Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 27, Number 1—January 2021

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


Results of JCV sequencing across samples from an immunocompromised patient with encephalitis, Boston, Massachusetts, USA*

Specimen Method Total reads† Unique JCV reads‡ % Genome assembled, by segment§
Mean depth, by genome segment§
Small Medium Large Small Medium Large
CSF mNGS, MSSPE 1,917,836,676 894 100 80 90 14.3 3.7 5.3
Cerebellum, frozen mNGS, MSSPE 1,031,252,808 558 98 66 100 9.4 1.3 6.1
Cerebellum, FFPE mNGS, hybrid capture 38,974,996 294 70 56 90 7.1 1.2 3.1
Cortex, frozen mNGS, MSSPE 729,867,496 3,652 100 100 100 61.6 15.2 40.2
Cortex, FFPE mNGS, hybrid capture 101,331,284 518 100 72 91 20.1 2.1 4.5

*Methods detailed in Appendix. CSF, cerebrospinal fluid; FFPE, formalin-fixed, paraffin-embedded; JCV, Jamestown Canyon virus; mNGS, metagenomic next-generation sequencing; MSSPE, metagenomic sequencing with spiked primer enrichment.
†Total reads reflect the number of raw reads that were generated from each sample.
‡Unique JCV reads reflects removal of PCR duplicates and mapping to JCV reference sequences.
§Small, 989 nt; Medium, 4,509 nt; Large, 6,960 nt.

Main Article

1These authors contributed equally to this article.

2These senior authors contributed equally to this article.

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

Page created: September 23, 2020
Page updated: December 21, 2020
Page reviewed: December 21, 2020
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.