The central nervous system’s proteogenomic and spatial imprint upon systemic viral infections with SARS-CoV-2

In COVID-19 neurological alterations are noticed during the systemic viral infection. Various pathophysiological mechanisms on the central nervous system (CNS) have been suggested in the past two years, including the viral neurotropism hypothesis. Nevertheless, neurological complications can also occur independent of neurotropism and at different stages of the disease and may be persistent. Previous autopsy studies of the CNS from patients with severe COVID-19 show infiltration of macrophages and T lymphocytes, especially in the perivascular regions as well as pronounced microglial activation, but without signs of viral encephalitis. However, there is an ongoing debate about long-term changes and cytotoxic effects in the CNS due to the systemic inflammation. Here, we show the brain-specific host response during and after COVID-19. We profile single-nucleus transcriptomes and proteomes of brainstem tissue from deceased COVID-19 patients who underwent rapid autopsy. We detect a disease phase-dependent inflammatory type-I interferon response in acute COVID-19 cases. Integrating single-nucleus RNA sequencing and spatial transcriptomics, we could localize two patterns of reaction to severe systemic inflammation. One neuronal with direct focus on cranial nerve nuclei and one diffusely affecting the whole brainstem, the latter reflecting a bystander effect that spreads throughout the vascular unit and alters the transcriptional state of oligodendrocytes, microglia and astrocytes. Our results indicate that even without persistence of SARS-CoV-2 in the CNS, the tissue activates highly protective mechanisms, which also cause functional disturbances that may explain the neurological symptoms of COVID-19, triggered by strong systemic type-I IFN signatures in the periphery. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germanys Excellence Strategy EXC-2049-390688087, as well as SFB TRR 167 and HE 3130/6-1 to F.L.H., CRC130 P17 to H.R. and A.E.H., HA 5354/10-1 to A.E.H. and RA 2491/1-1 to H.R.; by the German Center for Neurodegenerative Diseases (DZNE) Berlin, by the European Union (PHAGO, 115976; Innovative Medicines Initiative-2; FP7-PEOPLE-2012-ITN: NeuroKine) and by the Ministry for Science and Education of Lower Saxony through the program Niedersachsisches Vorab to J.F. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics commitee of Charite Universitymedicine Berlin Chariteplatz 1, 10117 Berlin (Germany) gave ethical approval for this study under the following registration numbers: EA1/144/13, EA2/066/20, EA1/075/19 and EA1/076/20. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.