Divergent and self-reactive immune responses in the CNS of COVID-19 patients

Background: One third of COVID-19 patients develop significant neurological symptoms, yet SARS-CoV-2 is rarely detected in central nervous system (CNS) tissue, suggesting a potential role for parainfectious processes, including neuroimmune responses. Methods: We examined immune parameters in CSF and blood samples from a cohort of hospitalized patients with COVID-19 and significant neurological complications (n=6), compared to SARS-CoV-2 uninfected controls (Fig1A). Immune cells were characterized by single cell RNA and repertoire sequencing. Intrathecal antibodies were assessed for anti-viral and auto-reactivity by ELISA, mouse brain immunostaining, phage display, and IP-MS. Results: Through single cell and parallel cytokine analyses of CSF and paired plasma, we found divergent T cell responses in the CNS compartment, including increased levels of IL-1B and IL-12-associated innate and adaptive immune cell activation (Fig1B). We found evidence of clonal expansion of B cells in the CSF, with B cell receptor sequences that were unique from those observed in peripheral blood B cells (Fig1C), suggesting a divergent intrathecal humoral response to SARS-CoV-2. Indeed, all COVID-19 cases examined had anti-SARS-antibodies. Next, we directly examined whether CSF resident antibodies targeted self-antigens and found a significant burden of CNS autoimmunity, with the CSF from most patients recognizing neural self-antigens. COVID-19 CSF produced immunoreactive staining of specific anatomic regions of the brain including cortical neurons, olfactory bulb, thalamus, and cerebral vasculature. Finally, we produced a panel of monoclonal antibodies from patients' CSF and peripheral blood, and show that these target both anti-viral and anti-neural antigens-including one CSF-derived mAb specific for the spike protein that also recognizes neural tissue (Fig1D). Conclusion: This immune survey reveals evidence of a compartmentalized and self-reactive immune response in the CNS in COVID-19 patients with neurologic symptoms. We identified both innate and adaptive anti-viral immune responses, as well as humoral autoimmunity that appears to be unique to the CNS during SARS-CoV-2 infection. These data suggest a potential role for autoimmunity in contributing to neurological symptoms, and merit further investigation to the potential role of autoantibodies in post-acute COVID-19 neurological symptoms.