Deep sequencing reveals persistence of cell-associated mumps vaccine virus in chronic encephalitis

Abstract

Routine childhood vaccination against measles, mumps and rubella has virtually abolished virus-related morbidity and mortality. Notwithstanding this, we describe here devastating neurological complications associated with the detection of live-attenuated mumps virus Jeryl Lynn (MuV^JL5) in the brain of a child who had undergone successful allogeneic transplantation for severe combined immunodeficiency (SCID). This is the first confirmed report of MuV^JL5 associated with chronic encephalitis and highlights the need to exclude immunodeficient individuals from immunisation with live-attenuated vaccines. The diagnosis was only possible by deep sequencing of the brain biopsy. Sequence comparison of the vaccine batch to the MuV^JL5 isolated from brain identified biased hypermutation, particularly in the matrix gene, similar to those found in measles from cases of SSPE. The findings provide unique insights into the pathogenesis of paramyxovirus brain infections.

Fig. 1

a Patient timeline presenting important clinical events (m.o. = months old) and immune recovery of CD3+ CD4+ T cells over this period. b MRI brain scan showing coronal T2-weighted FLAIR (FLuid Attenuated Inversion Recovery) and axial post-contrast T1-weighted images with bilateral basal ganglia lesions (white arrows) and enhancing cortical and deep grey matter lesions (black arrows). The pattern was typical of those described in subacute panencephalitis

Fig. 2

Much of the cortex showed significant tissue damage with neuronal loss. There was prominent reactive gliosis composed of plump astrocytosis with abundant eosinophilic cytoplasm and immunoreactivity for glial fibrillary acidic protein (GFAP) (a, e) with relative sparing of the superficial layers of the cortex. Some areas showed perivascular lymphocytosis and collections of macrophages (a, c). In others, with better neuronal preservation, there were foci of microglial nodules, neuronophagia, generalised microgliosis (demonstrated on CD68 staining b, d)) and patchy parenchymal and perivascular lymphocytes, the majority of which were positive for the T cell markers (f). Occasional foci of mineralisation were observed, but there was no vasculitis and no viral inclusions. The pathological changes extended into the underlying white matter (data not shown), which showed patchy loss of myelin staining on luxol fast blue. There was focal chronic inflammation in the leptomeninges. Mumps immunohistochemistry was positive in a neuronal pattern (g, h). We observed no specific staining for other pathogens HSV1 or 2, CMV, EBV, toxoplasma, JC virus, bacteria (Gram and Gram Twort), acid-fast bacteria (Ziehl-Neelson) or fungi (Grocott), and no evidence of intracellular or intranuclear viral inclusion bodies. a, b Haematoxylin and eosin (H&E), c, d CD68 immunohistochemistry, e GFAP immunohistochemistry, f CD3 immunohistochemistry. Scale bars-b, h 50 μm, a, c, d, e, g 100 μm, f 200 μm

Fig. 3

Fixed (defined to have frequency greater than 75 %) missense substitutions in the MuV^JL5-London brain mumps virus genome. The amino acid changes are plotted along the genome, colour-coded for each viral protein. The black dashed lines are the missense changes pre-existing as minor variants in the genome of the vaccine virus. The predicted CTL epitopes are also indicated