Volume 27, Number 1—January 2021
Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in Patient Receiving Rituximab
|Specimen||Method||Total reads†||Unique JCV reads‡||% Genome assembled, by segment§
||Mean depth, by genome segment§
|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.
1These authors contributed equally to this article.
2These senior authors contributed equally to this article.
3Current affiliation: Emory University, Atlanta, Georgia, USA.