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Table 1 Results of unbiased metagenomic deep sequencing and conventional diagnostic tests on intraocular fluid samples

From: Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens

Subject Clinical diagnosis Sample type MDS PCR RT- PCR Culture
Total culture read pairs Percentage unique non-host read pairs Organism (number of unique read pairs) HSV-1 HSV-2 VZV CMV T. gondii RV
1 Anterior uveitis Aqueous fluid 16,919,211 0.003 HSV-1 (423) Pos Neg Neg Neg Neg NA NA
2 Panuveitis Vitreous fluid 4,551,967 0.10 C. neoformans (8469) Neg Neg Neg Neg Neg NA C. neoformans
3 Panuveitis Vitreous fluid 10,759,511 0.02 T. gondii (1853) Neg Neg Neg Neg Pos NA NA
4 Panuveitis (noninfectious) Aqueous fluid 9,548,748 0.01 Neg Neg Neg Neg Neg Neg NA NA
5 Epiretinal membrane (noninflammatory) Vitreous fluid 7,167,502 0.04 Neg NA NA NA NA NA NA NA
6 Anterior and intermediate uveitis Aqueous fluid, right eye 1,684,220 0.41 RV (585) NA NA NA NA NA Pos NA
Vitreous fluid, left eye 12,111,540 0.01 RV (10) Neg Neg Neg Neg Neg NA NA
  Control H20 983,525 4.13 NA NA NA NA NA NA NA
  1. MDS correctly identified known infections in subjects 1–3. Subjects 4 and 5 had non-infectious ocular disease and had negative MDS testing for pathogens. RV was identified via MDS in subject 6 and confirmed by the California Department of Public Health’s RT-PCR assay. Abbreviations: Pos, positive; Neg, negative; NA, not applicable; RT-PCR, reverse transcription polymerase chain reaction; HSV-1, herpes simplex virus-1; HSV-2, herpes simplex virus-2; VZV, varicella zoster virus; CMV, cytomegalovirus; T. gondii, Toxoplasma gondii; RV, rubella virus; C. neoformans, Cryptococcus neoformans