Virology

María Carla Saleh is Full Professor at Institut Pasteur, where she directs the Viruses and RNAi unit within the department of Virology. She studies the antiviral response in insects and develops new vector control strategies to eliminate mosquito-borne diseases. During her postdoctoral training at the University of California, San Francisco, USA, she discovered that RNA interference was the antiviral immune system of insects. Félix Augusto Rey directs the Structural Virology unit of Institut Pasteur, France, where he studies the entry mechanisms of lipid-enveloped viruses into cells by using structural approaches. Previously, he has been junior group leader at the CNRS and was chair of Institut Pasteur�s Virology department between 2004 and 2012. During his post-doctoral training at Harvard University, USA, he determined the first structure of a flavivirus envelope protein.

Introduction xi
María-Carla SALEH and Félix AUGUSTO REY

Chapter 1 DNA Viruses 1
Lindsey M COSTANTINI and Blossom DAMANIA

1.1 Introduction to DNA viruses 1

1.1.1 What are the most abundant DNA viruses? 2

1.1.2 Human DNA viruses 4

1.2 Taxonomy and structure 6

1.2.1 Small DNA tumor virus, e.g human papillomavirus 7

1.2.2 Large DNA tumor virus, e.g Kaposi’s sarcoma-associated herpesvirus 7

1.3 Genomes 8

1.3.1 HPV, a small DNA tumor virus genome 9

1.3.2 KSHV, a large DNA tumor virus genome 10

1.4 Gene expression and regulation 10

1.4.1 Small DNA tumor virus gene expression, the HPV example 12

1.4.2 Large DNA tumor virus gene expression, the KSHV example 13

1.4.3 DNA virus inhibition of cellular gene expression 14

1.5 Infectious cycle 15

1.5.1 Small DNA tumor virus life cycle, the HPV example 16

1.5.2 Large DNA tumor virus life cycle, the KSHV example 18

1.6 Viral-induced cellular survival 20

1.6.1 Small DNA tumor virus enhancement of cell survival, e.g HPV 21

1.6.2 Large DNA tumor virus enhancement of cell survival, e.g KSHV 21

1.7 Disease prevalence and prevention 22

1.7.1 HPV, a small tumor DNA virus and disease associations 22

1.7.2 KSHV, a large DNA tumor virus and disease associations 24

1.8 Conclusion 25

1.9 References 26

Chapter 2 Double-stranded RNA Viruses 33
Michelle M. ARNOLD, Albie VAN DIJK and Susana LÓPE

2.1 Introduction 33

2.2 Rotaviruses 37

2.2.1 Virion structure 37

2.2.2 Genome 38

2.2.3 Virus entry 39

2.2.4 Transcription, replication and genome segment sorting 40

2.2.5 Host cell interactions: protein synthesis 41

2.2.6 Innate immune evasion 42

2.3 Reoviruses 43

2.3.1 The use of reovirus as an anti-cancer agent 43

2.3.2 Virion structure 43

2.3.3 Genome 44

2.3.4 Virus entry 44

2.3.5 Transcription and protein synthesis 45

2.3.6 RNA packaging and virion assembly 46

2.3.7 Innate immune evasion 48

2.4 Orbiviruses 49

2.4.1 Virion structure 51

2.4.2 Genome 51

2.4.3 Replication cycle 51

2.4.4 Virus entry 52

2.4.5 Transcription, (+)ssRNA selection and packaging, replication 52

2.4.6 Innate immune evasion 54

2.5 Concluding remarks and future challenges to understand dsRNA virus biology 55

2.6 References 56

Chapter 3 Negative-strand RNA Viruses 69
Rachel FEARNS

3.1 Introduction 69

3.2 Replication cycles of negative-strand RNA viruses 70

3.2.1 The order Mononegavirales 70

3.2.2 The order Bunyavirales 73

3.2.3 The order Articulavirales 77

3.2.4 The genus Deltavirus 78

3.2.5 Summary of viral replication cycles 80

3.3 The transcription and replication machinery of the negative-strand RNA viruses 80

3.3.1 Overview of the different negative-strand RNA virus polymerases 80

3.3.2 Orthomyxovirus polymerases and their transcription and replication mechanisms 81

3.3.3 The bunyavirus polymerase 85

3.3.4 The mononegavirus polymerases and their transcription and replication mechanisms 86

3.3.5 Concluding remarks 90

3.4 References 91

Chapter 4 Viral Epitranscriptomics 105
Rachel NETZBAND and Cara T PAGER

4.1 Introduction 105

4.1.1 What are epitranscriptomic marks? 105

4.1.2 How are epitranscriptomic marks installed? 106

4.2 The tools of RNA modification discovery 106

4.2.1 Chromatography and mass spectrometry 107

4.2.2 Sequencing methods for PTM detection 109

4.3 RNA modifications deposited by viral enzymes 113

4.3.1 Capping of 5’ end of viral RNA by viral methyltransferases 113

4.3.2 2’O-methylation of viral RNA 114

4.4 Editing of viral RNA by cellular enzymes 120

4.4.1 Editing of uridine-to-pseudouridine (Ψ) 121

4.4.2 Editing of adenosine-to-inosine 123

4.5 Deposition of RNA modifications on viral RNA by cellular enzymes 129

4.5.1 Role of N6-methyladenosine (m6A) on viral gene expression 129

4.5.2 Role of 5-methylcytosine (m5C) in viral gene expression 136

4.5.3 The viral epitranscriptome 139

4.6 Conclusion 140

4.7 References 141

Chapter 5 Defective Viral Particles 159
Carolina B LÓPEZ

5.1 Introduction 159

5.2 Discovery of defective viral genomes and early research 160

5.3 Classes of defective viral genomes 166

5.3.1 Mutations and frame shifts 168

5.3.2 Deletion DVGs 168

5.3.3 Copy-back and snap-back DVGs 169

5.3.4 Others 169

5.4 Impacts on the virus–host interaction 170

5.4.1 Interference with virus replication 170

5.4.2 Stimulation of the immune response 171

5.4.3 Antivirals and vaccines 173

5.4.4 Establishment of virus persistence 174

5.4.5 Impact on virus spread 175

5.5 Host factors affecting DVG accumulation and activity 175

5.6 Conclusion 176

5.7 References 176

Chapter 6 Enteric Viruses and the Intestinal Microbiota 197
Matthew PHILLIPS, Bria F DUNLAP, Megan T BALDRIDGE and Stephanie M KARST

6.1 Introduction 197

6.2 Enteric picornaviruses 198

6.2.1 Intestinal microbiota enhance poliovirus stability 200

6.2.2 Bacterial glycans facilitate virion attachment to target cells 200

6.2.3 Intestinal microbiota promote poliovirus recombination 200

6.3 Mouse mammary tumor virus 201

6.3.1 MMTV binds LPS, which in turn promotes a tolerogenic immune environment conducive to viral persistence 202

6.3.2 MMTV incorporates host LPS-binding proteins into its envelope 202

6.4 Reoviruses 204

6.4.1 Intestinal microbiota enhance reovirus stability 204

6.4.2 Immunostimulatory properties of bacterial flagellin inhibit rotavirus infection 206

6.4.3 Segmented filamentous bacteria have direct and indirect antiviral activity against rotavirus 207

6.4.4 How to reconcile the seemingly contradictory observations of bacterial enhancement and bacterial suppression of rotavirus infection 207

6.5 Noroviruses 208

6.5.1 Intestinal microbiota can promote norovirus infection 209

6.5.2 Intestinal microbiota can trigger antiviral immune responses during norovirus infection 211

6.6 Astroviruses 213

6.6.1 Host interferon responses reduce astrovirus replication and infection 214

6.6.2 Dysbiosis can occur after AstV infection 214

6.6.3 In vivo and in vitro culture systems for AstV pathogenesis studies 215

6.7 Overall conclusion 216

6.8 References 217

Chapter 7 Plant–Virus–Vector Interactions 227
Swapna Priya RAJARAPU, Diane E ULLMAN, Marilyne UZEST, Dorith ROTENBERG, Norma A ORDAZ and Anna E WHITFIELD

7.1 Introduction 227

7.2 Non-circulative virus transmission 228

7.2.1 Vectors of non-circulative viruses 230

7.2.2 Virus–vector interactions are highly specific 231

7.2.3 Capsid strategy 232

7.2.4 Helper strategy 232

7.3 Circulative virus transmission 234

7.3.1 Vectors of circulative viruses 234

7.4 Receptors in vectors of non-circulative viruses 235

7.4.1 Receptors in aphid stylets 236

7.4.2 Receptors in vector foreguts 237

7.5 Receptors in vectors of circulative viruses 237

7.5.1 Circulative virus binding and transcytosis 237

7.5.2 Circulative virus receptors 238

7.6 Circulative, propagative virus binding and entry 239

7.6.1 Circulative, propagative viruses binding and entry 239

7.6.2 Receptors in vectors of circulative, propagative viruses 241

7.6.3 Vertical transmission of propagative, circulative viruses 242

7.7 Virus transmission morphs for non-circulative viruses 243

7.8 “Omics” tools for studying virus–arthropod interactions 243

7.9 Vector innate immunity in response to viruses 247

7.10 Host and vector manipulation by plant viruses 250

7.10.1 Indirect (plant-mediated) manipulation of insect vectors by plant viruses 250

7.10.2 Direct manipulation of insect vectors by plant viruses 260

7.10.3 Mode of transmission and virus manipulation of plant hosts leading to enhanced vector transmission 262

7.11 Summary points 263

7.12 Acknowledgments 264

7.13 References 265

Chapter 8 Evolution and Origin of Human Viruses 289
Rachele CAGLIANI, Alessandra MOZZI, Chiara PONTREMOLI, Manuela SIRONI

8.1 Introduction 289

8.2 Origin and ancient evolutionary history of human viruses 290

8.2.1 Origin and ancient evolutionary history of human-infecting RNA viruses 290

8.2.2 Origin and ancient evolutionary history of human-infecting reverse-transcribing viruses 295

8.2.3 Origin and ancient evolutionary history of human-infecting DNA viruses 298

8.3 Sources of viral genetic diversity 303

8.4 Viral evolution and host range 307

8.5 Recent evolution of human RNA viruses – selected examples 313

8.6 Conclusion 319

8.7 References 320

List of Authors 341

Index 345