INDEX

A B

Adaptive immunity ...... 79 , 289 Bacillus anthracis ...... 439 , 451 , 669 , 680 Adenovirus ...... 10 , 12 , 335 Baculovirus ...... 211–213 , 365 , 368 , 438 Adjuvant ...... 6 , 7 , 10 , 15–17 , 40 , 43 , 47 , 125 , 128 , 129 , 131 , Baculovirus–insect cell system ...... 365 , 366 , 368 , 438 136 , 154 , 158–159 , 162 , 203 , 208 , 247 , 253 , 263 , BALB/c mice ...... 66 , 71 , 142 , 324–326 , 426 , 431 , 266 , 271 , 289–298 , 301 , 308 , 378 , 395 , 417 , 497 , 432 , 434 , 543 , 552 , 561 , 565 , 629 , 716 , 719 499 , 501 , 502 , 506 , 511 , 526 , 548 , 549 , 631 , 636 , Basic Local Alignment Search Tool (BLAST) ...... 182 , 184 , 638 , 645 , 683 , 684 , 697 , 698 , 700 , 715 , 716 , 719 , 187 , 227 , 237 , 430 , 472 , 743 775 , 781 , 796 , 820–824 , 826 , 828 , 831 B cells Aeromonad septicaemia ...... 203–208 epitope prediction ...... 53 Aeromonas sobria ...... 204–206 , 208 immunity ...... 761 Ag85B ...... 378 , 750 BepiPred ...... 53 , 54 Agrobacterium tumefaciens...... 551 , 556 , 581–595 , Betanodavirus ...... 211–222 597–599 , 601 , 603–605 , 610 , 611 BHK-21 cells...... 315 , 317 , 319–323 Allergy vaccine ...... 511 BioEdit sequence alignment editor ...... 53 Alphavirus ...... 313–326 Bioinformatics ...... 40 , 139 , 142 , 143 , 145 , 149 , 213 , Analytic vaccinology ...... 779 , 781 , 782 216–217 , 275 , 278 , 280 , 430 , 431 , 434 , 550 , Anaplasma phagocytophilum ...... 275 , 276 , 281–285 727–738 Animal model .... 123–132 , 167 , 313 , 314 , 434 , 530 , 657 , 671 , Biopanning ...... 423 , 427 708 , 742 , 777 , 778 BLAST . See Basic Local Alignment Search Tool (BLAST) Anthrax vaccine ...... 669 Bone marrow derived dendritic cells (BMDC) ...... 698 Anti-arthropod vaccine ...... 262 Borrelia burgdorferi ...... 6 Antibiotic abuse ...... 301 Botulinum neurotoxin (BoNTs) ...... 621 , 622 , 629 , 630 Antibiotic resistance ...... 48 , 193 , 366 , 369 , 530 , 583 Botulism ...... 621 , 622 Antibody epitope mapping ...... 134 Bovine tropical theileriosis...... 459 Antibody readouts ...... 79–80 Antigen ...... 6 , 7 , 9–15 , 19 , 20 , 24 , 40 , 51 , 52 , 55 , 56 , 59 , 60 C screening ...... 281–285 , 600 C57BL/6 mice ...... 157 , 325 , 354 , 359 , 360 , 502 , 506 , Antigen-specific T cells ...... 77–87 , 530 , 535 507 , 537 , 543 Anti-Hyalomma vaccine ...... 459 Cancer vaccine ...... 313 , 774 Anti-tick vaccine ...... 243–257 , 261 Candida albicans ...... 500–502 , 504–508 Antiviral DNA vaccines ...... 225–237 Candidiasis ...... 500–501 Antiviral drugs ...... 104 Carassius auratus langsdorfii ...... 194 Aquaculture ...... 181 , 203 , 211 , 225 , 226 Carbohydrate vaccine ...... 410 , 547 , 775 Arenavirus Cathepsin ...... 123 , 135–137 , 139–148 GP-expressing cells ...... 351 , 352 Cationic peptides ...... 290 , 291 , 294–297 rescue systems ...... 351 , 352 Cellular immunity ...... 149 , 162 , 167 , 170 reverse genetics ...... 352 , 362 Ceramic hydroxyapatite chromatography ...... 511 , 513–517 Attachment protein ...... 104 CFP10 gene ...... 380 , 381 , 387 , 390 Avian metapneumovirus ...... 103–120 Chagas disease ...... 683 , 684

Sunil Thomas (ed.), Vaccine Design: Methods and Protocols, Volume 2: Vaccines for Veterinary Diseases, Methods in Molecular Biology, vol. 1404, DOI 10.1007/978-1-4939-3389-1, © Springer Science+Business Media New York 2016 849 VACCINE DESIGN 850 Index Chicken ...... 6 , 7 , 9 , 11 , 14 , 22 , 77–86 , 89 , 103 , DsRed ...... 598 , 600 , 602 , 607 , 613 165–176 , 313 , 736 Dynamic light scattering (DLS) ...... 400–401 , 446 , Chicken viral vaccines ...... 77 , 86 450–451 , 677 , 709 Chimeric flavivirus ...... 19 Chitosan ...... 16 , 697–713 E Chlamydia ...... 500 Eastern blotting Cholera toxin B (CTB) subunit ...... 511–518 , 548 , Ebola virus ...... 108 , 109 , 313 , 325 , 597 549 , 553 , 557 , 562 EditSeq ...... 53 , 54 Cholera vaccine ...... 511 Edward Jenner ...... 835 , 836 , 843 Climate change ...... 135 Electroporation ...... 17 , 41 , 44 , 48 , 124 , 127 , 316 , 318–320 , Cloning...... 40 , 43 , 45 , 61–63 , 72 , 74 , 90–95 , 130 , 139–140 , 466 , 474 , 505 , 512 , 514 , 556 , 584 , 585 , 592 , 626 , 142–146 , 148 , 159 , 161 , 168–170 , 188 , 214 , 630 , 689 217–219 , 222 , 228–229 , 233 , 235 , 317 , 353 , 355 , ELISA . See Enzyme linked immunosorbent assay (ELISA) 369 , 372 , 390 , 393 , 439–444 , 462–464 , 469–471 , ELISpot...... 79 , 170 , 173–175 , 531 , 535–538 504 , 516 , 522 , 526 , 530 , 533 , 537 , 551 , 553–556 , ElliPro web server ...... 53 563 , 598–602 , 609–610 , 617 , 624–626 , 684–687 Emulsification ...... 635–649 , 656 Clostridial toxin ...... 621 Enterotoxigenic E. coli (ETEC) ...... 511 , 763 Clostridium botulinum ...... 621 , 622 , 624 Enzyme linked immunosorbent assay (ELISA) ...... 62 , 66 , ClustalW ...... 184 , 230 , 232 , 248 , 550 , 552 71 , 115 , 124 , 131 , 155 , 156 , 160 , 161 , 169 , 170 , Cold chain ...... 7 , 166 , 636 173 , 174 , 195 , 198–200 , 229 , 236 , 249 , 254 , 262 , α Competent DH5 cells ...... 67 , 68 , 124 , 127 , 168 , 171 , 218 , 263 , 267 , 268 , 272 , 291 , 296 , 302 , 304 , 309 , 310 , 231 , 234 , 338 , 340 , 465 , 471–473 , 488 , 530 , 685 325 , 371 , 373 , 429–431 , 433 , 434 , 507 , 552 , Conformation-specific vaccines ...... 13 558–559 , 607 , 663 , 678 , 710 , 712 , 717 , 720 Copyright ...... 791 , 795 , 797–800 , 809 EpiJen ...... 762–765 , 767 Coronaviruses ...... 13 EpiTOP ...... 762–764 , 766 , 767 COS-7 cells ...... 142 , 146–147 , 172 Epitope ...... 11 , 19 , 21 , 61 , 148 , 165 , 168 , 208 , 211 , 217 , CpG ODN ...... 289–298 , 308 253 , 301 , 334 , 378 , 394 , 423 , 431 , 483–494 , 519 , Current good manufacturing practice (cGMP) ...... 776 , 779 , 531 , 532 , 535 , 536 , 538 , 741 , 761–766 , 818 , 780 , 782 , 783 821–824 , 831–833 Cytotoxic CD8+ T cells (CTL) ...... 14 , 15 , 78 , 168 , 353 , Escherichia coli (E. coli ) ...... 6–8 , 11 , 23 , 27 , 39–41 , 44–46 , 354 , 363 , 535 , 538 , 543 , 651 , 684 63 , 64 , 67 , 68 , 95 , 124 , 127 , 136 , 139 , 143 , 146 , D 148 , 154 , 156 , 158 , 161 , 162 , 168 , 171 , 211–215 , 219 , 231 , 234 , 262 , 264 , 282–283 , 330–332 , 336 , Data analysis ...... 81 , 82 , 250 , 404 , 448 , 743 338 , 340 , 379 , 381 , 387 , 388 , 391 , 424 , 427–429 , Degradation pathways ...... 394 , 397 , 400 437–455 , 459–481 , 483–485 , 488 , 490 , 491 , 493 , Delta inulin ...... 410–411 498 , 501–507 , 511–518 , 520 , 526 , 530 , 549 , 558 , Dendritic cell (DC) 581 , 599 , 601 , 602 , 610 , 622 , 624 , 626 , 628 , 630 , based therapy ...... 535–536 669 , 672 , 673 , 685 , 693 vaccine ...... 289 Excipient ...... 394–397 , 399 , 400 , 403 , 405 , 406 , Deoxyribonucleic acid (DNA) 408 , 410 , 412 , 413 , 415 , 775 nanostructures...... 301 , 306–308 , 310 scaffolded vaccines ...... 301–310 F vaccine ...... 11 , 59–75 , 123 , 135 , 137 , 138 , 142 , 145–147 , Fasciola gigantica ...... 123 , 135 , 138 149 , 154 , 155 , 157–159 , 165–169 , 172 , 176 , 181 , Fasciola hepatica ...... 123 , 135 , 136 211 , 225 , 227 , 230 , 301 , 314 , 741–743 , 745 , 747 , Fasciolosis ...... 11 , 123 , 135–138 750 , 751 FASTA ...... 53 , 55 , 185–187 , 232 , 728 , 755–758 , 764–767 virus ...... 12 , 227 , 233 , 581 Filamentous bacteriophage ...... 423 , 483–494 Diagnostics ...... 581 , 838 , 845 Fish pasteurellosis ...... 181–192 DLS . See Dynamic light scattering (DLS) Fish vaccine ...... 193–201 , 203 , 206 , 207 DNAstar ...... 53 , 213 , 230 , 464 , 480 Flavivirus ...... 366–368 , 370 DNA vaccine database (DNAVaxDB)...... 741–751 Flow cytometry...... 62 , 70 , 74 , 79–82 , 307–308 , 334 , DOLOP ...... 183 , 187 345 , 536 , 538 , 540 , 663 , 665 Drug screening ...... 519–528 Food and Drug Administration (FDA) ...... 408 , 773 , Drugs of abuse ...... 301 774 , 777 , 778 , 780 , 782–785 , 808 , 824–826 , 828 VACCINE DESIGN 851 Index Forced degradation ...... 394 Immune epitope database (IEDB) ...... 762 , 765 , 766 , 770 Formulation ...... 16 , 23 , 24 , 40 , 43 , 61 , 145 , 167 , 181 , 247 , Immune response ...... 7–9 , 14–17 , 22 , 26 , 51 , 52 , 60 , 61 , 249 , 253 , 289–298 , 393–417 , 424 , 425 , 431–433 , 123 , 131 , 135–137 , 139 , 149 , 153 , 154 , 165 , 166 , 514 , 516 , 624 , 628 , 631 , 640 , 644 , 669–671 , 673 , 168 , 173–176 , 193 , 194 , 197 , 198 , 200 , 211 , 225 , 675 , 693 , 697 , 698 , 700 , 706 , 710–712 , 775 , 779 , 244 , 245 , 247 , 253 , 280 , 289 , 313 , 325 , 329 , 365 , 792 , 793 , 796 , 802 , 816 , 818 , 822 , 828 , 831 , 832 378 , 393 , 423 , 431–434 , 498 , 527 , 535 , 549 , 612 , Freeze-drying ...... 294 , 397 , 410–416 , 643 631 , 635 , 638 , 658–661 , 671 , 683 , 684 , 700 , 712 , Freeze-thaw ...... 332 , 342 , 346 , 362 , 394 , 395 , 410–416 715 , 741 , 742 , 748 , 762 , 779 , 794 , 816 , 823 , 824 , Fungal vaccine ...... 745 832 , 843 Fusion chimeric gene ...... 550 , 553 Immunofluorescence assay (IFA)...... 92 , 98 Fusion protein ...... 62 , 73 , 75 , 253 , 270 , 314 , 381 , 389 , Immunogenicity ...... 11 , 12 , 19 , 104 , 105 , 116–117 , 168 , 438 , 440 , 460 , 503 , 548–550 , 552–553 , 559 , 561 , 247 , 301 , 302 , 309 , 314 , 394 , 412 , 430 , 437 , 452 , 563 , 598 , 613 , 822–825 454 , 483 , 484 , 529–545 , 548 , 671 , 677 , 715 , 716 , 761–770 , 777–781 , 822 G Immunoinformatics ...... 753 GeneMark ...... 182 , 185 , 186 , 191 Immunology ...... 51 , 80 , 351 , 708 , 742 , 762 Gene stacking ...... 598 , 602 , 609 Immunoproteomics ...... 519 , 524 Genetic adjuvants ...... 166 , 169 Immunotherapy ...... 289 Genetic vaccination ...... 61 Infectious laryngotracheitis virus (ILTV) ...... 10 , 89–100 Ginbuna crucian carp ...... 194 Influenza vaccine ...... 366 , 396 , 397 , 408 , 410 , 715 GLIMMER ...... 182 , 185 , 186 , 191 Influenza virus ...... 15 , 77 , 313 Glycoprotein Inhibition adherence assay ...... 181 , 182 , 184–185 glycoprotein B (gB) ...... 89–100 Innate immunity ...... 15 , 61 , 211 glycoprotein D (gD) ...... 89–100 Insect cells ...... 232 , 247 , 365–373 , 406 , 438 Guinea pig ...... 378 , 628 , 781 Intellectual property (IP) ...... 791–810 , 835–846 strategy ...... 793 , 803 H Intradermal (ID) ...... 131 , 147 , 165 , 538 , 652 delivery ...... 715 HEK293 cells ...... 317 , 322 , 323 Intranasal vaccination ...... 697–713 Hemagglutinin ...... 313 , 366 , 367 , 393–417 , 597 In vivo imaging ...... 62 , 430 Hepatitis A vaccine ...... 797 Ixodes scapularis ...... 275 , 276 , 278 , 281 , 282 , 284 , 285 Hepatitis B vaccine ...... 782 , 797 , 805 Ixodida ...... 250 , 280 Hepatitis B virus (HBV) ...... 378 , 379 , 437 , 440 , 483 , 569 Hepatitis B virus core VLP (HBc-VLP) ...... 377–391 J Hepatitis C virus (HCV) ...... 534 , 762 Heterologous gene-sequences ...... 370 Japanese encephalitis vaccine ...... 367 High Five cells ...... 365 , 368–373 Japanese encephalitis virus ...... 365–373 History of medicine ...... 24 , 715 K Holotoxin ...... 511 , 549 Host microRNA response elements ...... 727–738 Kozak sequence ...... 61 , 72 , 167 , 533 Human cytomegalovirus (HCMV) ...... 170 Human immunodeficiency virus (HIV) vaccine ...... 843 L Human leukocytc antigen (HLA)-typing ...... 538 , 753 , Lactic acid bacteria ...... 500 754 , 761 Lactobacillus casei ...... 500 , 501 , 505 , 507 Human papillomavirus (HPV) ...... 366 , 437 , 438 , 440 , Lasergene ...... 108 , 213 483 , 569 , 651 , 773 LaSota vaccine strain ...... 89 , 90 , 104 Humoral immunity ...... 154 , 169 , 194 , 651 LCMV . See Lymphocytic choriomeningitis virus (LCMV) Hyalomma anatolicum ...... 459–462 , 469–470 , 479 Leishmania vaccine...... 6 Hybridoma ...... 363 Lentiviral vectors ...... 537 Hybrid particles ...... 483 , 484 Lipofectamine ...... 65 , 70 , 91 , 96 , 97 , 100 , 106 , 110 , I 111 , 146 , 155 , 157 , 169 , 172 , 354 , 532 , 685 , 687 LipoP...... 183 , 187 Immersion vaccine ...... 18 , 203–208 Liposome ...... 290–294 , 297 , 636 , 644 , 646 , 651–667 Immobilized metal affinity chromatography Liver disease ...... 131 (IMAC) ...... 141 , 511 , 515 , 517 , 607 , 613 Liver flukes ...... 135–151 VACCINE DESIGN 852 Index Live vaccine ...... 12 , 89 , 199 O Long-hairpin RNA ...... 227 Long term protection ...... 244 One Health ...... 24 , 28 Luria-Bertani (LB) medium...... 41 , 44 , 63 , 172 , 231 , Oral immunization ...... 17 , 693 520 , 623 Oral rabies vaccine ...... 547–565 Lyme disease ...... 285 Oral vaccine ...... 10 , 11 , 22 , 24 , 497–509 , 547 , 549 Lymphocytic choriomeningitis virus (LCMV) ...... 351–363 Outer membrane protein (Omp) H ...... 51–56 Lyophilization ...... 334 , 393–396 , 410 , 412–414 , 417 , 628 , Ovine retrovirus ...... 59 635–649 , 680 , 721 P

M Paramyxoviridae ...... 104 , 108 , 109 Maedi-visna virus (MVV) ...... 59–75 Pasteurella multocida ...... 51–56 Malaria vaccine ...... 597–613 Patent ...... 792 , 794–799 , 802 , 806–809 , 813–821 , 824–830 , Measles ...... 104 , 773 835–846 Meningococcal vaccines...... 782 Patent law ...... 795 , 813 , 814 , 819 , 820 , 823 , 835–838 , 844 MetaMHCIpan ...... 754 , 759 Pathogen ...... 5–10 , 12–17 , 21–23 , 25 , 26 , 39 , 51 , 52 , 55 , MHC class I binding prediction ...... 765–766 77 , 78 , 103 , 104 , 153 , 165–167 , 176 , 185 , 193 , MHC I ...... 79 , 166 , 538 , 543 , 754 , 761–765 194 , 196 , 203 , 204 , 225 , 226 , 229 , 230 , 236 , 261 , MHC II ...... 52 , 54 , 56 , 60 , 166 , 529 , 754 , 757 , 275 , 280 , 289 , 329 , 330 , 367 , 378 , 432 , 434 , 437 , 758 , 761 , 762 , 764 , 765 442 , 511 , 535 , 542 , 547 , 548 , 635 , 651 , 743 , MHC2MIL ...... 754 , 755 , 757 , 758 745–747 , 750 , 753 , 762 , 775 , 843 MHC2SKpan ...... 754 , 755 , 757 , 758 Pathogen-associated molecular patterns Microneedle arrays ...... 651–667 (PAMPs) ...... 15 , 289 , 529 , 635 , 683 Mimotope ...... 423 , 427 , 431 , 434 pelB signal sequence ...... 511 Modular cloning ...... 602 Penaeus monodon ...... 226 , 227 , 232 Molecular display ...... 497–509 Pentamer staining ...... 535 Monoclonal antibodies (MAbs) ...... 43 , 78 , 92 , 98 , 195 , Peptide binding ...... 753 , 762 , 763 , 765 , 767 196 , 198–200 , 597 , 653 , 761 Peptide libraries ...... 423 Montanide ...... 16 , 253 , 283 Peptide vaccine ...... 51–56 , 423–435 Motile Aeromonas species ...... 204 Perca fluviatilis ...... 203–208 Mucoadhesivity ...... 697 , 699 , 700 , 702 , 705–706 Perch ...... 203–208 Mucosal immune response ...... 697 , 707 pET expression system ...... 511 Mucosal vaccine ...... 651–667 Phage dispilay ...... 423–435 Multivalent vaccines ...... 20–21 , 135 , 824 Photobacteriosis ...... 181 Mumps ...... 104 Photobacterium damselae subsp. piscicida Mycobacterium bovis ...... 6 , 8 , 12 , 23–24 , 743 , 745–750 (Pdp ) ...... 181 , 182 , 184 , 186 , 188–191 Mycobacterium tuberculosis (Mtb) ...... 167 , 377 , 378 , 380 , Physicochemical degradation ...... 393 383 , 387 , 745–748 , 750 , 764–769 Pichia pastoris expression system ...... 124–127 Mycoplasma hyopneumoniae ...... 39–49 Plague ...... 805 Plant breeders’ rights ...... 794 , 795 , 800–801 , 809 N Plant expression vector ...... 551 , 553–556 , 581–583 , 601 Plasmid DNA vaccine ...... 227 , 774 , 775 Nanoparticles...... 301 , 485 , 652 , 674–680 , 697–705 , Plasmid Vaccine Ontology (VO) identifier ...... 742 708–711 Plasmodium falciparum ...... 597 , 609 , 612 , 613 Nanoparticle vaccine ...... 669 PLGA based nanoparticles ...... 669 , 671 , 677 Newcastle disease virus (NDV) ...... 13 , 89–100 , 104 , Pneumococcal vaccine ...... 782 108 , 109 , 167 Polysaccharides ...... 16 , 786 Nicotiana benthamiana ...... 582 , 584 , 587 , 598 , 605 , 606 , Poly-ε-caprolactone ...... 697–713 608–609 Post-transcriptional gene silencing (PTGS) ...... 226 , 582 Nipah virus ...... 104 Poultry ...... 6 , 9 , 13 , 17 , 21 , 22 , 26 , 52 , 77 , 89 , Nocardia seriolae ...... 193–197 , 199 , 200 103 , 104 , 165 , 169 Nocardiosis ...... 193 , 194 , 196 Powder delivery ...... 715–722 Nonhuman primates ...... 762 Prime-boost ...... 12 , 61 , 62 VACCINE DESIGN 853 Index Prokaryotic expression ...... 212 , 215 , 219 , 459–462 , 476–478 SignalP ...... 40 , 183 , 187 , 191 PROTEAN ...... 43 , 46 , 53–55 Silicon wafer ...... 653–655 Proteasome cleavage ...... 763 Single-cycle infectious arenavirus ...... 352 Protective immune response ...... 20 , 137 , 149 , 669 , 741 , 822 Site-directed mutagenesis ...... 43–44 , 105 , 109–110 Protein display ...... 498 Skin vaccination ...... 715–722 Protein H...... 52 Sodium dodecyl sulfate-polyacrylamide gel electrophoresis Protein vaccine ...... 10 , 11 , 47 , 135–137 , 139–145 , (SDS-PAGE) ...... 42 , 45 , 46 , 125 , 128 , 141 , 149 , 154 , 366 , 377–391 , 782 145 , 147 , 158 , 162 , 213 , 220–222 , 264 , 265 , 270 , Protozoa ...... 7 , 153 , 683 , 684 271 , 283 , 322 , 323 , 389 , 400 , 407–411 , 415 , 416 , pShuttle vectors ...... 330–332 , 335–336 , 338–340 , 347 441 , 446 , 447 , 465 , 467 , 468 , 473 , 476 , 479 , 484 , PSORT ...... 183 , 186 , 187 486–488 , 491–492 , 513–517 , 524 , 528 , 531 , 552 , Public health ...... 22 , 154 , 301 , 715 , 791 , 792 , 803 , 804 , 559 , 560 , 573 , 576 , 578 , 590 , 591 , 607–609 , 623 , 806 , 808 , 837 , 842 , 844–845 627 , 630 , 640 , 646 , 674 , 781 Pulmonary infection ...... 329 Stability ...... 105 , 114–116 , 208 , 228 , 302 , 304 , 306–307 , pVIII coat protein ...... 484 330 , 333 , 335 , 346–348 , 361 , 378 , 393–397 , 400–406 , 410–417 , 461 , 612 , 671 , 698 , 699 , 782 R Structure-based vaccines ...... 165 Rabies ...... 6 , 17 , 26 , 548 , 549 , 553 , 715 , 794 Subunit vaccine...... 9 , 10 , 12 , 15 , 77 , 154 , 181 , 225 , 301 , Rabies glycoprotein (RGP) ...... 548–549 , 552–554 , 557–559 365 , 378 , 410–411 , 547 , 549 , 635 , 637 , 741 , 763 Recombinant arenavirus ...... 352 Swine enzootic pneumonia ...... 39 Recombinant fd phage ...... 484 Swiss-Prot ...... 762 Recombinant PAD4 ...... 669 , 671–672 , 674 , 679 Synthetic vaccine ...... 301 , 483 Recombinant protein production...... 124–125 , 365 Systems biology ...... 275 Recombinant toxoid ...... 622 Systems vaccinology ...... 742 Recombinant vaccine ...... 10 , 11 , 39–49 , 175 , 188 , T 622 , 628 , 632 Recombinant virus ...... 91 , 98 , 105 , 118 , 321 , 326 , 332 TAP binding ...... 763 Replication-defective adenovirus vectors ...... 329–348 Tarmogen ...... 529 , 530 , 533–538 , 543 Reporter genes ...... 61 , 72 , 321 , 598 T cells Reporter virus ...... 610 epitope ...... 761 , 763 Reverse genetics ...... 89 , 103–120 vaccine , 529–545 Reverse vaccinology ...... 39 , 181–192 , 246 , 247 TEPITOPEpan ...... 754 , 755 , 757 , 758 Rhabdoviridae ...... 108 , 109 Tetanus toxoid ...... 208

Rhipicephalus ( Boophilus ) microplus ...... 245 , 261 , 459 T h -cell agretope prediction ...... 54 Ricin ...... 555–557 Theileria annulata ...... 459 , 460 Ricin toxin B (RTB) chain ...... 549 T-helper cell ...... 54 , 60 Ricinus communis ...... 549 , 553 , 555 Therapeutic vaccine ...... 537 , 774 , 777 Rickettsiales ...... 275 Thermal degradation ...... 410 , 415 RNA interference (RNAi) ...... 225–237 , 281 , 284–285 Tick-borne encephalitis ...... 261 RNAmmer...... 183 , 186 Ticks RNA virus ...... 13 , 26 , 72 , 104 , 108 , 226 , 227 , 233 , control ...... 243 , 261–272 351 , 352 , 581 vaccine , 275–285 Rotavirus ...... 549 TMpred ...... 183 S Toxoid...... 621–632 , 782 Toxoplasma gondii ...... 6 , 7 , 153 , 154 , 157–159 , 161 , 162 Saccharomyces cerevisiae ...... 139 , 143 , 148 , 438 , 483 , 498 , Toxoplasmosis...... 153–162 499 , 501 , 503 , 505–507 , 529 , 530 , 532 , 533 , 549 Trademark ...... 791 , 793 , 795 , 797–798 , 803 , 807 , 809 Salmonella vector ...... 11 , 683 Trade-Related Aspects of Intellectual Property Rights Secretory IgA (sIgA) ...... 548 , 697 , 712 (TRIPs) ...... 795 , 805–806 , 808 , 837 , 838 , 843 Sheep ...... 6 , 59 , 135 , 138 , 153 , 154 , 204 , 250 , 253 , Transducing units ...... 490–491 276 , 460 , 488 Transgenic parasite ...... 11 Short-hairpin RNA ...... 226–228 Transient plant expression ...... 597–613 Shrimp ...... 225–237 , 698 TrEMBL ...... 762 VACCINE DESIGN 854 Index Trypanosoma cruzi vaccine ...... 683–685 Veterinary vaccine ...... 3–28 Tuberculosis (TB) ...... 6 , 8 , 12 , 14 , 24 , 377–391 , 745 , 807 Vibrio cholerae ...... 512 , 553 Tumor endothelial marker ...... 669 Vibrio parahaemolyticus ...... 519 , 520 , 522–524 , 527 Tumor vaccine ...... 325 , 536–537 VIOLIN . See Vaccine Investigation and Online Information Turkey rhinotracheitis virus ...... 103 Network (VIOLIN) Type III secretion ...... 204 Viral coat proteins ...... 483 , 569 Viral methyltransferase ...... 104 U Viral molecular clone . 330 , 332–334 , 340 , 341 , 344 , 346–348 UniProt ...... 762 Viral nervous necrosis (VNN) ...... 211 United States Patent and Trade Mark Office Viral proteins ...... 225 , 313 , 365 , 393 , 416 , 438 , 581–595 (USPTO) ...... 814 , 815 , 818 , 821 , 829 , 835 , Viral rescue ...... 91 , 96–97 , 332 , 334 , 336–337 , 341–342 , 347 , 839 , 840 348 , 352 , 356 , 362 Viral vaccine vectors ...... 351–363 , 782 V Virus like particles (VLPs) analysis...... 448–453 Vaccine purification , 445–446 design ...... 55 , 78 , 329–348 , 423–435 , 671 , 741–751 Virus vector 10 , 19 , 21 , 40 , 352 , 353 , 358 , 359 , 362 , 363 , 581 innovation ...... 791 , 805 Visceral leishmaniasis ...... 6 purification ...... 213 regulation ...... 570 , 582 , 605 , 773 , 778–781 , 783 , 785 , 809 W screening ...... 519–528 Water-borne diseases ...... 204 Vaccine adjuvant-delivery system (VADS) ...... 635–649 , Web Ontology Language (OWL) ...... 751 651–667 Western blotting ...... 46–47 , 147 , 157 , 169 , 173 , 236 , Vaccine-induced protective immunity ...... 548 322 , 371 , 372 , 488 , 493 , 521 , 524 , 560 , 573 , 576 , Vaccine Investigation and Online Information Network 578 , 781 (VIOLIN) ...... 5 , 741–743 , 745 , 747 World Trade Organization (WTO) ...... 837 , 838 Vaccinomics ...... 275–285 Vaxign ...... 748–751 Y VaxiJen ...... 762–764 , 767 Vector purification ...... 333 , 337 , 342–343 Yellow fever vaccine ...... 367 Vector quality control ...... 330 , 334–335 , 337–338 , 344–346 Z Vero cells ...... 106 , 110–115 , 117 , 118 , 157 , 158 , 362 Vesicular stomatitis virus ...... 108 , 109 Zoonotic diseases...... 6 , 11 , 21 , 23 , 135