Tissue-specific autoantibody signatures reveal immune alterations undetected by routine serology in long COVID

Abstract Long COVID affects a substantial proportion of individuals recovering from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, yet its underlying pathophysiology remains poorly understood. Although autoimmunity is increasingly implicated in disease pathogenesis, routine diagnostics frequently fail to detect relevant immune dysregulation. To address this gap, we analyzed sera from Long COVID patients ( n = 114) and pre-pandemic controls ( n = 36) using tissue-based Western blotting targeting cardiac, pulmonary, and vascular antigens, alongside standard ANA HEp-2 testing. Longitudinal samples were additionally evaluated to assess autoantibody dynamics. Autoantibodies were detected in the majority of patients (83% vs. 53% in controls; p < 0.05), showing a dominant cardiovascular pattern. While cardiac (54% vs. 33% in controls; p = 0.16) and pulmonary (34% vs. 30% in controls; p = 0.50) prevalences did not reach significance, vascular autoreactivity was markedly elevated in Long COVID (34% vs. 8% in controls; p < 0.05). Responses exhibited broad polyreactivity and IgM dominance, with longitudinal follow-up showing persistent IgM and the emergence of additional isotypes. Clinically, cardiac autoreactivity was associated with hypertension and headache, while the overall autoreactivity correlated with anosmia and ageusia. In contrast, ANA HEp-2 testing showed no discriminatory value or clinical associations. Distinct autoreactivity patterns further aligned with female sex and clinical parameters (C-reactive protein, creatinine, troponin, body mass index). Together, these findings reveal a high burden of tissue-specific autoantibodies invisible to standard ANA screening. This persistent, IgM-skewed profile suggests ongoing immune dysregulation and may reflect a previously underrecognized component of the immunological response in long COVID, highlighting the need for targeted immunodiagnostic approaches beyond routine serology.