signatures of Illness Trajectories: Comparative FLow-based Immune Profiling (FLIP) in Long COVID 2260564

Abstract

Abstract Introduction Infection-associated chronic illnesses (IACIs) such as Long COVID (LC) and Post-Treatment Lyme Disease Syndrome (PTLDS) reveal a gap in our understanding of immune resolution after infection. Some patients experience persistent fatigue, cognitive dysfunction, post-exertional malaise, dysautonomia, musculoskeletal pain, and allergy-like symptomes. Although triggered by distinct pathogens (SARS-CoV-2 for L; B. burgdorferi for PTLD), these conditions share overlapping clinical and immunological features, suggesting convergent pathways of post-infectious immune dysregulation. Current serological assays quantify bulk antibody titers but fail to resolve the functional antibody diversity that may determine recovery versus chronicity–highlighting the need for mechanistic biomarkers of disease trajectory. Methods To address this, the Tal Lab developed FLow-based Immune Profiling (FLIP), a high-dimensional serological assay quantifying pathogen-bound antibodies across IgD, IgM, IgA, IgE, and IgG1—4 subclasses using live pathogens or antigen-coated beads as bait. FLIP captures effector-function—relevant antibody heterogeneity, revealing ratiometric patterns that encode immune trajectory. We established FLIP for LC, analyzing plasma from the RECOVER cohort to characterize SARS-CoV-2—specific and total antibody distributions, and compared these with the MAESTRO PTLDS cohort, where FLIP had identified antibody ratios predictive of symptom persistence. Results Our results show that (i) FLIP can be adapted to small-particle pathogens (viruses), enabling high-resolution mapping of SARS-CoV-2—specific repertoires, and (ii) distinct ratiometric antibody architectures differentiate recovery from persistence across both patient cohorts, supporting their potential use as predictive biomarkers of post-infectious outcomes. Conclusion Our findings establish FLIP as a versatile platform for dissecting humoral immune responses and provide a foundation for predictive diagnostics and immune-targeted interventions in IACIs. Funding Source n/a Topic Categories Immune Mechanisms of Human Disease (HUM)