A3SS, alternative 3' splice site; A5SS, alternative 5' splice site; ACACA, Acetyl-CoA Carboxylase Alpha; AKR1C2, Aldo-Keto Reductase Family 1 Member C2; ANKS1A, Ankyrin Repeat And Sterile Alpha Motif Domain Containing 1A; ANOS1, Anosmin 1; AOX1, Aldehyde Oxidase 1; APOBEC3G, Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3G; APOL1/6, Apolipoprotein L1/6; ARID2, AT-Rich Interaction Domain 2; AUTS2, Activator Of Transcription And Developmental Regulator AUTS2; Alternative splicing; Astrocytes; BCL11B, BAF Chromatin Remodeling Complex Subunit BCL11B; BCL9L, BCL9 Transcription Coactivator-like; BDKRB2, Bradykinin Receptor B2; BDNF, Brain Derived Neurotrophic Factor; BEND3, BEN Domain Containing 3; BSA, bovine serum albumin; BST2, Bone Marrow Stromal Cell Antigen 2; CALB1, Calbindin 1; CAMK2A, Calcium/Calmodulin Dependent Protein Kinase II Alpha; CD, complement determinant; CDKN1C, Cyclin Dependent Kinase Inhibitor 1C; CFAP61, Cilia And Flagella Associated Protein 61; CHRNA3, Cholinergic Receptor Nicotinic Alpha 3 Subunit; CHRNB4, Cholinergic Receptor Nicotinic Beta 4 Subunit; CLIC5, Chloride Intracellular Channel 5; CMPK2, Cytidine/Uridine Monophosphate Kinase 2; CNS, central nervous system; CNTN2, Contactin 2; CREG2, Cellular Repressor Of E1A Stimulated Genes 2; CXADR, Coxsackievirus B-Adenovirus Receptor; CYYR1, Cysteine And Tyrosine Rich 1; DACH1, Dachshund Family Transcription Factor 1; DAPI, diamidino-2-phenylindole; DCC, Netrin 1 Receptor; DCX, Doublecortin; DDX60, DExD/H-Box Helicase 60; DDX60L, DExD/H-Box 60 Like; DE, differentially expressed; DENV, Dengue virus; DIRAS2, DIRAS Family GTPase 2; DLX1/5/6, Distal-Less Homeobox 1/5/6; DNMT3B, DNA Methyltransferase 3 Beta; DPYSL2, Dihydropyrimidinase Like 2; EBF1, EBF Transcription Factor 1; EGF, Epidermal Growth Factor; ELAVL2/4, ELAV Like RNA Binding Protein 2/4; EPHB1, EPH Receptor B1; EPSTI1, Epithelial Stromal Interaction 1; ERBB4, Erb-B2 Receptor Tyrosine Kinase 4; ES, exon skipping; ESRRG, Estrogen Related Receptor Gamma; FGFb, Fibroblast Growth Factor 2; FPKM, Fragments Per Kilobase of transcript per Million mapped reads; FUT9, Fucosyltransferase 9; G2E3, G2/M−Phase Specific E3 Ubiquitin Protein Ligase; GABRG2, Gamma-Aminobutyric Acid Type A Receptor Subunit Gamma 2; GAPDH, Glyceraldehyde-3-Phosphate Dehydrogenase; GAS2L3, Growth Arrest Specific 2 Like 3; GAS7, Growth Arrest Specific 7; GATAD2B, GATA Zinc Finger Domain Containing 2B; GFAP, Glial Fibrillary Acidic Protein; GIPC2, GIPC PDZ Domain Containing Family Member 2; GLRA2, Glycine Receptor Alpha 2; GNG2, G Protein Subunit Gamma 2; GO, gene ontology; GOLGA4, Golgin A4; GRIN2A, Glutamate Ionotropic Receptor NMDA Type Subunit 2A; GSEA, gene set enrichment analysis; HERC5/6, HECT And RLD Domain Containing E3 Ubiquitin Protein Ligase 5/6; HEYL, Hes Related Family BHLH Transcription Factor With YRPW Motif Like; HPRT1, Hypoxanthine Phosphoribosyltransferase 1; HS, hot-spot; HSPA6, Heat Shock Protein Family A (Hsp70) Member 6; HUDD (ELAV4), Hu-Antigen D/ELAV Like Neuron-Specific RNA Binding Protein 4; IFI6, Interferon Alpha Inducible Protein 6; IFIH1 (MDA5), Interferon Induced With Helicase C Domain 1/Melanoma Differentiation-Associated Protein 5; IFIT1-3, Interferon Induced Protein With Tetratricopeptide Repeats 1­3; IFITM1/2, Interferon Induced Transmembrane Protein 1/2; IFN, interferon; IGB, Integrated Genome Browser; IL6, Interleukin 6; IR, intron retention; ISG20, Interferon Stimulated Exonuclease Gene 20; ISGF3, Interferon-Stimulated Gene Factor 3 Gamma; ISGs, interferon-stimulated genes; JEV, Japanese encephalitis virus; KCND2, Potassium Voltage-Gated Channel Subfamily D Member 2; KCNK10, Potassium Two Pore Domain Channel Subfamily K Member 10; KCNS2, Potassium Voltage-Gated Channel Modifier Subfamily S Member 2; KIT, KIT Proto-Oncogene, Receptor Tyrosine Kinase; KLHDC8A, Kelch Domain Containing 8A; KLHL13, Kelch Like Family Member 13; KRR1, KRR1 Small Subunit Processome Component Homolog; LCOR, Ligand Dependent Nuclear Receptor Corepressor; LEKR1, Leucine, Glutamate And Lysine Rich 1; LGI1, Leucine Rich Glioma Inactivated 1; LRRTM3, Leucine Rich Repeat Transmembrane Neuronal 3; LSV, local splicing variation; LUZP2, Leucine Zipper Protein 2; MAN1A1, Mannosidase Alpha Class 1A Member 1; MAP2, Microtubule Associated Protein 2; MBNL2, Muscleblind Like Splicing Regulator 2; MCTP1, Multiple C2 And Transmembrane Domain Containing 1; MMP13, Matrix Metallopeptidase 13; MN1, MN1 Proto-Oncogene, Transcriptional Regulator; MOI, multiplicity of infection; MTUS2, Microtubule Associated Scaffold Protein 2; MX2, MX Dynamin Like GTPase 2; MYCN, MYCN Proto-Oncogene, BHLH Transcription Factor; NAV1, Neuron Navigator 1; NCAM1, Neural Cell Adhesion Molecule 1; NDRG4, N-Myc Downstream-Regulated Gene 4 Protein; NEK7, NIMA Related Kinase 7; NFASC, Neurofascin; NKAIN1, Sodium/Potassium Transporting ATPase Interacting 1; NMI, N-Myc And STAT Interactor 2; NRAP, Nebulin Related Anchoring Protein; NRARP, NOTCH Regulated Ankyrin Repeat Protein; NREP, Neuronal Regeneration Related Protein; NRN1, Neuritin 1; NS3, flaviviral non-structural protein 3; NXPH2, Neurexophilin 2; NYNRIN, NYN Domain And Retroviral Integrase Containing; Neurons; Neuropathogenesis; OAS, 2'-5'-Oligoadenylate Synthetase; OASL, 2'-5'-Oligoadenylate Synthetase Like; ONECUT2, ONECUT-2 Homeodomain Transcription Factor; OPCML, Opioid Binding Protein/Cell Adhesion Molecule Like; OTX2, Orthodenticle Homeobox 2; PBS, phosphate buffer saline; PBX1, Pre-B-Cell Leukemia Transcription Factor 1; PCDH18/20, Protocadherin 18/20; PFKFB3, 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3; PIK3C2B, Phosphatidylinositol-4-Phosphate 3-Kinase Catalytic Subunit Type 2 Beta; PIP4P2, Phosphatidylinositol-4,5-Bisphosphate 4-Phosphatase 2; PLCH1, Phospholipase C Eta 1; POU3F4, Brain-Specific Homeobox/POU Domain Protein 4; PPM1L, Protein Phosphatase, Mg2+/Mn2+ Dependent 1L; PPP1R17, Protein Phosphatase 1 Regulatory Subunit 17; PRDM12, PR Domain Zinc Finger Protein 12; PSI, percent selective index; PSRC1, Proline And Serine Rich Coiled-Coil 1; PTPN5, Protein Tyrosine Phosphatase Non-Receptor Type 5; PTPRH, Protein Tyrosine Phosphatase Receptor Type H; RAPGEF5, Rap Guanine Nucleotide Exchange Factor 5; RBFOX1, RNA Binding Fox-1 Homolog 1; RIG-I (DDX58), Retinoic Acid-Inducible Gene 1 Protein; RNF212, Ring Finger Protein 212; RNVU1, RNA, Variant U1 Small Nuclear; RSAD2, Radical S-Adenosyl Methionine Domain Containing 2; RTL8B, Retrotransposon Gag Like 8B; Response to infection; SAMD9, Sterile Alpha Motif Domain Containing 9; SEMA3E, Semaphorin 3E; SH3TC2, SH3 Domain And Tetratricopeptide Repeats 2; SHF, Src Homology 2 Domain Containing F; SHISAL1, Shisa Like 1; SIAH3, Siah E3 Ubiquitin Protein Ligase Family Member 3; SIRPA, Signal Regulatory Protein Alpha; SLITRK5, SLIT And NTRK Like Family Member 5; SNP, single-nucleotide polymorphism; SOGA1, Suppressor Of Glucose, Autophagy Associated 1; SPSB4, SplA/Ryanodine Receptor Domain And SOCS Box Containing 4; ST6GAL1, ST6 Beta-Galactoside Alpha-2,6-Sialyltransferase 1; TBC1D30, TBC1 Domain Family Member 30; TBEV, Tick-borne encephalitis virus; TFAP2A, Transcription Factor AP-2 Alpha; TFAP2B, Transcription Factor AP-2 Beta; THSD7A, Thrombospondin Type 1 Domain Containing 7A; THUMPD2, THUMP Domain-Containing Protein 2/SAM-Dependent Methyltransferase; TIPARP, TCDD Inducible Poly(ADP-Ribose) Polymerase; TM4SF18, Transmembrane 4 L Six Family Member 18; TMC8, Transmembrane Channel Like 6; TMEM229B, Transmembrane Protein 229B; TMTC1, Transmembrane O-Mannosyltransferase Targeting Cadherins 1; TNFSF10, TNF Superfamily Member 10; TRHDE, Thyrotropin Releasing Hormone Degrading Enzyme; TRIM38, Tripartite Motif Containing 38; TSHZ1, Teashirt Zinc Finger Homeobox 1; Tick-borne encephalitis virus; Transcriptomics; USP18, Ubiquitin Specific Peptidase 18/ISG15-Specific-Processing Protease; UTR, untranslated region; UTS2R, Urotensin 2 Receptor; WNV, West Nile virus; XAF1, XIAP Associated Factor 1; XRN1, 5'-3' Exoribonuclease 1; ZIKV, Zika virus; ZMAT3, Zinc Finger Matrin-Type 3; ZMYM5, Zinc Finger MYM-Type Containing 5; ZNF124, Zinc Finger Protein 124; ZNF730, Zinc Finger Protein 730; gRNA, genomic TBEV RNA; hNSC, human neural stem cells; lncRNA, long non-coding RNA; mRNA, messenger RNA; miRNA; miRNA, micro RNA; ncRNA, non-coding RNA; pc-mRNA, protein-coding mRNA; qRT-PCR, quantitative reverse transcription real-time PCR; snRNP, small nuclear ribonucleoproteins; vd-sRNA, virus-derived small RNA