Neurological Manifestations of COVID-19 Feature T Cell Exhaustion and Dedifferentiated Monocytes in Cerebrospinal Fluid

Patients suffering from Coronavirus disease 2019 (COVID-19) can develop neurological sequelae, such as headache and neuroinflammatory or cerebrovascular disease. These conditions—termed here as Neuro-COVID—are more frequent in patients with severe COVID-19. To understand the etiology of these neurological sequelae, we utilized single-cell sequencing and examined the immune cell profiles from the cerebrospinal fluid (CSF) of Neuro-COVID patients compared with patients with non-inflammatory and autoimmune neurological diseases or with viral encephalitis. The CSF of Neuro-COVID patients exhibited an expansion of dedifferentiated monocytes and of exhausted CD4 + T cells. Neuro-COVID CSF leukocytes featured an enriched interferon signature; however, this was less pronounced than in viral encephalitis. Repertoire analysis revealed broad clonal T cell expansion and curtailed interferon response in severe compared with mild Neuro-COVID patients. Collectively, our findings document the CSF immune compartment in Neuro-COVID patients and suggest compromised antiviral responses in this setting. Graphical Abstract Highlights • Single-cell atlas of cerebrospinal fluid in Neuro-COVID and controls • Expansion of dedifferentiated monocytes and exhausted CD4 + T cells in Neuro-COVID • Less pronounced interferon signature in Neuro-COVID than in viral encephalitis • Curtailed interferon-response in severe Neuro-COVID Neurological manifestations associated with COVID-19 (Neuro-COVID) are recognized but under-studied. Using single-cell transcriptomics, Heming et al. identify expansion of dedifferentiated monocytes and exhausted CD4 + T cells in the cerebral spinal fluid of Neuro-COVID patients. This work provides a basis for improved understanding of the neurological sequelae associated with COVID-19.