Introduction to Modern Virology

Preface xvii About the companion website xix PART I THE NATURE OF VIRUSES 1 Chapter 1 Towards a definition of a virus 3 1.1 Discovery of viruses 4 1.2 Multiplication of viruses 5 1.3 The virus multiplication cycle 6 1.4 Viruses can be defined in chemical terms 7 1.5 Multiplication of bacterial and animal viruses is fundamentally similar 10 1.6 Viruses can be manipulated genetically 11 1.7 Properties of viruses 11 1.8 Origin of viruses 12 Key points 12 Further reading 12 Chapter 2 The structure of virus particles 13 2.1 Virus particles are constructed from subunits 13 2.2 The structure of filamentous viruses and nucleoproteins 14 2.3 The structure is of isometric virus particles 15 2.4 Enveloped (membrane-bound) virus particles 24 2.5 Virus particles with head-tail morphology 27 2.6 Frequency of occurrence of different virus particle morphologies 28 2.7 Principles of disassemply: virus particles are metastable 28 Key points 29 Further reading 29 Chapter 3 Classification of viruses 30 3.1 Classification on the basis of disease 30 3.2 Classification on the basis of host organism 31 3.3 Classification on the basis of virus particle morphology 31 3.4 Classification on the basis of viral nucleic acids 32 3.5 Classification on the basis of taxonomy 34 3.6 Satellites, viroids and prions 35 Key points 37 Further reading 38 Chapter 4 The evolution of viruses 39 4.1 Mechanisms of virus evolution 40 4.2 The potential for rapid evolution: mutation and quasispecies 40 4.3 Rapid evolution: recombination 43 4.4 Rapid evolution: reassortment 43 4.5 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 5.1 Culturing wild virus isolates 52 5.2 Enumeration of viruses 54 5.3 Measuring infectious virus titres 55 5.4 Measuring physical virus titres 57 5.5 Detecting virus in a sample 58 5.6 Understanding virus replication cycles 62 5.7 Viral genetics and reverse genetics 63 5.8 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 6.1 Infection of animal cells: the nature and importance of receptors 69 6.2 Infection of animal cells: enveloped viruses 73 6.3 Infection of animal cells: non-enveloped viruses 78 6.4 Infection of plant cells 80 6.5 Infection of bacteria 81 6.6 Infection of cells: post-entry events 82 6.7 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 7.1 The universal mechanism of DNA synthesis 87 7.2 Replication of circular double-stranded DNA genomes 90 7.3 Replication of linear double-stranded DNA genomes that can form circles 93 7.4 Replication of linear double-stranded DNA genomes that do not circularize 96 7.5 Replication of single-stranded circular DNA genomes 100 7.6 Replication of single-stranded linear DNA genomes 100 7.7 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 8.1 Nature and diversity of RNA virus genomes 106 8.2 Regulatory elements for RNA virus genome synthesis 106 8.3 Synthesis of the RNA genome of Baltimore class 3 viruses 111 8.4 Synthesis of the RNA genome of Baltimore class 4 viruses 111 8.5 Synthesis of the RNA genome of Baltimore class 5 viruses 115 8.6 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 9.1 The retrovirus replication cycle 122 9.2 Discovery of reverse transcription 122 9.3 Retroviral reverse transcriptase 123 9.4 Mechanism of retroviral reverse transcription 125 9.5 Integration of retroviral DNA into cell DNA 128 9.6 Production of retrovirus progeny genomes 130 9.7 Spumaviruses: retrovirus with unusual features 131 9.8 The hepadnavirus replication cycle 131 9.9 Mechanism of hepadnavirus reverse transcription 131 9.10 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 10.1 The DNA viruses and retroviruses: Baltimore classes 1, 2, 6 and 7 137 10.2 Polyomaviruses 138 10.3 Papillomaviruses 142 10.4 Adenoviruses 144 10.5 Herpesviruses 147 10.6 Poxviruses 149 10.7 Parvoviruses 149 10.8 Retroviruses 150 10.9 Hepadnaviruses 153 10.10 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 11.1 The RNA viruses: Baltimore classes 3, 4 and 5 157 11.2 Reoviruses 158 11.3 Picornaviruses 163 11.4 Alphaviruses 164 11.5 Coronaviruses 166 11.6 Negative sense RNA viruses with segmented genomes 169 11.7 Orthomyxoviruses 169 11.8 Arenaviruses 173 11.9 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 12.1 Self-assembly from mature virion components 180 12.2 Assembly of viruses with a helical structure 180 12.3 Assembly of viruses with an isometric structure 184 12.4 Assembly of complex viruses 187 12.5 Sequence-dependent and -independent packaging of virus DNA in virus particles 189 12.6 The assembly of enveloped viruses 190 12.7 Segmented virus genomes: the acquisition of multiple nucleic acid molecules 194 12.8 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 13.1 Innate immune responses in vertebrates - discovery of interferon 202 13.2 Induction of type 1 interferon responses 203 13.3 Virus countermeasures to innate immunity 207 13.4 TRIM proteins and immunity 209 13.5 Intrinsic resistance to viruses in vertebrates 210 13.6 Innate and intrinsic immunity and the outcome of infection 212 13.7 RNAi is an important antiviral mechanism in invertebrates and plants 212 13.8 Detecting and signalling infection in invertebrates and plants 214 13.9 Virus resistance mechanisms in bacteria and archaea 215 Key points 216 Questions 217 References 217 Chapter 14 The adaptive immune response 218 14.1 General features of the adaptive immune system 219 14.2 Cell-mediated immunity 221 14.3 Antibody-mediated humoral immunity 226 14.4 Virus evasion of adaptive immunity 232 14.5 Age and adaptive immunity 233 14.6 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 15.1 Acutely cytopathogenic infections 238 15.2 Persistent infections 238 15.3 Latent infections 241 15.4 Transforming infections 243 15.5 Abortive infections 243 15.6 Null infections 244 15.7 How do animal viruses kill cells? 244 Key points 246 Questions 247 Further reading 247 Chapter 16 Animal virus-host interactions 248 16.1 Cause and effect: Koch's postulates 248 16.2 A classification of virus-host interactions 249 16.3 Acute infections 252 16.4 Subclinical infections 253 16.5 Persistent and chronic infections 254 16.6 Latent infections 256 16.7 Slowly progressive diseases 257 16.8 Virus-induced tumours 258 Key points 259 Questions 260 Further reading 260 Chapter 17 Mechanisms in virus latency 261 17.1 The latent interaction of virus and host 261 17.2 Gene expression and the lytic and lysogenic life of bacteriophage lambda 263 17.3 Herpes simplex virus latency 270 17.4 Epstein-Barr virus latency 274 17.5 Latency in other herpesviruses 275 17.6 HIV-1 latency 277 Key points 277 Questions 278 Further reading 278 Chapter 18 Transmission of viruses 279 18.1 Virus transmission cycles 279 18.2 Barriers to transmission 281 18.3 Routes of horizontal transmission in animals 282 18.4 Vertical transmission 285 18.5 Vector-borne viruses and zoonotic transmission 287 18.6 Epidemiology of virus infections 289 18.7 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 19.1 A survey of human viral pathogens 295 19.2 Factors affecting the relative incidence of viral disease 297 19.3 Factors determining the nature and severity of viral disease 299 19.4 Common signs and symptoms of viral infection 301 19.5 Acute viral infection 1: gastrointestinal infections 302 19.6 Acute viral infection 2: respiratory infections 304 19.7 Acute viral infection 3: systemic spread 306 19.8 Acute viral disease: conclusions 306 Key points 307 Questions 308 Further reading 308 Chapter 20 Influenza virus infection 309 20.1 The origins of human influenza viruses 309 20.2 Influenza virus replication 315 20.3 Influenza virus infection and disease 316 20.4 Virus determinants of disease 321 20.5 Host factors in influenza virus disease 322 20.6 The immune response and influenza virus 323 20.7 Anti-influenza treatment 324 Key points 325 Questions 326 Further reading 326 Chapter 21 HIV and AIDS 327 21.1 Origins and spread of the HIV pandemic 327 21.2 Molecular biology of HIV 330 21.3 HIV transmission and tropism 338 21.4 Course of HIV infection: pathogenesis and disease 339 21.5 Immunological abnormalities during HIV infection 342 21.6 Prevention and control of HIV infection 343 Key points 345 Questions 346 Further reading 346 Chapter 22 Viral hepatitis 347 22.1 The signs and symptoms of hepatitis 347 22.2 Hepatitis A virus infections 349 22.3 Hepatitis E virus infections 350 22.4 Hepatitis B virus infections 352 22.5 Hepatitis D virus infections 355 22.6 Hepatitis C virus infections 356 Key points 359 Questions 361 Further reading 361 Chapter 23 Vector-borne infections 362 23.1 Arboviruses and their hosts 362 23.2 Yellow fever virus 363 23.3 Dengue virus 367 23.4 Chikungunya virus 369 23.5 West Nile virus in the USA 372 Key points 375 Questions 375 Further reading 375 Chapter 24 Exotic and emerging viral infections 376 24.1 Ebola and Marburg viruses: emerging filoviruses 377 24.2 Hendra and Nipah viruses: emerging paramyxoviruses 381 24.3 SARS and MERS: emerging coronaviruses 383 24.4 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 25.1 Immortalization, transformation and tumourigenesis 389 25.2 Oncogenic viruses 390 25.3 Polyomaviruses, papillomaviruses and adenoviruses: the small DNA tumour viruses as experimental models 394 25.4 Papillomaviruses and human cancer 398 25.5 Polyomaviruses and human cancer 399 25.6 Herpesvirus involvement in human cancers 400 25.7 Retroviruses as experimental model tumour viruses 402 25.8 Retroviruses and naturally-occurring tumours 404 25.9 Hepatitis viruses and liver cancer 405 25.10 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 26.1 The principles of vaccination 411 26.2 Whole virus vaccines 412 26.3 Advantages, disadvantages and difficulties associated with whole virus vaccines 415 26.4 Subunit vaccines 420 26.5 Advantages, disadvantages and difficulties associated with subunit vaccines 421 26.6 Considerations for the generation and use of vaccines 422 26.7 Adverse reactions and clinical complications with vaccines 423 26.8 Eradication of virus diseases by vaccination 425 26.9 Immunotherapy for virus infections 428 26.10 Adverse reactions and clinical complications with immunotherapy 429 Key points 429 Questions 430 Further reading 430 Chapter 27 Antiviral therapy 431 27.1 Scope and limitations of antiviral therapy 431 27.2 Antiviral therapy for herpesvirus infections 432 27.3 Antiviral therapy for influenza virus infections 434 27.4 Antiviral therapy for HIV infections 435 27.5 Antiviral therapy for hepatitis virus infections 439 27.6 Therapy for other virus infections 440 Key Points 441 Questions 441 Further Reading 442 Chapter 28 Prion diseases 443 28.1 The spectrum of prion diseases 443 28.2 The prion hypothesis 444 28.3 The aetiology of prion diseases 447 28.4 Prion disease pathogenesis 448 28.5 Bovine spongiform encephalopathy (BSE) 451 28.6 BSE and the emergence of variant CJD 453 28.7 Concerns about variant CJD in the future 454 28.8 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 29.1 The economics of virus infections of humans 462 29.2 The economics of virus infections of animals 464 29.3 The economics of virus infections of plants 466 29.4 The Netherlands tulip market crash 469 Key points 470 Further reading 470 Chapter 30 Recombinant viruses: making viruses work for us 472 30.1 Recombinant viruses as vaccines 473 30.2 Recombinant viruses for gene therapy 474 30.3 Retroviral vectors for gene therapy 476 30.4 Adenovirus vectors for gene therapy 478 30.5 Parvovirus vectors for gene therapy 480 30.6 Oncolytic viruses for cancer therapy 480 30.7 Recombinant viruses in the laboratory 482 Key points 482 Questions 482 Further reading 483 Chapter 31 Viruses: shaping the planet 484 31.1 Virus infections can give a host an evolutionary advantage 484 31.2 Endogenous retroviruses and host biology 485 31.3 Bacteriophage can be pathogenicity determinants for their hosts 488 31.4 Cyanophage impacts on carbon fixation and oceanic ecosystems 488 31.5 Virology and society: for good or ill 489 Key points 490 Questions 490 Further reading 490 Index 491