Index

Note: Page numbers followed by "f" indicate figures, "t" indicate tables, and "b" indicate boxes.

A Animal cell culture

AAV2. See Adeno-associated virus type 2 (AAV2) immortalized cell lines, 26
ACE2. See Angiotensin converting enzyme 2 (ACE2) lytic eukaryotic viruses, 26, 27f
Acquired immune deficiency syndrome (AIDS), 119, measles, 26–27
283–286 poliovirus, 26
Acute respiratory disease, 26–27 single-burst type, 26
Adaptive immune responses virus infection, 27–28
ADCC, 243–246 Antibody-dependent cellular cytotoxicity (ADCC),
CD8+ (suppressor) phenotype, 242 242–246
cell-mediated immunity, 242, 248f Antibody-dependent enhancement (ADE), 132
cell-surface proteins, 240, 243f Antigenic drift, 319
cytotoxic T-lymphocytes (CTLs), 242–244 Antiretrovirals (ARVs), 285
direct virus neutralization, 241 Antitermination, 168–169
evasion of immune responses by viruses Apoptosis, 232–234, 235f, 261
complement cascade, 246 Arboviruses
cytokines, 245 arthropod-borne viruses, 320
humoral immunity, 245–246 bunya viruses, 320, 323–325
MHC-II-restricted antigen presentation, 244 complex transmission pattern, 320, 320f
MHC-I-restricted antigen presentation, 244 control of insect vectors, 320
NK cell lysis, 245 emerging viruses, 320
humoral immune response, 240 flaviviruses, 320–323
IgM, IgA, 239–240, 240f orbiviruses, 320
immunoglobulin (Ig) structure, 239–240, 240f togaviruses, 320
kinetics of the immune response, 240, 241f vaccines, 320
mammalian antibodies, 240 Arthropod-infecting baculoviruses, 75–77
secretory IgA, 240–241 ARVs. See Antiretrovirals (ARVs)
sites of virus entry, 242, 250f ATLV. See Adult T cell leukemia virus (ATLV)
in vertebrates, 239–240 Atomic force microscopy (AFM), 46
Adeno-associated viruses (AAVs), particle, 4, 5f, 305
Adeno-associated virus type 2 (AAV2), 305 B
Adenovirus E3- 11.6K protein, 282 Bacterial pathogens, 353
Adenoviruses, 69, 70f, 178–180, 180f, 184–185, 204–210, Bacterial σ (sigma) factors, 168–169
208–209f, 296–298 Bacteriocins, 221
Adult T cell leukemia virus (ATLV), 328–329 Bacteriophage λ
Aerosols, 330–331 control of expression, 169–173, 171f
African cassava mosaic virus, 12, 227 integration of genome, 172f
African swine fever virus, 74–75 Bacteriophage M13, 159–160
Agrobacterium tumefaciens, 37–38 Baculovirus particles, 79f
AIDS. See Acquired immune deficiency syndrome Baltimore classification, 143–144, 144t
(AIDS) Bats, 340–341
Alphaviruses, 323–325 B-cell epitopes, 242–243, 245–246
Alzheimer’s syndrome, 360–361 B-cell lymphomas, 283, 301
Ambisense virus genomes, 197–198, 198f Belpaoviruses, 96
Amniotic fluid, 322–323 Betacoronaviruses, 341
Angiotensin converting enzyme 2 (ACE2), 344 “Biggiephage”, 219

379
380 Index

Biocontrol agent, 352 Clustered regularly interspaced short palindromic

Bioterrorism, 351–353 repeats (CRISPRs)
Biowarfare, 351–353 anti-CRISPR (acr) genes, 219
Bombali ebolavirus (BOMV), 338–339 cas genes, 218
Bovine coronaviruses (BCoVs), 349 CRISPR/Cas systems, in prokaryotes, 218–219, 220f
Bovine leukemia virus (BLV), 328 CRISPR-derived small RNAs (crRNAs), 218
Bovine papillomavirus 1 (BPV-1), 299 mimiviruses, 219–221
Bovine spongiform encephalopathy (BSE), 362–365 protospacer adjacent motif (PAM), 219
Bunya viruses, 195f, 197–198, 320, 323–325 recombinant DNA technology, 221
Burkitt’s lymphoma, 283 RNAs, 218
small interfering RNA (siRNA), 218
C type I, II and III systems, 218–219
Camelpox virus, 352 type IV system, 219
Caspases, 234–235 CNS. See Central nervous system (CNS)
Cauliflower mosaic virus (CaMV), 35, 201–202, 202f, Coat protein (CP), 62
212 Constant macromolecular synthesis, 280–281
Caulimoviruses, 97 Coronaviruses, 187, 191–193, 194f
Caveolin-dependent endocytosis, 139 COVID-19 vaccines, 350
CCHFV. See Crimean Congo hemorrhagic fever virus Creutzfeldt-Jakob disease (CJD), 365
(CCHFV) Crimean Congo hemorrhagic fever virus (CCHFV),
CD4+ T-helper cells, 284 309, 324
Cell penetration, 282 CRISPR-associated (cas) genes, 218
Cell transformation, 290–292 Crown gall disease, 37–38
Cell-transforming retroviruses, 291–292, 292t Cryoelectron microscopy (cryoEM), 45
Cellular endonucleases, 63–64 Cryoelectron tomography, 46
Cellular mechanism, 292, 293f Cutaneous lymphoma, 329
Cellular receptor molecules, 80 CWD. See Chronic wasting disease (CWD)
Central nervous system (CNS), 368 Cystoviruses, 73
CFS. See Chronic fatigue syndrome (CFS) Cytopathic effects, 280–281
Chamberland-Pasteur filter, 10 Cytotoxins, 234
Chemotherapy
antiviral drugs, 268–269, 269t D
attachment phase of replication, 271–277 Damage-associated molecules patterns (DAMPs),
blocking viral replication, 272–273 230–231
chemotherapeutic index, 268–270 Defective-interfering (DI) particles, 260
development of chemotherapies, 270 Dengue fever, 321
hepatitis C virus (HCV), 273 Dengue hemorrhagic fever (DHF), 287
HIV replication and expression, 274 Dengue virus infections, 287
penetration/uncoating stages, virus replication, 272 Dependovirus, 184–185, 185f
vaccination, 268–269 Dictyostelium intermediate repeat sequence (DIRS), 94
virion maturation and release, 274–277 Disrupt virus latency, 285–286
virus gene expression, blocking, 274 DNA-dependent RNA polymerase holoenzyme,
Chikungunya virus (CHIKV), 324 168–169
Chimpanzees, 285–286 DNA looping, 173
Chronic fatigue syndrome (CFS), 289, 349 DNA microarrays, 177
Chronic immune activation, 285–286 Double-stranded DNA, 146, 153
Chronic transforming retrovirus genomes, 295–296 Double-stranded RNA, 147–148
Chronic wasting disease (CWD), 363 dsDNA viruses, 92f
Circular Rep-encoding single-stranded (CRESS) DNA Dysentery, 13
viruses, 186
Cirrhosis, 303 E
CJD. See Creutzfeldt-Jakob disease (CJD) Ebola virus disease (EVD), 58
Clinical course of AIDS, 283–284 Ebola virus particle, 73f
 Index 381
EIAV. See Equine infectious anemia virus (EIAV) prokaryote to, 101
Electron microscope, 22f RdRp relatedness, 103
pandemic COVID-19, 23 Eukaryote ssDNA viruses, 91f
TMV, 21 Eukaryotic virus receptors, 128, 128f
Electron microscopy (EM), 45
Electrophoresis, 44 F
Elongation initiation factor III (eiFIII), 202 Fas/TNF inhibition, 235
Endogenous retroviruses (ERVs) Fecal contamination, 289
biomarker, 106 Feline immunodeficiency virus (FIV), 329
comparison, 105 Feline spongiform encephalopathy (FSE), 363
extracellular vesicles (EVs), 106 FHV. See Fock house virus (FHV)
gag genes, 106 Fibrinogen-related peptides (FREPS), 230–231
HERV LTRs, 106 Filoviruses
human ERVs, 105 Ebola viruses, 331–334, 333f
KoRV LTRs, 106–107 later Ebola virus disease outbreaks, 335–338, 336t
retrotransposons, 105 Marburg virus, 331–332
syncytins, 105 Sudan virus (SUDV), 334–335
Endogenous viral elements (EVEs) transmission, Ebola viruses, 338–339
evolution of, 108–110, 109f Filterable viruses, 11
NCLDVs, 108–110 FIV. See Feline immunodeficiency virus (FIV)
paleovirology, 107 Flaviviruses, 193, 210–211, 287, 321–323
RNA and DNA viruses, 107 Fock house virus (FHV), 326–327
viral sequences, 108–110, 108f Foot and mouth disease virus (FMDV), 11
VP35 homologue, 110 FSE. See Feline spongiform encephalopathy (FSE)
Enteric cytopathic human orphan (ECHO)
viruses, 129 G
Enteroviruses, 289 GAVI. See Global Alliance for Vaccines and
Enveloped virions Immunization (GAVI)
budding, 71f Geminiviruses, 68f, 185–186
HIV-1, 70–71 Gene expression
host membrane proteins, 78 posttranscriptional stages, 168
nucleoprotein, 72f, 73 regulatory loops, 168
rhabdo- and bunyaviruses, 73 Genetic information, 167–169, 177, 179f, 197–198, 206
spikes, 70 Genetic limitations, 167
Epidemiology, 122–123 Genetic switches, 168–169
Epigenetics, 177 Genome, 357
Epstein-Barr virus (EBV), 283, 300–302 Genome replication
Equine infectious anemia virus (EIAV), 329 and gene expression, 143–154
Eukaryote DNA viruses information flow, 144, 144f
caulimoviruses, 97 RNA genomes, 145
double-stranded DNA genomes, 91 Glandular fever, 283
hepadnaviruses, 97 Global Alliance for Vaccines and Immunization (GAVI),
origins, 90–91 340
retroelements, 93–101 Global virome, 121–122
reverse transcriptase, 93 Granzymes, 234
source, 91 Guillain-Barré syndrome, 288, 322–323
Eukaryote gene expression, 174–177
Eukaryote RNA viruses H
dsRNA replication intermediates, 103 Hantaviruses, 352–353
genomes, 103 Hantavirus pulmonary syndrome (HPS), 330–331
intermediates, 101 HBV. See Hepatitis B virus (HBV)
origin, 102f HDV. See Hepatitis delta virus (HDV)
polymerase, 101 Helical nucleocapsids, 62–65
382 Index

Helper viruses, 115, 115f I

Hematopoietic abnormalities, 283 Icosahedral symmetry, 160
Hemolytic-uremic syndrome, 289 IL-2. See Interleukin 2 (IL-2)
Hemorrhagic fevers, 352–353 Immune activation, 282
Hemorrhagic fever with renal syndrome (HFRS), Immune responses
330–331 adaptive immune responses in vertebrates, 239–246
Hendra virus (HeV), 339 innate immune responses, 230–239
Hepadnaviruses, 97, 199–201, 204–206 virus infections in animals, 229–230
Hepatitis B virus (HBV), 34–35, 199–202, 200f, 258–259, Immunodeficiency, 283
264, 302–304 Inflammation, 282
Hepatitis C virus, 304 Influenza A H1N1 virus, 352
Hepatitis delta virus (HDV) Influenza viruses, 129, 130f, 186, 194, 196f, 196t,
genome expression, 360, 360f 287–288
group of infectious agents, 360 “Asian flu”, 1957-58, 314–315, 314f
HDV virion, 359, 359f bovine coronavirus, 311
host-cell RNA polymerase II, 358 discovery, 314
properties, HDV, 357–358, 358t and HN protein, 130
satellites, 357, 358t “Hong Kong Flu”, 1968-69, 315–316, 315f
structure, 357–358, 359f influenza A pandemics, 311, 312f, 319
viroids, 357, 358t M2 protein, 164
Hepatocellular carcinoma (HCC), 302 pandemic outbreaks, 311
Herd immunity, 256, 258, 262 “Russian flu”, 1977, 316
Herpes simplex virus (HSV/HHV-1), 282 “Spanish flu” pandemic 1918-20, 311–312
Herpesviruses, 180–184, 206–207, 282–283, 289 “Swine flu” pandemic, 2009, 316–319, 317f
Herpesvirus saimirii, 282–283 Innate immune responses
Herpesvirus virion, 77f invertebrate innate defenses, 230–231
Hershey-Chase experiment, 25, 25f PAMPs in plants, 230
HeV. See Hendra virus (HeV) vertebrate innate defenses
HFRS. See Hemorrhagic fever with renal syndrome active defenses, 231–232
(HFRS) interferons (IFNs), 236–239
HHVs. See Human herpesviruses (HHVs) passive defenses, 231
Highly active antiretroviral therapy (HAART), 276 viruses and apoptosis, 232–236
HIV. See Human immunodeficiency virus (HIV) Interferons (IFNs)
HIV-1. See Human immunodeficiency virus type 1 avian retroviruses, 236
(HIV-1) cellular regulatory activities, 238
HPS. See Hantavirus pulmonary syndrome (HPS) as cellular regulatory proteins, 236–237
HTLV. See Human T-cell leukemia virus (HTLV) discovery, 236, 236f
Human B-lymphocytes, 301 effects, 238
Human encephalitis, 323 IFN-α, 237
Human hepatitis viruses, 327–328 IFN-β, 237
Human hepatocellular carcinoma (HCC), 305 IFN-γ, 237
Human herpesviruses (HHVs), 327 mechanisms
Human immunodeficiency virus (HIV), double-stranded (ds) RNA, 237
131–132, 282 metabolic inhibitors, 237
Human immunodeficiency virus type 1 (HIV-1), virus infection, 237
70–71, 329 2´,5´-oligo A synthetase and PKR, 238–239, 238f
Human papillomaviruses (HPVs), 298, 304–305 side effects, 239
Human retroviruses, 162–163, 328–329 therapeutic uses, 239, 239t
Human T-cell leukemia virus (HTLV), 201, 204–206, type I IFN, 238
205f, 210, 296, 305, 328–329 types, 236–237
Hyperimmune response, 301 Interleukin 2 (IL-2), 328–329
Hyperplasia, 228 Internal ribosomal entry site (IRES), 210–211, 211f
Hypoplasia, 228 Isometric nucleocapsids, 65–67
 Index 383
K Middle East respiratory syndrome coronavirus
Kaposi sarcoma-associated herpesvirus (MERS-CoV), 193, 344–345
(KSHV), 304 Mild disease, 310
Kaposi’s sarcoma (KS), 284 Mimiviruses, 77, 183–184, 219–221
Kawasaki disease (KD), 288 MIS-C. See Multisystem inflammatory syndrome in
Kawasaki-like hyperinflammatory syndrome, 288 children (MIS-C)
Koala retrovirus (KoRV, 106–107 Mitomycin C, 289–290
Koch’s postulates, 9 MMTV. See Mouse mammary tumor virus (MMTV)
KS. See Kaposi’s sarcoma (KS) Mobile genetic elements (MGEs), 93
KSHV. See Kaposi sarcoma-associated herpesvirus Molecular biology, 112, 123
(KSHV) Molecular cloning, 47
Molecular genetics, 112–113
Molecular virology, 40–42
L MS2 coliphage, 33
Lack of immune surveillance, 283 PhiX174 phage genome, 30
Latency-associated transcript (LAT), 261 PhiX174 phage sequencing, 33
Latent RNA, 261 physicochemical methods, 42–47
LAV. See Lymphadenopathy virus (LAV) potato spindle tuber disease, 31
Leviviridae, 169 reverse transcription and tumor viruses, 31–32
Long COVID, 349–350 RNA molecules, 31
Long intergenic region (LIR), 185, 186f simian vacuolating virus, 32
LUCA SV40 sequencing, 33–34
concept of, 89 Tour de force experiment, 30
feature of, 90 viral genome
hypothetical virome, 89 cloning, 32
Lymphadenopathy virus (LAV), 329 sequencing, 33
Lymphocytic choriomeningitis virus (LCMV), viroid, 34
259–260, 260f Monoclonal antibodies (mAbs), 43f, 337
Lymphoid/myeloid tumor, 283 Mononucleosis, 283
Lymphoid tumors, 283 Morbilliviruses, 340–341
Lymphoproliferation, 283 Mosaic disease, 10–12, 13f
Lysis of adenovirus-infected cells, 282 Mosquitoes, 287
Mouse hepatitis virus, 193
M Mouse mammary tumor virus (MMTV), 295–296, 300
Maize streak virus, 325–326 Multisystem inflammatory syndrome in children
Malignant tumor, 283 (MIS-C), 288
Marek’s disease virus, 282–283 Mumps virus, 64–65, 340–341
Mass spectroscopy (MS), 44 Murine leukemia virus (MLV), 213–214
Maternal antibodies, 310 Mutations, 116
Maturation, 160–161 Myalgic/myalgia encephalomyelitis (ME), 289
Mayaro virus, 325 Myovirus and siphovirus, 76f
MCV. See Merkel cell polyomavirus (MCV)
Measles, 310–311
virus, 64–65 N
virus infection, 286–287 Nasopharyngeal carcinoma (NPC), 301
Megavirus, 183–184 Natural killer (NK) cells, 232, 233f
Membrane fusion, 282 Necrosis, 228, 233–234
Merkel cell polyomavirus (MCV), 286b, 305 Negative feedback mechanism, 170–172
MERS-CoV. See Middle East respiratory syndrome Negatively-stained electron micrograph, 74
coronavirus (MERS-CoV) Neoplastic transformation, 290
7-Methyl guanosine triphosphate (m7Gppp), 188 Neural progenitor cells, 322–323
Microarray technology, 177 Neuraminidase (NA) protein, 129
MicroRNAs (miRNAs), 176, 248–249, 261 Neurological disorders, 289
384 Index

Nipah virus (NiV), 339–340, 352–353 classes II-VII, 227

Nonstructural protein NS3, 322–323 in cowpea mosaic virus (CPMV), 226–227
NPC. See Nasopharyngeal carcinoma (NPC) CP gene, 227
N protein, 170, 197 CRISPR/Cas, 229
Nuclear localization signals (NLSs), 202–204 horticultural production, 223
Nuclear magnetic resonance (NMR), 46 hypersensitive response, 228
Nuclear matrix, 174–175 innate immune response, 228
Nuclear pore complex, 142, 143f macroscopic symptoms, 228
Nucleic acid hybridization, 48f movement-related protein (MP) genes, 226–227
Nucleocytoplasmic large DNA viruses (NCLDV), peroxidases and polyphenoloxidase, 228–229
108–112 photosynthetic algae in oceans, 223
plant virus movement proteins, 226–227, 227f
O plasmodesmata, 225–227, 226–227f
Oncogenes, 291–292, 291t production of interferons (IFNs), 228
Open reading frames (ORFs), 168–169 routes of transmission
Operons, 168–169 arthropods, 224
Orthography, 57–58 bacteria, 223
Orthomyxoviruses, 187, 195f, 198 fungi, 223
mechanical transmission, 224
P nematodes, 223
Paillomaviruses, 178, 183–184, 214, 296–297 seeds, 223
Paramyxoviruses (PVs), 340–341 vegetative propagation/grafting, 223
Parvoviridae, 184–185 site of infection, 225–226
Parvovirus genomes, 184, 184–185f systemic resistance, 228–229
Parvovirus genomic hairpin sequences, 184, 184f tenuiviruses, 225
Passive defenses, 231 terrestrial plants, 223
Pathogen-associated molecular patterns (PAMPs), 228, transmission of plant viruses
230–231 by insects, 224
Pathogenicity, 279 nonpersistent/nonpropagative transmission, 224
Pattern-recognition receptors (PRRs), 230–231 persistent nonpropagative transmission, 225
PCP. See Pneumocystis carinii pneumonia (PCP) persistent/propagative transmission, 225
PCS. See Post COVID syndrome (PCS) semipersistent/nonpropagative, 224
Penetration virus coat protein (CP) genes, 229
animal cell entry, 137–140 Plant viruses, 128, 325–327
lysosomes, 138–139 Plasmodesmata, 225–227, 226–227f, 247
mitoviruses, 136 Pneumocystis carinii pneumonia (PCP), 284
plant and fungal cell entry, 135–136 Poliomyelitis/infantile paralysis, 12–13
prokaryote cell entry, 133–135 Polioviruses, 309–310
prokaryotes, 132 Polymerase chain reaction (PCR) technique, 48–49
receptor-mediated endocytosis, 134f, 138 qPCR, 48–49
Penton protein, 282 RT-PCR, 48–49
Perforin, 234, 242–243 SARS-CoV-2 infections, 48–49
Phage λ, 169 Polyomaviruses, 32, 34, 176, 178, 179f, 206–207
Phage therapy, 267 Popagative noncirculative vector, 326–327
Phagocytes, 230–231 Post COVID syndrome (PCS), 349
Phenotypic mixing, 120, 121f Posttranscriptional control of expression
Physiological stress, 172–173 adenovirus, 207–209, 209f
Picornavirus capsids, 128–129 AUG translation initiation codon, 210
Picornaviruses, 188–191, 190–191f, 210–211, 211f E1A polypeptides, 207–208
Pithovirus, 183–184 herpesviruses, 206–207
Plants, virus infections HTLV Rex and HIV Rev. proteins, 210
cauliflower mosaic virus, 224 interferons, 209–210
chaperonins and plasmodesmata-associated proteins, “leaky scanning” mechanism, 210
226–227 parvoviruses, 206–207
 Index 385
picornavirus genomes, 210–211, 211f Replication factories (RF), 187
polyomaviruses, 206–207 Replication-transcription complex (RTC), 193
ribosomal frameshifting, 212–214, 213f Retroelements (REs), 93–101
RNA pseudoknot, 212–214, 214f evolution, 95f
RNA transcript and finished polypeptide, 206 prokaryote, 94t
SARS-CoV-2, 214 Retroviruses, 282–283, 289
viral associated (VA) genes, 209–210 Retrovirus-like genomes, 174–175, 198–199, 199f, 212
Posttranscriptional gene silencing process, 228, 246 Retrovirus proteases, 161
Poxviruses, 78f, 182–183 Retrovirus protein kinases, 292, 294f
P22 podovirus, 76f Reverse-transcribing viruses, 96t
Primate T-lymphotropic viruses (PTLVs), 329 Reverse transcriptase (RT), 198–199, 212
Prion diseases phylogenetic trees, 93–94
chronic wasting disease (CWD), 363 retroposons, 94
conformational changes, 370, 371f Reverse-transcription (RT-PCR), 48–49
Doppel (Dpl) proteins, 367–368, 369f Reye’s syndrome, 287–288
endogenous gene/protein, 368, 369f Rhabdovirus particle, 62, 64f
feline spongiform encephalopathy (FSE), 363 Rhinovirus receptor binding, 128, 129f
human TSEs, 365–367 Ribosomal frameshifting, 207, 212–214, 213f
nucleic acid, 367 Ribosome “landing pad”, 210–211
pathology, 361 Rift Valley fever virus (RVFV), 309, 323–324
prion strain variation, 368 RNA, genetic material
radiation sensitivity, 367, 368f cDNA, 35
scrapie, 361–363, 362f Hershey- Chase experiment, 28
species barrier, 370 mRNA, 29
transgenic “knockout” Prnp0/0 mice, 370–371 nitrous acid, 28
transmissible mink encephalopathy (TME), 363 protein and DNA, 29
TSE in animals, 361 TMV virions, 28, 28f
Prion protein (PrP), 361 translation of viral, 28, 30f
Prokaryote gene expression viroid, 28, 31f
control of translation, 169 RNA interference (RNAi)
DNA-dependent RNA pol, 168–169 gene silencing, 246
genetic control mechanisms, 168–169 in mammals
operons, 168–169 antigenic drift, 255
Prokaryote ribocells, 168 antigenic shifts, 255–256, 271f
Prokaryotes, virus infection direct cell-cell contact, 253, 256f
CRISPRs (see Clustered regularly interspaced short dsRNAs, 249
palindromic repeats (CRISPRs)) historical influenza pandemics, 253, 257f
“primitive” organisms, 217 host immune response, 255
tailocins, 221–223 host-to-host transmission, 252–253
Protein-nucleic acid interactions, 80, 160 impact of innate immunity, 249
Protein-protein interactions, 297 localized and systemic virus infections,
PrP. See Prion protein (PrP) 253, 254t
PTLVs. See Primate T-lymphotropic viruses (PTLVs) mechanism and site of entry, 249
PVs. See Paramyxoviruses (PVs) miRNAs, 249
natural environment, 252
Q polarized epithelial cells, virus infection, 252, 254f
Quantitative PCR (qPCR), 48–49 retrovirus genomes (ERVs), 255
Quasicrystalline arrays, 162–163 siRNAs and miRNAs, 248
stem cells/mouse embryos, 248
R transmission of viruses, 248, 252f
Rabies vaccine, 9 viRNAs, 248
Rapid direct RNA sequencing (RNAseq), 177 viruses and routes of infection, 250–251, 251t
Recombinant protein vaccines, 264 virus pathogenesis, 249
Reoviruses, 187–188, 188t, 189f virus transmission patterns, 252, 253t
386 Index

RNA interference (RNAi) (Continued) Signal transducer and activator of transcription 2

pathways, 246 (STAT2), 238
in plants and insects Single-burst experiment, 24f, 25
dsRNA, 246–247 Single-hit process, 291
recombinant RNAi technology, 247 Single jelly-roll fold (SJR) proteins, 87–88
recovery phenotype, 247 Single-stranded DNA, 147
RNA-induced silencing complex (RISC), Single-stranded (+) sense RNA, 148–149
246–247 Single-stranded (–) sense RNA, 150–152
short interfering RNAs (siRNA), 246–247 SJR proteins. See Single jelly-roll fold (SJR) proteins
viral suppressors of RNAi (VSRs), 247 Small-angle neutron scattering, 46–47
posttranscriptional gene silencing process, 246 Smallpox, 310–311, 351–352
RNA polymerase (RNA pol), 168–170, 175–176, 175t Smallpox vaccine, 8–9
RNA pseudoknot, 212–214, 214f Solid tumor-causing virus, 13
RNA splicing, 185, 203f Spanish Flu, 14
RNA subgenomic promoter, 191 Spectroscopy, 43
RNA tumor viruses, 328 Sputnik virophage, 4
Rolling circle amplification (RCA), 186 35S RNA, 201–202
Rotaviruses, 352 ssDNA geminiviruses, 325
Rous sarcoma virus, 13 ssRNA- measles virus, 310
Rubulaviruses, 340–341 STEC. See Shiga toxin (Stx)-producing Escherichia coli
RVFV. See Rift Valley fever virus (RVFV) (STEC)
Subacute sclerosing panencephalitis (SSPE), 286–287
S Sudan virus (SUDV), 334–335
Saccharomyces cerevisiae, 371 Surface glycoproteins, 282
Sanger method, 33 SV40 T-antigen, 297
SARS. See Severe acute respiratory syndrome (SARS) Sylvan cycle, 325
SARS-CoV, 341–344, 343f Syncytia/fused cells, 282
SARS-CoV-2 Syngeneic LCMV-specific T-lymphocytes, 259–260
betacoronavirus-related sequence, 345
bioinformatics, 345 T
case fatality rate (CFR), 346 Tailocins
COVID-19, 345 bacteriocins, use, 221
dexamethasone, 347 daedalian capacity of bacteria, 221
Huanan Seafood Market, 345 ETEC and Clostridium difficile, 221
infection fatality rate (IFR), 346 flexible (F)/rigid (R) appearance, 221
personal protective equipment (PPE), 346 in Pseudomonas spp., 221, 222f
Public Health Emergency of International Concern R-type tailocin, 221, 222f
(PHEIC), 345 type VI secretion systems (T6SS), 221
Rhinolophus bats, 348 Tansfusion-related hepatitis, 328
variants of concern, 347–348 Tenuiviruses, 225
Satellite nucleic acids, 5 Terrestrial viruses
Satellite viruses emergence, 104, 104f
AAVs, 4 insects and plants, 104
classification, 5 Tissue tropism, 225, 254
replication, 4 T-lymphotropic, 282–283
“Selfish” gene, 168 TME. See Transmissible mink encephalopathy (TME)
Serological techniques, 41–42f Tobacco mosaic virus (TMV), 11, 11f
Serum hepatitis, 302 atomic-resolution structure, 36f
Severe acute respiratory coronavirus type 2 (SARS- denaturation, 44f
CoV-2), 193 fundamental types, 45
Severe acute respiratory syndrome (SARS), 341–350 genome, 35–36
Shiga toxin (Stx)-producing Escherichia coli structure, 36
(STEC), 289 symmetry, 62, 63f
Shope papillomavirus, 17 timeline, 36
 Index 387
Togaviruses, 191–193, 192f chronic pathologic conditions, 279
Tomato spotted wilt virus (TSWV), 326 direct effects, 279
Tomato yellow leaf curl virus (TYLCV-Is), 325 Epstein-Barr virus, 300–302
Trans-acting factors, 168 Hepatitis B virus, 302–304
Transcriptionally active DNA, 174–175 human disease, 289–290
Transcriptional regulatory genes, 184–185 immunodeficiency, 282–283
Transcription factors, 168 interferons, 279
Transcription of cellular genes, 283 interleukins, 279
Transcription promoters, 168 mechanisms, cellular injury, 280–282
Transferred DNA (T-DNA), 37–38 molecular determinants of virulence, 279–280
Transgenic hosts and viruses multiomics, 279–280
advantage, 37–38 side effects, immune response, 279
cell transfection, 39 viruses, 280, 282–283
description, 37 viruses and cancer, 300–305
generation, 38–39 virus-related diseases, 286–289
Transmembrane envelope glycoprotein of the virus Viral suppressors of RNAi (VSRs), 247
(gp41), 282 Virions
Transmissible mink encephalopathy (TME), 363 assembly process, 154
Transmissible spongiform encephalopathies (TSEs), bacterial virus-T4 phage/Enterobacteriophage T4, 60,
360–361 61f
trans-regulatory proteins, 283 budding, 154–155
TSWV. See Tomato spotted wilt virus (TSWV) complex/compound, 73–74
TYLCV-Is. See Tomato yellow leaf curl virus composition, 60–62
(TYLCV-Is) enveloped, 70–73
enzymatic activities, 81
formation, 156
U function, 60
Ultraviolet irradiation, 172–173 helical capsids, 62–63
nonstructural and host proteins, 78–80
V nucleoproteins, 61
Vaccine-associated paralytic poliomyelitis, 352 picornavirus capsids, 156–157, 156f
Vaccine-derived poliovirus type 2, 310 shapes and sizes, 58–60, 59f
Vaccinia virus (VV) genome, 265–266 structure, 23
van der Waal’s interactions, 42, 62 tailed, 157
Variant of CJD (vCJD), 366–367 Virions, crystallography
Varicella-zoster virus, 287–288 DNA, 25
Vector-borne viruses, 309 Escherichia coli bacteriophage, 24
Venezuelan equine encephalitis virus, 352 Hershey-Chase experiment, 25, 25f
Vertebrate innate defenses investigation, 23
active defenses one-step growth curve, 24f, 25
macrophages, 231–232 phage biology, 24
natural killer (NK) cells, 232, 233f Virocell, 7
phagocytic cells, 231 Viroids, 357
IFNs (see Interferons (IFNs)) Virology, history of, 1
passive defenses, 231 Viromics, 49–51
viruses and apoptosis, 232–233 Viromics, functional, 52
Viral pathogenesis Virophages, 93
acquired immunodeficiency syndrome (AIDS), Viroporins, 164
283–286 Virotherapy, 267
attenuated/avirulent strains, 279–280 Virus 2A protein, 281–282
bacteriophages, 289–290 Virus-attachment protein (VAP), 254, 271
cell transformation, 290–292 Virus-based gene therapy, 267
DNA viruses, 296–300 Virus-driven membrane fusion, 137–138
retroviruses, 294–296 Virus-encoded proteases, 161
388 Index

Virus envelope proteins, 163–164 ribozyviria, 57

Viruses and serological/immunological methods, 39–40
adnaviria, 57 taxonomic placement, 57
bacterial lysis and plaque assays, 12, 15f taxonomic ranks, 55–56
bioinformatics, 48–49, 50f, 51–52 vaccines, 8
classification, 55–58 varidnaviria, 57
concept, 2, 7–8 virologists and microbiologists, 2
current virus taxons, 56, 56t Virus genetics, 113–120
definition, 2 Virus genome coding strategies
duplodnaviria, 57 double-stranded DNA, 183–184
electron microscope, 21–23 adenoviruses, 178–180
emerging/re-emerging viruses, 307–308, 308t cytoplasm, 177
endemic mosquito transmitted viruses, 309 giant viruses, 183–184
in environment, 3 herpesviruses, 180–182
epidemics, 307–308 nuclear, 177
evolution, 7 polyomaviruses and papillomaviruses, 178
FMDV, 11 poxviruses, 182–183
genetic interactions with (+)sense RNA replication intermediates, 199–202
intramolecular recombination, 119 double-stranded RNA
nature and organization, 118 enzymes in reovirus particles, 188t
recombination, 118 genome RNA, 187–188
genomes types, 3, 4t maize streak virus genome, 186f
plasmids, 5 multipartite genomes, 187–188
polydnaviruses, 6–7 polyphyletic origin, 187
retrons, 6 secondary transcription, 187–188
satellite nucleic acids, 5 single-stranded DNA
satellite viruses, 4–5 adenovirus/herpesvirus superinfection, 184–185
viroids, 6, 6f CRESS DNA viruses, 186
history of discovery, 7–52 DNA repair processes, 184–185
local lesions, 16 long intergenic region (LIR), 185
metabolic energy, 3 Parvoviridae and Bidnaviridae, 184
Negri bodies, 12 Parvovirus genomes, 184, 184–185f
newly emerging viruses, 309 RNA splicing, 185, 203f
nongenetic interactions single-stranded (+) sense RNA
heterozygosity, 119–120 coronaviruses, 193, 194f
plant ssRNA+ viruses, 120 picorna-like viruses, gene expression, 190f
One Health, 309 picornaviruses, 189–191
origins, 84–85, 85f prokaryote ssRNA+ virus genomes, 188
orthography, 57–58 TMV genome, organization and mRNA
pandemics, 307–308 expression, 191f
pandoravirus, 2–3 Togaviruses, 191–193, 192f
physical properties, 43 virus genomes, 188
porcelain filters and discovery single-stranded (-) sense RNA
Chamberland filter, 10, 10f ambisense genome organization, 197–198
invention, 10 with DNA replication intermediates, 198–199
TMV, 11 full-length (+) sense RNA, 197
priority diseases, 307–308 orthomyxoviruses, 198
protein, 46, 46f trisegmented bunyaviruses, 198
purification single-stranded (–) sense RNA
biophysical studies, 19 either segmented/nonsegmented, 193–194
poxvirus, 19 full-length (+) sense RNA, 197
TMV, 20 influenza viruses, 194, 196f, 196t
ultracentrifuge, 19–20 monocistronic mRNAs, 194–195
recurrent epidemics/outbreaks, 307–308 paramyxoviruses, 195–196
riboviria, 57 virion RNA (vRNA), 194
 Index 389
Virus genomes “genetic”/DNA-based vaccines, 265
chemistry and structures, 83 killed whole-virion vaccines, 262
complexity live attenuated vaccines, 262
E. coli-infecting phage T4, 111 newer vaccine technologies, 263
eukaryotic hosts, 111 recombinant protein vaccines, 264
mimiviruses, 111–112 subunit vaccines, 262–263
prokaryotic hosts, 110–111 synthetic vaccines, 263–264
evolutionary origins, 84 VLP-based nanoparticle vaccines, 264
obligate intracellular parasites, 83 Virus variants, 114–118
single-stranded RNA, 83 genomes, 115
in size, 83–84 molecular biological techniques, 116
size/composition, 84 mutant viruses, 114
types, 83, 84t mutations, 114–115
uncoating RNA viruses, 116
ACE2, 142 VPg protein, 281–282
cell penetration, 141, 141f
DNA provirus, 142 W
picornaviruses, 141 West Nile virus (WNV), 309, 323
Virus hallmark genes, 86 Whiteflies, 325
eukaryotic RNA viruses, 87–88 WNV. See West Nile virus (WNV)
evolutionary lineages, 86
isometric capsid protein type, 88–89
replication modules, 86, 87t X
SJR fold proteins, 87–88 Xenotropic murine leukemia virus-related virus
Virus infections (XMRV), 289
abortive infection, 258 X-linked lymphoproliferative syndrome (XLP), 301
acute infection, 258 XMRV. See Xenotropic murine leukemia virus-related
chemotherapeutic index, 268–269 virus (XMRV)
chemotherapy, 268–277 X-ray crystallographers, 44–45
chronic infection, 258–259 X transcriptional trans-activator, 199–202, 200f
latent infection, 261
persistent infection, 259–260 Y
prevention and therapy see also Virus vaccines Yellow fever, 351–352
prophylactic viral vaccines, 262–267 Yellow Fever Research Institute in Uganda, 321
public and personal hygiene, 262 Yellow fever virus (YFV), 16, 19, 321
therapeutic vaccines, 266–267
viruses as therapeutics, 267–268 Z
virus vectors in gene therapy, 267–268, 268t Zamilon, 219–221
Virus receptors, 127 Z-DNA, 174–175
Virus-related diseases, 286–289 Zika virus (ZIKV), 309, 321
Virus replication Zoonoses
DNA viruses and RNA viruses, 125 filoviruses (see Filoviruses)
stages, 125–126, 126f hantaviruses, 330–331
Virus vaccines HIV, 329–330
DNA vaccines, 264–265 influenza A viruses, 329–330
egg-made influenza vaccines, 263 Zoonotic human diseases, 110