Detection of JC virus DNA in CSF of pediatric patients with non-PML neurological disorders

BACKGROUND: JC virus (JCV) is a human polyomavirus classically associated with progressive multifocal leukoencephalopathy (PML). Its role in other central nervous system (CNS) disorders - and the contribution of related polyomaviruses such as BK virus (BKV) and simian virus 40 (SV40) - remains poorly defined in pediatric populations, especially among immunocompromised patients. METHODS: We analysed 64 cerebrospinal fluid (CSF) specimens collected from children evaluated for suspected viral encephalitis or meningoencephalitis between March and October 2024. Broad-range and virus-specific PCR assays targeting conserved regions of the large T antigen (LT-ag) and VP1 genes were performed. Positive amplicons were confirmed by bidirectional Sanger sequencing and phylogenetic analysis. Associations with HIV status were assessed using chi-square tests. RESULTS: JCV DNA was detected in 4 of 64 samples (4/64; 6.3%), BKV DNA in 5 of 64 samples (5/64; 7.8%), and both viruses were co-detected in 3 samples (3/64; 4.7%). All positive detections occurred in HIV-positive patients (JCV: 4/19 HIV+; BKV: 5/19 HIV+), yielding statistically significant associations with HIV status (JCV p = 0.006; BKV p = 0.002). No SV40 DNA was identified. Phylogenetic reconstruction grouped patient sequences tightly with reference JCV and BKV strains, supporting authentic detection rather than laboratory contamination. CONCLUSIONS: These results provide molecular evidence that JCV and BKV can be detected in the CSF of pediatric patients with suspected CNS infection - predominantly in the setting of HIV-associated immunosuppression - and may represent underrecognized contributors to non-PML neurological disease. Larger, longitudinal studies integrating clinical, radiological and quantitative viral-load data are required to define causality and clinical impact.