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Progressive multifocal leukoencephalopathy (PML) is a rare central nervous system disease caused by John Cunningham (J.C.) virus reactivation in the setting of immunosuppression. We describe a young woman with chronic migraines, Factor V Leiden and prior intravenous drug use who presented with headache, fatigue and bilateral leg weakness. Imaging demonstrated stable subcortical T2/fluid-attenuated inversion recovery hyperintensities consistent with prior PML. During evaluation, she was found to have an autoimmune hepatitis flare associated with transient worsening of her neurologic deficits, suggesting PML recrudescence. This case highlights the potential for autoimmune-mediated perturbations in unmasking latent J.C. virus activity and underscores the importance of multidisciplinary care and ongoing research in managing atypical PML presentations.