Systematic SARS-CoV-2 screening in cerebrospinal fluid during the COVID-19 pandemic.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has emerged since December, 2019, and spread worldwide, causing the COVID-19 pandemic. Despite COVID-19 being a respiratory tract infection, the pathophysiology in both adults and children is incompletely understood. Neurological signs and symptoms—from headache to meningitis—have been reported in hospitalised patients.1, 2 SARS-CoV-2 can enter and replicate in neuronal cells in vitro, but the association between neurological manifestations and presence of SARS-CoV-2 in cerebrospinal fluid (CSF) has only been tested in a few cases, with one patient testing positive for SARS-CoV-2 in a case report and seven of seven patients testing negative in a case series.

We did retrospective systematic screening of all CSF samples (n=622) received at the virology laboratory of Lyon University Hospital during the COVID-19 epidemic (Feb 1 to May 11, 2020). In the appendix, a figure presents the number of COVID-19 cases and CSF samples screened during this period. Samples were screened for SARS-CoV-2 using a highly sensitive RT-PCR protocol from the Pasteur Institute. Overall, 578 CSF samples were tested, corresponding to 555 patients (aged 1 day to 90 years). 144 (25%) of 578 samples were from children (aged ≤15 years), whereas paediatric cases represented 31 (<1%) of 4304 patients with COVID-19. Notably, no peak in CSF sampling was noticed, as was seen for cases of COVID-19 (appendix), suggesting no increase in neurological diseases during the outbreak. Among the 555 patients, 171 (including 37 children) also had respiratory samples tested for SARS-CoV-2 within a period 3 weeks before and 4 weeks after CSF sampling was done; 23 patients (including five children) were positive for SARS-CoV-2 on respiratory samples.

All CSF samples were negative, except for two samples that were slightly positive for SARS-CoV-2 (cycle threshold [Ct]=32 and Ct=35) corresponding to post-mortem samples from two adults with confirmed COVID-19 (respectively, Ct=24 and Ct=22 in respiratory samples). This result was confirmed after a novel nucleic acid extraction of the initial sample. For one patient, a blood sample was available and was positive for SARS-CoV-2 (Ct=25) whereas brain biopsy samples from the two patients were negative, suggesting contamination of the CSF by blood. Importantly, the other 21 CSF samples from the patients with confirmed COVID-19 were negative (including one CSF sample collected post mortem).

To the best of our knowledge, our study is the largest screening for SARS-CoV-2 in CSF samples. SARS-CoV-2 detection in CSF during the outbreak in Lyon was very low (two of 578 samples). These data suggest that, although SARS-CoV-2 is able to replicate in neuronal cells in vitro, SARS-CoV-2 testing in CSF is not relevant in the general population. Our findings also emphasise the need for further studies to identify the potential role of the host-immune response on neurological manifestations in patients with COVID-19.