Index. Bag-1, 508, 509 Bayesian modeling, 4 Bax, 48, 307, 405 β-catenin, 508, 532, 533

Index Activating transcription factor 3 (ATF3), 508 Acute encephalomyelitis, 602 Acute viral infection, 60, 433 ADAR, 10, 286, 447, 448, 454, 657 Aggresomes, 227 Alb-urokinase plasminogen activator, 482 Alphavirus, 601 606, 611, 617, 618, 620 Alveolar fluid, 134 Alveolar macrophages, 135, 136, 162, 165, 176, 189, 309, 377 Akt, 119, 120, 124, 125, 277, 321, 333 337, 509, 540, 632, 633, 644 Anaphylatoxin complement fragments, 233 Anosmia, 232 Antigenic drift, 133, 146, 582 Antigenic-presenting cells, 404 Antigenic shift, 133 Antisense, 91, 94, 330 Antiviral immunity, 131, 132, 177, 178, 215, 218, 223, 419, 504 Apaf-1, 47, 639 Apolipoprotein E and B (Apo E; Apo B), 480, 482 Apoptosis inducing factor (AIF), 47, 638 640 Astrocyte response, 612 Atelectasis, 159 Atg5, 219 222, 531, 532 Atg8, 219, 531, 532 Atg12, 219, 221, 222, 531, 532 ATF-2/c-Jun, 116, 350 Autocrine or paracrine type I IFN signaling, 140 Autophagosomes, 219, 222, 223, 532 Autophagy, 209, 211, 218 223, 531, 532, 535 Autophagy-related genes, 218 Bag-1, 508, 509 Bayesian modeling, 4 Bax, 48, 307, 405 β-catenin, 508, 532, 533 Bcl-2, 35, 36, 405, 507, 509, 527, 609, 610, 640, 644 Bcl-family proteins, 507, 609 Bcl-xL, 337, 527, 644 679

680 Index BH3 (Bcl-2 homologous domain 3), 509 Bid, 405, 513, 639, 640 Bidirectional spread, 417 Biomarkers, 4, 5, 12, 20, 21 Blood-brain barrier, 214, 232, 415, 417, 603 Bronchiolitis, 157 159, 177, 185, 186, 188, 194, 195, 296 Bronchus associate lymphoid tissue (BALT), 142 Bunyaviridae, 248, 257, 263 Bystander injury, 611, 613 Bystander killing, 71 camp, 35, 37, 325, 328, 329 Cannabinoids, 235, 236 Caspase-3, 36, 37, 47, 327, 332, 333, 405, 514, 540, 639, 640, 643 Caspase-7, 332 Caspase-8, 36, 47, 48, 405, 638 641 Caspase-9, 47, 48, 335, 405, 639, 640 Caspase-10, 36 Caspase-recruiting domains (CARDs), 348 Cathepsin L, 304, 632 CCL2, 13, 37, 38, 194, 195, 428, 558, 561 CCL3, 38, 194, 195, 427, 428 CCL5, 13, 38, 166, 190 195, 203, 400, 427, 428, 561 CCL8, 554, 559, 560 Cell-mediated immune response, 71, 76 Cell surface marker, 38, 145 Cell surface receptors, 210, 476, 629 Cellular tropism, 401, 606 c-flip, 36, 554, 560 Chemokine receptor, 12, 68, 175, 398, 402, 404, 415, 427, 477 CCR5, 9, 11, 13, 34, 60, 61, 65, 67, 74, 194, 398, 400, 404, 415, 427, 428, 433, 477 CCR5-32 deletion, 65 CXCR3, 22, 402, 415, 427, 501 CXCR4, 9, 11, 34, 60, 65 Childhood morbidity, 159 Cholesterol trafficking, 38 Chronic hepatitis, 471, 473, 474, 486 489 Cilia, 134 Cirrhosis carcinoma, 446, 471, 473, 474, 485 Clades, 417 Classical pathway, 169, 480, 559 Coagulation disorders, 371, 380, 382 Collectin, 135, 136, 210 Complement system, 428 430, 480, 549, 550, 559 Congenital heart disease (CHD), 157, 160, 161 Connective tissue growth factor (CTGF), 510 COPD, 186, 187, 201 203 Conventional DCs (cdcs), 132, 133, 139 141 Coronavirus, 18, 219, 295 303, 321, 322, 531, 532. See also SARS-CoV Coxsackie and adenovirus receptor (CAR), 498, 499, 506, 526, 538

Index 681 Coxsackievirus B (CVB), 496, 498, 499, 502 508, 512, 513, 515, 516, 525, 526, 541 CVB3, 495 510, 512 515, 526, 527, 530, 532 536, 538 541 CVB4, 496, 498, 503, 505, 511 3A protein, 311, 312 2B protein, 514, 515 VP1 capsid protein, 497, 499, 526, 577 CpG motif, 211, 213 CTL response, 62, 73, 403 CXCL1, 194, 558, 561 CXCL8, 38, 190, 192, 194, 195, 501 CXCL9, 427, 501 CXCL10/IP10, 22, 38, 166, 190 194, 402, 403, 415, 423, 425, 427, 428, 501 503, 509, 554 Cyclooxygenase, 235, 333 Cyr 61, 508, 510 Cytochrome c, 47, 336, 405, 638 640, 643 Cytochrome c oxidase (COX5B/COX6B), 405 Cytokine and receptor IL-1α, 500, 504 IL-1β, 34, 43, 176, 178, 351, 377, 500, 506, 511, 512, 559, 616, 618 IL-1 receptor A (IL-1RA), 212, 377, 618, 620 IL-1 receptor associated kinase (IRAK), 212 IL-4, 48, 144, 200, 272, 275, 277, 459, 479, 500 IL-6, 34, 43, 44, 49, 62, 169, 176, 178, 283, 284, 309, 325, 330, 352, 377, 421, 425, 500, 501, 511, 557, 558, 560, 563, 583 IL-8, 34, 49, 136, 161, 166, 169, 176, 305, 309, 311, 333, 479, 501, 511, 539, 540, 557, 561 IL-10, 13, 35, 39, 43, 48, 49, 176, 178, 275, 277, 283, 330, 377, 457 459, 500, 501, 505, 583 IL-12, 13, 35, 39, 43, 48, 49, 176, 178, 275, 277, 283, 330, 377, 456 459, 500, 501, 505, 583 IL-12 Rβ1, 500 IL-13, 166, 186, 194, 200 203, 511 IL-18, 43, 235, 500 Cytokine regulation, 34, 193, 272 Cytopathic effect (CPE), 295, 304, 313, 326, 327, 332, 404, 508, 527, 533, 539, 590 Cytoskeleton, 36, 310 312, 485, 533, 557, 629 DAP5/p97/NAT1, 513 Decay accelerating factor (DAF), 498, 499, 526, 538, 540 Decoy death receptor DcR1/2, 640 Defensins, 131, 133, 135, 136, 188

682 Index Dengue virus, 306, 309, 547 550, 552 554, 556 559, 561 564, 566 Dicer, 10, 85 87, 89 96, 232 DNA binding domain, 420, 666, 667 DNA fragmentation, 327, 333, 335 Dominant negative, 122, 123, 168, 305, 330, 362, 422, 540, 640, 642 3-D organoid model of human, 590 Drosha, 85, 86, 89, 90, 92 Double-layered particles (DLP), 658 dsrna-dependent protein kinase (PKR), 22, 91, 112, 117, 118, 139, 193, 210, 219, 220, 236, 256, 286, 325, 349, 352, 355 357, 402, 421 423, 435, 447, 448, 480, 503, 554, 636, 656, 657, 672 Eastern equine encephalitis virus (EEV), 602 EBNA1, 222 Ebola virus (EBOV), 94, 345 354, 356 359, 361 363, 371 373, 375, 377 380, 382 385, 657 Ectodomain, 146, 215 Endocytosis, 33, 40, 41, 113, 114, 322, 393, 424, 473, 539, 629, 630, 635 Endoplasmic reticulum (ER), 42, 173, 277, 301, 311, 326, 393, 504, 514, 515, 660 Endosomes, 113, 190, 191, 209, 212, 214, 222, 629, 656 Eicosinoids, 234, 235 eif4gi, 504, 513 eif4gii, 513 Encephalomyocarditis virus, 221 Endothelial damage, 403, 547, 552, 553 Engulfed cargo, 218 Envelope glycoproteins, 450, 472, 473, 476, 477, 615 Epidermal growth factors (EGFR), 631, 633 Epithelial apoptosis, 160 Epizootic, 229 Epstein Barr virus (EBV), 87, 95, 222, 223, 457 E1-ubiquitin-activating enzyme, 528, 529, 670 E2-ubiquitin-conjugated enzyme, 528, 529, 671 E3-ubiquitin ligases, 670 Execution, 91, 219 Extra cellular signal regulated kinase 1 and 2 (ERK 1/2), 284, 328 Ex vivo model, 553, 590 Fas, 36, 40, 42, 43, 61, 143, 217, 220, 278, 306, 415, 433, 507, 554, 616, 638, 640 Fas apoptotic inhibitory molecule (FAIM), 306 Fas-associated death domain (FADD), 217, 220, 554, 560, 561, 638, 640 Filoviruses, 345, 346, 350, 353, 356, 363, 372, 375, 377, 379, 381, 383, 385 Flaccid paralysis, 392, 418

Index 683 Flaviviridae, 217, 391, 416, 445, 471, 472, 549 Focal adhesion kinase (FAK), 509 Formalin inactivated vaccine, 177, 204 Fulminant hemorrhagic disease, 371 Gamma delta T cells (γδ T cells), 198 Gastroenteritis, 575, 576, 579 584, 590, 591, 593, 594, 658 Gene expression omnibus (GEO) database, 3 Glial cell response, 611 Glycogen synthase kinase 3β (GSK 3β ), 333, 335, 336, 508, 633 Glycosylation, 71, 133, 215, 302, 394 Guanosine nucleotide analogue (loxoribine), 214 H539E, 215 Hantaviruses, 247 260, 262 264 G1 cytoplasmic tail, 258 260 pulmonary syndrome, 247, 249, 250 structure and genome, 248 Heat shock proteins, 295, 308, 537 Helper-T cell, 427 Hemagglutinin protein, 216 Hemorrhagic fevers (VHFs), 375 Hemorrhagic fever with renal syndromes (HFRS), 247, 249 251, 253, 255 Hepatitis C virus (HCV), 91, 94, 239, 261, 296, 227, 325, 445 462, 471 489, 657 HCV-like particles, 450, 476 Hepatocellular carcinoma (HCC), 445, 446, 471, 473, 474, 485 Herpes viruses, 88, 477, 532 Heterosubtypic immunity, 131, 146, 147 High-affinity immunoglobulin G Fc receptor, 476 High-density lipoprotein (HDL), 450 Highly active antiretroviral therapy (HAART), 36 HIV-1, 3, 4, 6 11, 15, 18, 21 23, 34, 38, 40, 42, 43, 45, 65, 66, 69 72, 83, 84, 89 96, 326, 356, 530, 537, 538, 540 gp120, 48, 70, 71, 76, 84, 326, 477 Nef, 31, 32, 38 43, 49, 74, 84, 89, 90, 92, 94 specific cellular immunity, 31 Tat, 9, 31 38, 42, 48, 49, 84, 90, 93 96, 356, 530 Virulence, 64, 66, 231, 273, 361, 362, 393, 394, 398, 401, 402, 420, 423, 426, 435, 498, 548, 582, 605, 607, 671 Host cell signaling pathway, 31, 349 Host immune responses, 59, 60, 64, 66, 253, 273, 275, 280, 407, 416, 424, 427, 434, 436, 445, 481, 577, 614 Host pathogen interaction, 296, 311 Host signature, 3, 4, 24 Human alpha defensin 1 (HNP-1), 136

684 Index Human beta defensin 1 (HBD1), 136 Human histo-blood group antigens (HBGAs), 577, 584 587, 591 Human leukocyte antigen (HLA), 13, 41, 42, 65, 67, 68, 73, 74, 404, 406, 407, 445, 449, 453 455, 460, 461, 484, 505, 506 Humoral immune response, 62, 69, 303, 371, 382, 449, 450, 484 Hyperinflation, 159 Hypermutation, 23, 286 Hypervariable region 1 (HVR-1), 450 ICAM1, 558 IFIT1, 563 IFITM1, 512, 563 IFN-α/β, 21, 22, 480 IFN-γ, 13, 22, 34, 65, 68, 71, 74, 75, 137, 144, 147, 234 236, 277, 282, 287, 309, 377, 400 402, 404, 419, 420, 423, 433, 435, 451, 453, 455, 483 485, 500 506, 511, 512, 565, 615, 616 IFN-β promoter stimulator (LPS-1), 217 IFN regulatory factors (IRFs), 22, 171, 172, 408, 420, 436, 671 IFN signaling pathway, 262, 281, 349, 427, 563, 655 657, 661, 666, 668 IFN-stimulated genes (ISGs), 117, 253, 255, 256, 258, 263, 406 408, 425, 426, 447, 448, 480, 481, 483, 485, 488, 502, 503, 507 IGTPase, 503 IκB-kinase β (IKKβ ), 121, 122, 170, 217, 641, 642 Immune antagonism, 132 Immunocompromise, 132, 231, 239, 392, 396, 579, 582, 645, 664 Immunodominant epitopes, 201 Immunotherapy, 617, 619 Indoleamine-pyrrole 2,3-dioxygenase (IDO), 404, 548, 551, 558, 564 566, 568 Inducible nitric oxide synthase (inos), 161, 504, 617 Inflammatory cytokines, 36, 43, 48, 62, 122, 132, 140, 143, 169, 176, 211, 212, 234, 273, 283, 302, 324, 347, 363, 378, 379, 396, 404, 422, 425, 433, 436, 501, 504, 505, 537, 539, 540, 552, 557, 563, 564 Inflammatory mediators, 160, 232, 233, 404, 612, 613 Influenza virus, 94, 109, 111, 115 125, 131 133, 135 149, 220, 326, 353, 355, 406 Inhibitor of apoptosis proteins (IAPs), 48, 634, 639 641 Inhibitory protein κb kinase (IKK) ε, 116, 118 121, 167, 169, 170, 213, 634, 641 Innate and adaptive immune responses, 59, 229, 269, 270, 313, 345, 415, 436, 614, 672 Innate antiviral immune response, 222, 476

Index 685 Innate cellular effectors, 137 Innate immune cells, 185, 186, 273, 379, 420, 446 Innate immune system, 89, 132, 133, 188, 209, 210, 223, 377, 428, 449 Interferon (IFN)-inducible protein, 210, 396 Intermediate subviral particles (ISVPs), 629, 630, 644 Internal ribosomal entry site (IRES), 497, 513 In vitro replicon systems, 590 IPS-1, 116, 118, 217, 222, 233, 253, 348, 354, 355, 448, 639, 643 IP10/CXCL-10, 501. See also chemokine IRAK1, 164, 564 IRAK4, 213, 564 ISRE, 172, 259, 260, 281, 282, 349, 350, 420, 423, 425, 426, 656, 657 JAK-STAT pathway, 22, 115, 174, 178, 656 Junctional adhesion molecules, 629 Jun-N-terminal kinase (JNK), 36, 37, 43, 44, 47, 123, 323, 324, 327, 333, 334, 337, 537, 540, 638, 639, 643, 644 Kruppel-like factor (KLF), 305 KSHV, 87, 88, 95, 657, 671 Kynureninase (KYNU), 558, 560, 566 La autoantigen, 499 LCMV, 75, 221, 282, 285, 286, 456, 458, 459, 657 Light chain 3 (LC3), 219, 531, 532 Lipoxygenase, 195, 235 Liver activation regulated chemokine (LARC), 478, 479 Long-term non-progressors (LTNPs), 64, 76 Low-density lipoprotein, 37, 480 Low molecular weight polypeptide-2 (LMP-2), 407, 484 Lysosome, 41, 213, 218, 220 222, 531, 535, 629 Macrophage derived chemokine (MDC), 501 Macrophage inflammatory protein-1 α (MIP-1α), 43, 48, 500 MAP kinase/erk kinase (MEK), 122, 123, 125, 331, 537 539, 632, 633, 635 Marburg virus (MARV), 345, 346, 371 373, 375, 378, 382 384 Matrix metalloproteinase (MMP), 34, 310, 510 Matrix protein 1 (MP1), 222 mbnip 21, 508 MCP-1, 13, 22, 37, 501, 511 MCP-2, 501, 559, 563 MCP-3, 13, 501 MCP-5, 427, 428, 501 MEKK, 643 Melanoma differentiation associated gene-5 (MDA-5), 116, 138, 166,

686 Index 193, 348, 354, 422, 425, 448, 559 MHC-related polypeptide, 484 Microarray, 20, 21, 96, 255, 258, 295, 304, 352, 357, 391, 392, 398, 405, 407, 408, 420, 430, 471, 474, 478, 481, 482, 485, 489, 495, 496, 500, 501, 509, 510, 515, 516, 553, 580 Microautophagy, 218 Microglia responses, 38, 612, 617 MicroRNA (mirna), 10, 83, 85 98, 232, 516 Mimic poly I:C, 215 Mitochondria antiviral signaling (MAVS), 141, 167, 169, 217, 253, 348, 448 Mitochondria outer membrane permeabilization (MOMP), 405 Mitogen-activated protein (MAP), 35, 123, 212, 284, 305, 321, 323, 325, 345, 362, 363, 513, 534, 536, 537, 636 Mitogen-activated protein kinase (MAPK), 35, 37, 40, 44, 46, 47, 111, 122, 123, 284, 305, 306, 321, 323 333, 337, 338, 534, 536, 537, 540, 564, 636 mrna metabolism, 15, 16 Measles virus (MV), 211, 216, 269, 270, 272 MV-induced immunosuppression, 275, 286, 287 Myeloid dendritic cells, 296, 233 Myeloid differentiation factor (MyD 88), 212, 506 Myxovirus resistance-1 (Mx1), 22, 119, 132, 139, 309, 349, 399, 406, 554 Mx2, 406, 554 MxA proteins, 256, 257, 349 Mx GTPase, 503, 504, 657 Native immunity, 252 Nature killer cells, 66, 131, 160, 197, 233, 379, 446, 501 Necrosis factor 1, 632 Neurodegeneration, 405, 612, 617 Neurokinin-1, 274 Neurotoxicity, 33, 36, 37, 48, 49 Neurovirulence, 219, 239, 391, 532, 602, 604, 608, 609 Neutralizing antibodies, 5, 63, 70, 145 147, 238, 248, 253, 383, 407, 427, 431, 432, 449 451, 457 Neutrophils, 135, 136, 233, 236, 238, 371, 404 NF-κB, 6, 7, 121, 165, 168, 170, 171, 306, 333, 337, 363, 425, 509, 633, 636, 643 NIK and IKK α, 170, 171 Nitric Oxide Synthase-1 (NOS-1), 234 236 NKG2D, 67, 137, 478 NKp44, 137 NKp46, 137 Norovirus, 575 594 virus-like particles (VLPs), 301, 363, 379, 385, 402, 577, 580, 583 585, 587

Index 687 Nucleotide-binding oligomerization domain (NOD) proteins, 210, 421 2,5 oligoadenylate synthetase (2-5 OAS), 447 OAS1, 554 OAS3, 554 OASL, 422, 554, 559 Oncolysis, 229, 230, 239, 627, 631, 635, 636, 646, 647 Orthomyxoviridae, 111 Osteopontin, 478, 479 Otitis media, 158, 159 OX40L, 196 P38 MAPK, 35, 40, 323 333, 337, 338, 537, 540 P53, 42, 43, 306 308, 502, 508, 509, 529, 530, 532, 533, 535 P90 ribosomal S6 kinase (RSK), 321, 329, 632, 644 PAMP, 262, 656 Paramyxoviridae, 157, 158, 217, 274 PARP, 513, 640 Passive antibody therapy, 186, 199 Pathogen associated molecular patterns (PAMPs), 138, 189, 204, 209 211, 233, 348, 421, 656 Pattern recognition receptors (PRRs), 133, 137, 157, 161, 163, 167, 168, 172, 185, 186, 189, 191, 209 212, 221, 223, 252, 253, 262, 274, 348, 421, 423, 425 PD-1 (programmed cell death 1), 75, 399, 456, 458, 459, 551 Pegylated interferon-alpha, 446 Perforin, 74, 75, 143, 197, 201, 287, 396, 417, 433 435, 507, 616 Perforin-Fas-mediated cytolytic mechanisms, 433 Peripheral blood mononuclear cells (PBMCs), 15, 18, 34, 192, 352, 458, 477, 487, 488 Perivascular, 160, 185, 186, 234, 603 Phagocytosis, 39, 136, 176, 210, 211, 613 Phosphatidylethanolamine, 219, 531 Phosphatidylinositide-dependent kinase 1 (PDK1), 329 Phosphatidylinositol-3-kinase (PI3K), 41 43, 45, 119, 120, 124, 125, 219, 277, 305, 333 336, 509, 515, 540, 632, 633, 644 PI3K/Akt, 119, 124, 125, 333, 334, 336, 509, 540, 632, 633, 644. See also Akt Picornaviridae, 217, 219, 496 Plasmacytoid, 116, 133, 165, 178, 190, 191, 196, 209, 211, 220, 233, 236, 283, 348, 352, 657, 668 Poly-A binding protein (PABP), 499, 513, 514 Polypyrimidine-tract binding protein (PTP), 499 Predictive gene set, 14, 19, 20 Primary infection and secondary infection, 5, 60 63, 66, 69, 144, 145, 147, 148, 198, 200 202, 285, 429, 549, 564, 565 Prophylaxis, 303, 383, 385

688 Index Protease 2A, 497, 513 Protease 3C, 497, 513 Proteasomal degradation, 258, 261, 655, 657, 670 Proteasome inhibitor, 530, 532, 534, 535, 642, 670 Proteasomes, 535, 666, 668, 670 Protein degradation, 118, 399, 525, 527 529, 532 534, 536 Protein kinase B (PKB), 335, 633 Protein modification, 38, 525, 530, 531, 534, 536 Protein ubiquitination and degradation, 247 Pseudo-particles, 474 PtdIns (3, 4, 5) P3, 335, 633 PtdIns (4, 5) P2, 633 Quasispecies, 394, 450, 460, 484 Raf/MEK/ERK, 122, 123, 125, 537, 632, 633 RANTES, 13, 37, 48, 65, 177, 357, 423, 425, 427, 511, 557 Ras signaling, 627, 630 632, 635, 644, 645, 647 Ras/Ral GEFs pathways, 634 Rhesus rotavirus (RRV), 661, 665, 668 Receptor DR4 and DR5, 562 Receptor interacting protein 1 (RIP1), 217, 554, 634 Recombinant norovirus, 577, 580, 584. See also norovirus Recombinant virus, 173, 605 Reovirus, 211, 215, 221, 627 632, 634 647, 663 Respiratory syncytial virus (RSV), 157 162, 164 166, 168, 170, 172 179, 185 195, 197 204, 211, 216, 221, 576, 580 asthma, 159, 185 187, 195, 201 204, 564 fusion protein, 211, 276, 362, 564 vaccination, 110, 149, 158, 187, 200, 204, 240, 384, 446, 604 Reticuloendothelial system, 232 Retinoid acid inducible gene-like receptor (RLR), 137, 138 Retrocyclin, 136 Retroviruses, 6, 10, 32, 87, 88, 91, 93, 111, 530 Rhabdoviridae, 217 Rho/Rac pathways, 634 Ribavirin, 188, 382, 446, 471, 474, 486 488 Ribonucleoprotein complex, 112 RNA-dependent RNA polymerase (RDRP), 248, 298, 353, 393, 394, 459, 526, 577, 578, 629, 630, 658 RNA helicases, 116, 138, 157, 161, 163, 166, 167, 209, 216, 217, 233, 253, 348, 354, 447, 448, 559, 656 RNAi suppressors, 88, 89 RNase L, 118, 236, 256, 396, 398, 402, 408, 422, 435, 503, 559, 657 RNA-specific adenosine deaminase 1 (ADAR 1), 447, 448 Rotavirus, 655, 658 672 RSAD2, 554

Index 689 SAPK/JNK, 638, 643 Sarcoma (src) family of kinases (p56 lck ), 506 SARS Coronavirus, 18, 297 299, 302, 303, 321 Scavenger receptor BI (SR-BI), 472 Sendai virus, 204, 214, 220, 260, 261, 354 Sialic-acid (neuraminic acid), 113 Signal transducer and activator of transcription 4 (STAT 4), 502 STAT1, 22, 69, 173, 174, 201, 236, 261, 270, 280 282, 332, 349 351, 358 361, 377, 399, 400, 406, 407, 426, 563 STAT2, 175, 270, 280, 281, 349, 350, 359, 360, 406, 426 Sindbis virus (SV), 601, 605, 608, 611, 614, 617 Single nucleotide polymorphism (SNP), 12, 13, 65, 397, 398, 422 Single-stranded RNA (ssrna), 107, 111, 116, 118, 138, 163, 190, 214, 220, 293, 416, 526, 549, 663 Siva, 508 Smac, 638 640, 643 Small interferon RNAs (sirna), 83, 85, 86, 88 92, 94, 95, 122, 168, 192, 193, 217, 257, 303, 309, 313, 358, 362, 533, 535, 559, 664 Spermidine/spermie N1-acetyltranferase (SAT), 405 Src, 39, 259, 537, 538 Stem cells, 232, 234, 280 Stress activated c-jun-n-terminal kinase (SAPK/JNK), 638, 643 Subacute sclerosing panencephalitis (SSPE), 269 271, 285, 286 Surfactant protein A (SP-A), 135, 136, 189 Surfactant protein D (SP-D), 135, 136, 311 Tank binding kinase (TBK1), 165, 167, 218, 247, 259 262, 264, 447, 634 TAR binding proteins (TRBP), 86, 91, 95, 96 Target of rapamycin (TOR), 219 T cell activation, 40, 196, 275, 278, 280, 284, 395, 456 T cell receptors (TCR), 39, 40, 43, 144, 198, 237, 259, 277, 432, 461 TFPI, 558 Th1 cytokine, 43, 192, 194, 272, 277, 503 Th2 cytokine, 43, 186, 192, 194, 200, 203, 272, 277 Tissue inhibitors of MMPs (TIMPs), 510 Tissue tropism, 395, 401, 498, 499, 502, 548 Toll-like receptors (TLRs), 21, 22, 116, 137, 138, 163, 164, 166, 168, 178, 186, 190, 193, 196,

690 Index 197, 209, 211 213, 216, 223, 233, 252, 262, 283, 348, 403, 421, 422, 656 TNF receptor-associated factor (TRAF), 169, 212, 217, 405, 506 TRAF-1, 47, 405 TRAF-2, 47, 217 TRAF-6, 164, 212, 213, 217, 506, 564 TNF-related apoptosis-inducing ligand (TRAIL), 36, 122, 220, 379, 478, 547, 551, 554, 556, 561 563, 566, 638, 640 642 Toll-receptor-domain-containing adaptor inducing IFN-β (TRIF), 22, 141, 164, 165, 191, 192, 212, 213, 217, 447 Transcriptomics, 303 Transforming growth factor-β (TGF-β ), 87, 88, 324, 457, 500, 502, 507, 510 Translational machinery, 308, 514, 590 TRIM22, 22, 554 Tumor necrosis factor superfamily (TNFSF14), 405 Two-phase model of secretion of type I IFN, 172 Tyrosine kinase 2 (Tyk2), 173, 330, 350, 394, 425, 426 Ubiquitination, 170, 247, 259, 261, 262, 264, 307, 528 531, 533, 534, 536, 641, 642, 655, 670, 672 Ubiquitin-like molecules, 118 Ubiquitin-proteasome system, 525, 527, 529 Ubiquitin-protein ligase, 528, 529, 655, 671 UDP-glucose ceramide glucosyltransferase (UGCG), 482, 560 3 -Untranslated regions (3 UTRs), 10, 85, 472, 497, 499 5 UTR, 91, 497, 499 Vaccination, 110, 149, 158, 187, 200, 204, 240, 384, 446, 604 VCAM1, 558 VEGF receptor, 33 Venezuelan equine encephalitis virus (VEEV), 384, 602 604, 606, 619 Vesicles, 41, 113, 210, 212, 218, 233, 302, 550 Vesicular stomatitis virus (VSV), 209, 214, 229, 286, 384, 477, 663 Very low density lipoprotein, 483 Viral encephalitis, 232, 239, 609 Viral escape, 455, 459 462, 475 Viral nucleocapsid, 309, 357, 393, 472, 478, 479 Virion infectivity, 38, 637 Virulence, 64, 66, 231, 273, 361, 362, 393, 394, 398, 401, 402, 420, 423, 426, 435, 498, 548, 582, 605, 607, 671 Virus Hemagglutinin (HA), 112 115, 121, 123, 145 147, 137, 146, 271, 272, 276 278, 284

Index 691 Virus host interactions, 124, 471, 472, 476, 477, 485, 489, 606, 647 Virus-induced signaling adaptor (VISA), 217, 253, 348, 448 Virus-like particles (VLPs), 301, 363, 379, 385, 402, 577, 580, 583 585, 587 VP1, 497 499, 526, 577, 578, 590, 658, 660 VP2, 497, 508, 577, 578, 658 VP24, 345, 350, 353, 357 362, 377 VP35, 345, 350, 353 358, 361, 657 VP40, 357, 363 VPg, 497, 577, 578, 589, 590 VPg-poly(U), 589 VSV encephalitis, 232 234, 238 Western equine encephalitis virus (WEEV), 602 604, 619 West Nile virus (WNV), 214, 391 409, 415 437, 433, 550, 556, 559, 618