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Volume 27, Number 1—January 2021
Dispatch

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

Isaac H. Solomon1Comments to Author , Vijay S. Ganesh1, Guixia Yu, Xian Ding Deng, Michael R. Wilson, Steve Miller, Tracey A. Milligan, Shibani S. Mukerji, Abigail Mathewson, Justin Linxweiler, Darlene Morse, Jana M. Ritter, J. Erin Staples, Holly Hughes, Carolyn V. Gould, Pardis C. Sabeti2, Charles Y. Chiu2, and Anne Piantadosi23
Author affiliations: Brigham and Women’s Hospital, Boston, Massachusetts, USA (I.H. Solomon, V.S. Ganesh, T.A. Milligan); Harvard Medical School, Boston (I.H. Solomon, V.S. Ganesh, T.A. Milligan, S.S. Mukerji, A. Piantadosi); Broad Institute, Cambridge, Massachusetts, USA (V.S. Ganesh, P.C. Sabeti, A. Piantadosi); University of California–San Francisco, San Francisco, California, USA (G. Yu, X.D. Deng, M.R. Wilson, S. Miller, C.Y. Chiu); Massachusetts General Hospital, Boston (S.S. Mukerji, A. Piantadosi); New Hampshire Division of Public Health Services, Concord, New Hampshire, USA (A. Mathewson, J. Linxweiler, D. Morse); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.M. Ritter); Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (J.E. Staples, H. Hughes, C.V. Gould); Harvard University, Cambridge (P.C. Sabeti); Harvard T.H. Chan School of Public Health, Boston (P.C. Sabeti); Howard Hughes Medical Institute, Chevy Chase, Maryland, USA (P.C. Sabeti)

Main Article

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.

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.

Main Article

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Main Article

1These authors contributed equally to this article.

2These senior authors contributed equally to this article.

3Current affiliation: Emory University, Atlanta, Georgia, USA.

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Page updated: December 21, 2020
Page reviewed: December 21, 2020
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