Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in Patient Receiving Rituximab

Abstract

A 56-year-old man receiving rituximab who had months of neurologic symptoms was found to have Jamestown Canyon virus in cerebrospinal fluid by clinical metagenomic sequencing. The patient died, and postmortem examination revealed extensive neuropathologic abnormalities. Deep sequencing enabled detailed characterization of viral genomes from the cerebrospinal fluid, cerebellum, and cerebral cortex.

Keywords: Jamestown Canyon virus; arbovirus; encephalitis; metagenomic next-generation sequencing; monoclonal antibody; orthobunyavirus; rituximab; vector-borne infections; viruses.

Figure 1

Brain imaging and autopsy findings in a case of chronic Jamestown Canyon virus (JCV) meningoencephalitis in a patient receiving rituximab, Boston, Massachusetts, USA. A) Brain magnetic resonance imaging T2-weighted fluid-attenuated inversion recovery showed mild atrophy with secondary ventriculomegaly but was otherwise unremarkable. B) Brain positron emission tomography with 2-deoxy-2-[fluorine-18] fluoro-D-glucose integrated with computed tomography showed global hypometabolism. Color scale ranges from blue-green (hypometabolic) to orange-white (hypermetabolic). C, D) Hematoxylin and eosin stained section of cerebral cortex at low magnification shows loss of neurons and perivascular chronic inflammation (C), compared with a JCV-negative control with a normal complement of cortical neurons (D). E, F) Higher-power magnification of cerebral cortex (E) and hippocampus (F) show microgliosis, microglial nodules, and neuronophagia (arrow). G, H) Severe Purkinje cell loss, Bergmann gliois (arrows), and microgliosis (arrowheads) of the molecular layer are present in the cerebellum (G), compared with a JCV-negative control with normal complement of Purkinje cells (H). I, J) Immunohistochemistry shows abundant perivascular, parenchymal, and leptomeningeal CD3+ T cells (I) and is negative for B-cell lineage–specific activator protein positive B cells (J). Panels C, D, I, and J, original magnification ×100; panels E, F, G, and H, original magnification ×200.

Figure 2

JCV genome analyses in a case of chronic JCV meningoencephalitis in a patient on rituximab, Boston, Massachusetts, USA. A) Maximum-likelihood phylogenetic tree of the coding region of the JCV small segment (nucleocapsid). Sequences from the patient (bold) were most closely related to a JCV strain isolated from Simsbury, Connecticut, USA (GenBank accession no. EF681842), with ≈70% bootstrap support. Clades A, B1, and B2 are as previously reported (9). B) Single-nucleotide polymorphisms (SNPs) observed between samples from patient in this study. The consensus genome derived from each sample was aligned to a mosquito-derived JCV sequence (GenBank accession nos. HM007356 [S segment], HM007357 [M segment], and HM007358 [L segment], all represented in the figure as HM00735X). For each sample in this study, the light gray bar indicates positions for which there was coverage of >3 reads. Using the sequence derived from CSF as the reference, positions with a SNP are marked with a star; black indicates a synonymous change, and red indicates a nonsynonymous change. Only high-confidence (confirmed) SNPs are shown in this figure; all SNPs observed are shown in Appendix Tables 3, 4. Sequence data is available under National Center for Biotechnology Information BioProject no. PRJNA662969 (GenBank accession nos. MW072986–MW073000). CSF, cerebrospinal fluid; FFPE, formalin-fixed, paraffin-embedded; JCV, Jamestown Canyon virus; L, large; M, medium; S, small.