Molecular and serological characterization of SARS-CoV-2 strains associated with viral encephalitis in Senegal during the COVID-19 pandemic.

Beyond its socio-economic impact, COVID-19 has been associated with respiratory, gastrointestinal, neurological and neuropsychiatric symptoms across many countries, including in Senegal. While the SARS-CoV-2 virus primarily targets the respiratory and cardiovascular systems, if not detected and treated early, it can invade the nervous system and lead to severe neurological complications. This study focuses on the molecular and serological characterization of the SARS-CoV-2 strains associated with encephalitis manifestations of the disease. The presence of the virus in the central nervous system was confirmed by RT-PCR and sequencing and also serological techniques. Genetic analysis identified Delta (B.1.617.2-like) and Eta (B.1.525-like) variants in encephalitis patients. In silico analysis revealed three mutations (p.Pro4619Leu, p.Ala103Pro and p.Thr40Ile) predicted to affect protein function, generating hypotheses regarding their possible involvement in neurological manifestations. Among 11 patients with SARS-CoV-2-associated encephalitis, 30% had SARS-CoV-2 IgG antibodies in their serum, and 20% had them in cerebrospinal fluid (CSF). As part of the surveillance system for infectious encephalitis in Senegal (ENSENE), our data provided evidence of SARS-CoV-2 involvement in the epidemiology of viral encephalitis during the COVID-19 pandemic. Similar approaches should be promoted in future studies to investigate the biological significance of these mutations and improve the diagnosis and management of neurological manifestations associated with SARS-CoV-2 infection.