Table. 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.