Metagenomic analysis of viral co-infection in autoimmune encephalitis patients within 72-hour detection interval

This study investigates the co-existence of viral infections and neuronal autoantibodies in encephalitis patients within a short detection interval (72 hours from symptom onset). Fifteen encephalitis patients showing concurrent viral infections and neuronal autoantibodies were analyzed using metagenomic next-generation sequencing (mNGS) between 2018 and 2025. Cerebrospinal fluid (CSF) samples revealed viral infections (HSV-1 in 5 patients, EBV in 10 patients) alongside neuronal autoantibodies (NMDA-R, CASPR2, LGI1, LON5, GFAP, GAD65, mGluR5). This dataset contains mNGS sequencing data from CSF samples, which may help understand the relationship between viral encephalitis and autoimmune encephalitis, and support early diagnosis and treatment strategies.