EP4713486A1 - Biomarkers for identifying infectious and non-infectious causes of neurological illness - Google Patents

Biomarkers for identifying infectious and non-infectious causes of neurological illness

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EP4713486A1
EP4713486A1 EP24840657.1A EP24840657A EP4713486A1 EP 4713486 A1 EP4713486 A1 EP 4713486A1 EP 24840657 A EP24840657 A EP 24840657A EP 4713486 A1 EP4713486 A1 EP 4713486A1
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group
rest
biomarkers
bacterial
cxcl9
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French (fr)
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Charles Chiu
Charles OMURA
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University of California
University of California Berkeley
University of California San Diego UCSD
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University of California
University of California Berkeley
University of California San Diego UCSD
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    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
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    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

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Abstract

Methods, compositions, systems, and kits for identifying infectious and noninfectious causes of neurological illness using select RNA gene biomarkers.

Description

Attorney Docket No.00138-015WO1 BIOMARKERS FOR IDENTIFYING INFECTIOUS AND NON-INFECTIOUS CAUSES OF NEUROLOGICAL ILLNESS CROSS REFERENCE TO RELATED APPLICATIONS [0001] This application claims priority under 35 U.S.C. §119 from Provisional Application Serial No.63/526,395, filed July 12, 2023, the disclosure of which is incorporated herein by reference for all purposes. FIELD [0002] The disclosure relates to the field of genomics and diagnostics, and more particularly to the use of RNA gene biomarkers for identifying infectious and non-infectious causes of neurological illness. BACKGROUND [0003] Traditional microbiological methods look for the pathogen to diagnose causes of infections. Diagnosis of neurological illnesses, including meningitis, encephalitis, and/or myelitis, is challenging, as currently available microbiologic tests for infection only identify approximately 50% of cases, and tests to identify non-infectious etiologies, such as autoimmune disease, are lacking. SUMMARY [0004] It was recognized herein the importance of host-pathogen interactions in infectious disease and the use of human RNA gene biomarkers in cerebrospinal fluid (CSF) to interrogate the patient host / immune response. The disclosure provides for processes or systems which leverage RNA metagenomic data from hundreds of CSF samples using a metagenomic next-generation sequencing (mNGS) assay in order to select human RNA expressed genes (RNA transcripts) that can be used along with a machine learning based classifier model to identify and potentially clinically diagnose infectious and non-infectious causes of neurological illness. The machine learning models can use panels of gene biomarkers (e.g., 35-60 RNA transcripts) to generate binary comparisons that differentiate between major etiologic categories: (1) autoimmune / non- infectious etiology, (2) viral infection, (3) bacterial infection, and (4) fungal infection. For example, there are sets of biomarkers that can discriminate between viral infection and the “rest” (all other categories), viral infection and bacterial infection, viral infection and autoimmune / non-infectious disease, etc. Additional gene panels have also been developed to differentiate categories via binary comparisons at higher levels of resolution (e.g., parasitic infection and “rest”, mycobacterial infection and “rest”, enterovirus D68 infection and non-enteroviral viral infection, etc.). The process or system disclosed herein leverages existing models (e.g., Attorney Docket No.00138-015WO1 neural networks, linear discriminant analysis, generalized linear models, etc.) with a novel algorithm (i.e., ranking Spearman classifier) for use with sets of RNA gene biomarkers of the disclosure. It was shown herein that the processes or systems of the disclosure generated probability estimates summing up to 100% the likelihood of a given etiology for the illness (e.g., 80% viral, 20% autoimmune / non-infectious). A clinical interpretation of these probability estimates can then be made, yielding a diagnostic test result that may be clinically actionable by medical care practitioners. [0005] The disclosure provides for human RNA gene biomarkers that can be used to develop a new generation of diagnostic tests for both infectious and non-infectious diagnoses based on a patient’s host response to infection. The availability of such tests has the potential to lower hospitalization costs and improve clinical outcomes for undiagnosed patients with neurological illness. [0006] In a particular embodiment, the disclosure provides a method of identifying infectious and non-infectious causes of neurological illness or disorder from a cerebrospinal fluid (CSF) sample from a subject, comprising: obtaining a cerebrospinal fluid (CSF) sample from a subject; measuring the gene expression profile of one or more RNA gene biomarkers from the subject's CSF sample, wherein the one or more RNA gene biomarkers are selected from the biomarkers listed in Table 1 and/or Table 2; and comparing the gene expression profile of the one or more RNA gene biomarkers from the subject's CSF sample with the gene expression profiles of RNA gene biomarkers from CSF samples from a population of subjects' that have known infectious and non-infectious causes of neurological illnesses or disorder. In another embodiment, the one or more RNA gene biomarkers are selected from the biomarkers listed in Table 1 or Table 2. In yet another embodiment, the one or more RNA gene biomarkers are selected from the biomarkers listed in Table 2. In a further embodiment, the one or more RNA gene biomarkers are selected from the RNA biomarkers listed in group (i), group (ii), group (iii) group (iv), group (v), group (vi), group (vii), group (viii), group (ix), group (x), group (xi), group (xii), group (xiii), group (xiv), group (xv), group (xvi), group (xvii), group (xviii), group (xix), group (xx), group (xxi), group (xxii), group (xxiii), group (xxiv), group (xxv), group (xxvi), group (xxvii), group (xxviii), group (xxix), and/or group (xxx): (i) ADAMTS12, ADD1, ADH5, ALDH1A2, ALDH3A1, ALOX15B, ARPC1A, ATP10D, AURKA, CACNB4, CASD1, CCL2, COX6B1, CXCL9, DAAM1, DDX23, DNMT3A, FAM198B, FBF1, FBXO41, FBXW11, FEM1A, FNIP2, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1RN, INTS6, IRF8, KCNK2, KIAA0232, MLXIP, MTURN, NET1, NOC3L, PHLDB1, PLEC, PNPLA2, PSMD10, Attorney Docket No.00138-015WO1 PSTPIP2, RASSF8, RHBDF2, RIMS1, RNF144B, RNF146, RSAD2, RUNX3, S100A9, SFPQ, SKI, SLC13A4, SLCO2B1, SNCAIP, TPGS2, TPRG1L, TPX2, TSC22D1, UBA6, UBE2L6, UBR4, WDR70, ZNF500, ZSCAN26, IFIT2, and IFIT3 [AINI v. 'rest']; (ii) ABCC5, ADGRL1, AFF2, AP4S1, BTBD11, CDCA7L, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IL1B, KCNJ2, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SLC15A4, SPARCL1, SYPL1, TIFA, and TMCC3 [Bacterial v. 'rest']; (iii) ABHD10, ACTG2, AMOTL2, BCL2, C12orf43, CD2AP, CDYL2, CHUK, CRABP1, CXCL8, CXCL9, DGKB, DRG1, EIF4E2, FAM122B, FAM198B, FBP1, FCF1, FGF1, GLCE, GMEB2, ITGB8, KCTD3, KHSRP, MAK16, MAST2, MED8, MID1, NDRG2, NRP1, NT5C3A, PAN2, PIGT, RBFOX2, RHBDF2, RRAGD, SPATS2L, TMEM126B, TMEM184C, TMEM64, TRIM38, TRMT2B, TSPYL4, TTC21B, TXLNG, UBA3, UGCG, VAT1L, and VPS26A [Fungal v. 'rest']; (iv) ARID3A, ATMIN, ATP1A3, AURKA, BCORL1, BHLHE41, BLZF1, C3, C3orf17, CACNA1F, CACNB4, CAPRIN2, CCT2, CD93, CHAMP1, CHST15, CRTC1, CXCL8, DDX60, DNM1L, EDEM2, EDEM3, EEF1A1, EEF1B2, EHD1, EIF3K, ELOVL7, ERAP1, FAM198B, FAM219B, FBRSL1, FBXL7, FOSL2, FPR3, GMFG, GRAMD1A, HELB, HERC6, HLA-DQA2, HMBS, HNRNPH3, IFFO2, IFI27, IFI44L, IFIT1, IL18, IL1B, IL2RB, INAFM2, INTS7, IRS2, KCTD3, KNSTRN, LAMP3, LIMK2, LPAR1, LPAR6, LY6E, MCPH1, MID1IP1, MKL2, MPP6, MROH1, MRPS6, MTURN, NUDT5, NUP133, NUP88, OAS1, OASL, OSGIN2, OTOF, PDCD10, PDIA4, PDS5A, PGM1, PHLDA1, PHLDB1, PLCD1, PLCD4, PRDM10, PRDM4, PTPRO, PTRH2, PXYLP1, RALGPS2, RETSAT, RGS18, RNF216, RSAD2, RSBN1, SCARF1, SDHAF3, SEMA6A, SESN1, SHISA9, SIAE, SIGLEC10, SLC11A1, SLC25A23, SLC31A1, SLC6A2, SMURF1, SNCAIP, SNX2, SOAT2, SPP1, STC2, TBC1D22B, TCN2, TET1, TLR7, TMEM106B, TMTC1, TNFSF10, TOX3, TUBG2, XAF1, ZMIZ1, ZNF410, ZNF614, ZNF621, ZNF831, UBC, USP18, VIM, FLNA, CXCL10, IL1RN, SELL, and EGR1 [Viral v. 'rest']; (v) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. Bacterial]; (vi) ABCD4, ALDH1A1, ANKRD13C, APOA1BP, APOL2, ATP10D, ATXN3, BAIAP2, BEST1, CCL2, CD2AP, CHIC1, CXCL8, CXCL9, DGKB, DNMBP, EIF4E2, ERMN, GATC, GBP3, GLCE, ITGB8, KCNK2, KHSRP, MAST2, MEAF6, MED24, MID1, MMRN1, MTPAP, MYH7, NET1, NOTCH1, P2RY14, P2RY2, PARK2, PLEK, RBFOX2, RECQL, RHBDF2, RRAGD, S100A8, TMEM63A, TPRG1L, TPX2, TSR1, TTPAL, TXLNG, UBR4, UGCG, ZNF76, CCND1, Attorney Docket No.00138-015WO1 PIM1, CCR1, CXCL10, IL1R2, IL1RN, CR1, FPR1, HK3, MNDA, and SLC2A3 [AINI v. Fungal]; (vii) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [Bacterial (typical & atypical) v. fungal]; (viii) ACP2, ADD1, ARHGAP4, ARL14EP, ARPC1A, ATP10D, AURKA, BAG5, BBS12, BCORL1, BLVRB, C3, CACNB4, CAMKK2, CAPRIN2, CASD1, CHST15, COX6B1, DAAM1, EEF1A1, EEF1B2, EFCAB1, ENO2, EPSTI1, ERAP1, FAM198B, FBF1, FGF1, FNIP2, GANAB, HELB, HELLS, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1B, IL1RN, IL2RB, INTS6, INTS7, IRF8, IRS2, ITGAV, KIAA0232, KNSTRN, LIMK2, LITAF, MCPH1, MPP6, MTURN, OAS1, PDCD4, PDIA4, PDS5A, PEX6, PGM1, PHAX, PHLDA1, PHLDB1, PLAU, PLCD4, PLEC, PPP1CC, PRDM10, PRDM4, PRPF4, PSMD10, PSTPIP2, PTPRO, RAB8A, RIMS1, RNF144B, RSAD2, SAMD9, SEC11A, SESN1, SFPQ, SIGLEC10, SKI, SLC11A1, SLC25A23, SMC2, SNCAIP, TMEM106B, TPRG1L, TRRAP, TUBG2, UBR4, VN1R1, ZBED4, and ZSCAN26 [AINI v. Viral]; (ix) ABCC5, ADGRL1, AFF2, ALDOC, BTBD11, CDCA7L, COL6A5, CPVL, CXCL9, DNPEP, ERICH3, FPR3, G0S2, H1F0, HN1L, HPCAL1, HYOU1, IGLL5, IL1B, IL1R1, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRRX1, RIPK2, SLC15A4, SPTA1, TIFA, TMCC3, TMEM52B, TRDMT1, USP18, and ZNF71 [bacterial (typical & atypical v. Viral]; (x) ABHD10, BLZF1, BTBD1, CD2AP, CDYL2, CHUK, CXCL8, DRG1, EIF3K, FAM198B, FBRSL1, GLCE, GMEB2, GTF3C2, IFI44L, IFIT1, IL1B, KHSRP, LY6E, MRPS6, MX2, MYBBP1A, NT5C3A, NUP133, P4HA1, PDHB, PIGT, RNF216, RRAGD, RSAD2, RSBN1, SEMA6A, SPATS2L, SPP1, TSR1, TTC21B, VPS26A, WDR75, and ZNF107 [Fungal v. Viral]; (xi) ABCA9, ABHD10, ACTA2, ACTN4, ADGRA3, AIP, AK5, ALDH1A2, AMER1, ANK2, ANP32A, APOD, ARMC6, ARRB2, ARRDC3, ATP9B, ATXN3, B3GALNT2, BCL2, BTAF1, BZRAP1, C12orf49, C15orf57, C1R, C2CD2, C2orf16, C5, C8orf33, CABIN1, CACHD1, CACNB4, CBX7, CD2, CDHR1, CDK12, CHST3, CNNM4, COL22A1, COPG2, CRIPT, CRY2, CSK, CSTF3, CXCL8, CXCL9, CYTH4, DDX5, DECR1, DNAH1, DNAH3, DNAJC19, DOK4, ECT2L, EIF3K, EIF4E2, EIF4E3, ELMO2, ELP5, EMC1, EPB41L5, EPPK1, ERI2, EXOC2, FADS6, FAM129C, FAM161B, FAM172A, FAM175A, FAM76A, FBXL12, FCF1, FGF2, FMOD, GPR160, GRB10, GRB2, HDAC7, HDGFRP3, HIVEP1, ICE2, IL18BP, INAFM2, INTS12, JKAMP, KCNF1, KDM2A, KHSRP, KIF24, KIFAP3, KLHL1, LANCL1, LILRB4, LIMD1, LSS, Attorney Docket No.00138-015WO1 MAP4K5, MAPK9, MAPRE1, MICB, MID1, MLKL, MME, MPI, MRE11A, MRPL22, NAV3, NBAS, NBPF11, NCF2, NCKAP5, NELL2, NID2, NRD1, NUTF2, OS9, OSBP, PAG1, PAN2, PARL, PDZD2, PHAX, PHF20, PHF24, PITPNM1, PLCB1, PLEKHG1, POGLUT1, POLI, PPP2R3A, PPP5C, PRR11, PSMA3, PSMB3, PTPN14, PTPN21, RAI14, RBFOX2, RGS12, RHOBTB3, RNF149, RNF217, RNF24, RNF8, RNFT1, RPF2, RRAGD, RXRB, S1PR3, SCRN1, SELL, SESN2, SF3A3, SGMS1, SGSM2, SLC25A11, SLC25A23, SLC30A7, SPACA6P, SPN, SSBP2, SYNPO2, TAPT1, TBC1D22A, TBC1D24, TCOF1, THAP5, THEMIS, TMED4, TPX2, TRIM38, TRMT1, TRMT2B, TRPM7, TSHZ1, TSPYL4, TTC17, TTPAL, TUBG2, TXNDC11, UBR4, ULK1, VAMP7, VPS13B, VPS26A, WDR45, YIPF5, YTHDF1, ZFAT, ZFP1, ZNF282, ZNF410, ZNF45, ZNF680, ZNHIT3, and ZRANB3 [Mold v. ‘rest’]; (xii) ABCA4, ABCG1, ACACA, ACP2, AGAP2, AGO3, ANAPC7, ANKLE2, ANKRD10, ANKRD36, ANLN, ANO7, AP5M1, ARHGAP20, ARHGEF17, ARSA, ASS1, ATG12, ATRN, BARD1, BPGM, BRD8, BRIP1, BUB1B, C16orf70, C22orf39, C6orf132, C7orf49, CAB39L, CARS, CBFA2T3, CCDC47, CCDC82, CCSAP, CD109, CD69, CDC23, CDK5RAP3, CEP250, CHI3L2, CHURC1, CLN6, CNTN1, COA3, COL9A3, CRIPT, CXCL11, CYC1, DBF4B, DERL1, DNASE1L1, EEF1G, EHBP1L1, EML3, EPM2AIP1, ERC2, ESCO2, FAM102B, FAM122A, FANCC, FBRSL1, FBXO31, FSCN3, GABPB2, GALNT14, GBAS, GID8, GPALPP1, GPD1L, GPR84, GRAMD1B, GRAP2, GTPBP1, H1F0, HAUS2, HAUS3, HCAR3, HFM1, HIST1H2BN, HMGA1, HVCN1, IFI27, IFI44L, IFIT2, IFIT3, IL17RD, IL1B, INTS2, ITGA5, ITGB7, KCTD3, KIF20B, LBR, LDLRAD3, LGALS3BP, LIMK1, LPAR5, LPIN2, LRRC1, LUC7L3, MAF, MAP3K15, 5-Mar, MARCO, MED22, MED27, MID1IP1, MMS19, MRPS6, MYO15A, NCDN, NCKAP1, NDUFAF4, NOC2L, NUP133, OTOF, OTUB2, P2RY12, PAPLN, PARP11, PARP15, PDE6B, PHF1, PLAC8, PNPLA2, POLD2, PPP2R1B, PRCP, PRDM4, PRKCE, PROK2, PRPF31, PRRX1, PSD4, PSMD10, PSTPIP2, PTBP1, PTBP2, PTGIS, QARS, RAB35, RASAL3, RASSF6, RBP3, RDH11, RER1, RGP1, RHOQ, RILP, RPA1, RPS6KA5, SASH3, SCAMP5, SESN1, SHC1, SLC11A1, SLC16A2, SLC24A1, SLC25A13, SLC25A17, SLC9A8, SLFN14, SMAD7, SMARCD1, SMC6, SMTN, SNCA, SOCS7, SPICE1, SPP1, SSTR3, TBL1X, TFDP1, THAP6, TIMM10B, TMEM108, TMEM159, TMEM63B, TNFRSF10A, TOLLIP, TPGS2, TPP2, TRAF2, TRIM35, TRPV2, TSPAN33, TYW3, USP14, USP38, UTP18, UTY, UVSSA, VCAM1, VPS72, WDR17, WDR47, WLS, XPNPEP3, ZBTB11, ZNF124, ZNF512B, ZNF546, ZNF639, ZNF687, ZNF740, ZNF765, and ZZZ3 [Flavivirus v. ‘rest’]; (xiii) AAR2, ACAA1, ACP2, ADAMTS2, AGPAT5, AKT2, ANKLE2, ANKRD54, ANO5, APBA3, APOL4, Attorney Docket No.00138-015WO1 APOLD1, ARHGAP24, ARSD, BAHD1, BCL7C, BDH1, BLNK, C10orf88, C12orf43, C2orf16, CASS4, CCDC170, CD101, CD274, CD7, CDC14B, CEACAM8, CENPC, CEP162, CFH, CHMP6, CLEC4M, CLK4, CLSTN1, COL5A1, COPS8, CRIPT, CS, CSF2RA, CSRNP2, CXCL11, CYB561, DAAM2, DCX, DDX20, DHRS7B, DIRC2, DMPK, EEFSEC, EGR3, EHD1, EHD3, EIF2B4, EPHX1, EPM2AIP1, ERO1B, FAM111B, FBP1, FPR3, G0S2, GALNT11, GATC, GBE1, GNPNAT1, GTF3C3, HCAR3, HERC6, HS6ST1, ICA1, IL12RB2, IL1R2, IQSEC2, KCNT2, KDM5D, KIAA1324, KLHL12, KPNA2, LAS1L, LCMT1, LGALS12, LRRCC1, LRSAM1, LTBP2, LZTFL1, MAP3K7CL, MCUR1, MEI1, MERTK, MFSD11, MGAT4B, MMAB, MRPS10, MRPS21, MTMR9, MUSK, MYBBP1A, MYO19, NATD1, NCKAP1, NCKIPSD, NPHP4, NRF1, NT5C3A, NUGGC, NUP43, OSGEP, P2RY14, PDPR, PEF1, PHGDH, PIM3, PISD, PLA2G12A, PLXNB2, PMS2, PNKP, POLD2, POU2AF1, PRICKLE3, PTGDS, PTPN13, R3HCC1L, RABGGTA, RABL2B, RAD17, RBFOX2, RFT1, RIC8B, RILPL2, RNF146, RNF5, ROCK2, RPRD1A, RUNX3, SCIN, SCRN3, 3-Sep, SHB, SHPK, SIAE, SLC16A7, SLC25A38, SLC39A10, SLC44A1, SLC8B1, SMCR5, SMIM12, SNAPC5, SNRK, SPATA20, SPRYD3, SRSF2, STEAP2, STK38L, STX2, TANK, TBPL1, TESK2, TICAM1, TJP1, TLDC1, TLR9, TMEM110, TMEM63A, TMEM70, TMEM87B, TNFSF13, TRAP1, TREM1, TRMT2A, TSHZ3, TSPAN17, TTC33, UBALD1, UCK2, UGCG, UQCR11, USP42, UTP14A, VIMP, VNN1, ZAP70, ZBED6, ZBTB3, ZBTB41, ZC4H2, ZCCHC14, ZDHHC17, ZNF486, ZNF542P, ZNF544, ZNF548, ZNF619, ZNF692, ZNF708, and ZNF720 [dimorphic fungi v. ‘rest’]; (xiv) AHNAK, AKAP10, ALDH1L1, ALDH3A2, ANGEL1, ANKRD17, ANKRD50, AQP10, ARHGEF17, ARID5B, ASAH1, ASUN, ATF6B, ATF7, ATXN7L2, ATXN7L3, ATXN7L3B, B4GALT4, BAHCC1, BCAP31, BCL6, BIN1, BMPR2, BRIP1, C11orf63, C5orf30, CAMKK2, CAPN1, CASP9, CD74, CDR1, CLIC5, CNOT3, COASY, CPSF7, CRISPLD1, CTTNBP2, CXCR1, DARS, DAZAP2, DDX10, DENND3, DFNA5, DHX15, DNAH6, DNAJA1, DNAJB6, EIF4G3, FTL, FYN, GABRB3, GALC, GCN1, GLE1, GLUD1, GNB2L1, HLA-DRB1, HR, IGF2BP3, IL18RAP, INTS2, INTU, JUNB, KANSL1L, KCNC2, KCNG1, KCNU1, KHDRBS1, KLF11, KLHL11, KLHL2, LAMA5, LARP4, LCA5L, LIMK2, LRRC4C, MAN2B2, MAPK6, MMRN2, MMS19, MPP7, MYH16, NDOR1, NDUFA6, NLGN2, NPY2R, NSRP1, NXN, PABPC4, PARP3, PJA2, PLAC8, PLCB1, PLEKHO1, PML, PNRC2, POP4, PPFIA2, PRDM2, PRDM7, PRDX1, PRELP, PSMA1, PSTK, PTGES3, PTPN21, PTPRO, R3HDM2, RAB7A, RC3H2, REV3L, RGL4, RIF1, RNF112, RNF170, ROR1, RPA2, RPE, RTN4IP1, SAMM50, SASH3, SCIN, SEC24B, SECISBP2L, SENP6, Attorney Docket No.00138-015WO1 SERF2, SESN3, SETD1A, SH3YL1, SIRT3, SLC39A11, SMARCA2, SMTN, SP3, SPOP, SPTBN2, SREK1IP1, SRPK1, SS18L1, ST6GALNAC1, STXBP5, TAOK1, TARBP1, TBC1D26, TECPR1, TESPA1, TIMM50, TMEM108, TMEM180, TMEM2, TNKS1BP1, TOB2, TRAF3IP3, TRAF5, TRPC5, TSC22D1, TUT1, TXNIP, TYRO3, TYRP1, UBE2H, UBE2R2, UNKL, VARS, VASP, VCAM1, VIT, VPS28, VPS8, VWDE, WDR73, WRN, ZC3H13, ZCCHC24, ZFAND6, ZFP36L2, ZMIZ1, ZNF197, ZNF469, ZNF521, ZNF608, ZNF721, ZNF780B, ZNF79, ZNRF2, ZSCAN25 [afm v. ‘rest’]; (xv) ALOX15, ASNS, BYSL, CD1E, CD209, CDC14B, CYP24A1, F13A1, GIPR, GTF2E1, JCHAIN, KLHDC8B, PIGX, SEMA4B, UCK2, ZBED8, ZIC1, and ZNF706 [worm v. ‘rest’]; (xvi) CCDC126, CXCL8, CXCL9, ERICH3, G0S2, IL1R2, KCNJ2, TNFAIP6, and UBD [mtb v. ‘rest’]; (xvii) ABHD14B, AHCY, ATP13A3, CCL2, CCL20, CD3E, COL1A1, CXCL9, CYP1B1, EFCAB2, FAM219B, FBXO25, HLA-DQB1, HSD17B4, IDO1, IGLL5, IL2RB, IL32, ITGB8, KLHL42, KRIT1, LETM1, LETMD1, LGALS3, MERTK, METTL9, MID1IP1, MOSPD2, MXI1, PI3, S100A8, SIGLEC10, SMCR8, SOD2, SPP1, ST3GAL5, UMPS, WIPI1, and ZNF253 [bacteria typical v. ‘rest’]; (xviii) ABCC5, ADGRL1, AFF2, AP4S1, ARL5A, B4GALT4, BTBD11, CCDC170, CDCA7L, CHST6, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IGLL5, ITGA8, KCNJ2, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SDPR, SLC15A4, SNX16, SYPL1, TIFA, TMCC3, TMEM52B, TPD52, TPGS2, TRIM36, and TUSC2 [bacteria atypical v. ‘rest’]; (xix) ABHD5, CD209, CWC15, DHX34, FADS2, FAM122B, FERMT3, FES, GPR183, HLA-DQA1, IFI44, KCNK2, KLHDC8B, LRRC9, METTL10, MS4A4A, NSDHL, PLCXD1, PLTP, PPM1G, PWP1, RBCK1, SKAP1, TADA2B, UCK2, and WBSCR16 [parasitic v. ‘rest’]; (xx) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. bacterial atypical]; (xxi) AHCY, ANKRD27, ATP2A3, CCL2, CD2, COBLL1, DNAH17, FAM219B, FBXO25, GALNT15, HSD17B4, IGLL5, KIAA1407, KIF3A, KRIT1, LETMD1, LILRA6, METTL9, MXI1, NLRP1, NOL8, NUCB1, PI3, PMP22, POLD4, POLL, PSTPIP2, RASAL3, RNF144B, RNPS1, S100A8, S100A9, SMCR8, TGFB3, TNFAIP2, and WIPI1 [AINI v. bacterial typical]; (xxii) ARHGAP25, AURKA, BCCIP, C2CD5, CCR7, CD209, CDYL2, CHEK2, CPM, CWC15, DDX19B, DHX34, FBF1, FZD3, GOLGA5, IDO1, IFI44, JCHAIN, KCNK2, KLC1, LRRC59, LRRC9, MAFB, METTL10, MRFAP1L1, MS4A4A, OLFML2B, POMP, PSTPIP2, PWP1, RBCK1, RIMS1, RNF146, RPF1, S100A8, SLAMF8, TNFRSF10B, Attorney Docket No.00138-015WO1 TRNT1, TTC9C, TYW3, and ZFAT [AINI v. parasitic]; (xxiii) ATF7IP2, ATP13A3, BLZF1, C3orf58, CCL2, CD36, CEP70, CXCL9, EYA2, FH, GPNMB, H1F0, HGS, HSD17B4, IGLL5, ITGB8, KATNAL2, MCUR1, RANBP6, REXO4, SFXN1, SIRT1, STMN4, ZNF430, and ZNF92 [bacteria atypical v. typical]; (xxiv) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [bacterial atypical v. fungal]; (xxv) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial atypical v. parasitic]; (xxvi) ABHD5, ADGRE1, BANK1, BCCIP, C16orf72, CD3E, COL1A1, CXCR1, CYP1B1, GATA3, GIN1, IDO1, IL32, IRAK2, JCHAIN, MOSPD2, NHS, PI3, POLR3D, PSPC1, PWP1, TIMP3, UMPS, ZGRF1, ZNF213, and ZNF407 [bacterial typical v. parasitic]; (xxvii) BLZF1, CHCHD3, CMTR1, COL1A1, CXCL1, CXCL8, DDX60, DNTTIP2, DUSP16, EDEM2, EDEM3, EFCAB2, EIF3F, FAM219B, IDO1, IL2RB, INAFM2, ITGB8, IWS1, LPAR6, MID1IP1, MXI1, NKG7, OTOF, PDE11A, PI3, PLTP, PPP3CC, PRDM4, RETSAT, SFXN1, SIGLEC10, SOD2, SPP1, TIMM10B, TNFSF10, and ZNF24 [bacterial typical v. viral]; (xxviii) A1CF, A2M, A2ML1, A4GALT, AAAS, AACS, AADACL4, AADAT, AAED1, AAGAB, AAMP, AAR2, AARS, AASDH, AASDHPPT, AATK, ABCA1, ABCA10, ABCA12, ABCA13, ABCA2, ABCA4, ABCA5, ABCA7, ABCA8, ABCA9, ABCB1, ABCB10, ABCB11, ABCB6, ABCB7, ABCB8, ABCC1, ABCC11, ABCC12, ABCC2, ABCC5, ABCD3, ABCD4, ABCF1, ABCF2, ABCG2, ABHD1, ABHD10, ABHD11, ABHD12B, ABHD14A, ABHD16A, ABHD17A, ABHD2, ABHD3, ABHD4, ABHD5, ABI2, ABL2, ABLIM3, ABR, ABT1, ABTB1, ACAA1, ACAA2, ACAD10, ACAD9, ACADL, ACADM, ACADS, ACAN, ACAP1, ACBD3, ACBD4, ACBD5, ACBD6, ACBD7, ACKR1, ACO1, ACOT11, ACOT13, ACOX1, ACOX2, ACOX3, ACPP, ACR, ACSBG1, ACSBG2, ACSL1, ACSL5, ACSL6, ACSS1, ACSS3, ACTG2, ACTL6A, ACTN1, ACTN4, ACTR1A, ACTR1B, ACTR8, ACVR1, ACVR1B, ACVRL1, ADAM15, ADAM20, ADAM29, ADAM30, ADAM33, ADAM9, ADAMDEC1, ADAMTS15, ADAMTS16, ADAMTS2, ADAMTS4, ADAMTS6, ADAMTS9, ADAMTSL4, ADAP2, ADAT2, ADCK1, ADCY3, ADCY9, ADD2, ADD3, ADGB, ADGRA3, ADGRE1, ADGRE2, ADGRF5, ADGRG2, ADGRG4, ADGRG6, ADGRL2, ADGRL3, ADGRL4, ADH1B, ADI1, ADNP2, ADORA2A-AS1, ADPRM, ADRA1A, Attorney Docket No.00138-015WO1 ADRA2A, AEBP2, AFF4, AFMID, AGBL5, AGFG2, AGL, AGPAT1, AGPAT5, AGPS, AGTPBP1, AHCTF1, AHCYL1, AHNAK2, AHSA2, AIDA, AIFM1, AK3, AKAP11, AKAP12, AKAP9, AKIRIN2, ALDH1A1, ALDH2, ALDH7A1, ALG1, ALG12, ALG9, ALKBH8, ALOX15, ALPK1, AMDHD1, AMIGO2, AMMECR1L, AMPD2, AMPD3, ANAPC1, ANAPC13, ANAPC4, ANKFY1, ANKIB1, ANKMY2, ANKRD13D, ANKRD20A5P, ANKRD28, ANKRD36C, ANKRD42, ANKRD62, ANLN, ANTXR1, AP3M1, AP5Z1, APOBEC3G, APOBR, APOD, APOPT1, APPL1, AQP4, ARFGAP3, ARHGEF37, ARID3A, ARMC6, ARNT2, ARV1, ATF6B, ATG16L1, ATG9B, ATOX1, ATP12A, ATP13A2, ATP1B2, ATP2B2, ATPAF1, BAP1, BATF2, BAX, BCAP29, BMPR2, BRMS1, BRPF1, BTBD18, BTF3L4, BUB1, BUD13, C12orf65, C16orf62, C16orf71, C17orf51, C1orf27, C2CD5, C3orf38, C5, C5orf63, C6orf132, C8orf33, C8orf49, CABLES1, CAD, CAMK4, CANT1, CASK, CASP7, CBX7, CCDC149, CCSAP, CD24, CD244, CDCA3, CDKL1, CECR6, CELSR1, CHN2, CLCN3, CLUAP1, CLUH, CMTR2, CNOT8, COMMD9, COPG2, CSRP2BP, DAAM2, DBNL, DCLRE1A, DDX46, DNAAF5, DNAH1, DOK4, EIF2AK3, EIF2B1, ELMOD3, EMC4, EML3, EPN2, FAF2, FAM160B2, FAM35A, FAM69A, FZD3, GFM1, GLIS3, GPR137B, GRK5, HMBOX1, HNRNPA1L2, HRH1, INSIG2, KIAA0319L, LAMP3, LIG1, LRIG2, NFATC2IP, OAZ2, OGG1, PAQR8, PARL, PCGF3, PCMTD2, PLAUR, PRPF19, PTPN7, RAD1, RBCK1, RBPMS, RFX1, RPS4Y1, SCAF1, SH3PXD2B, SNTA1, STRADA, STXBP4, TAF5L, TBRG4, TOM1L2, ZNF397, ZNF597, ZNF71, ZNF721, and ZSWIM6 [fungal v. parasitic]; (xxix) ANAPC4, APLP1, BLZF1, CLPX, CRYL1, DESI2, FADS2, FAM122B, FBN3, FES, GRWD1, HERC5, HEXA, HLA-DQA1, IFIT1, KLHDC8B, MTURN, MYO1D, NSDHL, PLCXD1, PLTP, PWP1, RAB11FIP4, SKAP1, SLC35D2, SPOCK1, SPP1, TADA2B, TLR7, TMTC3, UCK2, ZNF213, ZNF407 [parasitic v. viral]; and (xxx) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial both v. parasitic]. In yet another embodiment, the one or more RNA gene biomarkers are selected from group (i)-(iv) and comprise at least one or more from each group: (i) UBR4, RHDBF2, S100A9, PSTPIP2 and/or ALS2CR12/Casp8 [AINI v. 'rest']; (ii) PI3, NELFCD, MERTk, WDR93, and/or RIPK2 [Bacterial v. 'rest']; (iii) CXCL8, NT5C3A, TRMT1, SSPN, and/or SOD1 [Fungal v. 'rest']; and/or (iv) IFI44L, IFIT1, IRPS3A, CXCL8 and/or PRDM10[Viral v. 'rest'] In yet a further embodiment, the subject is a human patient that is suspected of having a neurological illness or disorder. In another embodiment, the neurological illness or disorder is selected from encephalitis, cavernous sinus thrombosis, Attorney Docket No.00138-015WO1 brain abscess, encephalomyelitis, meningitis, meningoencephalitis, basal ganglia disease, dyskinesia, athetosis, chorea, myoclonus, tremor, restless leg syndrome, tauopathy, frontotemporal dementia, Lewy bodies dementia, posterior cortical atrophy, vascular dementia, Leigh syndrome, multiple sclerosis, epilepsy, seizures, migraine, stroke, sleep disorder, intercranial hypertension, cerebral edema, intracranial hypotension, brain herniation, Reye syndrome, hepatic encephalopathy, toxic encephalopathy, Hashimoto's encephalopathy, static encephalopathy, Friedreich's ataxia, ataxia-telangiectasia, primary lateral sclerosis, Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. In yet another embodiment, the encephalitis, encephalomyelitis, meningitis, or meningoencephalitis is caused by a bacterium, virus, fungus, or parasite. In a further embodiment, the bacterium is selected from Group B Streptococcus, Escherichia coli, Listeria monocytogenes, Neisseria meningitides, Streptococcus pneumoniae and Haemophiles influenzae. In yet a further embodiment, the virus is selected from non-polio enteroviruses, mumps virus, Herpesviruses, Measles virus, Influenza virus, Arboviruses, and lymphocytic choriomeningitis virus. In another embodiment, the fungus is selected from Aspergillus, Candida Albicans, Coccidioides Immitis, Cryptococcus Neoformans, Histoplasma, and Mucormycosis. In yet another embodiment, the parasite is selected from Angiostrongylus cantonensis, Baylisascaris procyonis, and Gnathostoma spinigerum. In a further embodiment, the gene expression profile of one or more RNA biomarkers is measured using a metagenomic next-generation sequencing (mNGS) assay. In yet a further embodiment, the CSF samples from the population of subjects, are from subjects that have neurological illnesses or disorders selected from encephalitis, cavernous sinus thrombosis, brain abscess, encephalomyelitis, meningitis, meningoencephalitis, basal ganglia disease, dyskinesia, athetosis, chorea, myoclonus, tremor, restless leg syndrome, tauopathy, frontotemporal dementia, Lewy bodies dementia, posterior cortical atrophy, vascular dementia, Leigh syndrome, multiple sclerosis, epilepsy, seizures, migraine, stroke, sleep disorder, intercranial hypertension, cerebral edema, intracranial hypotension, brain herniation, Reye syndrome, hepatic encephalopathy, toxic encephalopathy, Hashimoto's encephalopathy, static encephalopathy, Friedreich's ataxia, ataxia-telangiectasia, primary lateral sclerosis, Alzheimer's disease, Parkinson's disease, Huntington's disease, and/or amyotrophic lateral sclerosis. In another embodiment, the encephalitis, encephalomyelitis, meningitis, or meningoencephalitis is caused by a bacterium, virus, fungus, or parasite. In yet another embodiment, the bacterium is selected from Group B Streptococcus, Escherichia coli, Listeria monocytogenes, Neisseria meningitides, Attorney Docket No.00138-015WO1 Streptococcus pneumoniae and Haemophiles influenzae. In a further embodiment, the virus is selected from non-polio enteroviruses, mumps virus, Herpesviruses, Measles virus, Influenza virus, Arboviruses, and lymphocytic choriomeningitis virus. In yet a further embodiment, the fungus is selected from Aspergillus, Candida Albicans, Coccidioides Immitis, Cryptococcus Neoformans, Histoplasma, and Mucormycosis. In another embodiment, the parasite is selected from Angiostrongylus cantonensis, Baylisascaris procyonis, and Gnathostoma spinigerum. In yet another embodiment, unsupervised hierarchical clustering is used to compare the the gene expression profile of the one or more RNA biomarkers from the subject's CSF sample with the gene expression profiles of RNA biomarkers from CSF samples from a population of subjects' that have known infectious and non-infectious causes of neurological illnesses or disorder. [0007] In a certain embodiment, the disclosure also provides a computer implemented method to select for the identification of RNA gene biomarkers associated with a neurological illness based on host response classification using a machine learning model, the method comprising the steps: (1) assembling a dataset of RNA metagenomic data from hundreds of CSF samples; (2) randomly splitting the dataset into a training and test subset based upon selected features and targets, wherein the selected features and targets include viral, bacterial, fungal, parasitic, and/or autoimmune/non-infectious (AINI) host response classifiers; (3) training a machine learning model with the training subset to predict and rank biomarkers that have a high degree of association with the host response classifiers for a neurological illness; and (4) testing the machine learning model with the testing subset by comparing testing predictions to actual targets to generate an accuracy or prediction score, retraining the machine learning model in step (3) until a statistically significant accuracy or prediction score is achieved. In another embodiment, biomarkers that have a high degree of association with the host response classifiers is determined based on measuring a linear correlation between the biomarker and the host response classifiers. In yet another embodiment, the linear correlation is measured using Pearson correlation coefficient (r). In yet another embodiment, the computer implemented method is implemented using a graphic processing unit (GPU) or an artificial intelligence accelerator of a cloud-based server. In one embodiment, the computer implemented method is trained using RNA gene biomarkers selected from the RNA biomarkers listed in group (i), group (ii), group (iii) group (iv), group (v), group (vi), group (vii), group (viii), group (ix), group (x), group (xi), group (xii), group (xiii), group (xiv), group (xv), group (xvi), group (xvii), group (xviii), group (xix), group (xx), group (xxi), group (xxii), group (xxiii), group (xxiv), group (xxv), group (xxvi), group Attorney Docket No.00138-015WO1 (xxvii), group (xxviii), group (xxix), and/or group (xxx): (i) ADAMTS12, ADD1, ADH5, ALDH1A2, ALDH3A1, ALOX15B, ARPC1A, ATP10D, AURKA, CACNB4, CASD1, CCL2, COX6B1, CXCL9, DAAM1, DDX23, DNMT3A, FAM198B, FBF1, FBXO41, FBXW11, FEM1A, FNIP2, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1RN, INTS6, IRF8, KCNK2, KIAA0232, MLXIP, MTURN, NET1, NOC3L, PHLDB1, PLEC, PNPLA2, PSMD10, PSTPIP2, RASSF8, RHBDF2, RIMS1, RNF144B, RNF146, RSAD2, RUNX3, S100A9, SFPQ, SKI, SLC13A4, SLCO2B1, SNCAIP, TPGS2, TPRG1L, TPX2, TSC22D1, UBA6, UBE2L6, UBR4, WDR70, ZNF500, ZSCAN26, IFIT2, and IFIT3 [AINI v. 'rest']; (ii) ABCC5, ADGRL1, AFF2, AP4S1, BTBD11, CDCA7L, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IL1B, KCNJ2, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SLC15A4, SPARCL1, SYPL1, TIFA, and TMCC3 [Bacterial v. 'rest']; (iii) ABHD10, ACTG2, AMOTL2, BCL2, C12orf43, CD2AP, CDYL2, CHUK, CRABP1, CXCL8, CXCL9, DGKB, DRG1, EIF4E2, FAM122B, FAM198B, FBP1, FCF1, FGF1, GLCE, GMEB2, ITGB8, KCTD3, KHSRP, MAK16, MAST2, MED8, MID1, NDRG2, NRP1, NT5C3A, PAN2, PIGT, RBFOX2, RHBDF2, RRAGD, SPATS2L, TMEM126B, TMEM184C, TMEM64, TRIM38, TRMT2B, TSPYL4, TTC21B, TXLNG, UBA3, UGCG, VAT1L, and VPS26A [Fungal v. 'rest']; (iv) ARID3A, ATMIN, ATP1A3, AURKA, BCORL1, BHLHE41, BLZF1, C3, C3orf17, CACNA1F, CACNB4, CAPRIN2, CCT2, CD93, CHAMP1, CHST15, CRTC1, CXCL8, DDX60, DNM1L, EDEM2, EDEM3, EEF1A1, EEF1B2, EHD1, EIF3K, ELOVL7, ERAP1, FAM198B, FAM219B, FBRSL1, FBXL7, FOSL2, FPR3, GMFG, GRAMD1A, HELB, HERC6, HLA-DQA2, HMBS, HNRNPH3, IFFO2, IFI27, IFI44L, IFIT1, IL18, IL1B, IL2RB, INAFM2, INTS7, IRS2, KCTD3, KNSTRN, LAMP3, LIMK2, LPAR1, LPAR6, LY6E, MCPH1, MID1IP1, MKL2, MPP6, MROH1, MRPS6, MTURN, NUDT5, NUP133, NUP88, OAS1, OASL, OSGIN2, OTOF, PDCD10, PDIA4, PDS5A, PGM1, PHLDA1, PHLDB1, PLCD1, PLCD4, PRDM10, PRDM4, PTPRO, PTRH2, PXYLP1, RALGPS2, RETSAT, RGS18, RNF216, RSAD2, RSBN1, SCARF1, SDHAF3, SEMA6A, SESN1, SHISA9, SIAE, SIGLEC10, SLC11A1, SLC25A23, SLC31A1, SLC6A2, SMURF1, SNCAIP, SNX2, SOAT2, SPP1, STC2, TBC1D22B, TCN2, TET1, TLR7, TMEM106B, TMTC1, TNFSF10, TOX3, TUBG2, XAF1, ZMIZ1, ZNF410, ZNF614, ZNF621, ZNF831, UBC, USP18, VIM, FLNA, CXCL10, IL1RN, SELL, and EGR1 [Viral v. 'rest']; (v) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. Bacterial]; (vi) Attorney Docket No.00138-015WO1 ABCD4, ALDH1A1, ANKRD13C, APOA1BP, APOL2, ATP10D, ATXN3, BAIAP2, BEST1, CCL2, CD2AP, CHIC1, CXCL8, CXCL9, DGKB, DNMBP, EIF4E2, ERMN, GATC, GBP3, GLCE, ITGB8, KCNK2, KHSRP, MAST2, MEAF6, MED24, MID1, MMRN1, MTPAP, MYH7, NET1, NOTCH1, P2RY14, P2RY2, PARK2, PLEK, RBFOX2, RECQL, RHBDF2, RRAGD, S100A8, TMEM63A, TPRG1L, TPX2, TSR1, TTPAL, TXLNG, UBR4, UGCG, ZNF76, CCND1, PIM1, CCR1, CXCL10, IL1R2, IL1RN, CR1, FPR1, HK3, MNDA, and SLC2A3 [AINI v. Fungal]; (vii) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [Bacterial (typical & atypical) v. fungal]; (viii) ACP2, ADD1, ARHGAP4, ARL14EP, ARPC1A, ATP10D, AURKA, BAG5, BBS12, BCORL1, BLVRB, C3, CACNB4, CAMKK2, CAPRIN2, CASD1, CHST15, COX6B1, DAAM1, EEF1A1, EEF1B2, EFCAB1, ENO2, EPSTI1, ERAP1, FAM198B, FBF1, FGF1, FNIP2, GANAB, HELB, HELLS, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1B, IL1RN, IL2RB, INTS6, INTS7, IRF8, IRS2, ITGAV, KIAA0232, KNSTRN, LIMK2, LITAF, MCPH1, MPP6, MTURN, OAS1, PDCD4, PDIA4, PDS5A, PEX6, PGM1, PHAX, PHLDA1, PHLDB1, PLAU, PLCD4, PLEC, PPP1CC, PRDM10, PRDM4, PRPF4, PSMD10, PSTPIP2, PTPRO, RAB8A, RIMS1, RNF144B, RSAD2, SAMD9, SEC11A, SESN1, SFPQ, SIGLEC10, SKI, SLC11A1, SLC25A23, SMC2, SNCAIP, TMEM106B, TPRG1L, TRRAP, TUBG2, UBR4, VN1R1, ZBED4, and ZSCAN26 [AINI v. Viral]; (ix) ABCC5, ADGRL1, AFF2, ALDOC, BTBD11, CDCA7L, COL6A5, CPVL, CXCL9, DNPEP, ERICH3, FPR3, G0S2, H1F0, HN1L, HPCAL1, HYOU1, IGLL5, IL1B, IL1R1, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRRX1, RIPK2, SLC15A4, SPTA1, TIFA, TMCC3, TMEM52B, TRDMT1, USP18, and ZNF71 [bacterial (typical & atypical v. Viral]; (x) ABHD10, BLZF1, BTBD1, CD2AP, CDYL2, CHUK, CXCL8, DRG1, EIF3K, FAM198B, FBRSL1, GLCE, GMEB2, GTF3C2, IFI44L, IFIT1, IL1B, KHSRP, LY6E, MRPS6, MX2, MYBBP1A, NT5C3A, NUP133, P4HA1, PDHB, PIGT, RNF216, RRAGD, RSAD2, RSBN1, SEMA6A, SPATS2L, SPP1, TSR1, TTC21B, VPS26A, WDR75, and ZNF107 [Fungal v. Viral]; (xi) ABCA9, ABHD10, ACTA2, ACTN4, ADGRA3, AIP, AK5, ALDH1A2, AMER1, ANK2, ANP32A, APOD, ARMC6, ARRB2, ARRDC3, ATP9B, ATXN3, B3GALNT2, BCL2, BTAF1, BZRAP1, C12orf49, C15orf57, C1R, C2CD2, C2orf16, C5, C8orf33, CABIN1, CACHD1, CACNB4, CBX7, CD2, CDHR1, CDK12, CHST3, CNNM4, COL22A1, COPG2, CRIPT, CRY2, CSK, Attorney Docket No.00138-015WO1 CSTF3, CXCL8, CXCL9, CYTH4, DDX5, DECR1, DNAH1, DNAH3, DNAJC19, DOK4, ECT2L, EIF3K, EIF4E2, EIF4E3, ELMO2, ELP5, EMC1, EPB41L5, EPPK1, ERI2, EXOC2, FADS6, FAM129C, FAM161B, FAM172A, FAM175A, FAM76A, FBXL12, FCF1, FGF2, FMOD, GPR160, GRB10, GRB2, HDAC7, HDGFRP3, HIVEP1, ICE2, IL18BP, INAFM2, INTS12, JKAMP, KCNF1, KDM2A, KHSRP, KIF24, KIFAP3, KLHL1, LANCL1, LILRB4, LIMD1, LSS, MAP4K5, MAPK9, MAPRE1, MICB, MID1, MLKL, MME, MPI, MRE11A, MRPL22, NAV3, NBAS, NBPF11, NCF2, NCKAP5, NELL2, NID2, NRD1, NUTF2, OS9, OSBP, PAG1, PAN2, PARL, PDZD2, PHAX, PHF20, PHF24, PITPNM1, PLCB1, PLEKHG1, POGLUT1, POLI, PPP2R3A, PPP5C, PRR11, PSMA3, PSMB3, PTPN14, PTPN21, RAI14, RBFOX2, RGS12, RHOBTB3, RNF149, RNF217, RNF24, RNF8, RNFT1, RPF2, RRAGD, RXRB, S1PR3, SCRN1, SELL, SESN2, SF3A3, SGMS1, SGSM2, SLC25A11, SLC25A23, SLC30A7, SPACA6P, SPN, SSBP2, SYNPO2, TAPT1, TBC1D22A, TBC1D24, TCOF1, THAP5, THEMIS, TMED4, TPX2, TRIM38, TRMT1, TRMT2B, TRPM7, TSHZ1, TSPYL4, TTC17, TTPAL, TUBG2, TXNDC11, UBR4, ULK1, VAMP7, VPS13B, VPS26A, WDR45, YIPF5, YTHDF1, ZFAT, ZFP1, ZNF282, ZNF410, ZNF45, ZNF680, ZNHIT3, and ZRANB3 [Mold v. ‘rest’]; (xii) ABCA4, ABCG1, ACACA, ACP2, AGAP2, AGO3, ANAPC7, ANKLE2, ANKRD10, ANKRD36, ANLN, ANO7, AP5M1, ARHGAP20, ARHGEF17, ARSA, ASS1, ATG12, ATRN, BARD1, BPGM, BRD8, BRIP1, BUB1B, C16orf70, C22orf39, C6orf132, C7orf49, CAB39L, CARS, CBFA2T3, CCDC47, CCDC82, CCSAP, CD109, CD69, CDC23, CDK5RAP3, CEP250, CHI3L2, CHURC1, CLN6, CNTN1, COA3, COL9A3, CRIPT, CXCL11, CYC1, DBF4B, DERL1, DNASE1L1, EEF1G, EHBP1L1, EML3, EPM2AIP1, ERC2, ESCO2, FAM102B, FAM122A, FANCC, FBRSL1, FBXO31, FSCN3, GABPB2, GALNT14, GBAS, GID8, GPALPP1, GPD1L, GPR84, GRAMD1B, GRAP2, GTPBP1, H1F0, HAUS2, HAUS3, HCAR3, HFM1, HIST1H2BN, HMGA1, HVCN1, IFI27, IFI44L, IFIT2, IFIT3, IL17RD, IL1B, INTS2, ITGA5, ITGB7, KCTD3, KIF20B, LBR, LDLRAD3, LGALS3BP, LIMK1, LPAR5, LPIN2, LRRC1, LUC7L3, MAF, MAP3K15, 5-Mar, MARCO, MED22, MED27, MID1IP1, MMS19, MRPS6, MYO15A, NCDN, NCKAP1, NDUFAF4, NOC2L, NUP133, OTOF, OTUB2, P2RY12, PAPLN, PARP11, PARP15, PDE6B, PHF1, PLAC8, PNPLA2, POLD2, PPP2R1B, PRCP, PRDM4, PRKCE, PROK2, PRPF31, PRRX1, PSD4, PSMD10, PSTPIP2, PTBP1, PTBP2, PTGIS, QARS, RAB35, RASAL3, RASSF6, RBP3, RDH11, RER1, RGP1, RHOQ, RILP, RPA1, RPS6KA5, SASH3, SCAMP5, SESN1, SHC1, SLC11A1, SLC16A2, SLC24A1, SLC25A13, SLC25A17, SLC9A8, SLFN14, SMAD7, SMARCD1, SMC6, SMTN, SNCA, SOCS7, SPICE1, SPP1, SSTR3, TBL1X, TFDP1, Attorney Docket No.00138-015WO1 THAP6, TIMM10B, TMEM108, TMEM159, TMEM63B, TNFRSF10A, TOLLIP, TPGS2, TPP2, TRAF2, TRIM35, TRPV2, TSPAN33, TYW3, USP14, USP38, UTP18, UTY, UVSSA, VCAM1, VPS72, WDR17, WDR47, WLS, XPNPEP3, ZBTB11, ZNF124, ZNF512B, ZNF546, ZNF639, ZNF687, ZNF740, ZNF765, and ZZZ3 [Flavivirus v. ‘rest’]; (xiii) AAR2, ACAA1, ACP2, ADAMTS2, AGPAT5, AKT2, ANKLE2, ANKRD54, ANO5, APBA3, APOL4, APOLD1, ARHGAP24, ARSD, BAHD1, BCL7C, BDH1, BLNK, C10orf88, C12orf43, C2orf16, CASS4, CCDC170, CD101, CD274, CD7, CDC14B, CEACAM8, CENPC, CEP162, CFH, CHMP6, CLEC4M, CLK4, CLSTN1, COL5A1, COPS8, CRIPT, CS, CSF2RA, CSRNP2, CXCL11, CYB561, DAAM2, DCX, DDX20, DHRS7B, DIRC2, DMPK, EEFSEC, EGR3, EHD1, EHD3, EIF2B4, EPHX1, EPM2AIP1, ERO1B, FAM111B, FBP1, FPR3, G0S2, GALNT11, GATC, GBE1, GNPNAT1, GTF3C3, HCAR3, HERC6, HS6ST1, ICA1, IL12RB2, IL1R2, IQSEC2, KCNT2, KDM5D, KIAA1324, KLHL12, KPNA2, LAS1L, LCMT1, LGALS12, LRRCC1, LRSAM1, LTBP2, LZTFL1, MAP3K7CL, MCUR1, MEI1, MERTK, MFSD11, MGAT4B, MMAB, MRPS10, MRPS21, MTMR9, MUSK, MYBBP1A, MYO19, NATD1, NCKAP1, NCKIPSD, NPHP4, NRF1, NT5C3A, NUGGC, NUP43, OSGEP, P2RY14, PDPR, PEF1, PHGDH, PIM3, PISD, PLA2G12A, PLXNB2, PMS2, PNKP, POLD2, POU2AF1, PRICKLE3, PTGDS, PTPN13, R3HCC1L, RABGGTA, RABL2B, RAD17, RBFOX2, RFT1, RIC8B, RILPL2, RNF146, RNF5, ROCK2, RPRD1A, RUNX3, SCIN, SCRN3, 3-Sep, SHB, SHPK, SIAE, SLC16A7, SLC25A38, SLC39A10, SLC44A1, SLC8B1, SMCR5, SMIM12, SNAPC5, SNRK, SPATA20, SPRYD3, SRSF2, STEAP2, STK38L, STX2, TANK, TBPL1, TESK2, TICAM1, TJP1, TLDC1, TLR9, TMEM110, TMEM63A, TMEM70, TMEM87B, TNFSF13, TRAP1, TREM1, TRMT2A, TSHZ3, TSPAN17, TTC33, UBALD1, UCK2, UGCG, UQCR11, USP42, UTP14A, VIMP, VNN1, ZAP70, ZBED6, ZBTB3, ZBTB41, ZC4H2, ZCCHC14, ZDHHC17, ZNF486, ZNF542P, ZNF544, ZNF548, ZNF619, ZNF692, ZNF708, and ZNF720 [dimorphic fungi v. ‘rest’]; (xiv) AHNAK, AKAP10, ALDH1L1, ALDH3A2, ANGEL1, ANKRD17, ANKRD50, AQP10, ARHGEF17, ARID5B, ASAH1, ASUN, ATF6B, ATF7, ATXN7L2, ATXN7L3, ATXN7L3B, B4GALT4, BAHCC1, BCAP31, BCL6, BIN1, BMPR2, BRIP1, C11orf63, C5orf30, CAMKK2, CAPN1, CASP9, CD74, CDR1, CLIC5, CNOT3, COASY, CPSF7, CRISPLD1, CTTNBP2, CXCR1, DARS, DAZAP2, DDX10, DENND3, DFNA5, DHX15, DNAH6, DNAJA1, DNAJB6, EIF4G3, FTL, FYN, GABRB3, GALC, GCN1, GLE1, GLUD1, GNB2L1, HLA-DRB1, HR, IGF2BP3, IL18RAP, INTS2, INTU, JUNB, KANSL1L, KCNC2, KCNG1, KCNU1, KHDRBS1, KLF11, KLHL11, KLHL2, LAMA5, LARP4, LCA5L, LIMK2, LRRC4C, Attorney Docket No.00138-015WO1 MAN2B2, MAPK6, MMRN2, MMS19, MPP7, MYH16, NDOR1, NDUFA6, NLGN2, NPY2R, NSRP1, NXN, PABPC4, PARP3, PJA2, PLAC8, PLCB1, PLEKHO1, PML, PNRC2, POP4, PPFIA2, PRDM2, PRDM7, PRDX1, PRELP, PSMA1, PSTK, PTGES3, PTPN21, PTPRO, R3HDM2, RAB7A, RC3H2, REV3L, RGL4, RIF1, RNF112, RNF170, ROR1, RPA2, RPE, RTN4IP1, SAMM50, SASH3, SCIN, SEC24B, SECISBP2L, SENP6, SERF2, SESN3, SETD1A, SH3YL1, SIRT3, SLC39A11, SMARCA2, SMTN, SP3, SPOP, SPTBN2, SREK1IP1, SRPK1, SS18L1, ST6GALNAC1, STXBP5, TAOK1, TARBP1, TBC1D26, TECPR1, TESPA1, TIMM50, TMEM108, TMEM180, TMEM2, TNKS1BP1, TOB2, TRAF3IP3, TRAF5, TRPC5, TSC22D1, TUT1, TXNIP, TYRO3, TYRP1, UBE2H, UBE2R2, UNKL, VARS, VASP, VCAM1, VIT, VPS28, VPS8, VWDE, WDR73, WRN, ZC3H13, ZCCHC24, ZFAND6, ZFP36L2, ZMIZ1, ZNF197, ZNF469, ZNF521, ZNF608, ZNF721, ZNF780B, ZNF79, ZNRF2, ZSCAN25 [afm v. ‘rest’]; (xv) ALOX15, ASNS, BYSL, CD1E, CD209, CDC14B, CYP24A1, F13A1, GIPR, GTF2E1, JCHAIN, KLHDC8B, PIGX, SEMA4B, UCK2, ZBED8, ZIC1, and ZNF706 [worm v. ‘rest’]; (xvi) CCDC126, CXCL8, CXCL9, ERICH3, G0S2, IL1R2, KCNJ2, TNFAIP6, and UBD [mtb v. ‘rest’]; (xvii) ABHD14B, AHCY, ATP13A3, CCL2, CCL20, CD3E, COL1A1, CXCL9, CYP1B1, EFCAB2, FAM219B, FBXO25, HLA-DQB1, HSD17B4, IDO1, IGLL5, IL2RB, IL32, ITGB8, KLHL42, KRIT1, LETM1, LETMD1, LGALS3, MERTK, METTL9, MID1IP1, MOSPD2, MXI1, PI3, S100A8, SIGLEC10, SMCR8, SOD2, SPP1, ST3GAL5, UMPS, WIPI1, and ZNF253 [bacteria typical v. ‘rest’]; (xviii) ABCC5, ADGRL1, AFF2, AP4S1, ARL5A, B4GALT4, BTBD11, CCDC170, CDCA7L, CHST6, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IGLL5, ITGA8, KCNJ2, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SDPR, SLC15A4, SNX16, SYPL1, TIFA, TMCC3, TMEM52B, TPD52, TPGS2, TRIM36, and TUSC2 [bacteria atypical v. ‘rest’]; (xix) ABHD5, CD209, CWC15, DHX34, FADS2, FAM122B, FERMT3, FES, GPR183, HLA-DQA1, IFI44, KCNK2, KLHDC8B, LRRC9, METTL10, MS4A4A, NSDHL, PLCXD1, PLTP, PPM1G, PWP1, RBCK1, SKAP1, TADA2B, UCK2, and WBSCR16 [parasitic v. ‘rest’]; (xx) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. bacterial atypical]; (xxi) AHCY, ANKRD27, ATP2A3, CCL2, CD2, COBLL1, DNAH17, FAM219B, FBXO25, GALNT15, HSD17B4, IGLL5, KIAA1407, KIF3A, KRIT1, LETMD1, LILRA6, METTL9, MXI1, NLRP1, NOL8, NUCB1, PI3, PMP22, POLD4, POLL, PSTPIP2, RASAL3, RNF144B, RNPS1, S100A8, Attorney Docket No.00138-015WO1 S100A9, SMCR8, TGFB3, TNFAIP2, and WIPI1 [AINI v. bacterial typical]; (xxii) ARHGAP25, AURKA, BCCIP, C2CD5, CCR7, CD209, CDYL2, CHEK2, CPM, CWC15, DDX19B, DHX34, FBF1, FZD3, GOLGA5, IDO1, IFI44, JCHAIN, KCNK2, KLC1, LRRC59, LRRC9, MAFB, METTL10, MRFAP1L1, MS4A4A, OLFML2B, POMP, PSTPIP2, PWP1, RBCK1, RIMS1, RNF146, RPF1, S100A8, SLAMF8, TNFRSF10B, TRNT1, TTC9C, TYW3, and ZFAT [AINI v. parasitic]; (xxiii) ATF7IP2, ATP13A3, BLZF1, C3orf58, CCL2, CD36, CEP70, CXCL9, EYA2, FH, GPNMB, H1F0, HGS, HSD17B4, IGLL5, ITGB8, KATNAL2, MCUR1, RANBP6, REXO4, SFXN1, SIRT1, STMN4, ZNF430, and ZNF92 [bacteria atypical v. typical]; (xxiv) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [bacterial atypical v. fungal]; (xxv) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial atypical v. parasitic]; (xxvi) ABHD5, ADGRE1, BANK1, BCCIP, C16orf72, CD3E, COL1A1, CXCR1, CYP1B1, GATA3, GIN1, IDO1, IL32, IRAK2, JCHAIN, MOSPD2, NHS, PI3, POLR3D, PSPC1, PWP1, TIMP3, UMPS, ZGRF1, ZNF213, and ZNF407 [bacterial typical v. parasitic]; (xxvii) BLZF1, CHCHD3, CMTR1, COL1A1, CXCL1, CXCL8, DDX60, DNTTIP2, DUSP16, EDEM2, EDEM3, EFCAB2, EIF3F, FAM219B, IDO1, IL2RB, INAFM2, ITGB8, IWS1, LPAR6, MID1IP1, MXI1, NKG7, OTOF, PDE11A, PI3, PLTP, PPP3CC, PRDM4, RETSAT, SFXN1, SIGLEC10, SOD2, SPP1, TIMM10B, TNFSF10, and ZNF24 [bacterial typical v. viral]; (xxviii) A1CF, A2M, A2ML1, A4GALT, AAAS, AACS, AADACL4, AADAT, AAED1, AAGAB, AAMP, AAR2, AARS, AASDH, AASDHPPT, AATK, ABCA1, ABCA10, ABCA12, ABCA13, ABCA2, ABCA4, ABCA5, ABCA7, ABCA8, ABCA9, ABCB1, ABCB10, ABCB11, ABCB6, ABCB7, ABCB8, ABCC1, ABCC11, ABCC12, ABCC2, ABCC5, ABCD3, ABCD4, ABCF1, ABCF2, ABCG2, ABHD1, ABHD10, ABHD11, ABHD12B, ABHD14A, ABHD16A, ABHD17A, ABHD2, ABHD3, ABHD4, ABHD5, ABI2, ABL2, ABLIM3, ABR, ABT1, ABTB1, ACAA1, ACAA2, ACAD10, ACAD9, ACADL, ACADM, ACADS, ACAN, ACAP1, ACBD3, ACBD4, ACBD5, ACBD6, ACBD7, ACKR1, ACO1, ACOT11, ACOT13, ACOX1, ACOX2, ACOX3, ACPP, ACR, ACSBG1, ACSBG2, ACSL1, ACSL5, ACSL6, ACSS1, ACSS3, ACTG2, ACTL6A, ACTN1, ACTN4, ACTR1A, ACTR1B, ACTR8, ACVR1, ACVR1B, Attorney Docket No.00138-015WO1 ACVRL1, ADAM15, ADAM20, ADAM29, ADAM30, ADAM33, ADAM9, ADAMDEC1, ADAMTS15, ADAMTS16, ADAMTS2, ADAMTS4, ADAMTS6, ADAMTS9, ADAMTSL4, ADAP2, ADAT2, ADCK1, ADCY3, ADCY9, ADD2, ADD3, ADGB, ADGRA3, ADGRE1, ADGRE2, ADGRF5, ADGRG2, ADGRG4, ADGRG6, ADGRL2, ADGRL3, ADGRL4, ADH1B, ADI1, ADNP2, ADORA2A-AS1, ADPRM, ADRA1A, ADRA2A, AEBP2, AFF4, AFMID, AGBL5, AGFG2, AGL, AGPAT1, AGPAT5, AGPS, AGTPBP1, AHCTF1, AHCYL1, AHNAK2, AHSA2, AIDA, AIFM1, AK3, AKAP11, AKAP12, AKAP9, AKIRIN2, ALDH1A1, ALDH2, ALDH7A1, ALG1, ALG12, ALG9, ALKBH8, ALOX15, ALPK1, AMDHD1, AMIGO2, AMMECR1L, AMPD2, AMPD3, ANAPC1, ANAPC13, ANAPC4, ANKFY1, ANKIB1, ANKMY2, ANKRD13D, ANKRD20A5P, ANKRD28, ANKRD36C, ANKRD42, ANKRD62, ANLN, ANTXR1, AP3M1, AP5Z1, APOBEC3G, APOBR, APOD, APOPT1, APPL1, AQP4, ARFGAP3, ARHGEF37, ARID3A, ARMC6, ARNT2, ARV1, ATF6B, ATG16L1, ATG9B, ATOX1, ATP12A, ATP13A2, ATP1B2, ATP2B2, ATPAF1, BAP1, BATF2, BAX, BCAP29, BMPR2, BRMS1, BRPF1, BTBD18, BTF3L4, BUB1, BUD13, C12orf65, C16orf62, C16orf71, C17orf51, C1orf27, C2CD5, C3orf38, C5, C5orf63, C6orf132, C8orf33, C8orf49, CABLES1, CAD, CAMK4, CANT1, CASK, CASP7, CBX7, CCDC149, CCSAP, CD24, CD244, CDCA3, CDKL1, CECR6, CELSR1, CHN2, CLCN3, CLUAP1, CLUH, CMTR2, CNOT8, COMMD9, COPG2, CSRP2BP, DAAM2, DBNL, DCLRE1A, DDX46, DNAAF5, DNAH1, DOK4, EIF2AK3, EIF2B1, ELMOD3, EMC4, EML3, EPN2, FAF2, FAM160B2, FAM35A, FAM69A, FZD3, GFM1, GLIS3, GPR137B, GRK5, HMBOX1, HNRNPA1L2, HRH1, INSIG2, KIAA0319L, LAMP3, LIG1, LRIG2, NFATC2IP, OAZ2, OGG1, PAQR8, PARL, PCGF3, PCMTD2, PLAUR, PRPF19, PTPN7, RAD1, RBCK1, RBPMS, RFX1, RPS4Y1, SCAF1, SH3PXD2B, SNTA1, STRADA, STXBP4, TAF5L, TBRG4, TOM1L2, ZNF397, ZNF597, ZNF71, ZNF721, and ZSWIM6 [fungal v. parasitic]; (xxix) ANAPC4, APLP1, BLZF1, CLPX, CRYL1, DESI2, FADS2, FAM122B, FBN3, FES, GRWD1, HERC5, HEXA, HLA-DQA1, IFIT1, KLHDC8B, MTURN, MYO1D, NSDHL, PLCXD1, PLTP, PWP1, RAB11FIP4, SKAP1, SLC35D2, SPOCK1, SPP1, TADA2B, TLR7, TMTC3, UCK2, ZNF213, ZNF407 [parasitic v. viral]; and (xxx) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial both v. parasitic]. In yet another embodiment, the one or more RNA gene biomarkers are selected from group (i)-(iv) and comprise at least one or more from each group: (i) UBR4, RHDBF2, S100A9, PSTPIP2 and/or ALS2CR12/Casp8 [AINI v. 'rest']; (ii) PI3, NELFCD, Attorney Docket No.00138-015WO1 MERTk, WDR93, and/or RIPK2 [Bacterial v. 'rest']; (iii) CXCL8, NT5C3A, TRMT1, SSPN, and/or SOD1 [Fungal v. 'rest']; and/or (iv) IFI44L, IFIT1, IRPS3A, CXCL8 and/or PRDM10[Viral v. 'rest']. [0008] The disclosure also provides a method of diagnosing a subject comprising measuring a plurality of biomarkers in a sample from the subject and applying the measured biomarkers to the computer implemented trained model of the disclosure to identity whether the subject has a CNS viral, bacterial, fungal, parasitic, and/or autoimmune/non-infectious (AINI) disease. In one embodiment, the plurality of biomarkers are selected from the RNA biomarkers listed in group (i), group (ii), group (iii) group (iv), group (v), group (vi), group (vii), group (viii), group (ix), group (x), group (xi), group (xii), group (xiii), group (xiv), group (xv), group (xvi), group (xvii), group (xviii), group (xix), group (xx), group (xxi), group (xxii), group (xxiii), group (xxiv), group (xxv), group (xxvi), group (xxvii), group (xxviii), group (xxix), and/or group (xxx): (i) ADAMTS12, ADD1, ADH5, ALDH1A2, ALDH3A1, ALOX15B, ARPC1A, ATP10D, AURKA, CACNB4, CASD1, CCL2, COX6B1, CXCL9, DAAM1, DDX23, DNMT3A, FAM198B, FBF1, FBXO41, FBXW11, FEM1A, FNIP2, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1RN, INTS6, IRF8, KCNK2, KIAA0232, MLXIP, MTURN, NET1, NOC3L, PHLDB1, PLEC, PNPLA2, PSMD10, PSTPIP2, RASSF8, RHBDF2, RIMS1, RNF144B, RNF146, RSAD2, RUNX3, S100A9, SFPQ, SKI, SLC13A4, SLCO2B1, SNCAIP, TPGS2, TPRG1L, TPX2, TSC22D1, UBA6, UBE2L6, UBR4, WDR70, ZNF500, ZSCAN26, IFIT2, and IFIT3 [AINI v. 'rest']; (ii) ABCC5, ADGRL1, AFF2, AP4S1, BTBD11, CDCA7L, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IL1B, KCNJ2, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SLC15A4, SPARCL1, SYPL1, TIFA, and TMCC3 [Bacterial v. 'rest']; (iii) ABHD10, ACTG2, AMOTL2, BCL2, C12orf43, CD2AP, CDYL2, CHUK, CRABP1, CXCL8, CXCL9, DGKB, DRG1, EIF4E2, FAM122B, FAM198B, FBP1, FCF1, FGF1, GLCE, GMEB2, ITGB8, KCTD3, KHSRP, MAK16, MAST2, MED8, MID1, NDRG2, NRP1, NT5C3A, PAN2, PIGT, RBFOX2, RHBDF2, RRAGD, SPATS2L, TMEM126B, TMEM184C, TMEM64, TRIM38, TRMT2B, TSPYL4, TTC21B, TXLNG, UBA3, UGCG, VAT1L, and VPS26A [Fungal v. 'rest']; (iv) ARID3A, ATMIN, ATP1A3, AURKA, BCORL1, BHLHE41, BLZF1, C3, C3orf17, CACNA1F, CACNB4, CAPRIN2, CCT2, CD93, CHAMP1, CHST15, CRTC1, CXCL8, DDX60, DNM1L, EDEM2, EDEM3, EEF1A1, EEF1B2, EHD1, EIF3K, ELOVL7, ERAP1, FAM198B, FAM219B, FBRSL1, FBXL7, FOSL2, FPR3, GMFG, GRAMD1A, HELB, HERC6, HLA-DQA2, HMBS, HNRNPH3, IFFO2, IFI27, IFI44L, IFIT1, IL18, IL1B, IL2RB, INAFM2, INTS7, IRS2, Attorney Docket No.00138-015WO1 KCTD3, KNSTRN, LAMP3, LIMK2, LPAR1, LPAR6, LY6E, MCPH1, MID1IP1, MKL2, MPP6, MROH1, MRPS6, MTURN, NUDT5, NUP133, NUP88, OAS1, OASL, OSGIN2, OTOF, PDCD10, PDIA4, PDS5A, PGM1, PHLDA1, PHLDB1, PLCD1, PLCD4, PRDM10, PRDM4, PTPRO, PTRH2, PXYLP1, RALGPS2, RETSAT, RGS18, RNF216, RSAD2, RSBN1, SCARF1, SDHAF3, SEMA6A, SESN1, SHISA9, SIAE, SIGLEC10, SLC11A1, SLC25A23, SLC31A1, SLC6A2, SMURF1, SNCAIP, SNX2, SOAT2, SPP1, STC2, TBC1D22B, TCN2, TET1, TLR7, TMEM106B, TMTC1, TNFSF10, TOX3, TUBG2, XAF1, ZMIZ1, ZNF410, ZNF614, ZNF621, ZNF831, UBC, USP18, VIM, FLNA, CXCL10, IL1RN, SELL, and EGR1 [Viral v. 'rest']; (v) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. Bacterial]; (vi) ABCD4, ALDH1A1, ANKRD13C, APOA1BP, APOL2, ATP10D, ATXN3, BAIAP2, BEST1, CCL2, CD2AP, CHIC1, CXCL8, CXCL9, DGKB, DNMBP, EIF4E2, ERMN, GATC, GBP3, GLCE, ITGB8, KCNK2, KHSRP, MAST2, MEAF6, MED24, MID1, MMRN1, MTPAP, MYH7, NET1, NOTCH1, P2RY14, P2RY2, PARK2, PLEK, RBFOX2, RECQL, RHBDF2, RRAGD, S100A8, TMEM63A, TPRG1L, TPX2, TSR1, TTPAL, TXLNG, UBR4, UGCG, ZNF76, CCND1, PIM1, CCR1, CXCL10, IL1R2, IL1RN, CR1, FPR1, HK3, MNDA, and SLC2A3 [AINI v. Fungal]; (vii) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [Bacterial (typical & atypical) v. fungal]; (viii) ACP2, ADD1, ARHGAP4, ARL14EP, ARPC1A, ATP10D, AURKA, BAG5, BBS12, BCORL1, BLVRB, C3, CACNB4, CAMKK2, CAPRIN2, CASD1, CHST15, COX6B1, DAAM1, EEF1A1, EEF1B2, EFCAB1, ENO2, EPSTI1, ERAP1, FAM198B, FBF1, FGF1, FNIP2, GANAB, HELB, HELLS, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1B, IL1RN, IL2RB, INTS6, INTS7, IRF8, IRS2, ITGAV, KIAA0232, KNSTRN, LIMK2, LITAF, MCPH1, MPP6, MTURN, OAS1, PDCD4, PDIA4, PDS5A, PEX6, PGM1, PHAX, PHLDA1, PHLDB1, PLAU, PLCD4, PLEC, PPP1CC, PRDM10, PRDM4, PRPF4, PSMD10, PSTPIP2, PTPRO, RAB8A, RIMS1, RNF144B, RSAD2, SAMD9, SEC11A, SESN1, SFPQ, SIGLEC10, SKI, SLC11A1, SLC25A23, SMC2, SNCAIP, TMEM106B, TPRG1L, TRRAP, TUBG2, UBR4, VN1R1, ZBED4, and ZSCAN26 [AINI v. Viral]; (ix) ABCC5, ADGRL1, AFF2, ALDOC, BTBD11, CDCA7L, COL6A5, CPVL, CXCL9, Attorney Docket No.00138-015WO1 DNPEP, ERICH3, FPR3, G0S2, H1F0, HN1L, HPCAL1, HYOU1, IGLL5, IL1B, IL1R1, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRRX1, RIPK2, SLC15A4, SPTA1, TIFA, TMCC3, TMEM52B, TRDMT1, USP18, and ZNF71 [bacterial (typical & atypical v. Viral]; (x) ABHD10, BLZF1, BTBD1, CD2AP, CDYL2, CHUK, CXCL8, DRG1, EIF3K, FAM198B, FBRSL1, GLCE, GMEB2, GTF3C2, IFI44L, IFIT1, IL1B, KHSRP, LY6E, MRPS6, MX2, MYBBP1A, NT5C3A, NUP133, P4HA1, PDHB, PIGT, RNF216, RRAGD, RSAD2, RSBN1, SEMA6A, SPATS2L, SPP1, TSR1, TTC21B, VPS26A, WDR75, and ZNF107 [Fungal v. Viral]; (xi) ABCA9, ABHD10, ACTA2, ACTN4, ADGRA3, AIP, AK5, ALDH1A2, AMER1, ANK2, ANP32A, APOD, ARMC6, ARRB2, ARRDC3, ATP9B, ATXN3, B3GALNT2, BCL2, BTAF1, BZRAP1, C12orf49, C15orf57, C1R, C2CD2, C2orf16, C5, C8orf33, CABIN1, CACHD1, CACNB4, CBX7, CD2, CDHR1, CDK12, CHST3, CNNM4, COL22A1, COPG2, CRIPT, CRY2, CSK, CSTF3, CXCL8, CXCL9, CYTH4, DDX5, DECR1, DNAH1, DNAH3, DNAJC19, DOK4, ECT2L, EIF3K, EIF4E2, EIF4E3, ELMO2, ELP5, EMC1, EPB41L5, EPPK1, ERI2, EXOC2, FADS6, FAM129C, FAM161B, FAM172A, FAM175A, FAM76A, FBXL12, FCF1, FGF2, FMOD, GPR160, GRB10, GRB2, HDAC7, HDGFRP3, HIVEP1, ICE2, IL18BP, INAFM2, INTS12, JKAMP, KCNF1, KDM2A, KHSRP, KIF24, KIFAP3, KLHL1, LANCL1, LILRB4, LIMD1, LSS, MAP4K5, MAPK9, MAPRE1, MICB, MID1, MLKL, MME, MPI, MRE11A, MRPL22, NAV3, NBAS, NBPF11, NCF2, NCKAP5, NELL2, NID2, NRD1, NUTF2, OS9, OSBP, PAG1, PAN2, PARL, PDZD2, PHAX, PHF20, PHF24, PITPNM1, PLCB1, PLEKHG1, POGLUT1, POLI, PPP2R3A, PPP5C, PRR11, PSMA3, PSMB3, PTPN14, PTPN21, RAI14, RBFOX2, RGS12, RHOBTB3, RNF149, RNF217, RNF24, RNF8, RNFT1, RPF2, RRAGD, RXRB, S1PR3, SCRN1, SELL, SESN2, SF3A3, SGMS1, SGSM2, SLC25A11, SLC25A23, SLC30A7, SPACA6P, SPN, SSBP2, SYNPO2, TAPT1, TBC1D22A, TBC1D24, TCOF1, THAP5, THEMIS, TMED4, TPX2, TRIM38, TRMT1, TRMT2B, TRPM7, TSHZ1, TSPYL4, TTC17, TTPAL, TUBG2, TXNDC11, UBR4, ULK1, VAMP7, VPS13B, VPS26A, WDR45, YIPF5, YTHDF1, ZFAT, ZFP1, ZNF282, ZNF410, ZNF45, ZNF680, ZNHIT3, and ZRANB3 [Mold v. ‘rest’]; (xii) ABCA4, ABCG1, ACACA, ACP2, AGAP2, AGO3, ANAPC7, ANKLE2, ANKRD10, ANKRD36, ANLN, ANO7, AP5M1, ARHGAP20, ARHGEF17, ARSA, ASS1, ATG12, ATRN, BARD1, BPGM, BRD8, BRIP1, BUB1B, C16orf70, C22orf39, C6orf132, C7orf49, CAB39L, CARS, CBFA2T3, CCDC47, CCDC82, CCSAP, CD109, CD69, CDC23, CDK5RAP3, CEP250, CHI3L2, CHURC1, CLN6, CNTN1, COA3, COL9A3, CRIPT, CXCL11, CYC1, DBF4B, DERL1, DNASE1L1, EEF1G, EHBP1L1, EML3, EPM2AIP1, ERC2, ESCO2, FAM102B, FAM122A, FANCC, FBRSL1, Attorney Docket No.00138-015WO1 FBXO31, FSCN3, GABPB2, GALNT14, GBAS, GID8, GPALPP1, GPD1L, GPR84, GRAMD1B, GRAP2, GTPBP1, H1F0, HAUS2, HAUS3, HCAR3, HFM1, HIST1H2BN, HMGA1, HVCN1, IFI27, IFI44L, IFIT2, IFIT3, IL17RD, IL1B, INTS2, ITGA5, ITGB7, KCTD3, KIF20B, LBR, LDLRAD3, LGALS3BP, LIMK1, LPAR5, LPIN2, LRRC1, LUC7L3, MAF, MAP3K15, 5-Mar, MARCO, MED22, MED27, MID1IP1, MMS19, MRPS6, MYO15A, NCDN, NCKAP1, NDUFAF4, NOC2L, NUP133, OTOF, OTUB2, P2RY12, PAPLN, PARP11, PARP15, PDE6B, PHF1, PLAC8, PNPLA2, POLD2, PPP2R1B, PRCP, PRDM4, PRKCE, PROK2, PRPF31, PRRX1, PSD4, PSMD10, PSTPIP2, PTBP1, PTBP2, PTGIS, QARS, RAB35, RASAL3, RASSF6, RBP3, RDH11, RER1, RGP1, RHOQ, RILP, RPA1, RPS6KA5, SASH3, SCAMP5, SESN1, SHC1, SLC11A1, SLC16A2, SLC24A1, SLC25A13, SLC25A17, SLC9A8, SLFN14, SMAD7, SMARCD1, SMC6, SMTN, SNCA, SOCS7, SPICE1, SPP1, SSTR3, TBL1X, TFDP1, THAP6, TIMM10B, TMEM108, TMEM159, TMEM63B, TNFRSF10A, TOLLIP, TPGS2, TPP2, TRAF2, TRIM35, TRPV2, TSPAN33, TYW3, USP14, USP38, UTP18, UTY, UVSSA, VCAM1, VPS72, WDR17, WDR47, WLS, XPNPEP3, ZBTB11, ZNF124, ZNF512B, ZNF546, ZNF639, ZNF687, ZNF740, ZNF765, and ZZZ3 [Flavivirus v. ‘rest’]; (xiii) AAR2, ACAA1, ACP2, ADAMTS2, AGPAT5, AKT2, ANKLE2, ANKRD54, ANO5, APBA3, APOL4, APOLD1, ARHGAP24, ARSD, BAHD1, BCL7C, BDH1, BLNK, C10orf88, C12orf43, C2orf16, CASS4, CCDC170, CD101, CD274, CD7, CDC14B, CEACAM8, CENPC, CEP162, CFH, CHMP6, CLEC4M, CLK4, CLSTN1, COL5A1, COPS8, CRIPT, CS, CSF2RA, CSRNP2, CXCL11, CYB561, DAAM2, DCX, DDX20, DHRS7B, DIRC2, DMPK, EEFSEC, EGR3, EHD1, EHD3, EIF2B4, EPHX1, EPM2AIP1, ERO1B, FAM111B, FBP1, FPR3, G0S2, GALNT11, GATC, GBE1, GNPNAT1, GTF3C3, HCAR3, HERC6, HS6ST1, ICA1, IL12RB2, IL1R2, IQSEC2, KCNT2, KDM5D, KIAA1324, KLHL12, KPNA2, LAS1L, LCMT1, LGALS12, LRRCC1, LRSAM1, LTBP2, LZTFL1, MAP3K7CL, MCUR1, MEI1, MERTK, MFSD11, MGAT4B, MMAB, MRPS10, MRPS21, MTMR9, MUSK, MYBBP1A, MYO19, NATD1, NCKAP1, NCKIPSD, NPHP4, NRF1, NT5C3A, NUGGC, NUP43, OSGEP, P2RY14, PDPR, PEF1, PHGDH, PIM3, PISD, PLA2G12A, PLXNB2, PMS2, PNKP, POLD2, POU2AF1, PRICKLE3, PTGDS, PTPN13, R3HCC1L, RABGGTA, RABL2B, RAD17, RBFOX2, RFT1, RIC8B, RILPL2, RNF146, RNF5, ROCK2, RPRD1A, RUNX3, SCIN, SCRN3, 3-Sep, SHB, SHPK, SIAE, SLC16A7, SLC25A38, SLC39A10, SLC44A1, SLC8B1, SMCR5, SMIM12, SNAPC5, SNRK, SPATA20, SPRYD3, SRSF2, STEAP2, STK38L, STX2, TANK, TBPL1, TESK2, TICAM1, TJP1, TLDC1, TLR9, TMEM110, TMEM63A, TMEM70, TMEM87B, TNFSF13, TRAP1, Attorney Docket No.00138-015WO1 TREM1, TRMT2A, TSHZ3, TSPAN17, TTC33, UBALD1, UCK2, UGCG, UQCR11, USP42, UTP14A, VIMP, VNN1, ZAP70, ZBED6, ZBTB3, ZBTB41, ZC4H2, ZCCHC14, ZDHHC17, ZNF486, ZNF542P, ZNF544, ZNF548, ZNF619, ZNF692, ZNF708, and ZNF720 [dimorphic fungi v. ‘rest’]; (xiv) AHNAK, AKAP10, ALDH1L1, ALDH3A2, ANGEL1, ANKRD17, ANKRD50, AQP10, ARHGEF17, ARID5B, ASAH1, ASUN, ATF6B, ATF7, ATXN7L2, ATXN7L3, ATXN7L3B, B4GALT4, BAHCC1, BCAP31, BCL6, BIN1, BMPR2, BRIP1, C11orf63, C5orf30, CAMKK2, CAPN1, CASP9, CD74, CDR1, CLIC5, CNOT3, COASY, CPSF7, CRISPLD1, CTTNBP2, CXCR1, DARS, DAZAP2, DDX10, DENND3, DFNA5, DHX15, DNAH6, DNAJA1, DNAJB6, EIF4G3, FTL, FYN, GABRB3, GALC, GCN1, GLE1, GLUD1, GNB2L1, HLA-DRB1, HR, IGF2BP3, IL18RAP, INTS2, INTU, JUNB, KANSL1L, KCNC2, KCNG1, KCNU1, KHDRBS1, KLF11, KLHL11, KLHL2, LAMA5, LARP4, LCA5L, LIMK2, LRRC4C, MAN2B2, MAPK6, MMRN2, MMS19, MPP7, MYH16, NDOR1, NDUFA6, NLGN2, NPY2R, NSRP1, NXN, PABPC4, PARP3, PJA2, PLAC8, PLCB1, PLEKHO1, PML, PNRC2, POP4, PPFIA2, PRDM2, PRDM7, PRDX1, PRELP, PSMA1, PSTK, PTGES3, PTPN21, PTPRO, R3HDM2, RAB7A, RC3H2, REV3L, RGL4, RIF1, RNF112, RNF170, ROR1, RPA2, RPE, RTN4IP1, SAMM50, SASH3, SCIN, SEC24B, SECISBP2L, SENP6, SERF2, SESN3, SETD1A, SH3YL1, SIRT3, SLC39A11, SMARCA2, SMTN, SP3, SPOP, SPTBN2, SREK1IP1, SRPK1, SS18L1, ST6GALNAC1, STXBP5, TAOK1, TARBP1, TBC1D26, TECPR1, TESPA1, TIMM50, TMEM108, TMEM180, TMEM2, TNKS1BP1, TOB2, TRAF3IP3, TRAF5, TRPC5, TSC22D1, TUT1, TXNIP, TYRO3, TYRP1, UBE2H, UBE2R2, UNKL, VARS, VASP, VCAM1, VIT, VPS28, VPS8, VWDE, WDR73, WRN, ZC3H13, ZCCHC24, ZFAND6, ZFP36L2, ZMIZ1, ZNF197, ZNF469, ZNF521, ZNF608, ZNF721, ZNF780B, ZNF79, ZNRF2, ZSCAN25 [afm v. ‘rest’]; (xv) ALOX15, ASNS, BYSL, CD1E, CD209, CDC14B, CYP24A1, F13A1, GIPR, GTF2E1, JCHAIN, KLHDC8B, PIGX, SEMA4B, UCK2, ZBED8, ZIC1, and ZNF706 [worm v. ‘rest’]; (xvi) CCDC126, CXCL8, CXCL9, ERICH3, G0S2, IL1R2, KCNJ2, TNFAIP6, and UBD [mtb v. ‘rest’]; (xvii) ABHD14B, AHCY, ATP13A3, CCL2, CCL20, CD3E, COL1A1, CXCL9, CYP1B1, EFCAB2, FAM219B, FBXO25, HLA-DQB1, HSD17B4, IDO1, IGLL5, IL2RB, IL32, ITGB8, KLHL42, KRIT1, LETM1, LETMD1, LGALS3, MERTK, METTL9, MID1IP1, MOSPD2, MXI1, PI3, S100A8, SIGLEC10, SMCR8, SOD2, SPP1, ST3GAL5, UMPS, WIPI1, and ZNF253 [bacteria typical v. ‘rest’]; (xviii) ABCC5, ADGRL1, AFF2, AP4S1, ARL5A, B4GALT4, BTBD11, CCDC170, CDCA7L, CHST6, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IGLL5, ITGA8, KCNJ2, LZTS1, MEMO1, Attorney Docket No.00138-015WO1 MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SDPR, SLC15A4, SNX16, SYPL1, TIFA, TMCC3, TMEM52B, TPD52, TPGS2, TRIM36, and TUSC2 [bacteria atypical v. ‘rest’]; (xix) ABHD5, CD209, CWC15, DHX34, FADS2, FAM122B, FERMT3, FES, GPR183, HLA-DQA1, IFI44, KCNK2, KLHDC8B, LRRC9, METTL10, MS4A4A, NSDHL, PLCXD1, PLTP, PPM1G, PWP1, RBCK1, SKAP1, TADA2B, UCK2, and WBSCR16 [parasitic v. ‘rest’]; (xx) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. bacterial atypical]; (xxi) AHCY, ANKRD27, ATP2A3, CCL2, CD2, COBLL1, DNAH17, FAM219B, FBXO25, GALNT15, HSD17B4, IGLL5, KIAA1407, KIF3A, KRIT1, LETMD1, LILRA6, METTL9, MXI1, NLRP1, NOL8, NUCB1, PI3, PMP22, POLD4, POLL, PSTPIP2, RASAL3, RNF144B, RNPS1, S100A8, S100A9, SMCR8, TGFB3, TNFAIP2, and WIPI1 [AINI v. bacterial typical]; (xxii) ARHGAP25, AURKA, BCCIP, C2CD5, CCR7, CD209, CDYL2, CHEK2, CPM, CWC15, DDX19B, DHX34, FBF1, FZD3, GOLGA5, IDO1, IFI44, JCHAIN, KCNK2, KLC1, LRRC59, LRRC9, MAFB, METTL10, MRFAP1L1, MS4A4A, OLFML2B, POMP, PSTPIP2, PWP1, RBCK1, RIMS1, RNF146, RPF1, S100A8, SLAMF8, TNFRSF10B, TRNT1, TTC9C, TYW3, and ZFAT [AINI v. parasitic]; (xxiii) ATF7IP2, ATP13A3, BLZF1, C3orf58, CCL2, CD36, CEP70, CXCL9, EYA2, FH, GPNMB, H1F0, HGS, HSD17B4, IGLL5, ITGB8, KATNAL2, MCUR1, RANBP6, REXO4, SFXN1, SIRT1, STMN4, ZNF430, and ZNF92 [bacteria atypical v. typical]; (xxiv) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [bacterial atypical v. fungal]; (xxv) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial atypical v. parasitic]; (xxvi) ABHD5, ADGRE1, BANK1, BCCIP, C16orf72, CD3E, COL1A1, CXCR1, CYP1B1, GATA3, GIN1, IDO1, IL32, IRAK2, JCHAIN, MOSPD2, NHS, PI3, POLR3D, PSPC1, PWP1, TIMP3, UMPS, ZGRF1, ZNF213, and ZNF407 [bacterial typical v. parasitic]; (xxvii) BLZF1, CHCHD3, CMTR1, COL1A1, CXCL1, CXCL8, DDX60, DNTTIP2, DUSP16, EDEM2, EDEM3, EFCAB2, EIF3F, FAM219B, IDO1, IL2RB, INAFM2, ITGB8, IWS1, LPAR6, MID1IP1, MXI1, NKG7, OTOF, PDE11A, PI3, PLTP, PPP3CC, PRDM4, Attorney Docket No.00138-015WO1 RETSAT, SFXN1, SIGLEC10, SOD2, SPP1, TIMM10B, TNFSF10, and ZNF24 [bacterial typical v. viral]; (xxviii) A1CF, A2M, A2ML1, A4GALT, AAAS, AACS, AADACL4, AADAT, AAED1, AAGAB, AAMP, AAR2, AARS, AASDH, AASDHPPT, AATK, ABCA1, ABCA10, ABCA12, ABCA13, ABCA2, ABCA4, ABCA5, ABCA7, ABCA8, ABCA9, ABCB1, ABCB10, ABCB11, ABCB6, ABCB7, ABCB8, ABCC1, ABCC11, ABCC12, ABCC2, ABCC5, ABCD3, ABCD4, ABCF1, ABCF2, ABCG2, ABHD1, ABHD10, ABHD11, ABHD12B, ABHD14A, ABHD16A, ABHD17A, ABHD2, ABHD3, ABHD4, ABHD5, ABI2, ABL2, ABLIM3, ABR, ABT1, ABTB1, ACAA1, ACAA2, ACAD10, ACAD9, ACADL, ACADM, ACADS, ACAN, ACAP1, ACBD3, ACBD4, ACBD5, ACBD6, ACBD7, ACKR1, ACO1, ACOT11, ACOT13, ACOX1, ACOX2, ACOX3, ACPP, ACR, ACSBG1, ACSBG2, ACSL1, ACSL5, ACSL6, ACSS1, ACSS3, ACTG2, ACTL6A, ACTN1, ACTN4, ACTR1A, ACTR1B, ACTR8, ACVR1, ACVR1B, ACVRL1, ADAM15, ADAM20, ADAM29, ADAM30, ADAM33, ADAM9, ADAMDEC1, ADAMTS15, ADAMTS16, ADAMTS2, ADAMTS4, ADAMTS6, ADAMTS9, ADAMTSL4, ADAP2, ADAT2, ADCK1, ADCY3, ADCY9, ADD2, ADD3, ADGB, ADGRA3, ADGRE1, ADGRE2, ADGRF5, ADGRG2, ADGRG4, ADGRG6, ADGRL2, ADGRL3, ADGRL4, ADH1B, ADI1, ADNP2, ADORA2A-AS1, ADPRM, ADRA1A, ADRA2A, AEBP2, AFF4, AFMID, AGBL5, AGFG2, AGL, AGPAT1, AGPAT5, AGPS, AGTPBP1, AHCTF1, AHCYL1, AHNAK2, AHSA2, AIDA, AIFM1, AK3, AKAP11, AKAP12, AKAP9, AKIRIN2, ALDH1A1, ALDH2, ALDH7A1, ALG1, ALG12, ALG9, ALKBH8, ALOX15, ALPK1, AMDHD1, AMIGO2, AMMECR1L, AMPD2, AMPD3, ANAPC1, ANAPC13, ANAPC4, ANKFY1, ANKIB1, ANKMY2, ANKRD13D, ANKRD20A5P, ANKRD28, ANKRD36C, ANKRD42, ANKRD62, ANLN, ANTXR1, AP3M1, AP5Z1, APOBEC3G, APOBR, APOD, APOPT1, APPL1, AQP4, ARFGAP3, ARHGEF37, ARID3A, ARMC6, ARNT2, ARV1, ATF6B, ATG16L1, ATG9B, ATOX1, ATP12A, ATP13A2, ATP1B2, ATP2B2, ATPAF1, BAP1, BATF2, BAX, BCAP29, BMPR2, BRMS1, BRPF1, BTBD18, BTF3L4, BUB1, BUD13, C12orf65, C16orf62, C16orf71, C17orf51, C1orf27, C2CD5, C3orf38, C5, C5orf63, C6orf132, C8orf33, C8orf49, CABLES1, CAD, CAMK4, CANT1, CASK, CASP7, CBX7, CCDC149, CCSAP, CD24, CD244, CDCA3, CDKL1, CECR6, CELSR1, CHN2, CLCN3, CLUAP1, CLUH, CMTR2, CNOT8, COMMD9, COPG2, CSRP2BP, DAAM2, DBNL, DCLRE1A, DDX46, DNAAF5, DNAH1, DOK4, EIF2AK3, EIF2B1, ELMOD3, EMC4, EML3, EPN2, FAF2, FAM160B2, FAM35A, FAM69A, FZD3, GFM1, GLIS3, GPR137B, GRK5, HMBOX1, HNRNPA1L2, HRH1, INSIG2, KIAA0319L, LAMP3, LIG1, LRIG2, NFATC2IP, OAZ2, OGG1, PAQR8, Attorney Docket No.00138-015WO1 PARL, PCGF3, PCMTD2, PLAUR, PRPF19, PTPN7, RAD1, RBCK1, RBPMS, RFX1, RPS4Y1, SCAF1, SH3PXD2B, SNTA1, STRADA, STXBP4, TAF5L, TBRG4, TOM1L2, ZNF397, ZNF597, ZNF71, ZNF721, and ZSWIM6 [fungal v. parasitic]; (xxix) ANAPC4, APLP1, BLZF1, CLPX, CRYL1, DESI2, FADS2, FAM122B, FBN3, FES, GRWD1, HERC5, HEXA, HLA-DQA1, IFIT1, KLHDC8B, MTURN, MYO1D, NSDHL, PLCXD1, PLTP, PWP1, RAB11FIP4, SKAP1, SLC35D2, SPOCK1, SPP1, TADA2B, TLR7, TMTC3, UCK2, ZNF213, ZNF407 [parasitic v. viral]; and (xxx) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial both v. parasitic]. In yet another embodiment, the one or more RNA gene biomarkers are selected from group (i)-(iv) and comprise at least one or more from each group: (i) UBR4, RHDBF2, S100A9, PSTPIP2 and/or ALS2CR12/Casp8 [AINI v. 'rest']; (ii) PI3, NELFCD, MERTk, WDR93, and/or RIPK2 [Bacterial v. 'rest']; (iii) CXCL8, NT5C3A, TRMT1, SSPN, and/or SOD1 [Fungal v. 'rest']; and/or (iv) IFI44L, IFIT1, IRPS3A, CXCL8 and/or PRDM10[Viral v. 'rest']. DESCRIPTION OF DRAWINGS [0009] Figure 1 presents an overview of an embodiment of a process of the disclosure for the diagnosis of neurological illness based on host response classification using a machine model of the disclosure. As shown, in step 1, the CSF dataset is randomly split into training and test subsets for a targeted classification scheme, wherein 80% of the dataset is used to train the machine learning model, and 20% of the dataset is used to test the accuracy of the machine learning model. Once a machine learning model is trained, the accuracy of the model is determined by comparing testing predictions to actual target. If the model has achieved a desired level of accuracy, the model is used to predict which feature or target is implicated based on the host response classification. [0010] Figure 2 presents an embodiment of exemplary decision tree for a novel CSF host response classifier algorithm that can be used with the process and systems disclosed herein. [0011] Figure 3 presents an embodiment of implementation of a novel CSF host response classifier in a machine learning model of the disclosure. [0012] Figure 4 provides examples of host response classifier calls using a machine learning model of the disclosure in a method or system disclosed herein. [0013] Figure 5 demonstrates the performance of the host response classifier using the methods or systems disclosed herein. Attorney Docket No.00138-015WO1 [0014] Figure 6 provides an exemplary host response profiling for diagnosis of infections using a method or system of the disclosure. [0015] Figure 7A-B provides an example of host response profiling of CSF. (A) Machine learning based (least absolute shrinkage and selection operator, LASSO regression method) approaches were used to construct classifiers based on condensed (n=20-50) panels of differentially expressed genes that could discriminate between autoimmune / non- infectious, viral, bacterial, fungal and parasitic causes of meningoencephalitis. The final classifier, with accuracy for viral identification of ~90%, suggests that the patient's host response is likely viral, and possibly autoimmune, non-infectious encephalitis. (B) Heat map showing hierarchical clustering of Z-scores corresponding to the 66 genes from the viral versus autoimmune / non-infectious classifier (y-axis) across all available autoimmune / non- infectious samples (n=146) and viral samples (n=109), in conjunction with the host response profile from the patient's sample. The classification of the patient's host response as viral appears to be driven by upregulation of genes specific to the viral host response (dotted rectangle). [0016] Figure 8 depicts a block diagram for a system useful in the disclosure, wherein a system 130 includes a computer system 140 and the associated Internet 11 connection upon which an embodiment may be implemented and includes a bus 137, an interconnect, or other communication mechanism for communicating information, and a processor 138, commonly in the form of an integrated circuit, coupled with bus 137 for processing information and for executing the computer executable instructions. Computer system 140 also includes a main memory 134, such as a Random Access Memory (RAM) or other dynamic storage device, coupled to bus 137 for storing information and instructions to be executed by processor 138. [0017] Figure 9 provides a general schematic on the methodology of the disclosure. [0018] Figure 10 provides a general overview of the machine learning process used in the dislcosure. [0019] Figure 11 provides lasso coefficients for various gene expression profiles in various classifications. Also listed are a few of the top classifier genes. DETAILED DESCRIPTION [0020] Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art. See, e.g., Lackie, DICTIONARY OF CELL AND MOLECULAR BIOLOGY, Elsevier (4th ed.2007); Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Attorney Docket No.00138-015WO1 Harbor Lab Press (Cold Spring Harbor, NY 1989), both of which are incorporated herein by reference. All patents, patent applications, and publications mentioned herein are incorporated herein by reference in their entireties for all purposes. [0021] The term “a”, “an” or “the” is intended to mean “one or more”, e.g., a biomarker refers to one or more biomarkers unless otherwise made clear from the context of the text. [0022] The term “comprise,” and variations thereof such as “comprises” and “comprising,” when preceding the recitation of a step or an element, are intended to mean that the addition of further steps or elements is optional and not excluded. [0023] Also, the use of “or” means “and/or” unless stated otherwise. Similarly, “comprise,” “comprises,” “comprising” “include,” “includes,” and “including” are interchangeable and not intended to be limiting. [0024] It is to be further understood that where descriptions of various embodiments use the term “comprising,” those skilled in the art would understand that in some specific instances, an embodiment can be alternatively described using language “consisting essentially of” or “consisting of.” [0025] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs. Any methods and reagents similar or equivalent to those described herein can be used in the practice of the disclosed methods and compositions. [0026] The disclosure provides a number of acronyms for genes. The full name and related information for such genes and abbreviations/acronyms can be found using the HUGO Gene Nomenclature website (genenames.org). [0027] As used herein, the term “amplifying” refers to the process of synthesizing nucleic acid molecules that are complementary to one (or both strands) of a template nucleic acid molecule. Amplifying a nucleic acid molecule typically includes denaturing the template nucleic acid, particularly if the template nucleic acid is double-stranded, annealing one or more primers to the template nucleic acid at a temperature that is below the melting temperatures of the primers, and enzymatically elongating from the primers to generate an amplification product. Generally, synthesis initiates at the 3′ end of a primer and proceeds in a 5′ to 3′ direction along the template nucleic acid strand. Amplification typically requires the presence of deoxyribonucleoside triphosphates, a polymerase enzyme (e.g., DNA or RNA polymerase or T7 for in vitro transcription in TMA) and an appropriate buffer and/or co- factors for optimal activity of the polymerase enzyme (e.g., MgCl2 and/or KCl). Attorney Docket No.00138-015WO1 [0028] As used herein, the term “complement thereof” or “complementary” refers to a nucleic acid molecule that is optionally the same length as a target molecule of interest and possesses a structural (e.g., nucleotide) composition that is complementary (i.e., capable of conventional hydrogen base pairing) with the target molecule of interest, unless otherwise specified. Substantial complementarity refers to a nucleic acid molecule that is optionally the same length as the target molecule of interest but is greater than 90% complementary and less than 100% complementary to the target molecule of interest. [0029] As used herein, the terms “extension”, “extend” or “elongation” when used with respect to nucleic acid molecules refers to a biological process by which additional nucleotides (or nucleotide analogs) are incorporated into nucleic acid molecules. For example, a nucleic acid can be extended by a nucleotide incorporating enzyme, such as a polymerase or reverse transcriptase that typically adds sequentially, a nucleotide to the 3′ terminal end of the nucleic acid molecule (e.g., the freely available 3’-OH group). [0030] As used herein, “hybridization”, “hybridizing”, “anneal” and “annealing”, and the like, refer to a process of combining two complementary (or substantially complementary (e.g.., at least 90%) single-stranded DNA or RNA molecules so as to form a double-stranded molecule (DNA/DNA, DNA/RNA, RNA/RNA) through conventional hydrogen base pairing. Hybridization stringency is typically determined by the hybridization temperature and salt concentration of the hybridization buffer; e.g., high temperature and low salt provide high stringency hybridization conditions. Examples of salt concentration ranges and temperature ranges for different hybridization conditions are as follows: high stringency, approximately 0.01 M to approximately 0.05 M salt, hybridization temperature 5 °C to 10 °C below Tm; moderate stringency, approximately 0.16 M to approximately 0.33 M salt, hybridization temperature 20 °C to 29 °C below Tm; and low stringency, approximately 0.33 M to approximately 0.82 M salt, hybridization temperature 40 °C to 48 °C below Tm of duplex nucleic acids is calculated by standard methods well-known in the art (see, e.g., Maniatis, T., et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press: New York (1982); Casey, J., et al., Nucleic Acids Research 4:1539-1552 (1977); Bodkin, D. K., et al., Journal of Virological Methods 10(1):45-52 (1985); Wallace, R. B., et al., Nucleic Acids Research 9(4):879-894 (1981)). Algorithm prediction tools to estimate Tm are also publicly available (see, e.g., [http://] [tmcalculator.neb.com]). High stringency conditions for hybridization typically refer to conditions under which a nucleic acid molecule having complementarity (or substantial complementarity, e.g., greater than 90%, 95%, 98%, 99% Attorney Docket No.00138-015WO1 complementarity) to a target sequence predominantly hybridizes with the target sequence and does not hybridize to non-target or off-target sequences. [0031] In some embodiments, hybridizing refers to the annealing of RNA gene biomarker(s) to a complementary (or substantially complementary (e.g.., greater than 90% complementary)) template (or target) RNA or DNA sequence. In another embodiment, hybridizing can include annealing RNA gene biomarker(s) to an amplification product (e.g., cDNA molecule). Hybridization is typically carried out using moderate stringency or high stringency hybridization conditions to reduce background and nonspecific hybridizations. [0032] As used herein, the terms “identical” or “percent identity” in the context of two or more nucleic acid sequences, refers to two or more sequences that are the same or have a specified percentage of nucleotides that are the same (i.e., identical), when compared and aligned for maximum correspondence, e.g., as measured using one of the sequence comparison algorithms or by visual inspection. An exemplary algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST program, which are described in Altschul et al. (1990) “Basic local alignment search tool” J. Mol. Biol. 215:403-410, Gish et al. (1993) “Identification of protein coding regions by database similarity search” Nature Genet.3:266-272, Madden et al. (1996) “Applications of network BLAST server” Meth. Enzymol.266:113-141, Altschul et al. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs” Nucleic Acids Res. 25:3389-3402, and Zhang et al. (1997) “PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation” Genome Res.7:649-656. [0033] Other exemplary multiple sequence alignment computer programs include MAFFT ([https://] [mafft.cbrc.jp/alignment/software/]), MUSCLE ([https://] [www.ebi.ac.uk/Tools/msa/muscle/]), and CLUSTALW ([https://] [www.ebi.ac.uk/Tools/msa/clustalw2/]). Percent identity between two nucleic acid sequences is generally calculated using standard default parameters of the various methods or computer programs. A high degree of sequence identity, as used herein, between two nucleic acid molecules is typically at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, at least 99% identity, at least 99.5% identity, or any range of percent identity that includes or is between any two of the foregoing percentages (e.g., between 90% identity and 100% identity, between 95% identity and 98% identity, etc.). A moderate degree of sequence identity, as used herein, between two nucleic acid molecules is typically at least 80% identity, at least 82% identity, at least 83% identity, at least 84% Attorney Docket No.00138-015WO1 identity, at least 85% identity, at least 86% identity, at least 87% identity, at least 88% identity, at least 89% identity, or any range of percent identity that includes or is between any two of the foregoing percentages (e.g., between 80% identity and 90% identity, between 85% identity and 89% identity, etc.). A low degree of sequence identity, as used herein, between two nucleic acid molecules is typically at least 50% identity, at least 55% identity, at least 60% identity, at least 65% identity, at least 70% identity, at least 75% identity, at least 79% identity, or any range of percent identity that includes or is between any two of the foregoing percentages (e.g., between 50% identity and 70% identity, 55% identity and 75% identity). For example, a sample from a subject, (e.g., suspected of being infected with Zika virus) can have a high degree of sequence identity to a reference taxon of pathogenic microorganisms (e.g., Flavivirus) and a low degree of sequence identity to bacterial pathogenic microorganisms (e.g., Streptococcus, Clostridium, Salmonella and Mycobacterium). [0034] The term "microorganism" or “microbial organism” is used in its broadest sense and includes bacteria, fungi, parasites, protozoa, and viruses. [0035] As used herein, a “modified nucleotide” or “nucleotide analog” in the context of nucleic acids (e.g., an RNA gene biomarker) refers to incorporation of a non-naturally occurring nucleotide (e.g., a nucleotide other than A, G, T, C or U) in a nucleic acid, and whereby incorporation of the modified nucleotide or nucleotide analog does not hinder or prevent nucleic acid extension or elongation under suitable amplification conditions. Examples of nucleic acid modifications are described in, e.g., U.S. Pat. No.6,001,611. Other modified nucleotide substitutions may alter the stability of the oligonucleotide (e.g., modulate its Tm), or provide other desirable features (e.g., nuclease resistance). [0036] As used herein, the terms “nucleic acid”, “polynucleotide” and “oligonucleotide” refer to a polymeric form of nucleotides. The nucleotides may be deoxyribonucleotides (DNA), ribonucleotides (RNA), analogs thereof, or combinations thereof, and may be of any length. Polynucleotides may perform any function and may have any secondary and tertiary structures (e.g., hairpins, stem loop structures). Oligonucleotides refer to polymeric form of nucleotides typically having much shorter lengths than polynucleotides (e.g., ≤50 nt). The terms encompass known analogs of natural nucleotides and nucleotides that are modified in the base, sugar and/or phosphate moieties. Typically, analogs of a particular nucleotide have the same base-pairing specificity (e.g., an analog of A base pairs with T). An oligonucleotide may comprise one modified nucleotide or multiple modified nucleotides. Examples of modified nucleotides include fluorinated nucleotides, methylated nucleotides, and nucleotide analogs. The nucleotide structure may be modified Attorney Docket No.00138-015WO1 before or after a polymer is assembled. The terms also encompass nucleic acids comprising modified backbone residues or linkages that are synthetic, naturally occurring, and non- naturally occurring, and have similar binding properties as a reference polynucleotide (e.g., DNA or RNA). Examples of such analogs include, but are not limited to, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs), Locked Nucleic Acid (LNA) and morpholino structures. [0037] As used herein, the term “pathogen” refers to a virus, bacterium, protozoa, prion, archaea, fungus, algae, parasite, or other microbe (helminth) that causes or induces neurological disease or illness in a subject (e.g., a mammalian subject). The term includes both the disease-causing organism per se and toxins produced by the pathogen (e.g., Shiga toxins) present in a sample. Detection of a pathogen as set forth in the methods disclosed herein includes detection of a portion of the genome of the pathogen or a nucleic acid molecule using RNA gene biomarkers disclosed herein that are complementary or substantially complementary (i.e., at least 90% complementary) to a portion of the genome of the pathogen. [0038] As used herein, a “reagent” refers broadly to any agent used in a reaction, other than the analyte (e.g., nucleic acid molecule being analyzed). Illustrative reagents for a nucleic acid amplification reaction or sequencing assay include, but are not limited to, buffer, metal ions, polymerase, reverse transcriptase, primers, probes, template nucleic acid, nucleotides, labels, dyes, nucleases, adapters, oligo-coated beads, microparticles or droplets, and the like. Generally, reagents for enzymatic reactions include, for example, substrates, cofactors, buffers, metal ions, inhibitors, and/or activators. [0039] A “sample” refers to a biological sample such as sputum, blood, plasma, serum, urine, tissue and the like. In one embodiment, a sample refers to a cerebrospinal fluid (CSF) sample collected from a subject. CSF is a clear, colorless, watery fluid that flows in and around the brain and spinal cord. CSF acts like a cushion that helps protect the brain and spinal cord from sudden impact or injury. The fluid also removes waste products from the brain and helps the central nervous system work properly. Typically, a CSF sample is used to help diagnose diseases of the brain and spinal cord and other conditions that affect the central nervous system. To get a sample of CSF, a provider will do a spinal tap, also known as a lumbar puncture, by inserting a thin, hollow needle between two vertebrae in the lower spine and drawing forth a small amount of CSF for testing. Attorney Docket No.00138-015WO1 [0040] As used herein, the term “subject” refers to any member of the class animals, including, without limitation, humans and other primates, including non-human primates such as rhesus macaques, chimpanzees and other monkey and ape species; farm animals, such as cattle, sheep, pigs, goats and horses; domestic mammals, such as dogs and cats; laboratory animals, including rabbits, mice, rats and guinea pigs; birds and other reptiles, including domestic, wild, and game birds, such as chickens, turkeys, geese, ducks, lizards, alligators, and snakes; amphibians, including frogs, toads, salamanders, and newts; fish, such as salmon, and tilapia; and insects. The term does not denote a particular age or gender. Thus, adult, young, and newborn subjects are intended to be included as well as male and female subjects. In most instances, the subject is a host to the pathogen and the pathogen may rely on its ability to infect the host, for example the production of toxins, to enter cells and tissues within the host, and acquire host nutrients to maintain infectiousness. The term includes subjects who are experiencing or have experienced illness or disease associated with a particular taxon of pathogenic microorganisms or subjects who are infected (or suspected of being infected) with a particular taxon of pathogen but are not experiencing or demonstrating symptoms of illness or disease associated with the pathogen. [0041] As used herein, a “target” refers to a molecule of interest to be detected in a sample by using the RNA gene biomarkers disclosed herein. In some embodiments, two or more target molecules are detected, e.g., two or more RNA gene biomarkers disclosed herein. In some embodiments, the two or more target molecules may be related to each other (e.g., nucleic acids from the same taxon, genus, or species of pathogens). In some embodiments, the target nucleic can be from the host subject that is indicative of a neurological illness or disease that is not caused by an infectious pathogen. In an alternate embodiment, the target is a target DNA, target RNA or target nucleic acid from an infectious pathogen. In a further embodiment, the infectious pathogen is associated with a neurological illness or disease (e.g., bacterial, or viral meningitis). [0042] As used herein, the terms “treatment” and “treating” and the like, refer to methods or compositions for amelioration of a neurological disease or illness including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or delaying the onset of symptoms; slowing in the rate of degeneration or decline; making the final point of degeneration less debilitating; and/or improving a subject's physical or mental well-being. [0043] As used herein, “Polymerase Chain Reaction (PCR)” refers to a process in which one or more nucleic acid molecules are amplified typically through the use of one or Attorney Docket No.00138-015WO1 more primers under suitable amplification conditions. PCR is described in U.S. Pat. Nos. 4,683,195; 4,683,202; and 4,965,188; Saiki et al., 1985, Science 230:1350-1354; Mullis et al., 1986, Cold Springs Harbor Symp. Quant. Biol.51:263-273; and Mullis and Faloona, 1987, Methods Enzymol.155:335-350. The development and application of PCR are described extensively in the literature. For example, a range of PCR-related topics are discussed in PCR Technology--principles and applications for DNA amplification, 1989, (ed. H. A.Erlich) Stockton Press, New York; PCR Protocols: A guide to methods and applications, 1990, (ed. M. A. Innis et al.) Academic Press, San Diego; and PCR Strategies, 1995, (ed. M. A. Innis et al.) Academic Press, San Diego. Commercial vendors, such as ThermoFisher Scientific (Waltham, Conn.) market PCR reagents and publish PCR protocols. [0044] Since its inception, various amplification techniques have been described as variants or derivatives of PCR including, but not limited to, Ligase Chain Reaction (LCR, Wu and Wallace, 1989, Genomics 4:560-569 and Barany, 1991, Proc. Natl. Acad. Sci. USA 88:189-193); Polymerase Ligase Chain Reaction (Barany, 1991, PCR Methods and Applic. 1:5-16); Gap-LCR (PCT Patent Publication No. WO 90/01069); Repair Chain Reaction (European Patent Publication No.439,182 A2), 3SR (Kwoh et al., 1989, Proc. Natl. Acad. Sci. USA 86:1173-1177; Guatelli et al., 1990, Proc. Natl. Acad. Sci. USA 87:1874-1878; PCT Patent Publication No. WO 92/0880A), NASBA (U.S. Pat. No.5,130,238), Nested-Patch PCR (Varley and Mitra, (2008) Genome Research, 18:1844-50), asymmetric PCR (Wooddell & Burgess, (1996) Genome Research, 6:886-892), anchored PCR (Loh, (1991) Methods, 2, 1:11-19) inverse PCR (Ochman et al., (1988) Genetics, 120 (3):621-23), real-time quantitative PCR (Real Time-PCR) or quantitative PCR (qPCR) (Watson et al., (2004). Molecular Biology of the Gene (Fifth ed.). San Francisco: Benjamin Cummings), transcription based amplification system (TAS), strand displacement amplification (SDA), rolling circle amplification (RCA), hyper-branched RCA (HRCA) and Rapid Amplification of cDNA ends (RACE) (Lagarde et al., (2016), Nat. Comm., 7:1233. Additionally, digital PCR is a technique that allows quantitative measurement of the number of target molecules in a sample. The basic premise is to divide a large sample into a number of smaller subvolumes (partitioned volumes), whereby the subvolumes contain on average a low number or single copy of target. By counting the number of successful amplification reactions in the subvolumes, one can deduce the starting copy number of the target molecule in the starting volume (US Patent 8,722,334). [0045] Described herein are methods, compositions, systems, and kits for identifying RNA gene biomarkers that can specifically identify the causes of both non-infectious and Attorney Docket No.00138-015WO1 infectious diseases that cause neurological illness. These methods are useful in the areas of diagnosis of pathogenic neurological infections, epidemiology, and disease surveillance, among others. [0046] Acute neurological illnesses such as meningitis and encephalitis are devastating syndromes, remaining undiagnosed in a majority of cases. The diagnostic workup for many patients requires extensive, and often negative, serial testing that utilizes a combination of culture, antigen, serologic, and molecular methods, resulting in delayed or missed diagnoses and increased costs. Cerebrospinal fluid (CSF) sample volume is often limiting, so that only a fraction of desired tests are able to be performed. Given the high burden of encephalitis-associated hospitalizations in the United States, there is a large unmet clinical need for better and more timely diagnostics for this syndrome, both to identify and to exclude infectious etiologies. [0047] Diagnosis of neurological illnesses, including meningitis, encephalitis, and/or myelitis, is challenging, as currently available microbiologic tests for infection only identify approximately 50% of cases, and tests to identify non-infectious etiologies, such as autoimmune disease, are lacking. A metagenomic next-generation sequencing (mNGS) assay to identify causative pathogens, including viruses, bacteria, fungi, and parasites, in a single assay is leveraged herein. More specifically, the RNA metagenomic data generated from CSF samples using the mNGS assay is used to select human RNA expressed genes (RNA transcripts) that can be used along with a machine learning based classifier model to identify and clinically diagnose infectious and non-infectious causes of neurological illness. These models use panels of RNA gene biomarkers (e.g., 35-60 RNA gene biomarkers) to generate binary comparisons that can differentiate between major etiologic categories: (1) autoimmune / non-infectious etiology, (2) viral infection, (3) bacterial infection, and (4) fungal infection. For example, there are sets of biomarkers that have been used to train a machine learning based classifier model to discriminate between viral infection and the “rest” (all other categories), viral infection and bacterial infection, viral infection, and autoimmune / non- infectious disease, etc. Additional gene panels have been generated to differentiate categories via binary comparisons at higher levels of resolution (e.g., parasitic infection and “rest”, mycobacterial infection and “rest”, enterovirus D68 infection and non-enteroviral viral infection, etc.). In addition, a new algorithm (i.e., ranking Spearman classifier) has been developed to train machine learning models (neural networks, linear discriminant analysis, generalized linear models, etc.) with these sets of RNA gene biomarkers. When these biomarkers are coupled with a model, probability estimates summing to 100% are provided Attorney Docket No.00138-015WO1 of the likelihood of a given etiology for the illness (e.g., 80% viral, 20% autoimmune / non- infectious). A clinical interpretation of these probability estimates can then be made, yielding a diagnostic test result that is clinically actionable by medical care practitioners. [0048] In various embodiments, techniques are provided for determining a central nervous system (CNS) disease, infection or disorder in a subject (e.g., a human subject) without knowledge of a CNS disease, infection or disorder (e.g., a preexisting CNS disease, infection or disorder) in the subject. The techniques may utilize the computing system 130 described with respect to FIG.8 to determine levels of two or more biomarkers in a biological sample of the subject, and, according to the levels, determine a probabilistic assessment of the subject having a particular CNS disease, infection or disorder selected from autoimmune disease or non-infectious, viral infection, bacterial infection, and fungal infection. In some embodiments, the biomarkers and biomarker combinations are to be measured in cerebral spinal fluid (CSF) from various subjects that have or have not been diagnosed with a CNS disease, infection or disorder. Examples of subjects from which such a sample may be obtained and utilized in accordance with various embodiments discussed herein include, but are not limited to, asymptomatic subjects that have not developed a CNS disease, infection or disorder, subjects manifesting or exhibiting one or more symptoms of a CNS disease, infection or disorder, subjects predisposed to a CNS disease, infection or disorder, subjects suspected of having a CNS disease, infection or disorder, subjects not undergoing treatment for a CNS disease, infection or disorder and the like. [0049] In various embodiments, biomarkers and biomarker combinations are selected from known biomarkers that have been shown to have some diagnostic utility for CNS disease, infection or disorder. For example, a measurement of the level of the biomarkers is predictive a CNS disease, infection or disorder. In some embodiments, biomarkers and biomarker combinations are identified or determined as potential biomarkers of a CNS disease, infection or disorder. For example, a measurement of the level of the biomarkers has not been demonstrated previously to be predictive for a CNS disease, infection or disorder. In other embodiments, biomarkers and biomarker combinations are selected from biomarkers that are autonomously identified as potential biomarkers of a CNS disease, infection or disorder from databases of data, e.g., data mined from medical publications. For example, a measurement of the level of the biomarkers has not been demonstrated previously to be predictive for a CNS disease, infection or disorder. In some embodiments, the biomarkers and combination of biomarkers include any combination of the biomarkers set forth in Tables 1, and/or 2. In other embodiments, the biomarkers and combination of biomarkers include any Attorney Docket No.00138-015WO1 combination of the biomarkers set forth in Tables 1 and/or 2, and one or more other biomarkers that has not been demonstrated previously to be predictive for the development of a CNS disease, infection or disorder. [0050] In order to identify or predict a CNS disease, infection or disorder a mathematical model may be used to generate “classifiers” to discriminate between viral infection and the “rest” (all other categories), viral infection and bacterial infection, viral infection, and autoimmune / non-infectious disease, etc. Mathematical models useful in accordance with various embodiments include those using either supervised or unsupervised learning. In some embodiments, the mathematical model chosen uses supervised learning in conjunction with a “training population” to evaluate each of the possible combination of biomarkers. In some embodiments, the mathematical model used is selected from the following: a regression model, a logistic regression model, a neural network, a clustering model, principal component analysis, nearest neighbor classifier analysis, linear discriminant analysis, quadratic discriminant analysis, a support vector machine, a decision tree, a genetic algorithm, classifier optimization using bagging, classifier optimization using boosting, classifier optimization using the Random Subspace Method, a projection pursuit, and weighted voting. In certain embodiments, a logistic regression model is used. In another embodiment, a neural network model is used. In yet another embodiment, mathematical models can be used in combination. [0051] Populations used for training input into the mathematical model should be chosen so as to result in statistically significant resulting biomarker combinations. In some embodiments, the reference or training population includes between 10 and 30 subjects. In another embodiment, the training population contains between 30 and 50 subjects. In still other embodiments, the reference population includes two or more populations each containing between 50 and 100, 100 and 500, between 500 and 1000, or more than 1000 subjects. Typically, the training population includes roughly equivalent numbers of individuals that have a CNS disease, infection or disorder and individuals that do not have a CNS disease, infection or disorder as well as populations from each of a CNS disease, a CNS infection-viral, a CNS infection-bacterial, and a CNS infection-fungal. For purposes of characterizing the individual populations as having or not having a CNS disease, infection or disorder, any traditional method of diagnosis or a CNS disease or infection can be used. In some embodiments, the phenotypic characteristics of the two populations used in the training set are as similar as possible but for the phenotypic characteristic of having or not Attorney Docket No.00138-015WO1 having a CNS disease, infection or disorder. In another embodiment, the populations are age and sex matched. [0052] A logistic regression model uses an equation as the representation where input values (x) are combined linearly using weights or coefficient values (b) to predict an output value (y). In some embodiments, the input values (x) include the levels of the two or more biomarkers in a biological sample, and the output value (y) being modeled is binary, e.g., a differentiator between subjects that, e.g., have a CNS autoimmune disease and the “rest” (e.g., CNS infection with a virus, fungi or bacteria etc.). The coefficient values (b) of the logistic regression algorithm may be estimated from the training data. In various embodiments, the logistic regression model may be used to test various combinations of two or more of the biomarkers to generate classifiers. The classifiers may be in the form of equations where the data representing the measured values of each of the biomarkers in the equation is multiplied by a weighted coefficient as generated by the regression model. In some embodiments, one or more weighted coefficients are a time dependent variable. For example, the training data may be grouped, classified, or identified based at least on a time dependent variable such as a time to diagnosis. The time to diagnosis variable indicates the time from when a biological sample having levels of the two or more biomarkers was obtained from the subject to the time of subject being diagnosed with a CNS disease, infection or disorder. As such, the time to diagnosis variable allows for the classifiers to take into consideration the effect of the time to diagnosis variable on the predictive nature of the two or more biomarkers. The classifiers generated can be used to analyze input data from a test subject and provide risk assessment data. [0053] In some embodiments, the logistic regression model is fit by a maximum likelihood estimation. In other words, the coefficients are determined by maximum likelihood. A likelihood is a conditional probability. The likelihood function measures the probability of observing the particular set of variable values that occur in the sample data set. It is written as the probability of the product of the variables. The higher the likelihood function, the higher the probability of observing the variables in the sample. Maximum likelihood estimation involves finding the coefficients that makes the log of the likelihood function as large as possible or −2 times the log of the likelihood function as small as possible. In maximum likelihood estimation, some initial estimates of the coefficients are made. Then the likelihood of the data given these coefficient estimates is computed. The coefficient estimates are improved each time the data is recalculated. This process is repeated Attorney Docket No.00138-015WO1 until the coefficient estimates do not change much (for example, a change of less than 0.01 or 0.001 in the probability). [0054] In some embodiments, the classifiers or logistic regression equations are evaluated using one or more of the following methods: cross validation, Leave One out Cross Validation, n-fold cross validation, or jackknife analysis using standard statistical methods. In certain embodiments, each classifier is evaluated for its ability to properly characterize those individuals of the training population, which were not used to generate the classifier. In some embodiments, the method used to evaluate the classifier for its ability to characterize each individual of the training population is a method, which evaluates the classifiers sensitivity (TPF, true positive fraction) and 1-specificity (TNF, true negative fraction). In certain embodiments, the method used to test the classifier is Receiver Operating Characteristic (ROC), which provides several parameters to evaluate both the sensitivity and specificity of the diagnostic result of the classifier generated. The ROC area (area under the curve (AUC)) may be used to evaluate the equations. For example, an ROC area greater than 0.5, 0.6, 0.7, 0.8, 0.9 and 1.0. A perfect ROC area score of 1.0 indicates a classifier, which is both 100% sensitive and 100% specific. [0055] The disclosure thus provides a computer implemented method to select for the identification of additional RNA gene biomarkers associated with a neurological illness based on host response classification using a machine learning model, the method comprising the steps: (1) assembling a dataset of RNA metagenomic data from hundreds of CSF samples; (2) randomly splitting the dataset into a training and test subset based upon selected features and targets, wherein the selected features and targets include viral, bacterial, fungal, parasitic, and/or autoimmune/non-infectious (AINI) host response classifiers; (3) training a machine learning model with the training subset to predict and rank biomarkers that have a high degree of association with the host response classifiers for a neurological illness; and (4) testing the machine learning model with the testing subset by comparing testing predictions to actual targets to generate an accuracy or prediction score, retraining the machine learning model in step (3) until a statistically significant accuracy or prediction score is achieved. In a further embodiment, biomarkers that have a high degree of association with the host response classifiers is determined based on measuring a linear correlation between the biomarker and the host response classifiers. In a further embodiment, linear correlation is measured using Pearson correlation coefficient (r). In yet a further embodiment, the computer implemented model is implemented using a graphic processing unit (GPU) or an artificial intelligence accelerator of a cloud-based server. Attorney Docket No.00138-015WO1 [0056] In a particular embodiment, the disclosure provides a method of identifying infectious and non-infectious causes of neurological illness or disorder from a sample (e.g., a CSF sample) obtained from a subject, comprising: obtaining a sample (e.g., a CSF sample) from a subject; measuring the gene expression profile of one or more RNA gene biomarkers from the subject's CSF sample, wherein the one or more RNA gene biomarkers are selected from the biomarkers listed in Table 1 and/or Table 2; and applying the gene expression profile of the one or more RNA gene biomarkers from the subject's CSF sample to a machine learning system trained as described herein using gene expression profiles of RNA gene biomarkers from CSF samples from a population of subjects' that have known infectious and non-infectious causes of neurological illnesses or disorder. In another embodiment, the one or more RNA gene biomarkers are selected from the biomarkers listed in Table 1 or Table 2. In yet another embodiment, the one or more RNA gene biomarkers are selected from the biomarkers listed in Table 2. [0057] Table 1. Four main categories of genes used with the classifier AUTOIMMUNE / BACTERIAL FUNGAL VS. VIRAL VS. NONINFECTIOU VS. "REST" "REST" "REST" Attorney Docket No.00138-015WO1 HERC5 RIPK2 KHSRP EEF1B2 HMGA1 RPE MAK16 EHD1 Attorney Docket No.00138-015WO1 IFIT2 NUP88 IFIT3 OAS1 Attorney Docket No.00138-015WO1 TLR7 TMEM106B [0058 ] a e prov es a ur er rea own o cass ers an su-cass ers. [0059] Table 2: Gene Classifier Gene Classifier ADAMTS1 Attorney Docket No.00138-015WO1 ABCA12 fungal vs parasitic 18 FBF1 AINI vs rest ABCA13 fungal vs parasitic 19 FBXO41 AINI vs rest Attorney Docket No.00138-015WO1 ACAD9 fungal vs parasitic 62 UBE2L6 AINI vs rest ACADL fungal vs parasitic 63 UBR4 AINI vs rest Attorney Docket No.00138-015WO1 bacterial_atypical vs ACTN4 fungal vs parasitic 22 STMN4 bacterial_typical bacterial atypical vs Attorney Docket No.00138-015WO1 bacterial_atypical vs ADD3 fungal vs parasitic 23 PRRX1 fungal bacterial atypical vs Attorney Docket No.00138-015WO1 bacterial_atypical vs AGPS fungal vs parasitic 9 KCNJ10 parasitic bacterial atypical vs Attorney Docket No.00138-015WO1 ANKRD20 A5P fungal vs parasitic 20 MID1IP1 bacterial_typical vs viral ANKRD28 f n l r iti 21 MXI1 b tril t i l irl Attorney Docket No.00138-015WO1 C16orf71 fungal vs parasitic 25 POLL AINI vs bacterial_tyical C17orf51 fungal vs parasitic 26 PSTPIP2 AINI vs bacterial_tyical Attorney Docket No.00138-015WO1 EMC4 fungal vs parasitic 32 NOTCH1 AINI vs fungal EML3 fungal vs parasitic 33 P2RY14 AINI vs fungal Attorney Docket No.00138-015WO1 311 ZNF597 fungal vs parasitic 312 ZNF71 fungal vs parasitic Attorney Docket No.00138-015WO1 38 COPG2 mold_vs_rest 38 CEP250 flavivirus_vs_rest 39 CRIPT mold_vs_rest 39 CHI3L2 flavivirus_vs_rest Attorney Docket No.00138-015WO1 INAFM2 mold_vs_rest 81 IFI27 flavivirus_vs_rest INTS12 mold_vs_rest 82 IFI44L flavivirus_vs_rest Attorney Docket No.00138-015WO1 POGLUT1 mold_vs_rest 125 POLD2 flavivirus_vs_rest POLI mold_vs_rest 126 PPP2R1B flavivirus_vs_rest Attorney Docket No.00138-015WO1 TRMT1 mold_vs_rest 169 SPP1 flavivirus_vs_rest TRMT2B mold_vs_rest 170 SSTR3 flavivirus_vs_rest Attorney Docket No.00138-015WO1 AGPAT5 dimorphic_fungi_vs_rest 4 ANGEL1 AFM_vs_rest AKT2 dimorphic_fungi_vs_rest 5 ANKRD17 AFM_vs_rest Attorney Docket No.00138-015WO1 DIRC2 dimorphic_fungi_vs_rest 47 EIF4G3 AFM_vs_rest DMPK dimorphic_fungi_vs_rest 48 FTL AFM_vs_rest Attorney Docket No.00138-015WO1 MGAT4B dimorphic_fungi_vs_rest 90 PJA2 AFM_vs_rest MMAB dimorphic_fungi_vs_rest 91 PLAC8 AFM_vs_rest Attorney Docket No.00138-015WO1 RUNX3 dimorphic_fungi_vs_rest 134 SPOP AFM_vs_rest SCIN dimorphic_fungi_vs_rest 135 SPTBN2 AFM_vs_rest Attorney Docket No.00138-015WO1 UQCR11 dimorphic_fungi_vs_rest 177 ZNF197 AFM_vs_rest USP42 dimorphic_fungi_vs_rest 178 ZNF469 AFM_vs_rest Attorney Docket No.00138-015WO1 ATP13A3 bacterial_typical vs rest 2 AFF2 bacterial_atypical vs rest CCL2 bacterial_typical vs rest 3 AP4S1 bacterial_atypical vs rest Attorney Docket No.00138-015WO1 3 BCL2 fungal vs rest 3 DHX34 parasitic vs rest 4 C12orf43 fungal vs rest 4 FADS2 parasitic vs rest Attorney Docket No.00138-015WO1 UGCG fungal vs rest VAT1L fungal vs rest Attorney Docket No.00138-015WO1 HMBS viral vs rest 39 IL1B AINI vs viral HNRNPH3 viral vs rest 40 IL1RN AINI vs viral Attorney Docket No.00138-015WO1 PTRH2 viral vs rest 83 SLC11A1 AINI vs viral PXYLP1 viral vs rest 84 SLC25A23 AINI vs viral l l l l l l l l l l l l l l l l l l l l l l l l l l l l Attorney Docket No.00138-015WO1 FLNA viral vs rest CXCL10 viral vs rest Attorney Docket No.00138-015WO1 23 TMCC3 bacterial_both vs AINI 24 TPGS2 bacterial_both vs AINI Attorney Docket No.00138-015WO1 ZNF569 bacterial_both vs fungal 37 WDR75 fungal vs viral ZNF720 bacterial_both vs fungal 38 ZNF107 fungal vs viral al al al al al al al al al al al al al al al al al al al al al al al al Attorney Docket No.00138-015WO1 bacterial_atypical vs PDLIM1 viral 24 ST3GAL5 bacterial_typical vs fungal bacterial atypical vs al al al al al Attorney Docket No.00138-015WO1 bacterial_typical vs JCHAIN parasitic 14 IL1B bacterial_both vs rest bacterial typical vs Attorney Docket No.00138-015WO1 18 KCNK2 AINI vs parasitic 18 NSDHL parasitic vs viral 19 KLC1 AINI vs parasitic 19 PLCXD1 parasitic vs viral [0060] In a particular embodiment, the disclosure provides for selecting one or more RNA gene biomarkers from Table 2, wherein the RNA gene biomarkers are selected from the RNA biomarkers listed in group (i), group (ii), group (iii) group (iv), group (v), group (vi), group (vii), group (viii), group (ix), group (x), group (xi), group (xii), group (xiii), group (xiv), group (xv), group (xvi), group (xvii), group (xviii), group (xix), group (xx), group (xxi), group (xxii), group (xxiii), group (xxiv), group (xxv), group (xxvi), group (xxvii), group (xxviii), group (xxix), and/or group (xxx): (i) ADAMTS12, ADD1, ADH5, ALDH1A2, ALDH3A1, ALOX15B, ARPC1A, ATP10D, AURKA, CACNB4, CASD1, CCL2, COX6B1, CXCL9, DAAM1, DDX23, DNMT3A, FAM198B, FBF1, FBXO41, FBXW11, FEM1A, FNIP2, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1RN, INTS6, IRF8, KCNK2, KIAA0232, MLXIP, MTURN, NET1, NOC3L, PHLDB1, PLEC, PNPLA2, PSMD10, PSTPIP2, RASSF8, RHBDF2, RIMS1, RNF144B, RNF146, RSAD2, RUNX3, S100A9, SFPQ, SKI, Attorney Docket No.00138-015WO1 SLC13A4, SLCO2B1, SNCAIP, TPGS2, TPRG1L, TPX2, TSC22D1, UBA6, UBE2L6, UBR4, WDR70, ZNF500, ZSCAN26, IFIT2, and IFIT3 [AINI v. 'rest']; (ii) ABCC5, ADGRL1, AFF2, AP4S1, BTBD11, CDCA7L, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IL1B, KCNJ2, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SLC15A4, SPARCL1, SYPL1, TIFA, and TMCC3 [Bacterial v. 'rest']; (iii) ABHD10, ACTG2, AMOTL2, BCL2, C12orf43, CD2AP, CDYL2, CHUK, CRABP1, CXCL8, CXCL9, DGKB, DRG1, EIF4E2, FAM122B, FAM198B, FBP1, FCF1, FGF1, GLCE, GMEB2, ITGB8, KCTD3, KHSRP, MAK16, MAST2, MED8, MID1, NDRG2, NRP1, NT5C3A, PAN2, PIGT, RBFOX2, RHBDF2, RRAGD, SPATS2L, TMEM126B, TMEM184C, TMEM64, TRIM38, TRMT2B, TSPYL4, TTC21B, TXLNG, UBA3, UGCG, VAT1L, and VPS26A [Fungal v. 'rest']; (iv) ARID3A, ATMIN, ATP1A3, AURKA, BCORL1, BHLHE41, BLZF1, C3, C3orf17, CACNA1F, CACNB4, CAPRIN2, CCT2, CD93, CHAMP1, CHST15, CRTC1, CXCL8, DDX60, DNM1L, EDEM2, EDEM3, EEF1A1, EEF1B2, EHD1, EIF3K, ELOVL7, ERAP1, FAM198B, FAM219B, FBRSL1, FBXL7, FOSL2, FPR3, GMFG, GRAMD1A, HELB, HERC6, HLA-DQA2, HMBS, HNRNPH3, IFFO2, IFI27, IFI44L, IFIT1, IL18, IL1B, IL2RB, INAFM2, INTS7, IRS2, KCTD3, KNSTRN, LAMP3, LIMK2, LPAR1, LPAR6, LY6E, MCPH1, MID1IP1, MKL2, MPP6, MROH1, MRPS6, MTURN, NUDT5, NUP133, NUP88, OAS1, OASL, OSGIN2, OTOF, PDCD10, PDIA4, PDS5A, PGM1, PHLDA1, PHLDB1, PLCD1, PLCD4, PRDM10, PRDM4, PTPRO, PTRH2, PXYLP1, RALGPS2, RETSAT, RGS18, RNF216, RSAD2, RSBN1, SCARF1, SDHAF3, SEMA6A, SESN1, SHISA9, SIAE, SIGLEC10, SLC11A1, SLC25A23, SLC31A1, SLC6A2, SMURF1, SNCAIP, SNX2, SOAT2, SPP1, STC2, TBC1D22B, TCN2, TET1, TLR7, TMEM106B, TMTC1, TNFSF10, TOX3, TUBG2, XAF1, ZMIZ1, ZNF410, ZNF614, ZNF621, ZNF831, UBC, USP18, VIM, FLNA, CXCL10, IL1RN, SELL, and EGR1 [Viral v. 'rest']; (v) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. Bacterial]; (vi) ABCD4, ALDH1A1, ANKRD13C, APOA1BP, APOL2, ATP10D, ATXN3, BAIAP2, BEST1, CCL2, CD2AP, CHIC1, CXCL8, CXCL9, DGKB, DNMBP, EIF4E2, ERMN, GATC, GBP3, GLCE, ITGB8, KCNK2, KHSRP, MAST2, MEAF6, MED24, MID1, MMRN1, MTPAP, MYH7, NET1, NOTCH1, P2RY14, P2RY2, PARK2, PLEK, RBFOX2, Attorney Docket No.00138-015WO1 RECQL, RHBDF2, RRAGD, S100A8, TMEM63A, TPRG1L, TPX2, TSR1, TTPAL, TXLNG, UBR4, UGCG, ZNF76, CCND1, PIM1, CCR1, CXCL10, IL1R2, IL1RN, CR1, FPR1, HK3, MNDA, and SLC2A3 [AINI v. Fungal]; (vii) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [Bacterial (typical & atypical) v. fungal]; (viii) ACP2, ADD1, ARHGAP4, ARL14EP, ARPC1A, ATP10D, AURKA, BAG5, BBS12, BCORL1, BLVRB, C3, CACNB4, CAMKK2, CAPRIN2, CASD1, CHST15, COX6B1, DAAM1, EEF1A1, EEF1B2, EFCAB1, ENO2, EPSTI1, ERAP1, FAM198B, FBF1, FGF1, FNIP2, GANAB, HELB, HELLS, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1B, IL1RN, IL2RB, INTS6, INTS7, IRF8, IRS2, ITGAV, KIAA0232, KNSTRN, LIMK2, LITAF, MCPH1, MPP6, MTURN, OAS1, PDCD4, PDIA4, PDS5A, PEX6, PGM1, PHAX, PHLDA1, PHLDB1, PLAU, PLCD4, PLEC, PPP1CC, PRDM10, PRDM4, PRPF4, PSMD10, PSTPIP2, PTPRO, RAB8A, RIMS1, RNF144B, RSAD2, SAMD9, SEC11A, SESN1, SFPQ, SIGLEC10, SKI, SLC11A1, SLC25A23, SMC2, SNCAIP, TMEM106B, TPRG1L, TRRAP, TUBG2, UBR4, VN1R1, ZBED4, and ZSCAN26 [AINI v. Viral]; (ix) ABCC5, ADGRL1, AFF2, ALDOC, BTBD11, CDCA7L, COL6A5, CPVL, CXCL9, DNPEP, ERICH3, FPR3, G0S2, H1F0, HN1L, HPCAL1, HYOU1, IGLL5, IL1B, IL1R1, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRRX1, RIPK2, SLC15A4, SPTA1, TIFA, TMCC3, TMEM52B, TRDMT1, USP18, and ZNF71 [bacterial (typical & atypical v. Viral]; (x) ABHD10, BLZF1, BTBD1, CD2AP, CDYL2, CHUK, CXCL8, DRG1, EIF3K, FAM198B, FBRSL1, GLCE, GMEB2, GTF3C2, IFI44L, IFIT1, IL1B, KHSRP, LY6E, MRPS6, MX2, MYBBP1A, NT5C3A, NUP133, P4HA1, PDHB, PIGT, RNF216, RRAGD, RSAD2, RSBN1, SEMA6A, SPATS2L, SPP1, TSR1, TTC21B, VPS26A, WDR75, and ZNF107 [Fungal v. Viral]; (xi) ABCA9, ABHD10, ACTA2, ACTN4, ADGRA3, AIP, AK5, ALDH1A2, AMER1, ANK2, ANP32A, APOD, ARMC6, ARRB2, ARRDC3, ATP9B, ATXN3, B3GALNT2, BCL2, BTAF1, BZRAP1, C12orf49, C15orf57, C1R, C2CD2, C2orf16, C5, C8orf33, CABIN1, CACHD1, CACNB4, CBX7, CD2, CDHR1, CDK12, CHST3, CNNM4, COL22A1, COPG2, CRIPT, CRY2, CSK, CSTF3, CXCL8, CXCL9, CYTH4, DDX5, Attorney Docket No.00138-015WO1 DECR1, DNAH1, DNAH3, DNAJC19, DOK4, ECT2L, EIF3K, EIF4E2, EIF4E3, ELMO2, ELP5, EMC1, EPB41L5, EPPK1, ERI2, EXOC2, FADS6, FAM129C, FAM161B, FAM172A, FAM175A, FAM76A, FBXL12, FCF1, FGF2, FMOD, GPR160, GRB10, GRB2, HDAC7, HDGFRP3, HIVEP1, ICE2, IL18BP, INAFM2, INTS12, JKAMP, KCNF1, KDM2A, KHSRP, KIF24, KIFAP3, KLHL1, LANCL1, LILRB4, LIMD1, LSS, MAP4K5, MAPK9, MAPRE1, MICB, MID1, MLKL, MME, MPI, MRE11A, MRPL22, NAV3, NBAS, NBPF11, NCF2, NCKAP5, NELL2, NID2, NRD1, NUTF2, OS9, OSBP, PAG1, PAN2, PARL, PDZD2, PHAX, PHF20, PHF24, PITPNM1, PLCB1, PLEKHG1, POGLUT1, POLI, PPP2R3A, PPP5C, PRR11, PSMA3, PSMB3, PTPN14, PTPN21, RAI14, RBFOX2, RGS12, RHOBTB3, RNF149, RNF217, RNF24, RNF8, RNFT1, RPF2, RRAGD, RXRB, S1PR3, SCRN1, SELL, SESN2, SF3A3, SGMS1, SGSM2, SLC25A11, SLC25A23, SLC30A7, SPACA6P, SPN, SSBP2, SYNPO2, TAPT1, TBC1D22A, TBC1D24, TCOF1, THAP5, THEMIS, TMED4, TPX2, TRIM38, TRMT1, TRMT2B, TRPM7, TSHZ1, TSPYL4, TTC17, TTPAL, TUBG2, TXNDC11, UBR4, ULK1, VAMP7, VPS13B, VPS26A, WDR45, YIPF5, YTHDF1, ZFAT, ZFP1, ZNF282, ZNF410, ZNF45, ZNF680, ZNHIT3, and ZRANB3 [Mold v. ‘rest’]; (xii) ABCA4, ABCG1, ACACA, ACP2, AGAP2, AGO3, ANAPC7, ANKLE2, ANKRD10, ANKRD36, ANLN, ANO7, AP5M1, ARHGAP20, ARHGEF17, ARSA, ASS1, ATG12, ATRN, BARD1, BPGM, BRD8, BRIP1, BUB1B, C16orf70, C22orf39, C6orf132, C7orf49, CAB39L, CARS, CBFA2T3, CCDC47, CCDC82, CCSAP, CD109, CD69, CDC23, CDK5RAP3, CEP250, CHI3L2, CHURC1, CLN6, CNTN1, COA3, COL9A3, CRIPT, CXCL11, CYC1, DBF4B, DERL1, DNASE1L1, EEF1G, EHBP1L1, EML3, EPM2AIP1, ERC2, ESCO2, FAM102B, FAM122A, FANCC, FBRSL1, FBXO31, FSCN3, GABPB2, GALNT14, GBAS, GID8, GPALPP1, GPD1L, GPR84, GRAMD1B, GRAP2, GTPBP1, H1F0, HAUS2, HAUS3, HCAR3, HFM1, HIST1H2BN, HMGA1, HVCN1, IFI27, IFI44L, IFIT2, IFIT3, IL17RD, IL1B, INTS2, ITGA5, ITGB7, KCTD3, KIF20B, LBR, LDLRAD3, LGALS3BP, LIMK1, LPAR5, LPIN2, LRRC1, LUC7L3, MAF, MAP3K15, 5-Mar, MARCO, MED22, MED27, MID1IP1, MMS19, MRPS6, MYO15A, NCDN, NCKAP1, NDUFAF4, NOC2L, NUP133, OTOF, OTUB2, P2RY12, PAPLN, PARP11, PARP15, PDE6B, PHF1, PLAC8, PNPLA2, POLD2, PPP2R1B, PRCP, PRDM4, PRKCE, PROK2, PRPF31, PRRX1, PSD4, PSMD10, PSTPIP2, PTBP1, PTBP2, PTGIS, QARS, RAB35, RASAL3, RASSF6, RBP3, RDH11, RER1, RGP1, RHOQ, RILP, RPA1, RPS6KA5, SASH3, SCAMP5, SESN1, SHC1, SLC11A1, SLC16A2, SLC24A1, SLC25A13, SLC25A17, SLC9A8, SLFN14, SMAD7, SMARCD1, SMC6, SMTN, SNCA, SOCS7, Attorney Docket No.00138-015WO1 SPICE1, SPP1, SSTR3, TBL1X, TFDP1, THAP6, TIMM10B, TMEM108, TMEM159, TMEM63B, TNFRSF10A, TOLLIP, TPGS2, TPP2, TRAF2, TRIM35, TRPV2, TSPAN33, TYW3, USP14, USP38, UTP18, UTY, UVSSA, VCAM1, VPS72, WDR17, WDR47, WLS, XPNPEP3, ZBTB11, ZNF124, ZNF512B, ZNF546, ZNF639, ZNF687, ZNF740, ZNF765, and ZZZ3 [Flavivirus v. ‘rest’]; (xiii) AAR2, ACAA1, ACP2, ADAMTS2, AGPAT5, AKT2, ANKLE2, ANKRD54, ANO5, APBA3, APOL4, APOLD1, ARHGAP24, ARSD, BAHD1, BCL7C, BDH1, BLNK, C10orf88, C12orf43, C2orf16, CASS4, CCDC170, CD101, CD274, CD7, CDC14B, CEACAM8, CENPC, CEP162, CFH, CHMP6, CLEC4M, CLK4, CLSTN1, COL5A1, COPS8, CRIPT, CS, CSF2RA, CSRNP2, CXCL11, CYB561, DAAM2, DCX, DDX20, DHRS7B, DIRC2, DMPK, EEFSEC, EGR3, EHD1, EHD3, EIF2B4, EPHX1, EPM2AIP1, ERO1B, FAM111B, FBP1, FPR3, G0S2, GALNT11, GATC, GBE1, GNPNAT1, GTF3C3, HCAR3, HERC6, HS6ST1, ICA1, IL12RB2, IL1R2, IQSEC2, KCNT2, KDM5D, KIAA1324, KLHL12, KPNA2, LAS1L, LCMT1, LGALS12, LRRCC1, LRSAM1, LTBP2, LZTFL1, MAP3K7CL, MCUR1, MEI1, MERTK, MFSD11, MGAT4B, MMAB, MRPS10, MRPS21, MTMR9, MUSK, MYBBP1A, MYO19, NATD1, NCKAP1, NCKIPSD, NPHP4, NRF1, NT5C3A, NUGGC, NUP43, OSGEP, P2RY14, PDPR, PEF1, PHGDH, PIM3, PISD, PLA2G12A, PLXNB2, PMS2, PNKP, POLD2, POU2AF1, PRICKLE3, PTGDS, PTPN13, R3HCC1L, RABGGTA, RABL2B, RAD17, RBFOX2, RFT1, RIC8B, RILPL2, RNF146, RNF5, ROCK2, RPRD1A, RUNX3, SCIN, SCRN3, 3-Sep, SHB, SHPK, SIAE, SLC16A7, SLC25A38, SLC39A10, SLC44A1, SLC8B1, SMCR5, SMIM12, SNAPC5, SNRK, SPATA20, SPRYD3, SRSF2, STEAP2, STK38L, STX2, TANK, TBPL1, TESK2, TICAM1, TJP1, TLDC1, TLR9, TMEM110, TMEM63A, TMEM70, TMEM87B, TNFSF13, TRAP1, TREM1, TRMT2A, TSHZ3, TSPAN17, TTC33, UBALD1, UCK2, UGCG, UQCR11, USP42, UTP14A, VIMP, VNN1, ZAP70, ZBED6, ZBTB3, ZBTB41, ZC4H2, ZCCHC14, ZDHHC17, ZNF486, ZNF542P, ZNF544, ZNF548, ZNF619, ZNF692, ZNF708, and ZNF720 [dimorphic fungi v. ‘rest’]; (xiv) AHNAK, AKAP10, ALDH1L1, ALDH3A2, ANGEL1, ANKRD17, ANKRD50, AQP10, ARHGEF17, ARID5B, ASAH1, ASUN, ATF6B, ATF7, ATXN7L2, ATXN7L3, ATXN7L3B, B4GALT4, BAHCC1, BCAP31, BCL6, BIN1, BMPR2, BRIP1, C11orf63, C5orf30, CAMKK2, CAPN1, CASP9, CD74, CDR1, CLIC5, CNOT3, COASY, CPSF7, CRISPLD1, CTTNBP2, CXCR1, DARS, DAZAP2, DDX10, DENND3, DFNA5, DHX15, DNAH6, DNAJA1, DNAJB6, EIF4G3, FTL, FYN, GABRB3, GALC, GCN1, GLE1, GLUD1, GNB2L1, HLA-DRB1, HR, IGF2BP3, IL18RAP, INTS2, INTU, JUNB, Attorney Docket No.00138-015WO1 KANSL1L, KCNC2, KCNG1, KCNU1, KHDRBS1, KLF11, KLHL11, KLHL2, LAMA5, LARP4, LCA5L, LIMK2, LRRC4C, MAN2B2, MAPK6, MMRN2, MMS19, MPP7, MYH16, NDOR1, NDUFA6, NLGN2, NPY2R, NSRP1, NXN, PABPC4, PARP3, PJA2, PLAC8, PLCB1, PLEKHO1, PML, PNRC2, POP4, PPFIA2, PRDM2, PRDM7, PRDX1, PRELP, PSMA1, PSTK, PTGES3, PTPN21, PTPRO, R3HDM2, RAB7A, RC3H2, REV3L, RGL4, RIF1, RNF112, RNF170, ROR1, RPA2, RPE, RTN4IP1, SAMM50, SASH3, SCIN, SEC24B, SECISBP2L, SENP6, SERF2, SESN3, SETD1A, SH3YL1, SIRT3, SLC39A11, SMARCA2, SMTN, SP3, SPOP, SPTBN2, SREK1IP1, SRPK1, SS18L1, ST6GALNAC1, STXBP5, TAOK1, TARBP1, TBC1D26, TECPR1, TESPA1, TIMM50, TMEM108, TMEM180, TMEM2, TNKS1BP1, TOB2, TRAF3IP3, TRAF5, TRPC5, TSC22D1, TUT1, TXNIP, TYRO3, TYRP1, UBE2H, UBE2R2, UNKL, VARS, VASP, VCAM1, VIT, VPS28, VPS8, VWDE, WDR73, WRN, ZC3H13, ZCCHC24, ZFAND6, ZFP36L2, ZMIZ1, ZNF197, ZNF469, ZNF521, ZNF608, ZNF721, ZNF780B, ZNF79, ZNRF2, ZSCAN25 [afm v. ‘rest’]; (xv) ALOX15, ASNS, BYSL, CD1E, CD209, CDC14B, CYP24A1, F13A1, GIPR, GTF2E1, JCHAIN, KLHDC8B, PIGX, SEMA4B, UCK2, ZBED8, ZIC1, and ZNF706 [worm v. ‘rest’]; (xvi) CCDC126, CXCL8, CXCL9, ERICH3, G0S2, IL1R2, KCNJ2, TNFAIP6, and UBD [mtb v. ‘rest’]; (xvii) ABHD14B, AHCY, ATP13A3, CCL2, CCL20, CD3E, COL1A1, CXCL9, CYP1B1, EFCAB2, FAM219B, FBXO25, HLA-DQB1, HSD17B4, IDO1, IGLL5, IL2RB, IL32, ITGB8, KLHL42, KRIT1, LETM1, LETMD1, LGALS3, MERTK, METTL9, MID1IP1, MOSPD2, MXI1, PI3, S100A8, SIGLEC10, SMCR8, SOD2, SPP1, ST3GAL5, UMPS, WIPI1, and ZNF253 [bacteria typical v. ‘rest’]; (xviii) ABCC5, ADGRL1, AFF2, AP4S1, ARL5A, B4GALT4, BTBD11, CCDC170, CDCA7L, CHST6, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IGLL5, ITGA8, KCNJ2, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SDPR, SLC15A4, SNX16, SYPL1, TIFA, TMCC3, TMEM52B, TPD52, TPGS2, TRIM36, and TUSC2 [bacteria atypical v. ‘rest’]; (xix) ABHD5, CD209, CWC15, DHX34, FADS2, FAM122B, FERMT3, FES, GPR183, HLA-DQA1, IFI44, KCNK2, KLHDC8B, LRRC9, METTL10, MS4A4A, NSDHL, PLCXD1, PLTP, PPM1G, PWP1, RBCK1, SKAP1, TADA2B, UCK2, and WBSCR16 [parasitic v. ‘rest’]; (xx) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, Attorney Docket No.00138-015WO1 RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. bacterial atypical]; (xxi) AHCY, ANKRD27, ATP2A3, CCL2, CD2, COBLL1, DNAH17, FAM219B, FBXO25, GALNT15, HSD17B4, IGLL5, KIAA1407, KIF3A, KRIT1, LETMD1, LILRA6, METTL9, MXI1, NLRP1, NOL8, NUCB1, PI3, PMP22, POLD4, POLL, PSTPIP2, RASAL3, RNF144B, RNPS1, S100A8, S100A9, SMCR8, TGFB3, TNFAIP2, and WIPI1 [AINI v. bacterial typical]; (xxii) ARHGAP25, AURKA, BCCIP, C2CD5, CCR7, CD209, CDYL2, CHEK2, CPM, CWC15, DDX19B, DHX34, FBF1, FZD3, GOLGA5, IDO1, IFI44, JCHAIN, KCNK2, KLC1, LRRC59, LRRC9, MAFB, METTL10, MRFAP1L1, MS4A4A, OLFML2B, POMP, PSTPIP2, PWP1, RBCK1, RIMS1, RNF146, RPF1, S100A8, SLAMF8, TNFRSF10B, TRNT1, TTC9C, TYW3, and ZFAT [AINI v. parasitic]; (xxiii) ATF7IP2, ATP13A3, BLZF1, C3orf58, CCL2, CD36, CEP70, CXCL9, EYA2, FH, GPNMB, H1F0, HGS, HSD17B4, IGLL5, ITGB8, KATNAL2, MCUR1, RANBP6, REXO4, SFXN1, SIRT1, STMN4, ZNF430, and ZNF92 [bacteria atypical v. typical]; (xxiv) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [bacterial atypical v. fungal]; (xxv) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial atypical v. parasitic]; (xxvi) ABHD5, ADGRE1, BANK1, BCCIP, C16orf72, CD3E, COL1A1, CXCR1, CYP1B1, GATA3, GIN1, IDO1, IL32, IRAK2, JCHAIN, MOSPD2, NHS, PI3, POLR3D, PSPC1, PWP1, TIMP3, UMPS, ZGRF1, ZNF213, and ZNF407 [bacterial typical v. parasitic]; (xxvii) BLZF1, CHCHD3, CMTR1, COL1A1, CXCL1, CXCL8, DDX60, DNTTIP2, DUSP16, EDEM2, EDEM3, EFCAB2, EIF3F, FAM219B, IDO1, IL2RB, INAFM2, ITGB8, IWS1, LPAR6, MID1IP1, MXI1, NKG7, OTOF, PDE11A, PI3, PLTP, PPP3CC, PRDM4, RETSAT, SFXN1, SIGLEC10, SOD2, SPP1, TIMM10B, TNFSF10, and ZNF24 [bacterial typical v. viral]; (xxviii) A1CF, A2M, A2ML1, A4GALT, AAAS, AACS, AADACL4, AADAT, AAED1, AAGAB, AAMP, AAR2, AARS, AASDH, AASDHPPT, AATK, ABCA1, Attorney Docket No.00138-015WO1 ABCA10, ABCA12, ABCA13, ABCA2, ABCA4, ABCA5, ABCA7, ABCA8, ABCA9, ABCB1, ABCB10, ABCB11, ABCB6, ABCB7, ABCB8, ABCC1, ABCC11, ABCC12, ABCC2, ABCC5, ABCD3, ABCD4, ABCF1, ABCF2, ABCG2, ABHD1, ABHD10, ABHD11, ABHD12B, ABHD14A, ABHD16A, ABHD17A, ABHD2, ABHD3, ABHD4, ABHD5, ABI2, ABL2, ABLIM3, ABR, ABT1, ABTB1, ACAA1, ACAA2, ACAD10, ACAD9, ACADL, ACADM, ACADS, ACAN, ACAP1, ACBD3, ACBD4, ACBD5, ACBD6, ACBD7, ACKR1, ACO1, ACOT11, ACOT13, ACOX1, ACOX2, ACOX3, ACPP, ACR, ACSBG1, ACSBG2, ACSL1, ACSL5, ACSL6, ACSS1, ACSS3, ACTG2, ACTL6A, ACTN1, ACTN4, ACTR1A, ACTR1B, ACTR8, ACVR1, ACVR1B, ACVRL1, ADAM15, ADAM20, ADAM29, ADAM30, ADAM33, ADAM9, ADAMDEC1, ADAMTS15, ADAMTS16, ADAMTS2, ADAMTS4, ADAMTS6, ADAMTS9, ADAMTSL4, ADAP2, ADAT2, ADCK1, ADCY3, ADCY9, ADD2, ADD3, ADGB, ADGRA3, ADGRE1, ADGRE2, ADGRF5, ADGRG2, ADGRG4, ADGRG6, ADGRL2, ADGRL3, ADGRL4, ADH1B, ADI1, ADNP2, ADORA2A-AS1, ADPRM, ADRA1A, ADRA2A, AEBP2, AFF4, AFMID, AGBL5, AGFG2, AGL, AGPAT1, AGPAT5, AGPS, AGTPBP1, AHCTF1, AHCYL1, AHNAK2, AHSA2, AIDA, AIFM1, AK3, AKAP11, AKAP12, AKAP9, AKIRIN2, ALDH1A1, ALDH2, ALDH7A1, ALG1, ALG12, ALG9, ALKBH8, ALOX15, ALPK1, AMDHD1, AMIGO2, AMMECR1L, AMPD2, AMPD3, ANAPC1, ANAPC13, ANAPC4, ANKFY1, ANKIB1, ANKMY2, ANKRD13D, ANKRD20A5P, ANKRD28, ANKRD36C, ANKRD42, ANKRD62, ANLN, ANTXR1, AP3M1, AP5Z1, APOBEC3G, APOBR, APOD, APOPT1, APPL1, AQP4, ARFGAP3, ARHGEF37, ARID3A, ARMC6, ARNT2, ARV1, ATF6B, ATG16L1, ATG9B, ATOX1, ATP12A, ATP13A2, ATP1B2, ATP2B2, ATPAF1, BAP1, BATF2, BAX, BCAP29, BMPR2, BRMS1, BRPF1, BTBD18, BTF3L4, BUB1, BUD13, C12orf65, C16orf62, C16orf71, C17orf51, C1orf27, C2CD5, C3orf38, C5, C5orf63, C6orf132, C8orf33, C8orf49, CABLES1, CAD, CAMK4, CANT1, CASK, CASP7, CBX7, CCDC149, CCSAP, CD24, CD244, CDCA3, CDKL1, CECR6, CELSR1, CHN2, CLCN3, CLUAP1, CLUH, CMTR2, CNOT8, COMMD9, COPG2, CSRP2BP, DAAM2, DBNL, DCLRE1A, DDX46, DNAAF5, DNAH1, DOK4, EIF2AK3, EIF2B1, ELMOD3, EMC4, EML3, EPN2, FAF2, FAM160B2, FAM35A, FAM69A, FZD3, GFM1, GLIS3, GPR137B, GRK5, HMBOX1, HNRNPA1L2, HRH1, INSIG2, KIAA0319L, LAMP3, LIG1, LRIG2, NFATC2IP, OAZ2, OGG1, PAQR8, PARL, PCGF3, PCMTD2, PLAUR, PRPF19, PTPN7, RAD1, RBCK1, RBPMS, RFX1, RPS4Y1, SCAF1, SH3PXD2B, SNTA1, STRADA, STXBP4, TAF5L, TBRG4, TOM1L2, ZNF397, ZNF597, ZNF71, ZNF721, and ZSWIM6 [fungal v. parasitic]; Attorney Docket No.00138-015WO1 (xxix) ANAPC4, APLP1, BLZF1, CLPX, CRYL1, DESI2, FADS2, FAM122B, FBN3, FES, GRWD1, HERC5, HEXA, HLA-DQA1, IFIT1, KLHDC8B, MTURN, MYO1D, NSDHL, PLCXD1, PLTP, PWP1, RAB11FIP4, SKAP1, SLC35D2, SPOCK1, SPP1, TADA2B, TLR7, TMTC3, UCK2, ZNF213, ZNF407 [parasitic v. viral]; and (xxx) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial both v. parasitic]. [0061] In yet another embodiment, the one or more RNA gene biomarkers are selected from group (i)-(iv) and comprise at least one or more from each group: (i) UBR4, RHDBF2, S100A9, PSTPIP2 and/or ALS2CR12/Casp8 [AINI v. 'rest']; (ii) PI3, NELFCD, MERTk, WDR93, and/or RIPK2 [Bacterial v. 'rest']; (iii) CXCL8, NT5C3A, TRMT1, SSPN, and/or SOD1 [Fungal v. 'rest']; and/or (iv) IFI44L, IFIT1, IRPS3A, CXCL8 and/or PRDM10[Viral v. 'rest']. [0062] In yet another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) above and comprise at least the RNA gene biomarkers of PRDM4 and RHBDF2. In yet a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of PRDM4, RHBDF2, COBLL1, S100A9, MTURN, PSTPIP2, FGF1, CCL2, HLF, and CXCL9. In another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of PRDM4, RHBDF2, COBLL1, S100A9, MTURN, PSTPIP2, FGF1, CCL2, HLF, CXCL9, SLC13A4, FAM198B, APOA1BP, RIMS1, TPRG1L, ZSCAN26, DDX23, FBF1, HMGA1, and RNF144B. In yet another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of PRDM4, RHBDF2, COBLL1, S100A9, MTURN, PSTPIP2, FGF1, CCL2, HLF, CXCL9, SLC13A4, FAM198B, APOA1BP, RIMS1, TPRG1L, ZSCAN26, DDX23, FBF1, HMGA1, RNF144B, PGAP2, RSAD2, ADD1, IFI27, ZNF500, FBXW11, HNRNPH3, IL1RN, ALDH3A1, and FEM1A. In a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarker of CDKN1B. In yet a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of CDKN1B, MERTK, WIPI1, PRRX1, and ADGRL1. In another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of CDKN1B, MERTK, WIPI1, PRRX1, ADGRL1, HN1L, MXI1, FAM172A, SPARC, and CYP1B1. In yet another embodiment, the Attorney Docket No.00138-015WO1 one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of CDKN1B, MERTK, WIPI1, PRRX1, ADGRL1, HN1L, MXI1, FAM172A, SPARC, CYP1B1, INAFM2, SOD2, ZNF395, PDLIM1, and SPP1. In another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarker of NT5C3A and TSPYL4. In yet another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of NT5C3A, TSPYL4, CD2AP, FBP1, UGCG, KHSRP, MID1, MAST2, RBFOX2, and CXCL9. In a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of NT5C3A, TSPYL4, CD2AP, FBP1, UGCG, KHSRP, MID1, MAST2, RBFOX2, CXCL9, FAM122B, RRAGD, FGF1, GMEB2, DRG1, and CXCL8. In yet a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarker of ZNF621, and EEF1B2. In another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of ZNF621, EEF1B2, LPAR6, CXCL8, ANLN, EEF1A1, LAMP3, PRDM10, XAF1, and RNF216. In yet another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of ZNF621, EEF1B2, LPAR6, CXCL8, ANLN, EEF1A1, LAMP3, PRDM10, XAF1, RNF216, TMC3, IL1B, CAPRIN2, NUP133, TLR7, MTURN, SEMA6A, BCORL1, INTS7 and FAM219B. In a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of ZNF621, EEF1B2, LPAR6, CXCL8, ANLN, EEF1A1, LAMP3, PRDM10, XAF1, RNF216, TMC3, IL1B, CAPRIN2, NUP133, TLR7, MTURN, SEMA6A, BCORL1, INTS7, FAM219B, CRX, C3, LILRB1, RSBN1, SNCAIP, FBRSL1, TBC1D22B, PLCD1, HERC6, and MID1IP1. In yet a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarker of RUNX3 and S100A9. In another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of FRAS1, PSTPIP2, PDZD8, LETMD1, PRCC, PI3, TMEM104, and RIMS1. In yet another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of FRAS1, PSTPIP2, PDZD8, LETMD1, PRCC, PI3, TMEM104, RIMS1, GEN1, RNF144B, GANAB, RIPK2, ZN76, ADGRL1, ZNF507, IL1RN, MTFR1, and KCNJ2. In a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of FRAS1, PSTPIP2, PDZD8, Attorney Docket No.00138-015WO1 LETMD1, PRCC, PI3, TMEM104, RIMS1, GEN1, RNF144B, GANAB, RIPK2, ZN76, ADGRL1, ZNF507, IL1RN, MTFR1, KCNJ2, BARD1, IRAK3, SPARC, OL1, and POLL. In yet a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarker of CXCL9 and TMEM259. In another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of CXCL9, TMEM259, RHBDF2, ERMN, RRAGD, ZNF76, CCL2, TMEM63A, ATP10D, and NOTCH1. In yet another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of CXCL9, TMEM259, RHBDF2, ERMN, RRAGD, ZNF76, CCL2, TMEM63A, ATP10D, NOTCH1, CXCL8, GLCE, EIF4E2, DNMBP, S100A8, TPRG1L, KHSRP, RECQL, GATC, and TXLNG. In a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of CXCL9, TMEM259, RHBDF2, ERMN, RRAGD, ZNF76, CCL2, TMEM63A, ATP10D, NOTCH1, CXCL8, GLCE, EIF4E2, DNMBP, S100A8, TPRG1L, KHSRP, RECQL, GATC, TXLNG, PARK2, ITGB8, APOL2, RBFOX2, P2RY14, FGF1, ANKRD13C, CHIC1, BEST1, and TTPAL. In yet a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarker of COL1A2 and LETM1. In another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of COL1A2, LETM1, UGCG, CD209, FBXO22, CCDC170, NT5C3A, BCL2, CDC14B, and RPF2. In yet another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of COL1A2, LETM1, UGCG, CD209, FBXO22, CCDC170, NT5C3A, BCL2, CDC14B, RPF2, S100A12, COX19, EBI3, MED8, MERTK, P2RY2, NTRK3, GMEB2, and LETMD1. In a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of COL1A2, LETM1, UGCG, CD209, FBXO22, CCDC170, NT5C3A, BCL2, CDC14B, RPF2, S100A12, COX19, EBI3, MED8, MERTK, P2RY2, NTRK3, GMEB2, LETMD1, DRG1, YIPF5, LDLRAD3, CDKN1B, and DUSP16. In yet a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarker of TRRAP and OASL. In another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of TRRAP, OASL, PRDM10, TNFSF10, PHLDB1, UBE2G1, PDS5A, CXCL9, PLEC, and IRF8. In yet another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the Attorney Docket No.00138-015WO1 RNA gene biomarkers of TRRAP, OASL, PRDM10, TNFSF10, PHLDB1, UBE2G1, PDS5A, CXCL9, PLEC, IRF8, MTURN, TMEM106B, FGF1, RAB8A, IRS2, PTPRO, UBR4, TUBG2, ARHGAP4, and CCL2. In a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of TRRAP, OASL, PRDM10, TNFSF10, PHLDB1, UBE2G1, PDS5A, CXCL9, PLEC, IRF8, MTURN, TMEM106B, FGF1, RAB8A, IRS2, PTPRO, UBR4, TUBG2, ARHGAP4, CCL, PRDM4, CACNB4, BCORL1, RNF144B, EEF1A1, SLC10A7, PHLDA1, IFI27, SKI, and ACP2. In yet a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarker of PI3 and CPVL. In another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of PI3, CPVL, SPP1, SPTA1, GRAMD1A, IFI44L, SOD2, MS4A6A, MTA1, and ZAP70. In yet another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of PI3, CPVL, SPP1, SPTA1, GRAMD1A, IFI44L, SOD2, MS4A6A, MTA1, ZAP70, CXCL8, FPR3, HN1L, TCN2, INAFM2, TNFSF10, ZNF395, IL2RB, and SIGLEC10. In a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of PI3, CPVL, SPP1, SPTA1, GRAMD1A, IFI44L, SOD2, MS4A6A, MTA1, ZAP70, CXCL8, FPR3, HN1L, TCN2, INAFM2, TNFSF10, ZNF395, IL2RB, SIGLEC10, MMP2, RETSAT, ADGRL1, MXI1, and PRDM4. In yet a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarker of XAF1 and CXCL8. In another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of XAF1, CXCL8, RSAD2, RRAGD, FAM198B, NUP133, BLZF1, EIF3K, IFI44L, and KHSRP. In yet another embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of XAF1, CXCL8, RSAD2, RRAGD, FAM198B, NUP133, BLZF1, EIF3K, IFI44L, KHSRP, CD2AP, RSBN1, SEMA6A, GTF3C2, WDR75, IL1B, IFIT1, FBRSL1, VPS26A, and PDHB. In a further embodiment, the one or more RNA gene biomarkers are selected from groups (i)-(x) and comprise at least the RNA gene biomarkers of XAF1, CXCL8, RSAD2, RRAGD, FAM198B, NUP133, BLZF1, EIF3K, IFI44L, KHSRP, CD2AP, RSBN1, SEMA6A, GTF3C2, WDR75, IL1B, IFIT1, FBRSL1, VPS26A, PDHB, MX2, ABHD10, PIGT, RNF216, TTC21B, MYBBP1A, DRG1, TSR1, LY6E, and BTBD1. Attorney Docket No.00138-015WO1 [0063] The samples used in the methods disclosed herein are typically CSF samples obtained from an animal subject, particularly a mammalian subject such as a human. The methods, however, are not limited to CSF samples, as any type of sample (e.g., blood, plasma, urine, sputum, etc.) can used with the RNA gene biomarkers disclosed herein. In a certain embodiment, the CSF samples used in the methods disclosed herein are from a human patient. In a further embodiment, the human patient has, or is suspected of having, a neurological disease or illness. Examples of neurological diseases or illnesses include, but are not limited to, encephalitis, cavernous sinus thrombosis, brain abscess, encephalomyelitis, meningitis, meningoencephalitis, basal ganglia disease, dyskinesia, athetosis, chorea, myoclonus, tremor, restless leg syndrome, tauopathy, frontotemporal dementia, Lewy bodies dementia, posterior cortical atrophy, vascular dementia, Leigh syndrome, multiple sclerosis, epilepsy, seizures, migraine, stroke, sleep disorder, intercranial hypertension, cerebral edema, intracranial hypotension, brain herniation, Reye syndrome, hepatic encephalopathy, toxic encephalopathy, Hashimoto's encephalopathy, static encephalopathy, Friedreich's ataxia, ataxia-telangiectasia, primary lateral sclerosis, Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. [0064] The methods of the disclosure can further be used to identify whether a subject's neurological illness or disease is caused by an infectious pathogen or otherwise. In another embodiment, the subject has a neurological illness or disease selected from encephalitis, encephalomyelitis, meningitis, and meningoencephalitis that is suspected of being caused by an infectious pathogen. In a further embodiment, the infectious pathogen is a bacterium, virus, parasite, or fungus. In yet a further embodiment, the infectious agent is a bacterium selected from Group B Streptococcus, Escherichia coli, Listeria monocytogenes, Neisseria meningitides, Streptococcus pneumoniae and Haemophiles influenzae. In another embodiment, the infectious agent is a virus selected from non-polio enteroviruses, mumps virus, Herpesviruses, Measles virus, Influenza virus, Arboviruses, and lymphocytic choriomeningitis virus. In yet another embodiment, the infectious agent is a fungus selected from selected from Aspergillus, Candida Albicans, Coccidioides Immitis, Cryptococcus Neoformans, Histoplasma, and Mucormycosis. In a further embodiment, the infectious agent is a fungus selected selected from Angiostrongylus cantonensis, Baylisascaris procyonis, and Gnathostoma spinigerum. The methods of the disclosure can be used to identify an infectious agent selected from the group consisting of EBV, HIV, HHV-6, HHV-7, CMV, WNV, VZV, HSV-1, Mycobacterium tuberculosis complex, Powassan, Cryptococcus neoformans, HCV, JC virus, Coccidioides sp, HSV-2, BK virus, Toxoplasma gondii, Attorney Docket No.00138-015WO1 Adenovirus, Aspergillus sp, HBV, Rubella, Klebsiella pneumoniae, Streptococcus pneumoniae, Aspergillus fumigatus, Enterococcus faecalis, Haemophilus influenzae, Rhinovirus, St. Louis encephalitis virus, Streptococcus intermedius, Candida tropicalis, Coxsackievirus B5, HEV, Histoplasma capsulatum, Human polyomavirus 6, Staphylococcus aureus, Balamuthia mandrillaris, Cache valley virus, Citrobacter koseri, Coccidioides immitis, Enterovirus A71, Human parvovirus B19, Human polyoma virus 8 (Trichodysplasia spinulosa-associated polyomavirus), Human polyomavirus 10 (MW), Klebsiella aerogenes, LCMV, Mycobacterium fortuitum, Neisseria meningitidis, Nocardia farcinica, Streptococcus agalactiae, Streptococcus sp, Alternaria sp, Angiostrongylus cantonensis, Astrovirus VA1, Borrelia burgdorferi, Candida albicans, Candida famata, Coccidioides posadasii, Coronavirus 229E, Enterobacter aerogenes, Enterobacter cloacae, Enterococcus faecium, Enterovirus B, Enterovirus D68, Human polyomavirus 5 (Merkel cell), Mycobacterium avium, Mycoplasma hominis, Rotavirus, Rotavirus A, Serratia marcescens, Staphylococcus epidermidis, Streptococcus dysgalactiae, Taenia solium, Treponema pallidum, Acanthamoeba castellani, Acanthamoeba sp, Acinetobacter radioresistens, Actinomyces oris, Bacteroides sp, Bartonella henselae, Borrelia miyamotoi, Calicivirus, Candida glabrata, Candida lusitaniae, Candida parapsilosis, Candida utilis, Chlamydia psittaci, Colorado tick fever virus, Corynebacterium singular, Coxsackievirus A6, Cronobacter sakazakii, Cryptococcus gattii, Cutibacterium avidum, Dengue, Echovirus 18, Echovirus 30, Echovirus E6, Enterovirus B85, Epicoccum sp, Fusarium graminearum, Fusarium oxysporum, Fusarium sp, Fusobacterium necrophorum, Fusobacterium nucleatum, Gardnerella vaginalis, HHV-8, HTLV-2, Haemophilus parainfluenzae, Human parechovirus, Human parvovirus 4, Human polyomavirus 11, Jamestown Canyon virus, Kingella kingae, Klebsiella oxytoca, Klebsiella variicola, La Crosse, Legionella sp, Leptospira borgpetersenii, Leuconostoc sp, Measles, Moraxella catarrhalis, Mucorales sp, Mycobacterium choelonae, Mycobacterium sp, Mycoplasma pneumoniae, Naegleria Fowleri, Neisseria sp probable non- meningitidis, Norovirus, Pantoea sp, Parascaris equorum, Potosi virus, Powassan virus, Propionibacterium acnes, Proteus mirabilis, Pseudomonas aeruginosa, Rhizopus sp, Rothia mucilaginosa, SARS-CoV-2, Serratia marcecens, Serratia sp, Shewanella baltica, Sporothrix schenckii, Staphylococcus haemolyticus, Staphylococcus lugdunensis, Staphylococcus warneri, Streptococcus canis, Streptococcus mutans, Streptococcus pyogenes, Streptococcus viridans, Taenia sp, Tropheryma whipplei, Trypanozoma cruzi, Ureaplasma parvum, Ureaplasma urealyticum, Yellow fever virus, Yersinia pestis, and Zika. Attorney Docket No.00138-015WO1 [0065] The gene expression profile of one or more RNA gene biomarkers from the subject's sample can be measured using any number of gene expression systems known in the art, including, but not limited to mass sequencing, microarray, gene chips, qPCR, and bead chips. In a particular embodiment, the gene expression profile of one or more RNA biomarkers is measured using a metagenomic next-generation sequencing (mNGS) assay. Metagenomic next-generation sequencing (mNGS) provides a comprehensive method by which nearly all potential pathogens -viruses, bacteria, fungi, and parasites—can be accurately identified in a single assay (see Miller et al., Genome Research 29(5):831-342 (2019)). This approach is attractive for diagnosis of infectious diseases, as pathogens that cause an infectious syndrome commonly have nonspecific, overlapping clinical presentations (Washington 1996). Recent advances in sequencing technology and the development of rapid bioinformatics pipelines have enabled mNGS testing to be performed within a clinically actionable time frame. [0066] In yet another embodiment, the gene expression profile of the one or more RNA biomarkers from a subject's sample can be compared using unsupervised hierarchical clustering with the gene expression profiles of RNA biomarkers from CSF samples from a population of subjects' that have known infectious and non-infectious causes of neurological illnesses or disorder. Other gene-based clustering algorithms can also be used to compare the gene expression profile of the one or more RNA biomarkers from a subject's sample with the gene expression profiles of RNA biomarkers from CSF samples from a population of subjects, including agglomerative hierarchical clustering, CLICK, dynamical clustering, k- means, and self-organizing maps. [0067] The methods and compositions (i.e., RNA gene biomarkers) disclosed herein can provide complementary host response data to existing clinical mNGS assays (e.g., the UCSF CSF mNGS assay, licensed by Delve Bio, Inc.) that will improve the performance and utility of the existing assays. Further, The RNA gene biomarkers identified herein can be utilized in new multiplexed diagnostic tests for neurological illnesses using rapid, high throughput testing platforms (e.g., Genmark ePlex, Thermo-Fisher Taqman Array Cards, BioFire, Luyminex MagPix, etc.). The methods and compositions (i.e., RNA gene biomarkers) disclosed herein can also be used to identify host response targets to address specific clinical unmet needs in infectious diseases. The methods and compositions (i.e., RNA gene biomarkers) disclosed herein can be used to support existing outbreak investigations (e.g., yellow fever outbreak by the CDC, monkeypox, unusual autoimmune cases). The methods and compositions (i.e., RNA gene biomarkers) disclosed herein can Attorney Docket No.00138-015WO1 provide new gene targets for clinical unmet needs. Additionally, the methods and compositions (i.e., RNA gene biomarkers) disclosed herein may potentially be extendible to other sample types and clinical indications other than neurological illness. [0068] The following examples are meant to further illustrate, but not limit the invention as defined by the appended claims. EXAMPLES [0069] mNGS assay using CSF samples. Standard operating procedures (SOPs) in the clinical laboratory for processing and analyzing CSF samples by mNGS were established. Each of the “wet lab” and bioinformatics processing steps was optimized to ensure sensitive and accurate organism detection (Schlaberg et al.2017a). The mNGS assay workflow was performed as follows (Fig.1). Briefly, each CSF sample was first subjected to bead-beating to lyse organisms (see FIG.1A), followed by addition (“spiking”) of T1 (DNA) and MS2 (RNA) bacteriophages as an internal control (IC). Total nucleic acid was then extracted and split into two aliquots for construction of separate DNA and RNA libraries. Microbial sequences were enriched by antibody-based removal of methylated host DNA (for DNA libraries) or DNase treatment (for RNA libraries), followed by transposon-based library construction (see FIG.1B). Each sequencing run on an Illumina HiSeq instrument included up to eight samples, along with a negative “no template” control consisting of elution buffer, intended to allow for sensitive detection of contamination, and a positive control consisting of a mixture of seven representative pathogenic organisms (RNA virus, DNA virus, Gram- positive bacterium, Gram-negative bacterium, fungus, mold, and parasite). Sequence analysis was performed using the SURPI+ computational pipeline (see FIG.1C), an automated clinical version of the previously published SURPI (“sequencebased ultrarapid pathogen identification”) research pipeline (Naccache et al.2014). Receiver-operator curve analyses were performed as part of the accuracy study to determine optimal threshold values for organism detection, using 95 clinical CSF samples with established microbiological results. These pre-established thresholds were then finalized and used for all subsequent clinical mNGS runs. Each mNGS run was analyzed by experienced laboratory physicians, and results were generated for five categories per sample (RNA virus, DNA virus, bacteria, fungi, and parasite). Run quality control (QC) metrics included a minimum of 5 million reads per library, ≥100 reads per million for the IC T1 and MS2 phages in the DNA and RNA libraries, respectively, and positive qualitative detection of each of the seven organisms in the PC. [0070] All patents, patent applications, and publications mentioned herein are incorporated herein by reference in their entireties for all purposes.

Claims

Attorney Docket No.00138-015WO1 WHAT IS CLAIMED IS: 1. A method of identifying infectious and non-infectious causes of neurological illness or disorder from a cerebrospinal fluid (CSF) sample from a subject, comprising: obtaining a cerebrospinal fluid (CSF) sample from a subject; measuring the gene expression profile of one or more RNA gene biomarkers from the subject's CSF sample, wherein the one or more RNA gene biomarkers are selected from the biomarkers listed in Table 1 and/or Table 2; and comparing the gene expression profile of the one or more RNA gene biomarkers from the subject's CSF sample with the gene expression profiles of RNA gene biomarkers from CSF samples from a population of subjects' that have known infectious and non-infectious causes of neurological illnesses or disorder. 2. The method of claim 1, wherein the one or more RNA gene biomarkers are selected from the biomarkers listed in Table 1 or Table 2. 3. The method of claim 1, wherein the one or more RNA gene biomarkers are selected from the biomarkers listed in Table 2. 4. The method of claim 3, wherein the one or more RNA gene biomarkers are selected from the biomarkers listed in Table 2 are selected from the RNA biomarkers listed in group (i), group (ii), group (iii) group (iv), group (v), group (vi), group (vii), group (viii), group (ix), group (x), group (xi), group (xii), group (xiii), group (xiv), group (xv), group (xvi), group (xvii), group (xviii), group (xix), group (xx), group (xxi), group (xxii), group (xxiii), group (xxiv), group (xxv), group (xxvi), group (xxvii), group (xxviii), group (xxix), and/or group (xxx): (i) ADAMTS12, ADD1, ADH5, ALDH1A2, ALDH3A1, ALOX15B, ARPC1A, ATP10D, AURKA, CACNB4, CASD1, CCL2, COX6B1, CXCL9, DAAM1, DDX23, DNMT3A, FAM198B, FBF1, FBXO41, FBXW11, FEM1A, FNIP2, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1RN, INTS6, IRF8, KCNK2, KIAA0232, MLXIP, MTURN, NET1, NOC3L, PHLDB1, PLEC, PNPLA2, PSMD10, PSTPIP2, RASSF8, RHBDF2, RIMS1, RNF144B, RNF146, RSAD2, RUNX3, S100A9, SFPQ, SKI, SLC13A4, SLCO2B1, SNCAIP, TPGS2, TPRG1L, TPX2, TSC22D1, UBA6, UBE2L6, UBR4, WDR70, ZNF500, ZSCAN26, IFIT2, and IFIT3 [AINI v. 'rest']; Attorney Docket No.00138-015WO1 (ii) ABCC5, ADGRL1, AFF2, AP4S1, BTBD11, CDCA7L, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IL1B, KCNJ2, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SLC15A4, SPARCL1, SYPL1, TIFA, and TMCC3 [Bacterial v. 'rest']; (iii) ABHD10, ACTG2, AMOTL2, BCL2, C12orf43, CD2AP, CDYL2, CHUK, CRABP1, CXCL8, CXCL9, DGKB, DRG1, EIF4E2, FAM122B, FAM198B, FBP1, FCF1, FGF1, GLCE, GMEB2, ITGB8, KCTD3, KHSRP, MAK16, MAST2, MED8, MID1, NDRG2, NRP1, NT5C3A, PAN2, PIGT, RBFOX2, RHBDF2, RRAGD, SPATS2L, TMEM126B, TMEM184C, TMEM64, TRIM38, TRMT2B, TSPYL4, TTC21B, TXLNG, UBA3, UGCG, VAT1L, and VPS26A [Fungal v. 'rest']; (iv) ARID3A, ATMIN, ATP1A3, AURKA, BCORL1, BHLHE41, BLZF1, C3, C3orf17, CACNA1F, CACNB4, CAPRIN2, CCT2, CD93, CHAMP1, CHST15, CRTC1, CXCL8, DDX60, DNM1L, EDEM2, EDEM3, EEF1A1, EEF1B2, EHD1, EIF3K, ELOVL7, ERAP1, FAM198B, FAM219B, FBRSL1, FBXL7, FOSL2, FPR3, GMFG, GRAMD1A, HELB, HERC6, HLA-DQA2, HMBS, HNRNPH3, IFFO2, IFI27, IFI44L, IFIT1, IL18, IL1B, IL2RB, INAFM2, INTS7, IRS2, KCTD3, KNSTRN, LAMP3, LIMK2, LPAR1, LPAR6, LY6E, MCPH1, MID1IP1, MKL2, MPP6, MROH1, MRPS6, MTURN, NUDT5, NUP133, NUP88, OAS1, OASL, OSGIN2, OTOF, PDCD10, PDIA4, PDS5A, PGM1, PHLDA1, PHLDB1, PLCD1, PLCD4, PRDM10, PRDM4, PTPRO, PTRH2, PXYLP1, RALGPS2, RETSAT, RGS18, RNF216, RSAD2, RSBN1, SCARF1, SDHAF3, SEMA6A, SESN1, SHISA9, SIAE, SIGLEC10, SLC11A1, SLC25A23, SLC31A1, SLC6A2, SMURF1, SNCAIP, SNX2, SOAT2, SPP1, STC2, TBC1D22B, TCN2, TET1, TLR7, TMEM106B, TMTC1, TNFSF10, TOX3, TUBG2, XAF1, ZMIZ1, ZNF410, ZNF614, ZNF621, ZNF831, UBC, USP18, VIM, FLNA, CXCL10, IL1RN, SELL, and EGR1 [Viral v. 'rest']; (v) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. Bacterial]; (vi) ABCD4, ALDH1A1, ANKRD13C, APOA1BP, APOL2, ATP10D, ATXN3, BAIAP2, BEST1, CCL2, CD2AP, CHIC1, CXCL8, CXCL9, DGKB, DNMBP, EIF4E2, ERMN, GATC, GBP3, GLCE, ITGB8, KCNK2, KHSRP, MAST2, MEAF6, MED24, MID1, MMRN1, MTPAP, MYH7, NET1, NOTCH1, P2RY14, P2RY2, PARK2, PLEK, RBFOX2, RECQL, RHBDF2, RRAGD, S100A8, TMEM63A, TPRG1L, TPX2, TSR1, TTPAL, Attorney Docket No.00138-015WO1 TXLNG, UBR4, UGCG, ZNF76, CCND1, PIM1, CCR1, CXCL10, IL1R2, IL1RN, CR1, FPR1, HK3, MNDA, and SLC2A3 [AINI v. Fungal]; (vii) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [Bacterial (typical & atypical) v. fungal]; (viii) ACP2, ADD1, ARHGAP4, ARL14EP, ARPC1A, ATP10D, AURKA, BAG5, BBS12, BCORL1, BLVRB, C3, CACNB4, CAMKK2, CAPRIN2, CASD1, CHST15, COX6B1, DAAM1, EEF1A1, EEF1B2, EFCAB1, ENO2, EPSTI1, ERAP1, FAM198B, FBF1, FGF1, FNIP2, GANAB, HELB, HELLS, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1B, IL1RN, IL2RB, INTS6, INTS7, IRF8, IRS2, ITGAV, KIAA0232, KNSTRN, LIMK2, LITAF, MCPH1, MPP6, MTURN, OAS1, PDCD4, PDIA4, PDS5A, PEX6, PGM1, PHAX, PHLDA1, PHLDB1, PLAU, PLCD4, PLEC, PPP1CC, PRDM10, PRDM4, PRPF4, PSMD10, PSTPIP2, PTPRO, RAB8A, RIMS1, RNF144B, RSAD2, SAMD9, SEC11A, SESN1, SFPQ, SIGLEC10, SKI, SLC11A1, SLC25A23, SMC2, SNCAIP, TMEM106B, TPRG1L, TRRAP, TUBG2, UBR4, VN1R1, ZBED4, and ZSCAN26 [AINI v. Viral]; (ix) ABCC5, ADGRL1, AFF2, ALDOC, BTBD11, CDCA7L, COL6A5, CPVL, CXCL9, DNPEP, ERICH3, FPR3, G0S2, H1F0, HN1L, HPCAL1, HYOU1, IGLL5, IL1B, IL1R1, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRRX1, RIPK2, SLC15A4, SPTA1, TIFA, TMCC3, TMEM52B, TRDMT1, USP18, and ZNF71 [bacterial (typical & atypical v. Viral]; (x) ABHD10, BLZF1, BTBD1, CD2AP, CDYL2, CHUK, CXCL8, DRG1, EIF3K, FAM198B, FBRSL1, GLCE, GMEB2, GTF3C2, IFI44L, IFIT1, IL1B, KHSRP, LY6E, MRPS6, MX2, MYBBP1A, NT5C3A, NUP133, P4HA1, PDHB, PIGT, RNF216, RRAGD, RSAD2, RSBN1, SEMA6A, SPATS2L, SPP1, TSR1, TTC21B, VPS26A, WDR75, and ZNF107 [Fungal v. Viral]; (xi) ABCA9, ABHD10, ACTA2, ACTN4, ADGRA3, AIP, AK5, ALDH1A2, AMER1, ANK2, ANP32A, APOD, ARMC6, ARRB2, ARRDC3, ATP9B, ATXN3, B3GALNT2, BCL2, BTAF1, BZRAP1, C12orf49, C15orf57, C1R, C2CD2, C2orf16, C5, C8orf33, CABIN1, CACHD1, CACNB4, CBX7, CD2, CDHR1, CDK12, CHST3, CNNM4, COL22A1, COPG2, CRIPT, CRY2, CSK, CSTF3, CXCL8, CXCL9, CYTH4, DDX5, DECR1, DNAH1, DNAH3, DNAJC19, DOK4, ECT2L, EIF3K, EIF4E2, EIF4E3, ELMO2, Attorney Docket No.00138-015WO1 ELP5, EMC1, EPB41L5, EPPK1, ERI2, EXOC2, FADS6, FAM129C, FAM161B, FAM172A, FAM175A, FAM76A, FBXL12, FCF1, FGF2, FMOD, GPR160, GRB10, GRB2, HDAC7, HDGFRP3, HIVEP1, ICE2, IL18BP, INAFM2, INTS12, JKAMP, KCNF1, KDM2A, KHSRP, KIF24, KIFAP3, KLHL1, LANCL1, LILRB4, LIMD1, LSS, MAP4K5, MAPK9, MAPRE1, MICB, MID1, MLKL, MME, MPI, MRE11A, MRPL22, NAV3, NBAS, NBPF11, NCF2, NCKAP5, NELL2, NID2, NRD1, NUTF2, OS9, OSBP, PAG1, PAN2, PARL, PDZD2, PHAX, PHF20, PHF24, PITPNM1, PLCB1, PLEKHG1, POGLUT1, POLI, PPP2R3A, PPP5C, PRR11, PSMA3, PSMB3, PTPN14, PTPN21, RAI14, RBFOX2, RGS12, RHOBTB3, RNF149, RNF217, RNF24, RNF8, RNFT1, RPF2, RRAGD, RXRB, S1PR3, SCRN1, SELL, SESN2, SF3A3, SGMS1, SGSM2, SLC25A11, SLC25A23, SLC30A7, SPACA6P, SPN, SSBP2, SYNPO2, TAPT1, TBC1D22A, TBC1D24, TCOF1, THAP5, THEMIS, TMED4, TPX2, TRIM38, TRMT1, TRMT2B, TRPM7, TSHZ1, TSPYL4, TTC17, TTPAL, TUBG2, TXNDC11, UBR4, ULK1, VAMP7, VPS13B, VPS26A, WDR45, YIPF5, YTHDF1, ZFAT, ZFP1, ZNF282, ZNF410, ZNF45, ZNF680, ZNHIT3, and ZRANB3 [Mold v. ‘rest’]; (xii) ABCA4, ABCG1, ACACA, ACP2, AGAP2, AGO3, ANAPC7, ANKLE2, ANKRD10, ANKRD36, ANLN, ANO7, AP5M1, ARHGAP20, ARHGEF17, ARSA, ASS1, ATG12, ATRN, BARD1, BPGM, BRD8, BRIP1, BUB1B, C16orf70, C22orf39, C6orf132, C7orf49, CAB39L, CARS, CBFA2T3, CCDC47, CCDC82, CCSAP, CD109, CD69, CDC23, CDK5RAP3, CEP250, CHI3L2, CHURC1, CLN6, CNTN1, COA3, COL9A3, CRIPT, CXCL11, CYC1, DBF4B, DERL1, DNASE1L1, EEF1G, EHBP1L1, EML3, EPM2AIP1, ERC2, ESCO2, FAM102B, FAM122A, FANCC, FBRSL1, FBXO31, FSCN3, GABPB2, GALNT14, GBAS, GID8, GPALPP1, GPD1L, GPR84, GRAMD1B, GRAP2, GTPBP1, H1F0, HAUS2, HAUS3, HCAR3, HFM1, HIST1H2BN, HMGA1, HVCN1, IFI27, IFI44L, IFIT2, IFIT3, IL17RD, IL1B, INTS2, ITGA5, ITGB7, KCTD3, KIF20B, LBR, LDLRAD3, LGALS3BP, LIMK1, LPAR5, LPIN2, LRRC1, LUC7L3, MAF, MAP3K15, 5-Mar, MARCO, MED22, MED27, MID1IP1, MMS19, MRPS6, MYO15A, NCDN, NCKAP1, NDUFAF4, NOC2L, NUP133, OTOF, OTUB2, P2RY12, PAPLN, PARP11, PARP15, PDE6B, PHF1, PLAC8, PNPLA2, POLD2, PPP2R1B, PRCP, PRDM4, PRKCE, PROK2, PRPF31, PRRX1, PSD4, PSMD10, PSTPIP2, PTBP1, PTBP2, PTGIS, QARS, RAB35, RASAL3, RASSF6, RBP3, RDH11, RER1, RGP1, RHOQ, RILP, RPA1, RPS6KA5, SASH3, SCAMP5, SESN1, SHC1, SLC11A1, SLC16A2, SLC24A1, SLC25A13, SLC25A17, SLC9A8, SLFN14, SMAD7, SMARCD1, SMC6, SMTN, SNCA, SOCS7, SPICE1, SPP1, SSTR3, TBL1X, TFDP1, THAP6, TIMM10B, TMEM108, TMEM159, Attorney Docket No.00138-015WO1 TMEM63B, TNFRSF10A, TOLLIP, TPGS2, TPP2, TRAF2, TRIM35, TRPV2, TSPAN33, TYW3, USP14, USP38, UTP18, UTY, UVSSA, VCAM1, VPS72, WDR17, WDR47, WLS, XPNPEP3, ZBTB11, ZNF124, ZNF512B, ZNF546, ZNF639, ZNF687, ZNF740, ZNF765, and ZZZ3 [Flavivirus v. ‘rest’]; (xiii) AAR2, ACAA1, ACP2, ADAMTS2, AGPAT5, AKT2, ANKLE2, ANKRD54, ANO5, APBA3, APOL4, APOLD1, ARHGAP24, ARSD, BAHD1, BCL7C, BDH1, BLNK, C10orf88, C12orf43, C2orf16, CASS4, CCDC170, CD101, CD274, CD7, CDC14B, CEACAM8, CENPC, CEP162, CFH, CHMP6, CLEC4M, CLK4, CLSTN1, COL5A1, COPS8, CRIPT, CS, CSF2RA, CSRNP2, CXCL11, CYB561, DAAM2, DCX, DDX20, DHRS7B, DIRC2, DMPK, EEFSEC, EGR3, EHD1, EHD3, EIF2B4, EPHX1, EPM2AIP1, ERO1B, FAM111B, FBP1, FPR3, G0S2, GALNT11, GATC, GBE1, GNPNAT1, GTF3C3, HCAR3, HERC6, HS6ST1, ICA1, IL12RB2, IL1R2, IQSEC2, KCNT2, KDM5D, KIAA1324, KLHL12, KPNA2, LAS1L, LCMT1, LGALS12, LRRCC1, LRSAM1, LTBP2, LZTFL1, MAP3K7CL, MCUR1, MEI1, MERTK, MFSD11, MGAT4B, MMAB, MRPS10, MRPS21, MTMR9, MUSK, MYBBP1A, MYO19, NATD1, NCKAP1, NCKIPSD, NPHP4, NRF1, NT5C3A, NUGGC, NUP43, OSGEP, P2RY14, PDPR, PEF1, PHGDH, PIM3, PISD, PLA2G12A, PLXNB2, PMS2, PNKP, POLD2, POU2AF1, PRICKLE3, PTGDS, PTPN13, R3HCC1L, RABGGTA, RABL2B, RAD17, RBFOX2, RFT1, RIC8B, RILPL2, RNF146, RNF5, ROCK2, RPRD1A, RUNX3, SCIN, SCRN3, 3-Sep, SHB, SHPK, SIAE, SLC16A7, SLC25A38, SLC39A10, SLC44A1, SLC8B1, SMCR5, SMIM12, SNAPC5, SNRK, SPATA20, SPRYD3, SRSF2, STEAP2, STK38L, STX2, TANK, TBPL1, TESK2, TICAM1, TJP1, TLDC1, TLR9, TMEM110, TMEM63A, TMEM70, TMEM87B, TNFSF13, TRAP1, TREM1, TRMT2A, TSHZ3, TSPAN17, TTC33, UBALD1, UCK2, UGCG, UQCR11, USP42, UTP14A, VIMP, VNN1, ZAP70, ZBED6, ZBTB3, ZBTB41, ZC4H2, ZCCHC14, ZDHHC17, ZNF486, ZNF542P, ZNF544, ZNF548, ZNF619, ZNF692, ZNF708, and ZNF720 [dimorphic fungi v. ‘rest’]; (xiv) AHNAK, AKAP10, ALDH1L1, ALDH3A2, ANGEL1, ANKRD17, ANKRD50, AQP10, ARHGEF17, ARID5B, ASAH1, ASUN, ATF6B, ATF7, ATXN7L2, ATXN7L3, ATXN7L3B, B4GALT4, BAHCC1, BCAP31, BCL6, BIN1, BMPR2, BRIP1, C11orf63, C5orf30, CAMKK2, CAPN1, CASP9, CD74, CDR1, CLIC5, CNOT3, COASY, CPSF7, CRISPLD1, CTTNBP2, CXCR1, DARS, DAZAP2, DDX10, DENND3, DFNA5, DHX15, DNAH6, DNAJA1, DNAJB6, EIF4G3, FTL, FYN, GABRB3, GALC, GCN1, GLE1, GLUD1, GNB2L1, HLA-DRB1, HR, IGF2BP3, IL18RAP, INTS2, INTU, JUNB, KANSL1L, KCNC2, KCNG1, KCNU1, KHDRBS1, KLF11, KLHL11, KLHL2, LAMA5, Attorney Docket No.00138-015WO1 LARP4, LCA5L, LIMK2, LRRC4C, MAN2B2, MAPK6, MMRN2, MMS19, MPP7, MYH16, NDOR1, NDUFA6, NLGN2, NPY2R, NSRP1, NXN, PABPC4, PARP3, PJA2, PLAC8, PLCB1, PLEKHO1, PML, PNRC2, POP4, PPFIA2, PRDM2, PRDM7, PRDX1, PRELP, PSMA1, PSTK, PTGES3, PTPN21, PTPRO, R3HDM2, RAB7A, RC3H2, REV3L, RGL4, RIF1, RNF112, RNF170, ROR1, RPA2, RPE, RTN4IP1, SAMM50, SASH3, SCIN, SEC24B, SECISBP2L, SENP6, SERF2, SESN3, SETD1A, SH3YL1, SIRT3, SLC39A11, SMARCA2, SMTN, SP3, SPOP, SPTBN2, SREK1IP1, SRPK1, SS18L1, ST6GALNAC1, STXBP5, TAOK1, TARBP1, TBC1D26, TECPR1, TESPA1, TIMM50, TMEM108, TMEM180, TMEM2, TNKS1BP1, TOB2, TRAF3IP3, TRAF5, TRPC5, TSC22D1, TUT1, TXNIP, TYRO3, TYRP1, UBE2H, UBE2R2, UNKL, VARS, VASP, VCAM1, VIT, VPS28, VPS8, VWDE, WDR73, WRN, ZC3H13, ZCCHC24, ZFAND6, ZFP36L2, ZMIZ1, ZNF197, ZNF469, ZNF521, ZNF608, ZNF721, ZNF780B, ZNF79, ZNRF2, ZSCAN25 [afm v. ‘rest’]; (xv) ALOX15, ASNS, BYSL, CD1E, CD209, CDC14B, CYP24A1, F13A1, GIPR, GTF2E1, JCHAIN, KLHDC8B, PIGX, SEMA4B, UCK2, ZBED8, ZIC1, and ZNF706 [worm v. ‘rest’]; (xvi) CCDC126, CXCL8, CXCL9, ERICH3, G0S2, IL1R2, KCNJ2, TNFAIP6, and UBD [mtb v. ‘rest’]; (xvii) ABHD14B, AHCY, ATP13A3, CCL2, CCL20, CD3E, COL1A1, CXCL9, CYP1B1, EFCAB2, FAM219B, FBXO25, HLA-DQB1, HSD17B4, IDO1, IGLL5, IL2RB, IL32, ITGB8, KLHL42, KRIT1, LETM1, LETMD1, LGALS3, MERTK, METTL9, MID1IP1, MOSPD2, MXI1, PI3, S100A8, SIGLEC10, SMCR8, SOD2, SPP1, ST3GAL5, UMPS, WIPI1, and ZNF253 [bacteria typical v. ‘rest’]; (xviii) ABCC5, ADGRL1, AFF2, AP4S1, ARL5A, B4GALT4, BTBD11, CCDC170, CDCA7L, CHST6, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IGLL5, ITGA8, KCNJ2, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SDPR, SLC15A4, SNX16, SYPL1, TIFA, TMCC3, TMEM52B, TPD52, TPGS2, TRIM36, and TUSC2 [bacteria atypical v. ‘rest’]; (xix) ABHD5, CD209, CWC15, DHX34, FADS2, FAM122B, FERMT3, FES, GPR183, HLA-DQA1, IFI44, KCNK2, KLHDC8B, LRRC9, METTL10, MS4A4A, NSDHL, PLCXD1, PLTP, PPM1G, PWP1, RBCK1, SKAP1, TADA2B, UCK2, and WBSCR16 [parasitic v. ‘rest’]; (xx) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, Attorney Docket No.00138-015WO1 RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. bacterial atypical]; (xxi) AHCY, ANKRD27, ATP2A3, CCL2, CD2, COBLL1, DNAH17, FAM219B, FBXO25, GALNT15, HSD17B4, IGLL5, KIAA1407, KIF3A, KRIT1, LETMD1, LILRA6, METTL9, MXI1, NLRP1, NOL8, NUCB1, PI3, PMP22, POLD4, POLL, PSTPIP2, RASAL3, RNF144B, RNPS1, S100A8, S100A9, SMCR8, TGFB3, TNFAIP2, and WIPI1 [AINI v. bacterial typical]; (xxii) ARHGAP25, AURKA, BCCIP, C2CD5, CCR7, CD209, CDYL2, CHEK2, CPM, CWC15, DDX19B, DHX34, FBF1, FZD3, GOLGA5, IDO1, IFI44, JCHAIN, KCNK2, KLC1, LRRC59, LRRC9, MAFB, METTL10, MRFAP1L1, MS4A4A, OLFML2B, POMP, PSTPIP2, PWP1, RBCK1, RIMS1, RNF146, RPF1, S100A8, SLAMF8, TNFRSF10B, TRNT1, TTC9C, TYW3, and ZFAT [AINI v. parasitic]; (xxiii) ATF7IP2, ATP13A3, BLZF1, C3orf58, CCL2, CD36, CEP70, CXCL9, EYA2, FH, GPNMB, H1F0, HGS, HSD17B4, IGLL5, ITGB8, KATNAL2, MCUR1, RANBP6, REXO4, SFXN1, SIRT1, STMN4, ZNF430, and ZNF92 [bacteria atypical v. typical]; (xxiv) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [bacterial atypical v. fungal]; (xxv) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial atypical v. parasitic]; (xxvi) ABHD5, ADGRE1, BANK1, BCCIP, C16orf72, CD3E, COL1A1, CXCR1, CYP1B1, GATA3, GIN1, IDO1, IL32, IRAK2, JCHAIN, MOSPD2, NHS, PI3, POLR3D, PSPC1, PWP1, TIMP3, UMPS, ZGRF1, ZNF213, and ZNF407 [bacterial typical v. parasitic]; (xxvii) BLZF1, CHCHD3, CMTR1, COL1A1, CXCL1, CXCL8, DDX60, DNTTIP2, DUSP16, EDEM2, EDEM3, EFCAB2, EIF3F, FAM219B, IDO1, IL2RB, INAFM2, ITGB8, IWS1, LPAR6, MID1IP1, MXI1, NKG7, OTOF, PDE11A, PI3, PLTP, PPP3CC, PRDM4, RETSAT, SFXN1, SIGLEC10, SOD2, SPP1, TIMM10B, TNFSF10, and ZNF24 [bacterial typical v. viral]; (xxviii) A1CF, A2M, A2ML1, A4GALT, AAAS, AACS, AADACL4, AADAT, AAED1, AAGAB, AAMP, AAR2, AARS, AASDH, AASDHPPT, AATK, ABCA1, Attorney Docket No.00138-015WO1 ABCA10, ABCA12, ABCA13, ABCA2, ABCA4, ABCA5, ABCA7, ABCA8, ABCA9, ABCB1, ABCB10, ABCB11, ABCB6, ABCB7, ABCB8, ABCC1, ABCC11, ABCC12, ABCC2, ABCC5, ABCD3, ABCD4, ABCF1, ABCF2, ABCG2, ABHD1, ABHD10, ABHD11, ABHD12B, ABHD14A, ABHD16A, ABHD17A, ABHD2, ABHD3, ABHD4, ABHD5, ABI2, ABL2, ABLIM3, ABR, ABT1, ABTB1, ACAA1, ACAA2, ACAD10, ACAD9, ACADL, ACADM, ACADS, ACAN, ACAP1, ACBD3, ACBD4, ACBD5, ACBD6, ACBD7, ACKR1, ACO1, ACOT11, ACOT13, ACOX1, ACOX2, ACOX3, ACPP, ACR, ACSBG1, ACSBG2, ACSL1, ACSL5, ACSL6, ACSS1, ACSS3, ACTG2, ACTL6A, ACTN1, ACTN4, ACTR1A, ACTR1B, ACTR8, ACVR1, ACVR1B, ACVRL1, ADAM15, ADAM20, ADAM29, ADAM30, ADAM33, ADAM9, ADAMDEC1, ADAMTS15, ADAMTS16, ADAMTS2, ADAMTS4, ADAMTS6, ADAMTS9, ADAMTSL4, ADAP2, ADAT2, ADCK1, ADCY3, ADCY9, ADD2, ADD3, ADGB, ADGRA3, ADGRE1, ADGRE2, ADGRF5, ADGRG2, ADGRG4, ADGRG6, ADGRL2, ADGRL3, ADGRL4, ADH1B, ADI1, ADNP2, ADORA2A-AS1, ADPRM, ADRA1A, ADRA2A, AEBP2, AFF4, AFMID, AGBL5, AGFG2, AGL, AGPAT1, AGPAT5, AGPS, AGTPBP1, AHCTF1, AHCYL1, AHNAK2, AHSA2, AIDA, AIFM1, AK3, AKAP11, AKAP12, AKAP9, AKIRIN2, ALDH1A1, ALDH2, ALDH7A1, ALG1, ALG12, ALG9, ALKBH8, ALOX15, ALPK1, AMDHD1, AMIGO2, AMMECR1L, AMPD2, AMPD3, ANAPC1, ANAPC13, ANAPC4, ANKFY1, ANKIB1, ANKMY2, ANKRD13D, ANKRD20A5P, ANKRD28, ANKRD36C, ANKRD42, ANKRD62, ANLN, ANTXR1, AP3M1, AP5Z1, APOBEC3G, APOBR, APOD, APOPT1, APPL1, AQP4, ARFGAP3, ARHGEF37, ARID3A, ARMC6, ARNT2, ARV1, ATF6B, ATG16L1, ATG9B, ATOX1, ATP12A, ATP13A2, ATP1B2, ATP2B2, ATPAF1, BAP1, BATF2, BAX, BCAP29, BMPR2, BRMS1, BRPF1, BTBD18, BTF3L4, BUB1, BUD13, C12orf65, C16orf62, C16orf71, C17orf51, C1orf27, C2CD5, C3orf38, C5, C5orf63, C6orf132, C8orf33, C8orf49, CABLES1, CAD, CAMK4, CANT1, CASK, CASP7, CBX7, CCDC149, CCSAP, CD24, CD244, CDCA3, CDKL1, CECR6, CELSR1, CHN2, CLCN3, CLUAP1, CLUH, CMTR2, CNOT8, COMMD9, COPG2, CSRP2BP, DAAM2, DBNL, DCLRE1A, DDX46, DNAAF5, DNAH1, DOK4, EIF2AK3, EIF2B1, ELMOD3, EMC4, EML3, EPN2, FAF2, FAM160B2, FAM35A, FAM69A, FZD3, GFM1, GLIS3, GPR137B, GRK5, HMBOX1, HNRNPA1L2, HRH1, INSIG2, KIAA0319L, LAMP3, LIG1, LRIG2, NFATC2IP, OAZ2, OGG1, PAQR8, PARL, PCGF3, PCMTD2, PLAUR, PRPF19, PTPN7, RAD1, RBCK1, RBPMS, RFX1, RPS4Y1, SCAF1, SH3PXD2B, SNTA1, STRADA, STXBP4, TAF5L, TBRG4, TOM1L2, ZNF397, ZNF597, ZNF71, ZNF721, and ZSWIM6 [fungal v. parasitic]; Attorney Docket No.00138-015WO1 (xxix) ANAPC4, APLP1, BLZF1, CLPX, CRYL1, DESI2, FADS2, FAM122B, FBN3, FES, GRWD1, HERC5, HEXA, HLA-DQA1, IFIT1, KLHDC8B, MTURN, MYO1D, NSDHL, PLCXD1, PLTP, PWP1, RAB11FIP4, SKAP1, SLC35D2, SPOCK1, SPP1, TADA2B, TLR7, TMTC3, UCK2, ZNF213, ZNF407 [parasitic v. viral]; and (xxx) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial both v. parasitic]. 5. The method of claim 4, wherein the one or more RNA gene biomarkers are selected from group (i)-(iv) and comprise at least one or more from each group: (i) UBR4, RHDBF2, S100A9, PSTPIP2 and/or ALS2CR12/Casp8 [AINI v. 'rest']; (ii) PI3, NELFCD, MERTk, WDR93, and/or RIPK2 [Bacterial v. 'rest']; (iii) CXCL8, NT5C3A, TRMT1, SSPN, and/or SOD1 [Fungal v. 'rest']; and/or (iv) IFI44L, IFIT1, IRPS3A, CXCL8 and/or PRDM10[Viral v. 'rest']. 6. The method of any one of the preceding claims, wherein the subject is a human patient that is suspected of having a neurological illness or disorder. 7. The method of claim 6, wherein the neurological illness or disorder is selected from encephalitis, cavernous sinus thrombosis, brain abscess, encephalomyelitis, meningitis, meningoencephalitis, basal ganglia disease, dyskinesia, athetosis, chorea, myoclonus, tremor, restless leg syndrome, tauopathy, frontotemporal dementia, Lewy bodies dementia, posterior cortical atrophy, vascular dementia, Leigh syndrome, multiple sclerosis, epilepsy, seizures, migraine, stroke, sleep disorder, intercranial hypertension, cerebral edema, intracranial hypotension, brain herniation, Reye syndrome, hepatic encephalopathy, toxic encephalopathy, Hashimoto's encephalopathy, static encephalopathy, Friedreich's ataxia, ataxia-telangiectasia, primary lateral sclerosis, Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. 8. The method of claim 7, wherein the encephalitis, encephalomyelitis, meningitis, or meningoencephalitis is caused by a bacterium, virus, fungus, or parasite. Attorney Docket No.00138-015WO1 9. The method of claim 8, wherein the bacterium is selected from Group B Streptococcus, Escherichia coli, Listeria monocytogenes, Neisseria meningitides, Streptococcus pneumoniae and Haemophiles influenzae. 10. The method of claim 8, wherein the virus is selected from non-polio enteroviruses, mumps virus, Herpesviruses, Measles virus, Influenza virus, Arboviruses, and lymphocytic choriomeningitis virus. 11. The method of claim 8, wherein the fungus is selected from Aspergillus, Candida Albicans, Coccidioides Immitis, Cryptococcus Neoformans, Histoplasma, and Mucormycosis. 12. The method of claim 8, wherein the parasite is selected from Angiostrongylus cantonensis, Baylisascaris procyonis, and Gnathostoma spinigerum. 13. The method of any one of the preceding claims, wherein the gene expression profile of one or more RNA biomarkers is measured using a metagenomic next-generation sequencing (mNGS) assay. 14. The method of any one of the preceding claims, wherein the CSF samples from the population of subjects, are from subjects that have neurological illnesses or disorders selected from encephalitis, cavernous sinus thrombosis, brain abscess, encephalomyelitis, meningitis, meningoencephalitis, basal ganglia disease, dyskinesia, athetosis, chorea, myoclonus, tremor, restless leg syndrome, tauopathy, frontotemporal dementia, Lewy bodies dementia, posterior cortical atrophy, vascular dementia, Leigh syndrome, multiple sclerosis, epilepsy, seizures, migraine, stroke, sleep disorder, intercranial hypertension, cerebral edema, intracranial hypotension, brain herniation, Reye syndrome, hepatic encephalopathy, toxic encephalopathy, Hashimoto's encephalopathy, static encephalopathy, Friedreich's ataxia, ataxia-telangiectasia, primary lateral sclerosis, Alzheimer's disease, Parkinson's disease, Huntington's disease, and/or amyotrophic lateral sclerosis. 15. The method of claim 14, wherein the encephalitis, encephalomyelitis, meningitis, or meningoencephalitis is caused by a bacterium, virus, fungus, or parasite. Attorney Docket No.00138-015WO1 16. The method of claim 15, wherein the bacterium is selected from Group B Streptococcus, Escherichia coli, Listeria monocytogenes, Neisseria meningitides, Streptococcus pneumoniae and Haemophiles influenzae. 17. The method of claim 15, wherein the virus is selected from non-polio enteroviruses, mumps virus, Herpesviruses, Measles virus, Influenza virus, Arboviruses, and lymphocytic choriomeningitis virus. 18. The method of claim 15, wherein the fungus is selected from Aspergillus, Candida Albicans, Coccidioides Immitis, Cryptococcus Neoformans, and Mucormycosis. 19. The method of claim 15, wherein the parasite is selected from Angiostrongylus cantonensis, Baylisascaris procyonis, and Gnathostoma spinigerum. 20. The method of any one of the preceding claims, wherein unsupervised hierarchical clustering is used to compare the gene expression profile of the one or more RNA biomarkers from the subject's CSF sample with the gene expression profiles of RNA biomarkers from CSF samples from a population of subjects' that have known infectious and non-infectious causes of neurological illnesses or disorder. 21. A computer implemented method to select for the identification of RNA gene biomarkers associated with a neurological illness based on host response classification using a machine learning model, the method comprising: (1) assembling a dataset of RNA metagenomic data from CSF samples; (2) randomly splitting the dataset into a training and test subset based upon selected features and targets, wherein the selected features and targets include viral, bacterial, fungal, parasitic, and/or autoimmune/non-infectious (AINI) host response classifiers; (3) training a machine learning model with the training subset to predict and rank biomarkers that have a high degree of association with the host response classifiers for a neurological illness; and (4) testing the machine learning model with the testing subset by comparing testing predictions to actual targets to generate an accuracy or prediction score, retraining the machine learning model in step (3) until a statistically significant accuracy or prediction score is achieved. Attorney Docket No.00138-015WO1 22. The computer implemented method of claim 21, wherein biomarkers that have a high degree of association with the host response classifiers is determined based on measuring a linear correlation between the biomarker and the host response classifiers. 23. The computer implemented method of claim 22, wherein the linear correlation is measured using Pearson correlation coefficient (r). 24. The computer implemented method of any one of claims 21 to 23, wherein the computer implemented method is implemented using a graphic processing unit (GPU) or an artificial intelligence accelerator of a cloud-based server. 25. A method of diagnosing a subject comprising measuring a plurality of biomarkers in a sample from the subject and applying the measured biomarkers to the computer implemented method of claim 21 to identity whether the subject has a CNS viral, bacterial, fungal, parasitic, and/or autoimmune/non-infectious (AINI) disease. 26. The method of clam 25, wherein the biomarkers are one or more as listed in group (i), group (ii), group (iii) group (iv), group (v), group (vi), group (vii), group (viii), group (ix), group (x), group (xi), group (xii), group (xiii), group (xiv), group (xv), group (xvi), group (xvii), group (xviii), group (xix), group (xx), group (xxi), group (xxii), group (xxiii), group (xxiv), group (xxv), group (xxvi), group (xxvii), group (xxviii), group (xxix), and/or group (xxx): (i) ADAMTS12, ADD1, ADH5, ALDH1A2, ALDH3A1, ALOX15B, ARPC1A, ATP10D, AURKA, CACNB4, CASD1, CCL2, COX6B1, CXCL9, DAAM1, DDX23, DNMT3A, FAM198B, FBF1, FBXO41, FBXW11, FEM1A, FNIP2, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1RN, INTS6, IRF8, KCNK2, KIAA0232, MLXIP, MTURN, NET1, NOC3L, PHLDB1, PLEC, PNPLA2, PSMD10, PSTPIP2, RASSF8, RHBDF2, RIMS1, RNF144B, RNF146, RSAD2, RUNX3, S100A9, SFPQ, SKI, SLC13A4, SLCO2B1, SNCAIP, TPGS2, TPRG1L, TPX2, TSC22D1, UBA6, UBE2L6, UBR4, WDR70, ZNF500, ZSCAN26, IFIT2, and IFIT3 [AINI v. 'rest']; (ii) ABCC5, ADGRL1, AFF2, AP4S1, BTBD11, CDCA7L, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IL1B, KCNJ2, LZTS1, MEMO1, MUC17, Attorney Docket No.00138-015WO1 NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SLC15A4, SPARCL1, SYPL1, TIFA, and TMCC3 [Bacterial v. 'rest']; (iii) ABHD10, ACTG2, AMOTL2, BCL2, C12orf43, CD2AP, CDYL2, CHUK, CRABP1, CXCL8, CXCL9, DGKB, DRG1, EIF4E2, FAM122B, FAM198B, FBP1, FCF1, FGF1, GLCE, GMEB2, ITGB8, KCTD3, KHSRP, MAK16, MAST2, MED8, MID1, NDRG2, NRP1, NT5C3A, PAN2, PIGT, RBFOX2, RHBDF2, RRAGD, SPATS2L, TMEM126B, TMEM184C, TMEM64, TRIM38, TRMT2B, TSPYL4, TTC21B, TXLNG, UBA3, UGCG, VAT1L, and VPS26A [Fungal v. 'rest']; (iv) ARID3A, ATMIN, ATP1A3, AURKA, BCORL1, BHLHE41, BLZF1, C3, C3orf17, CACNA1F, CACNB4, CAPRIN2, CCT2, CD93, CHAMP1, CHST15, CRTC1, CXCL8, DDX60, DNM1L, EDEM2, EDEM3, EEF1A1, EEF1B2, EHD1, EIF3K, ELOVL7, ERAP1, FAM198B, FAM219B, FBRSL1, FBXL7, FOSL2, FPR3, GMFG, GRAMD1A, HELB, HERC6, HLA-DQA2, HMBS, HNRNPH3, IFFO2, IFI27, IFI44L, IFIT1, IL18, IL1B, IL2RB, INAFM2, INTS7, IRS2, KCTD3, KNSTRN, LAMP3, LIMK2, LPAR1, LPAR6, LY6E, MCPH1, MID1IP1, MKL2, MPP6, MROH1, MRPS6, MTURN, NUDT5, NUP133, NUP88, OAS1, OASL, OSGIN2, OTOF, PDCD10, PDIA4, PDS5A, PGM1, PHLDA1, PHLDB1, PLCD1, PLCD4, PRDM10, PRDM4, PTPRO, PTRH2, PXYLP1, RALGPS2, RETSAT, RGS18, RNF216, RSAD2, RSBN1, SCARF1, SDHAF3, SEMA6A, SESN1, SHISA9, SIAE, SIGLEC10, SLC11A1, SLC25A23, SLC31A1, SLC6A2, SMURF1, SNCAIP, SNX2, SOAT2, SPP1, STC2, TBC1D22B, TCN2, TET1, TLR7, TMEM106B, TMTC1, TNFSF10, TOX3, TUBG2, XAF1, ZMIZ1, ZNF410, ZNF614, ZNF621, ZNF831, UBC, USP18, VIM, FLNA, CXCL10, IL1RN, SELL, and EGR1 [Viral v. 'rest']; (v) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. Bacterial]; (vi) ABCD4, ALDH1A1, ANKRD13C, APOA1BP, APOL2, ATP10D, ATXN3, BAIAP2, BEST1, CCL2, CD2AP, CHIC1, CXCL8, CXCL9, DGKB, DNMBP, EIF4E2, ERMN, GATC, GBP3, GLCE, ITGB8, KCNK2, KHSRP, MAST2, MEAF6, MED24, MID1, MMRN1, MTPAP, MYH7, NET1, NOTCH1, P2RY14, P2RY2, PARK2, PLEK, RBFOX2, RECQL, RHBDF2, RRAGD, S100A8, TMEM63A, TPRG1L, TPX2, TSR1, TTPAL, TXLNG, UBR4, UGCG, ZNF76, CCND1, PIM1, CCR1, CXCL10, IL1R2, IL1RN, CR1, FPR1, HK3, MNDA, and SLC2A3 [AINI v. Fungal]; Attorney Docket No.00138-015WO1 (vii) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [Bacterial (typical & atypical) v. fungal]; (viii) ACP2, ADD1, ARHGAP4, ARL14EP, ARPC1A, ATP10D, AURKA, BAG5, BBS12, BCORL1, BLVRB, C3, CACNB4, CAMKK2, CAPRIN2, CASD1, CHST15, COX6B1, DAAM1, EEF1A1, EEF1B2, EFCAB1, ENO2, EPSTI1, ERAP1, FAM198B, FBF1, FGF1, FNIP2, GANAB, HELB, HELLS, HERC5, HMGA1, HNRNPH3, IFI27, IFI44L, IFIT1, IFIT5, IL1B, IL1RN, IL2RB, INTS6, INTS7, IRF8, IRS2, ITGAV, KIAA0232, KNSTRN, LIMK2, LITAF, MCPH1, MPP6, MTURN, OAS1, PDCD4, PDIA4, PDS5A, PEX6, PGM1, PHAX, PHLDA1, PHLDB1, PLAU, PLCD4, PLEC, PPP1CC, PRDM10, PRDM4, PRPF4, PSMD10, PSTPIP2, PTPRO, RAB8A, RIMS1, RNF144B, RSAD2, SAMD9, SEC11A, SESN1, SFPQ, SIGLEC10, SKI, SLC11A1, SLC25A23, SMC2, SNCAIP, TMEM106B, TPRG1L, TRRAP, TUBG2, UBR4, VN1R1, ZBED4, and ZSCAN26 [AINI v. Viral]; (ix) ABCC5, ADGRL1, AFF2, ALDOC, BTBD11, CDCA7L, COL6A5, CPVL, CXCL9, DNPEP, ERICH3, FPR3, G0S2, H1F0, HN1L, HPCAL1, HYOU1, IGLL5, IL1B, IL1R1, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRRX1, RIPK2, SLC15A4, SPTA1, TIFA, TMCC3, TMEM52B, TRDMT1, USP18, and ZNF71 [bacterial (typical & atypical v. Viral]; (x) ABHD10, BLZF1, BTBD1, CD2AP, CDYL2, CHUK, CXCL8, DRG1, EIF3K, FAM198B, FBRSL1, GLCE, GMEB2, GTF3C2, IFI44L, IFIT1, IL1B, KHSRP, LY6E, MRPS6, MX2, MYBBP1A, NT5C3A, NUP133, P4HA1, PDHB, PIGT, RNF216, RRAGD, RSAD2, RSBN1, SEMA6A, SPATS2L, SPP1, TSR1, TTC21B, VPS26A, WDR75, and ZNF107 [Fungal v. Viral]; (xi) ABCA9, ABHD10, ACTA2, ACTN4, ADGRA3, AIP, AK5, ALDH1A2, AMER1, ANK2, ANP32A, APOD, ARMC6, ARRB2, ARRDC3, ATP9B, ATXN3, B3GALNT2, BCL2, BTAF1, BZRAP1, C12orf49, C15orf57, C1R, C2CD2, C2orf16, C5, C8orf33, CABIN1, CACHD1, CACNB4, CBX7, CD2, CDHR1, CDK12, CHST3, CNNM4, COL22A1, COPG2, CRIPT, CRY2, CSK, CSTF3, CXCL8, CXCL9, CYTH4, DDX5, DECR1, DNAH1, DNAH3, DNAJC19, DOK4, ECT2L, EIF3K, EIF4E2, EIF4E3, ELMO2, ELP5, EMC1, EPB41L5, EPPK1, ERI2, EXOC2, FADS6, FAM129C, FAM161B, FAM172A, FAM175A, FAM76A, FBXL12, FCF1, FGF2, FMOD, GPR160, GRB10, GRB2, Attorney Docket No.00138-015WO1 HDAC7, HDGFRP3, HIVEP1, ICE2, IL18BP, INAFM2, INTS12, JKAMP, KCNF1, KDM2A, KHSRP, KIF24, KIFAP3, KLHL1, LANCL1, LILRB4, LIMD1, LSS, MAP4K5, MAPK9, MAPRE1, MICB, MID1, MLKL, MME, MPI, MRE11A, MRPL22, NAV3, NBAS, NBPF11, NCF2, NCKAP5, NELL2, NID2, NRD1, NUTF2, OS9, OSBP, PAG1, PAN2, PARL, PDZD2, PHAX, PHF20, PHF24, PITPNM1, PLCB1, PLEKHG1, POGLUT1, POLI, PPP2R3A, PPP5C, PRR11, PSMA3, PSMB3, PTPN14, PTPN21, RAI14, RBFOX2, RGS12, RHOBTB3, RNF149, RNF217, RNF24, RNF8, RNFT1, RPF2, RRAGD, RXRB, S1PR3, SCRN1, SELL, SESN2, SF3A3, SGMS1, SGSM2, SLC25A11, SLC25A23, SLC30A7, SPACA6P, SPN, SSBP2, SYNPO2, TAPT1, TBC1D22A, TBC1D24, TCOF1, THAP5, THEMIS, TMED4, TPX2, TRIM38, TRMT1, TRMT2B, TRPM7, TSHZ1, TSPYL4, TTC17, TTPAL, TUBG2, TXNDC11, UBR4, ULK1, VAMP7, VPS13B, VPS26A, WDR45, YIPF5, YTHDF1, ZFAT, ZFP1, ZNF282, ZNF410, ZNF45, ZNF680, ZNHIT3, and ZRANB3 [Mold v. ‘rest’]; (xii) ABCA4, ABCG1, ACACA, ACP2, AGAP2, AGO3, ANAPC7, ANKLE2, ANKRD10, ANKRD36, ANLN, ANO7, AP5M1, ARHGAP20, ARHGEF17, ARSA, ASS1, ATG12, ATRN, BARD1, BPGM, BRD8, BRIP1, BUB1B, C16orf70, C22orf39, C6orf132, C7orf49, CAB39L, CARS, CBFA2T3, CCDC47, CCDC82, CCSAP, CD109, CD69, CDC23, CDK5RAP3, CEP250, CHI3L2, CHURC1, CLN6, CNTN1, COA3, COL9A3, CRIPT, CXCL11, CYC1, DBF4B, DERL1, DNASE1L1, EEF1G, EHBP1L1, EML3, EPM2AIP1, ERC2, ESCO2, FAM102B, FAM122A, FANCC, FBRSL1, FBXO31, FSCN3, GABPB2, GALNT14, GBAS, GID8, GPALPP1, GPD1L, GPR84, GRAMD1B, GRAP2, GTPBP1, H1F0, HAUS2, HAUS3, HCAR3, HFM1, HIST1H2BN, HMGA1, HVCN1, IFI27, IFI44L, IFIT2, IFIT3, IL17RD, IL1B, INTS2, ITGA5, ITGB7, KCTD3, KIF20B, LBR, LDLRAD3, LGALS3BP, LIMK1, LPAR5, LPIN2, LRRC1, LUC7L3, MAF, MAP3K15, 5-Mar, MARCO, MED22, MED27, MID1IP1, MMS19, MRPS6, MYO15A, NCDN, NCKAP1, NDUFAF4, NOC2L, NUP133, OTOF, OTUB2, P2RY12, PAPLN, PARP11, PARP15, PDE6B, PHF1, PLAC8, PNPLA2, POLD2, PPP2R1B, PRCP, PRDM4, PRKCE, PROK2, PRPF31, PRRX1, PSD4, PSMD10, PSTPIP2, PTBP1, PTBP2, PTGIS, QARS, RAB35, RASAL3, RASSF6, RBP3, RDH11, RER1, RGP1, RHOQ, RILP, RPA1, RPS6KA5, SASH3, SCAMP5, SESN1, SHC1, SLC11A1, SLC16A2, SLC24A1, SLC25A13, SLC25A17, SLC9A8, SLFN14, SMAD7, SMARCD1, SMC6, SMTN, SNCA, SOCS7, SPICE1, SPP1, SSTR3, TBL1X, TFDP1, THAP6, TIMM10B, TMEM108, TMEM159, TMEM63B, TNFRSF10A, TOLLIP, TPGS2, TPP2, TRAF2, TRIM35, TRPV2, TSPAN33, TYW3, USP14, USP38, UTP18, UTY, UVSSA, VCAM1, VPS72, WDR17, WDR47, WLS, Attorney Docket No.00138-015WO1 XPNPEP3, ZBTB11, ZNF124, ZNF512B, ZNF546, ZNF639, ZNF687, ZNF740, ZNF765, and ZZZ3 [Flavivirus v. ‘rest’]; (xiii) AAR2, ACAA1, ACP2, ADAMTS2, AGPAT5, AKT2, ANKLE2, ANKRD54, ANO5, APBA3, APOL4, APOLD1, ARHGAP24, ARSD, BAHD1, BCL7C, BDH1, BLNK, C10orf88, C12orf43, C2orf16, CASS4, CCDC170, CD101, CD274, CD7, CDC14B, CEACAM8, CENPC, CEP162, CFH, CHMP6, CLEC4M, CLK4, CLSTN1, COL5A1, COPS8, CRIPT, CS, CSF2RA, CSRNP2, CXCL11, CYB561, DAAM2, DCX, DDX20, DHRS7B, DIRC2, DMPK, EEFSEC, EGR3, EHD1, EHD3, EIF2B4, EPHX1, EPM2AIP1, ERO1B, FAM111B, FBP1, FPR3, G0S2, GALNT11, GATC, GBE1, GNPNAT1, GTF3C3, HCAR3, HERC6, HS6ST1, ICA1, IL12RB2, IL1R2, IQSEC2, KCNT2, KDM5D, KIAA1324, KLHL12, KPNA2, LAS1L, LCMT1, LGALS12, LRRCC1, LRSAM1, LTBP2, LZTFL1, MAP3K7CL, MCUR1, MEI1, MERTK, MFSD11, MGAT4B, MMAB, MRPS10, MRPS21, MTMR9, MUSK, MYBBP1A, MYO19, NATD1, NCKAP1, NCKIPSD, NPHP4, NRF1, NT5C3A, NUGGC, NUP43, OSGEP, P2RY14, PDPR, PEF1, PHGDH, PIM3, PISD, PLA2G12A, PLXNB2, PMS2, PNKP, POLD2, POU2AF1, PRICKLE3, PTGDS, PTPN13, R3HCC1L, RABGGTA, RABL2B, RAD17, RBFOX2, RFT1, RIC8B, RILPL2, RNF146, RNF5, ROCK2, RPRD1A, RUNX3, SCIN, SCRN3, 3-Sep, SHB, SHPK, SIAE, SLC16A7, SLC25A38, SLC39A10, SLC44A1, SLC8B1, SMCR5, SMIM12, SNAPC5, SNRK, SPATA20, SPRYD3, SRSF2, STEAP2, STK38L, STX2, TANK, TBPL1, TESK2, TICAM1, TJP1, TLDC1, TLR9, TMEM110, TMEM63A, TMEM70, TMEM87B, TNFSF13, TRAP1, TREM1, TRMT2A, TSHZ3, TSPAN17, TTC33, UBALD1, UCK2, UGCG, UQCR11, USP42, UTP14A, VIMP, VNN1, ZAP70, ZBED6, ZBTB3, ZBTB41, ZC4H2, ZCCHC14, ZDHHC17, ZNF486, ZNF542P, ZNF544, ZNF548, ZNF619, ZNF692, ZNF708, and ZNF720 [dimorphic fungi v. ‘rest’]; (xiv) AHNAK, AKAP10, ALDH1L1, ALDH3A2, ANGEL1, ANKRD17, ANKRD50, AQP10, ARHGEF17, ARID5B, ASAH1, ASUN, ATF6B, ATF7, ATXN7L2, ATXN7L3, ATXN7L3B, B4GALT4, BAHCC1, BCAP31, BCL6, BIN1, BMPR2, BRIP1, C11orf63, C5orf30, CAMKK2, CAPN1, CASP9, CD74, CDR1, CLIC5, CNOT3, COASY, CPSF7, CRISPLD1, CTTNBP2, CXCR1, DARS, DAZAP2, DDX10, DENND3, DFNA5, DHX15, DNAH6, DNAJA1, DNAJB6, EIF4G3, FTL, FYN, GABRB3, GALC, GCN1, GLE1, GLUD1, GNB2L1, HLA-DRB1, HR, IGF2BP3, IL18RAP, INTS2, INTU, JUNB, KANSL1L, KCNC2, KCNG1, KCNU1, KHDRBS1, KLF11, KLHL11, KLHL2, LAMA5, LARP4, LCA5L, LIMK2, LRRC4C, MAN2B2, MAPK6, MMRN2, MMS19, MPP7, MYH16, NDOR1, NDUFA6, NLGN2, NPY2R, NSRP1, NXN, PABPC4, PARP3, PJA2, Attorney Docket No.00138-015WO1 PLAC8, PLCB1, PLEKHO1, PML, PNRC2, POP4, PPFIA2, PRDM2, PRDM7, PRDX1, PRELP, PSMA1, PSTK, PTGES3, PTPN21, PTPRO, R3HDM2, RAB7A, RC3H2, REV3L, RGL4, RIF1, RNF112, RNF170, ROR1, RPA2, RPE, RTN4IP1, SAMM50, SASH3, SCIN, SEC24B, SECISBP2L, SENP6, SERF2, SESN3, SETD1A, SH3YL1, SIRT3, SLC39A11, SMARCA2, SMTN, SP3, SPOP, SPTBN2, SREK1IP1, SRPK1, SS18L1, ST6GALNAC1, STXBP5, TAOK1, TARBP1, TBC1D26, TECPR1, TESPA1, TIMM50, TMEM108, TMEM180, TMEM2, TNKS1BP1, TOB2, TRAF3IP3, TRAF5, TRPC5, TSC22D1, TUT1, TXNIP, TYRO3, TYRP1, UBE2H, UBE2R2, UNKL, VARS, VASP, VCAM1, VIT, VPS28, VPS8, VWDE, WDR73, WRN, ZC3H13, ZCCHC24, ZFAND6, ZFP36L2, ZMIZ1, ZNF197, ZNF469, ZNF521, ZNF608, ZNF721, ZNF780B, ZNF79, ZNRF2, ZSCAN25 [afm v. ‘rest’]; (xv) ALOX15, ASNS, BYSL, CD1E, CD209, CDC14B, CYP24A1, F13A1, GIPR, GTF2E1, JCHAIN, KLHDC8B, PIGX, SEMA4B, UCK2, ZBED8, ZIC1, and ZNF706 [worm v. ‘rest’]; (xvi) CCDC126, CXCL8, CXCL9, ERICH3, G0S2, IL1R2, KCNJ2, TNFAIP6, and UBD [mtb v. ‘rest’]; (xvii) ABHD14B, AHCY, ATP13A3, CCL2, CCL20, CD3E, COL1A1, CXCL9, CYP1B1, EFCAB2, FAM219B, FBXO25, HLA-DQB1, HSD17B4, IDO1, IGLL5, IL2RB, IL32, ITGB8, KLHL42, KRIT1, LETM1, LETMD1, LGALS3, MERTK, METTL9, MID1IP1, MOSPD2, MXI1, PI3, S100A8, SIGLEC10, SMCR8, SOD2, SPP1, ST3GAL5, UMPS, WIPI1, and ZNF253 [bacteria typical v. ‘rest’]; (xviii) ABCC5, ADGRL1, AFF2, AP4S1, ARL5A, B4GALT4, BTBD11, CCDC170, CDCA7L, CHST6, CXCL9, DNPEP, EBI3, ERICH3, FAM206A, FH, H1F0, HPCAL1, IGLL5, ITGA8, KCNJ2, LZTS1, MEMO1, MUC17, NUP93, PDLIM1, PRCC, PRRX1, RIPK2, RPE, SDPR, SLC15A4, SNX16, SYPL1, TIFA, TMCC3, TMEM52B, TPD52, TPGS2, TRIM36, and TUSC2 [bacteria atypical v. ‘rest’]; (xix) ABHD5, CD209, CWC15, DHX34, FADS2, FAM122B, FERMT3, FES, GPR183, HLA-DQA1, IFI44, KCNK2, KLHDC8B, LRRC9, METTL10, MS4A4A, NSDHL, PLCXD1, PLTP, PPM1G, PWP1, RBCK1, SKAP1, TADA2B, UCK2, and WBSCR16 [parasitic v. ‘rest’]; (xx) ADCK3, BCKDHA, BTBD11, C2, CXCL9, EBNA1BP2, FH, HPCAL1, KCNJ2, LIG3, LMNB2, NR4A3, PDLIM1, POLB, PRCC, PSTPIP2, PTBP2, RIMS1, RIPK2, SFMBT1, SPARCL1, TAF1B, TIFA, TMCC3, TPGS2, TRIM27, VWA5B1, and ZNF76 [AINI v. bacterial atypical]; Attorney Docket No.00138-015WO1 (xxi) AHCY, ANKRD27, ATP2A3, CCL2, CD2, COBLL1, DNAH17, FAM219B, FBXO25, GALNT15, HSD17B4, IGLL5, KIAA1407, KIF3A, KRIT1, LETMD1, LILRA6, METTL9, MXI1, NLRP1, NOL8, NUCB1, PI3, PMP22, POLD4, POLL, PSTPIP2, RASAL3, RNF144B, RNPS1, S100A8, S100A9, SMCR8, TGFB3, TNFAIP2, and WIPI1 [AINI v. bacterial typical]; (xxii) ARHGAP25, AURKA, BCCIP, C2CD5, CCR7, CD209, CDYL2, CHEK2, CPM, CWC15, DDX19B, DHX34, FBF1, FZD3, GOLGA5, IDO1, IFI44, JCHAIN, KCNK2, KLC1, LRRC59, LRRC9, MAFB, METTL10, MRFAP1L1, MS4A4A, OLFML2B, POMP, PSTPIP2, PWP1, RBCK1, RIMS1, RNF146, RPF1, S100A8, SLAMF8, TNFRSF10B, TRNT1, TTC9C, TYW3, and ZFAT [AINI v. parasitic]; (xxiii) ATF7IP2, ATP13A3, BLZF1, C3orf58, CCL2, CD36, CEP70, CXCL9, EYA2, FH, GPNMB, H1F0, HGS, HSD17B4, IGLL5, ITGB8, KATNAL2, MCUR1, RANBP6, REXO4, SFXN1, SIRT1, STMN4, ZNF430, and ZNF92 [bacteria atypical v. typical]; (xxiv) AASDH, AMMECR1, ANTXR1, AP4S1, CCDC170, CDC14B, CFAP36, COG6, COL1A2, DHRS9, EBI3, ERICH3, FBXO22, FKBP3, FREM1, GMEB2, KCNJ2, NTRK3, NUP43, P2RY2, PADI3, PAN2, PFN2, PRRX1, RIPK2, RSAD1, SMIM3, SNX16, SOCS2, SOX4, SPN, SSB, TMEM50A, TMEM52B, TRDMT1, TXLNG, ZNF430, ZNF569, ZNF720, and ZNF805 [bacterial atypical v. fungal]; (xxv) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial atypical v. parasitic]; (xxvi) ABHD5, ADGRE1, BANK1, BCCIP, C16orf72, CD3E, COL1A1, CXCR1, CYP1B1, GATA3, GIN1, IDO1, IL32, IRAK2, JCHAIN, MOSPD2, NHS, PI3, POLR3D, PSPC1, PWP1, TIMP3, UMPS, ZGRF1, ZNF213, and ZNF407 [bacterial typical v. parasitic]; (xxvii) BLZF1, CHCHD3, CMTR1, COL1A1, CXCL1, CXCL8, DDX60, DNTTIP2, DUSP16, EDEM2, EDEM3, EFCAB2, EIF3F, FAM219B, IDO1, IL2RB, INAFM2, ITGB8, IWS1, LPAR6, MID1IP1, MXI1, NKG7, OTOF, PDE11A, PI3, PLTP, PPP3CC, PRDM4, RETSAT, SFXN1, SIGLEC10, SOD2, SPP1, TIMM10B, TNFSF10, and ZNF24 [bacterial typical v. viral]; (xxviii) A1CF, A2M, A2ML1, A4GALT, AAAS, AACS, AADACL4, AADAT, AAED1, AAGAB, AAMP, AAR2, AARS, AASDH, AASDHPPT, AATK, ABCA1, ABCA10, ABCA12, ABCA13, ABCA2, ABCA4, ABCA5, ABCA7, ABCA8, ABCA9, ABCB1, ABCB10, ABCB11, ABCB6, ABCB7, ABCB8, ABCC1, ABCC11, ABCC12, Attorney Docket No.00138-015WO1 ABCC2, ABCC5, ABCD3, ABCD4, ABCF1, ABCF2, ABCG2, ABHD1, ABHD10, ABHD11, ABHD12B, ABHD14A, ABHD16A, ABHD17A, ABHD2, ABHD3, ABHD4, ABHD5, ABI2, ABL2, ABLIM3, ABR, ABT1, ABTB1, ACAA1, ACAA2, ACAD10, ACAD9, ACADL, ACADM, ACADS, ACAN, ACAP1, ACBD3, ACBD4, ACBD5, ACBD6, ACBD7, ACKR1, ACO1, ACOT11, ACOT13, ACOX1, ACOX2, ACOX3, ACPP, ACR, ACSBG1, ACSBG2, ACSL1, ACSL5, ACSL6, ACSS1, ACSS3, ACTG2, ACTL6A, ACTN1, ACTN4, ACTR1A, ACTR1B, ACTR8, ACVR1, ACVR1B, ACVRL1, ADAM15, ADAM20, ADAM29, ADAM30, ADAM33, ADAM9, ADAMDEC1, ADAMTS15, ADAMTS16, ADAMTS2, ADAMTS4, ADAMTS6, ADAMTS9, ADAMTSL4, ADAP2, ADAT2, ADCK1, ADCY3, ADCY9, ADD2, ADD3, ADGB, ADGRA3, ADGRE1, ADGRE2, ADGRF5, ADGRG2, ADGRG4, ADGRG6, ADGRL2, ADGRL3, ADGRL4, ADH1B, ADI1, ADNP2, ADORA2A-AS1, ADPRM, ADRA1A, ADRA2A, AEBP2, AFF4, AFMID, AGBL5, AGFG2, AGL, AGPAT1, AGPAT5, AGPS, AGTPBP1, AHCTF1, AHCYL1, AHNAK2, AHSA2, AIDA, AIFM1, AK3, AKAP11, AKAP12, AKAP9, AKIRIN2, ALDH1A1, ALDH2, ALDH7A1, ALG1, ALG12, ALG9, ALKBH8, ALOX15, ALPK1, AMDHD1, AMIGO2, AMMECR1L, AMPD2, AMPD3, ANAPC1, ANAPC13, ANAPC4, ANKFY1, ANKIB1, ANKMY2, ANKRD13D, ANKRD20A5P, ANKRD28, ANKRD36C, ANKRD42, ANKRD62, ANLN, ANTXR1, AP3M1, AP5Z1, APOBEC3G, APOBR, APOD, APOPT1, APPL1, AQP4, ARFGAP3, ARHGEF37, ARID3A, ARMC6, ARNT2, ARV1, ATF6B, ATG16L1, ATG9B, ATOX1, ATP12A, ATP13A2, ATP1B2, ATP2B2, ATPAF1, BAP1, BATF2, BAX, BCAP29, BMPR2, BRMS1, BRPF1, BTBD18, BTF3L4, BUB1, BUD13, C12orf65, C16orf62, C16orf71, C17orf51, C1orf27, C2CD5, C3orf38, C5, C5orf63, C6orf132, C8orf33, C8orf49, CABLES1, CAD, CAMK4, CANT1, CASK, CASP7, CBX7, CCDC149, CCSAP, CD24, CD244, CDCA3, CDKL1, CECR6, CELSR1, CHN2, CLCN3, CLUAP1, CLUH, CMTR2, CNOT8, COMMD9, COPG2, CSRP2BP, DAAM2, DBNL, DCLRE1A, DDX46, DNAAF5, DNAH1, DOK4, EIF2AK3, EIF2B1, ELMOD3, EMC4, EML3, EPN2, FAF2, FAM160B2, FAM35A, FAM69A, FZD3, GFM1, GLIS3, GPR137B, GRK5, HMBOX1, HNRNPA1L2, HRH1, INSIG2, KIAA0319L, LAMP3, LIG1, LRIG2, NFATC2IP, OAZ2, OGG1, PAQR8, PARL, PCGF3, PCMTD2, PLAUR, PRPF19, PTPN7, RAD1, RBCK1, RBPMS, RFX1, RPS4Y1, SCAF1, SH3PXD2B, SNTA1, STRADA, STXBP4, TAF5L, TBRG4, TOM1L2, ZNF397, ZNF597, ZNF71, ZNF721, and ZSWIM6 [fungal v. parasitic]; (xxix) ANAPC4, APLP1, BLZF1, CLPX, CRYL1, DESI2, FADS2, FAM122B, FBN3, FES, GRWD1, HERC5, HEXA, HLA-DQA1, IFIT1, KLHDC8B, MTURN, MYO1D, Attorney Docket No.00138-015WO1 NSDHL, PLCXD1, PLTP, PWP1, RAB11FIP4, SKAP1, SLC35D2, SPOCK1, SPP1, TADA2B, TLR7, TMTC3, UCK2, ZNF213, ZNF407 [parasitic v. viral]; and (xxx) ADGRA2, AFF2, ATL2, CCDC170, CDKL3, DHX34, FCGR3B, FES, ICAM1, KCNJ10, LIG3, MBOAT2, NT5DC3, RBCK1, RIPK2, SFMBT1, SLC37A2, TMCC3, TUSC2, ZNF407, ZNF92, and ZRANB2 [bacterial both v. parasitic]. 27. The method of claim 26, wherein the one or more RNA gene biomarkers are selected from group (i)-(iv) and comprise at least one or more from each group: (i) UBR4, RHDBF2, S100A9, PSTPIP2 and/or ALS2CR12/Casp8 [AINI v. 'rest']; (ii) PI3, NELFCD, MERTk, WDR93, and/or RIPK2 [Bacterial v. 'rest']; (iii) CXCL8, NT5C3A, TRMT1, SSPN, and/or SOD1 [Fungal v. 'rest']; and/or (iv) IFI44L, IFIT1, IRPS3A, CXCL8 and/or PRDM10[Viral v. 'rest'].
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