Tables

Table 1. Clinical demographics

Supplementary Table 1. Subjects not meeting inclusion criteria due to known bacterial or fungal infection

Cerebrospinal fluid (CSF) total nucleated cells (TNC) and pathogen classification for the 14 cases excluded from analyses.

Supplementary Table 2. Subject-Level Clinical Details

Clinical details that include cerebrospinal fluid white blood cells, duration of infection prior to lumbar puncture and treatment provided for the 68 subjects in study. The number of infectious disease tests include tests performed during a MGH hospitalization; infectious disease tests performed prior to an MGH admission were not included. Abbreviations: AIDS, Acquired immunodeficiency syndrome; ALL, Acute lymphocytic leukemia; ANCA, Antineutrophil cytoplasmic antibodies; CLL, Chronic Lymphocytic Leukemia, CNS, Central Nervous System; CVID, Combined Variable Immunodeficiency; DLBCL, Diffuse large B-cell Lymphoma; GAD-65, glutamic acid decarboxylase 65-kilodalton isoform; HIV, Human Immunodeficiency Virus; HSV, Herpes Simplex Virus; HHV-6, Human Herpesvirus 6; ID, Infectious Disease; anti-NMDA-R, anti- N-methyl-D-aspartate receptor; PML, Progressive Multifocal Leukoencephalopathy; WNV, West Nile Virus; VZV, Varicella Zoster Virus

Supplementary Table 3. Clinical Followup for Subjects Listed as Unknown at Discharge

Chart review for subjects classified as unknown at hospital discharge.

Supplementary Table 4. Pathogenic taxa of interest classifications

Virus reads identified by KrakenUniq were manually inspected in Geneious and excluded as "Lab contaminant" if the reads matched a known virus commonly used in the laboratory, or if they matched the virus from a different subject in this study. Table hosted on https://figshare.com/articles/dataset/Tables/13266506

Supplementary Table 5. Sequencing Read Counts per Library - Computational Steps

Number of read counts per library identified at each step of computational processing. Table hosted on https://figshare.com/articles/dataset/Tables/13266506

Supplementary Table 6. Sequencing Read Counts by Subject - Computational Steps

Number of read counts per subject identified at each step of computational processing. Table hosted on https://figshare.com/articles/dataset/Tables/13266506

Supplementary Table 7. Enhanced sequencing metrics for positively identified taxa

RPM of positively identified taxa in each cell (without computational depletion). Empty cells correspond to 0 counts. Table hosted on https://figshare.com/articles/dataset/Tables/13266506

Supplementary Table 8. Detection of reads matching Blacklegged Tick Picorna-Like Virus (BTPLV)

Reads identified by Kaiju were aligned to BTPLV in Geneious and manually inspected. Table hosted on https://figshare.com/articles/dataset/Tables/13266506