To describe a rare case of infectious immunodeficiency-related vaccine-derived rubella virus (iVDRV) and common variable immunodeficiency (CVID) associated granulomatous disease involving the central nervous system (CNS).

A 38-year-old male with CVID and cutaneous granulomatous disease presented with tinnitus, hearing loss, diplopia, and imbalance. Magnetic resonance imaging of the brain showed pachymeningeal enhancement along the cavernous sinuses, internal auditory canals, and multiple cranial nerves. Cerebrospinal fluid (CSF) testing showed lymphocytic pleocytosis, hypoglycorrhachia, and elevated protein. The initial evaluation, including an infectious workup, was negative for a specific etiology. There was suspicion for CVID-associated granulomatous disease, so infliximab was initiated, in part due to excellent systemic response in the past. The patient showed a marked clinical and partial radiographic response to treatment that lasted more than 1.5 years. He ultimately developed a precipitous decline, with development of anosmia, ageusia, and blindness. Re-evaluation of CSF with metagenomic next-generation sequencing (mNGS) indicated iVDRV. Shortly thereafter, the patient developed disseminated rubella with multi-organ involvement. He received ribavirin and nitazoxanide but ultimately passed.

This rare case of iVDRV manifesting with CNS granulomatous disease has not previously been reported. The overlap with CVID-associated granulomatous disease makes diagnosis particularly challenging. mNGS provides a unique opportunity for diagnosing rare infectious diseases.