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Data from: Autoantibody landscapes in neurological Long COVID and post-COVID cognitive impairment show heterogeneity without a shared disease signature

Chakravarty, Debanjana1; Dandekar, Ravi1; Lashkari, Vishal D.1; Tilton, Iris1; McAlpine, Lindsay2; Chiarella, Jennifer2; Nelson, Allison2; Ngo, Thomas1; Chen, PeiXi1; Wang, Chung-Yu1; Saxena, Aditi1; Castillo-Rojas, Bryan1; Zorn, Kelsey1; Tribble, David R.3; Burgess, Timothy H.3; Rubin, Leah H.4; Richard, Stephanie A.3; Agan, Brian K.3; Pollett, Simon D.3; Farhadian, Shelli2; Spudich, Serena2; Pleasure, Samuel1; Wilson, Michael1

Research facility: University of California - San Francisco School of Medicine
Published Mar 27, 2026 on Dryad. https://doi.org/10.5061/dryad.kprr4xhkt

Data files

Abstract

Neurologic Long COVID (n-LC) includes persistent cognitive and autonomic symptoms after SARS-CoV-2 infection. Prior studies of post-COVID conditions have described diverse humoral autoreactivity, but findings are heterogeneous, and it remains unclear whether n-LC is associated with a consistent CNS-directed humoral signature. We performed a cross-cohort case-control analysis to detect autoantibodies in cerebrospinal fluid (CSF) and serum from n-LC participants. In the Yale COVID Mind Study, CSF from n-LC participants and from pre-pandemic and post-COVID asymptomatic controls was assessed by mouse brain immunofluorescence and proteome-wide phage immunoprecipitation sequencing (PhIP-seq), with candidate reactivities evaluated by orthogonal assays and supervised modeling. In the Epidemiology, Immunology, and Clinical Characteristics of Emerging Infectious Diseases with Pandemic Potential (IDCRP EPICC) cohort, post-COVID sera collected prior to iPhone- or iPad-based cognitive screening were profiled by PhIP-seq and compared between participants with and without cognitive impairment. CSF immunoreactivity on mouse brain tissue was observed in both n-LC and controls, with similar overall frequencies, although n-LC participants more often showed nuclear-predominant staining patterns. PhIP-seq identified sparse, largely patient-specific peptide reactivities to nuclear and neuronal proteins in CSF and serum. Supervised models provided limited discrimination between cases and controls. Candidate autoantigens had limited disease specificity on orthogonal testing. EPICC serum profiling similarly failed to distinguish individuals with and without cognitive impairment. Across cohorts and compartments, n-LC did not exhibit a shared autoantibody signature. These findings support the absence of a dominant, common CNS autoantibody-mediated mechanism in n-LC.