SARS-CoV-2 Is Not Detected in the Cerebrospinal Fluid of Encephalopathic COVID-19 Patients

Abstract

Neurologic manifestations of the novel coronavirus SARS-CoV-2 infection have received wide attention, but the mechanisms remain uncertain. Here, we describe computational data from public domain RNA-seq datasets and cerebrospinal fluid data from adult patients with severe COVID-19 pneumonia that suggest that SARS-CoV-2 infection of the central nervous system is unlikely. We found that the mRNAs encoding the ACE2 receptor and the TMPRSS2 transmembrane serine protease, both of which are required for viral entry into host cells, are minimally expressed in the major cell types of the brain. In addition, CSF samples from 13 adult encephalopathic COVID-19 patients diagnosed with the viral infection via nasopharyngeal swab RT-PCR did not show evidence for the virus. This particular finding is robust for two reasons. First, the RT-PCR diagnostic was validated for CSF studies using stringent criteria; and second, 61% of these patients had CSF testing within 1 week of a positive nasopharyngeal diagnostic test. We propose that neurologic sequelae of COVID-19 are not due to SARS-CoV-2 meningoencephalitis and that other etiologies are more likely mechanisms.

Keywords: COVID-19; CSF; SARS-CoV-2; cerebrospinal fluid; encephalopathy.

Figure 1

ACE2 and TMPRSS2 mRNAs are only minimally expressed in the brain. (A) Bulk RNA sequencing of normal human tissues in the GTEx portal shows that ACE2 and TMPRSS2 mRNAs are minimally expressed in the human brain (red box and arrows). (B) The Brain RNA-seq database, which is based on RNA-seq of sorted cellular populations, shows minimal expression of ACE2 and TMPRSS2 in brain cells, including neurons, glia, microglia and endothelial cells. The expression pattern of GRIN2A, which encodes the NMDA receptor 2A subunit in neurons, and GFAP, which encodes an intracellular filament found in astrocytes, are shown for comparison. (C) Similar information is found in the Allen Brain Atlas, which is based on single-cell RNA-seq of normal brain specimens. ACE2 and TMPRSS2 (red arrow) are minimally expressed. GRIN2A and GFAP are again shown for comparison. TPM, Transcripts Per Million mapped reads; FPKM, Fragments Per Kilobase of transcript per Million mapped reads; CPM, Counts Per Million mapped reads; OPC, Oligodendrocyte Precursor Cells; oligo, oligodendrocytes; endo, endothelial cells; VLMC/peri, Vascular and LeptoMeningeal Cells/pericytes; micro, microglia.

Figure 2

Time interval between COVID-19 diagnosis by nasopharyngeal swab and CSF testing. (A) The interval between CSF testing and the nasopharyngeal swab test is displayed for all 13 patients in the cohort. (B) Pie chart showing the distribution of interval between CSF and nasopharyngeal testing.