HANDBOOK OF FILTERABLE VIRUSES
PART I THE NATURE OF VIRUSES 1 Chapter 1 Towards a definition of a virus 3 11 Discovery of viruses 4 12 Multiplication of viruses 5 13 The virus multiplication cycle 6 14 Viruses can be defined in chemical terms 7 15 Multiplication of bacterial and animal viruses is fundamentally similar 10 16 Viruses can be manipulated genetically 11 17 Properties of viruses 11 18 Origin of viruses 12 Key points 12 Further reading 12 Chapter 2 The structure of virus particles 13 21 Virus particles are constructed from subunits 13 22 The structure of filamentous viruses and nucleoproteins 14 23 The structure is of isometric virus particles 15 24 Enveloped (membrane-bound) virus particles 24 25 Virus particles with head-tail morphology 27 26 Frequency of occurrence of different virus particle morphologies 28 27 Principles of disassemply: virus particles are metastable 28 Key points 29 Further reading 29 Chapter 3 Classification of viruses 30 31 Classification on the basis of disease 30 32 Classification on the basis of host organism 31 33 Classification on the basis of virus particle morphology 31 34 Classification on the basis of viral nucleic acids 32 35 Classification on the basis of taxonomy 34 36 Satellites, viroids and prions 35 Key points 37 Further reading 38 Chapter 4 The evolution of viruses 39 41 Mechanisms of virus evolution 40 42 The potential for rapid evolution: mutation and quasispecies 40 43 Rapid evolution: recombination 43 44 Rapid evolution: reassortment 43 45 Evolution to find a host, and subsequent co-evolution with the host 46 Key points 51 Questions 51 Further reading 51 Chapter 5 Techniques for studying viruses 52 51 Culturing wild virus isolates 52 52 Enumeration of viruses 54 53 Measuring infectious virus titres 55 54 Measuring physical virus titres 57 55 Detecting virus in a sample 58 56 Understanding virus replication cycles 62 57 Viral genetics and reverse genetics 63 58 Systems-level virology 63 Key points 65 Questions 65 Further reading 65 PART II VIRUS GROWTH IN CELLS 67 Chapter 6 The process of infection: I Virus attachment and entry into cells 69 61 Infection of animal cells: the nature and importance of receptors 69 62 Infection of animal cells: enveloped viruses 73 63 Infection of animal cells: non-enveloped viruses 78 64 Infection of plant cells 80 65 Infection of bacteria 81 66 Infection of cells: post-entry events 82 67 Virus entry: cell culture and the whole organism 84 Key points 84 Questions 84 Further reading 85 Chapter 7 The process of infection: IIA The replication of viral DNA 86 71 The universal mechanism of DNA synthesis 87 72 Replication of circular double-stranded DNA genomes 90 73 Replication of linear double-stranded DNA genomes that can form circles 93 74 Replication of linear double-stranded DNA genomes that do not circularize 96 75 Replication of single-stranded circular DNA genomes 100 76 Replication of single-stranded linear DNA genomes 100 77 Dependency versus autonomy among DNA viruses 103 Key points 103 Questions 103 Further reading 103 Chapter 8 The process of infection: IIB Genome replication in RNA viruses 105 81 Nature and diversity of RNA virus genomes 106 82 Regulatory elements for RNA virus genome synthesis 106 83 Synthesis of the RNA genome of Baltimore class 3 viruses 111 84 Synthesis of the RNA genome of Baltimore class 4 viruses 111 85 Synthesis of the RNA genome of Baltimore class 5 viruses 115 86 Synthesis of the RNA genome of viroids and hepatitis delta virus 118 Key points 119 Questions 119 Further reading 119 Chapter 9 The process of infection: IIC The replication of RNA viruses with a DNA intermediate and vice versa 121 91 The retrovirus replication cycle 122 92 Discovery of reverse transcription 122 93 Retroviral reverse transcriptase 123 94 Mechanism of retroviral reverse transcription 125 95 Integration of retroviral DNA into cell DNA 128 96 Production of retrovirus progeny genomes 130 97 Spumaviruses: retrovirus with unusual features 131 98 The hepadnavirus replication cycle 131 99 Mechanism of hepadnavirus reverse transcription 131 910 Comparing reverse transcribing viruses 134 Key points 134 Questions 134 Further reading 135 Chapter 10 The process of infection: IIIA Gene expression in DNA viruses and reverse-transcribing viruses 136 101 The DNA viruses and retroviruses: Baltimore classes 1, 2, 6 and 7 137 102 Polyomaviruses 138 103 Papillomaviruses 142 104 Adenoviruses 144 105 Herpesviruses 147 106 Poxviruses 149 107 Parvoviruses 149 108 Retroviruses 150 109 Hepadnaviruses 153 1010 DNA bacteriophages 154 Key points 154 Questions 155 Further reading 155 Chapter 11 The process of infection: IIIB Gene expression and its regulation in RNA viruses 156 111 The RNA viruses: Baltimore classes 3, 4 and 5 157 112 Reoviruses 158 113 Picornaviruses 163 114 Alphaviruses 164 115 Coronaviruses 166 116 Negative sense RNA viruses with segmented genomes 169 117 Orthomyxoviruses 169 118 Arenaviruses 173 119 Negative sense RNA viruses with non-segmented, single stranded genomes: rhabdoviruses and paramyxoviruses 174 Key points 177 Questions 178 Further reading 178 Chapter 12 The process of infection: IV The assembly of viruses 179 121 Self-assembly from mature virion components 180 122 Assembly of viruses with a helical structure 180 123 Assembly of viruses with an isometric structure 184 124 Assembly of complex viruses 187 125 Sequence-dependent and -independent packaging of virus DNA in virus particles 189 126 The assembly of enveloped viruses 190 127 Segmented virus genomes: the acquisition of multiple nucleic acid molecules 194 128 Maturation of virus particles 195 Key points 196 Questions 197 Further reading 197 PART III VIRUS INTERACTIONS WITH THE WHOLE ORGANISM 199 Chapter 13 Innate and intrinsic immunity 201 131 Innate immune responses in vertebrates – discovery of interferon 202 132 Induction of type 1 interferon responses 203 133 Virus countermeasures to innate immunity 207 134 TRIM proteins and immunity 209 135 Intrinsic resistance to viruses in vertebrates 210 136 Innate and intrinsic immunity and the outcome of infection 212 137 RNAi is an important antiviral mechanism in invertebrates and plants 212 138 Detecting and signalling infection in invertebrates and plants 214 139 Virus resistance mechanisms in bacteria and archaea 215 Key points 216 Questions 217 References 217 Chapter 14 The adaptive immune response 218 141 General features of the adaptive immune system 219 142 Cell-mediated immunity 221 143 Antibody-mediated humoral immunity 226 144 Virus evasion of adaptive immunity 232 145 Age and adaptive immunity 233 146 Interaction between the innate and adaptive immune systems 233 Key points 234 Questions 236 Further reading 236 Chapter 15 Interactions between animal viruses and cells 237 151 Acutely cytopathogenic infections 238 152 Persistent infections 238 153 Latent infections 241 154 Transforming infections 243 155 Abortive infections 243 156 Null infections 244 157 How do animal viruses kill cells? 244 Key points 246 Questions 247 Further reading 247 Chapter 16 Animal virus–host interactions 248 161 Cause and effect: Koch’s postulates 248 162 A classification of virus–host interactions 249 163 Acute infections 252 164 Subclinical infections 253 165 Persistent and chronic infections 254 166 Latent infections 256 167 Slowly progressive diseases 257 168 Virus-induced tumours 258 Key points 259 Questions 260 Further reading 260 Chapter 17 Mechanisms in virus latency 261 171 The latent interaction of virus and host 261 172 Gene expression and the lytic and lysogenic life of bacteriophage ? 263 173 Herpes simplex virus latency 270 174 Epstein-Barr virus latency 274 175 Latency in other herpesviruses 275 176 HIV-1 latency 277 Key points 277 Questions 278 Further reading 278 Chapter 18 Transmission of viruses 279 181 Virus transmission cycles 279 182 Barriers to transmission 281 183 Routes of horizontal transmission in animals 282 184 Vertical transmission 285 185 Vector-borne viruses and zoonotic transmission 287 186 Epidemiology of virus infections 289 187 Sustaining infection in populations 290 Key points 291 Questions 291 Further reading 291 PART IV VIRUSES AND HUMAN DISEASE 293 Chapter 19 Human viral disease: an overview 295 191 A survey of human viral pathogens 295 192 Factors affecting the relative incidence of viral disease 297 193 Factors determining the nature and severity of viral disease 299 194 Common signs and symptoms of viral infection 301 195 Acute viral infection 1: gastrointestinal infections 302 196 Acute viral infection 2: respiratory infections 304 197 Acute viral infection 3: systemic spread 306 198 Acute viral disease: conclusions 306 Key points 307 Questions 308 Further reading 308 Chapter 20 Influenza virus infection 309 201 The origins of human influenza viruses 309 202 Influenza virus replication 315 203 Influenza virus infection and disease 316 204 Virus determinants of disease 321 205 Host factors in influenza virus disease 322 206 The immune response and influenza virus 323 207 Anti-influenza treatment 324 Key points 325 Questions 326 Further reading 326 Chapter 21 HIV and AIDS 327 211 Origins and spread of the HIV pandemic 327 212 Molecular biology of HIV 330 213 HIV transmission and tropism 338 214 Course of HIV infection: pathogenesis and disease 339 215 Immunological abnormalities during HIV infection 342 216 Prevention and control of HIV infection 343 Key points 345 Questions 346 Further reading 346 Chapter 22 Viral hepatitis 347 221 The signs and symptoms of hepatitis 347 222 Hepatitis A virus infections 349 223 Hepatitis E virus infections 350 224 Hepatitis B virus infections 352 225 Hepatitis D virus infections 355 226 Hepatitis C virus infections 356 Key points 359 Questions 361 Further reading 361 Chapter 23 Vector-borne infections 362 231 Arboviruses and their hosts 362 232 Yellow fever virus 363 233 Dengue virus 367 234 Chikungunya virus 369 235 West Nile virus in the USA 372 Key points 375 Questions 375 Further reading 375 Chapter 24 Exotic and emerging viral infections 376 241 Ebola and Marburg viruses: emerging filoviruses 377 242 Hendra and Nipah viruses: emerging paramyxoviruses 381 243 SARS and MERS: emerging coronaviruses 383 244 Predicting the future: clues from analysis of the genomes of previously unknown viruses 386 Key points 386 Questions 386 Further reading 387 Chapter 25 Carcinogenesis and tumour viruses 388 251 Immortalization, transformation and tumourigenesis 389 252 Oncogenic viruses 390 253 Polyomaviruses, papillomaviruses and adenoviruses: the small DNA tumour viruses as experimental models 394 254 Papillomaviruses and human cancer 398 255 Polyomaviruses and human cancer 399 256 Herpesvirus involvement in human cancers 400 257 Retroviruses as experimental model tumour viruses 402 258 Retroviruses and naturally-occurring tumours 404 259 Hepatitis viruses and liver cancer 405 2510 Prospects for the control of virus-associated cancers 406 Key points 407 Questions 408 Further reading 408 Chapter 26 Vaccines and immunotherapy: the prevention of virus diseases 409 261 The principles of vaccination 411 262 Whole virus vaccines 412 263 Advantages, disadvantages and difficulties associated with whole virus vaccines 415 264 Subunit vaccines 420 265 Advantages, disadvantages and difficulties associated with subunit vaccines 421 266 Considerations for the generation and use of vaccines 422 267 Adverse reactions and clinical complications with vaccines 423 268 Eradication of virus diseases by vaccination 425 269 Immunotherapy for virus infections 428 2610 Adverse reactions and clinical complications with immunotherapy 429 Key points 429 Questions 430 Further reading 430 Chapter 27 Antiviral therapy 431 271 Scope and limitations of antiviral therapy 431 272 Antiviral therapy for herpesvirus infections 432 273 Antiviral therapy for influenza virus infections 434 274 Antiviral therapy for HIV infections 435 275 Antiviral therapy for hepatitis virus infections 439 276 Therapy for other virus infections 440 Key Points 441 Questions 441 Further Reading 442 Chapter 28 Prion diseases 443 281 The spectrum of prion diseases 443 282 The prion hypothesis 444 283 The aetiology of prion diseases 447 284 Prion disease pathogenesis 448 285 Bovine spongiform encephalopathy (BSE) 451 286 BSE and the emergence of variant CJD 453 287 Concerns about variant CJD in the future 454 288 Unresolved issues 455 Key points 456 Questions 456 Further reading 456 PART V VIROLOGY – THE WIDER CONTEXT 459 Chapter 29 The economic impact of viruses 461 291 The economics of virus infections of humans 462 292 The economics of virus infections of animals 464 293 The economics of virus infections of plants 466 294 The Netherlands tulip market crash 469 Key points 470 Further reading 470 Chapter 30 Recombinant viruses: making viruses work for us 472 301 Recombinant viruses as vaccines 473 302 Recombinant viruses for gene therapy 474 303 Retroviral vectors for gene therapy 476 304 Adenovirus vectors for gene therapy 478 305 Parvovirus vectors for gene therapy 480 306 Oncolytic viruses for cancer therapy 480 307 Recombinant viruses in the laboratory 482 Key points 482 Questions 482 Further reading 483 Chapter 31 Viruses: shaping the planet 484 311 Virus infections can give a host an evolutionary advantage 484 312 Endogenous retroviruses and host biology 485 313 Bacteriophage can be pathogenicity determinants for their hosts 488 314 Cyanophage impacts on carbon fixation and oceanic ecosystems 488 315 Virology and society: for good or ill 489 Key points 490 Questions 490 Further reading 490