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 xiMaría-Carla SALEH and Félix AUGUSTO REYChapter 1 DNA Viruses 1Lindsey M COSTANTINI and Blossom DAMANIA1.1 Introduction to DNA viruses 11.1.1 What are the most abundant DNA viruses? 21.1.2 Human DNA viruses 41.2 Taxonomy and structure 61.2.1 Small DNA tumor virus, e.g human papillomavirus 71.2.2 Large DNA tumor virus, e.g Kaposi’s sarcoma-associated herpesvirus 71.3 Genomes 81.3.1 HPV, a small DNA tumor virus genome 91.3.2 KSHV, a large DNA tumor virus genome 101.4 Gene expression and regulation 101.4.1 Small DNA tumor virus gene expression, the HPV example 121.4.2 Large DNA tumor virus gene expression, the KSHV example 131.4.3 DNA virus inhibition of cellular gene expression 141.5 Infectious cycle 151.5.1 Small DNA tumor virus life cycle, the HPV example 161.5.2 Large DNA tumor virus life cycle, the KSHV example 181.6 Viral-induced cellular survival 201.6.1 Small DNA tumor virus enhancement of cell survival, e.g HPV 211.6.2 Large DNA tumor virus enhancement of cell survival, e.g KSHV 211.7 Disease prevalence and prevention 221.7.1 HPV, a small tumor DNA virus and disease associations 221.7.2 KSHV, a large DNA tumor virus and disease associations 241.8 Conclusion 251.9 References 26Chapter 2 Double-stranded RNA Viruses 33Michelle M. ARNOLD, Albie VAN DIJK and Susana LÓPE2.1 Introduction 332.2 Rotaviruses 372.2.1 Virion structure 372.2.2 Genome 382.2.3 Virus entry 392.2.4 Transcription, replication and genome segment sorting 402.2.5 Host cell interactions: protein synthesis 412.2.6 Innate immune evasion 422.3 Reoviruses 432.3.1 The use of reovirus as an anti-cancer agent 432.3.2 Virion structure 432.3.3 Genome 442.3.4 Virus entry 442.3.5 Transcription and protein synthesis 452.3.6 RNA packaging and virion assembly 462.3.7 Innate immune evasion 482.4 Orbiviruses 492.4.1 Virion structure 512.4.2 Genome 512.4.3 Replication cycle 512.4.4 Virus entry 522.4.5 Transcription, (+)ssRNA selection and packaging, replication 522.4.6 Innate immune evasion 542.5 Concluding remarks and future challenges to understand dsRNA virus biology 552.6 References 56Chapter 3 Negative-strand RNA Viruses 69Rachel FEARNS3.1 Introduction 693.2 Replication cycles of negative-strand RNA viruses 703.2.1 The order Mononegavirales 703.2.2 The order Bunyavirales 733.2.3 The order Articulavirales 773.2.4 The genus Deltavirus 783.2.5 Summary of viral replication cycles 803.3 The transcription and replication machinery of the negative-strand RNA viruses 803.3.1 Overview of the different negative-strand RNA virus polymerases 803.3.2 Orthomyxovirus polymerases and their transcription and replication mechanisms 813.3.3 The bunyavirus polymerase 853.3.4 The mononegavirus polymerases and their transcription and replication mechanisms 863.3.5 Concluding remarks 903.4 References 91Chapter 4 Viral Epitranscriptomics 105Rachel NETZBAND and Cara T PAGER4.1 Introduction 1054.1.1 What are epitranscriptomic marks? 1054.1.2 How are epitranscriptomic marks installed? 1064.2 The tools of RNA modification discovery 1064.2.1 Chromatography and mass spectrometry 1074.2.2 Sequencing methods for PTM detection 1094.3 RNA modifications deposited by viral enzymes 1134.3.1 Capping of 5’ end of viral RNA by viral methyltransferases 1134.3.2 2’O-methylation of viral RNA 1144.4 Editing of viral RNA by cellular enzymes 1204.4.1 Editing of uridine-to-pseudouridine (Ψ) 1214.4.2 Editing of adenosine-to-inosine 1234.5 Deposition of RNA modifications on viral RNA by cellular enzymes 1294.5.1 Role of N6-methyladenosine (m6A) on viral gene expression 1294.5.2 Role of 5-methylcytosine (m5C) in viral gene expression 1364.5.3 The viral epitranscriptome 1394.6 Conclusion 1404.7 References 141Chapter 5 Defective Viral Particles 159Carolina B LÓPEZ5.1 Introduction 1595.2 Discovery of defective viral genomes and early research 1605.3 Classes of defective viral genomes 1665.3.1 Mutations and frame shifts 1685.3.2 Deletion DVGs 1685.3.3 Copy-back and snap-back DVGs 1695.3.4 Others 1695.4 Impacts on the virus–host interaction 1705.4.1 Interference with virus replication 1705.4.2 Stimulation of the immune response 1715.4.3 Antivirals and vaccines 1735.4.4 Establishment of virus persistence 1745.4.5 Impact on virus spread 1755.5 Host factors affecting DVG accumulation and activity 1755.6 Conclusion 1765.7 References 176Chapter 6 Enteric Viruses and the Intestinal Microbiota 197Matthew PHILLIPS, Bria F DUNLAP, Megan T BALDRIDGE and Stephanie M KARST6.1 Introduction 1976.2 Enteric picornaviruses 1986.2.1 Intestinal microbiota enhance poliovirus stability 2006.2.2 Bacterial glycans facilitate virion attachment to target cells 2006.2.3 Intestinal microbiota promote poliovirus recombination 2006.3 Mouse mammary tumor virus 2016.3.1 MMTV binds LPS, which in turn promotes a tolerogenic immune environment conducive to viral persistence 2026.3.2 MMTV incorporates host LPS-binding proteins into its envelope 2026.4 Reoviruses 2046.4.1 Intestinal microbiota enhance reovirus stability 2046.4.2 Immunostimulatory properties of bacterial flagellin inhibit rotavirus infection 2066.4.3 Segmented filamentous bacteria have direct and indirect antiviral activity against rotavirus 2076.4.4 How to reconcile the seemingly contradictory observations of bacterial enhancement and bacterial suppression of rotavirus infection 2076.5 Noroviruses 2086.5.1 Intestinal microbiota can promote norovirus infection 2096.5.2 Intestinal microbiota can trigger antiviral immune responses during norovirus infection 2116.6 Astroviruses 2136.6.1 Host interferon responses reduce astrovirus replication and infection 2146.6.2 Dysbiosis can occur after AstV infection 2146.6.3 In vivo and in vitro culture systems for AstV pathogenesis studies 2156.7 Overall conclusion 2166.8 References 217Chapter 7 Plant–Virus–Vector Interactions 227Swapna Priya RAJARAPU, Diane E ULLMAN, Marilyne UZEST, Dorith ROTENBERG, Norma A ORDAZ and Anna E WHITFIELD7.1 Introduction 2277.2 Non-circulative virus transmission 2287.2.1 Vectors of non-circulative viruses 2307.2.2 Virus–vector interactions are highly specific 2317.2.3 Capsid strategy 2327.2.4 Helper strategy 2327.3 Circulative virus transmission 2347.3.1 Vectors of circulative viruses 2347.4 Receptors in vectors of non-circulative viruses 2357.4.1 Receptors in aphid stylets 2367.4.2 Receptors in vector foreguts 2377.5 Receptors in vectors of circulative viruses 2377.5.1 Circulative virus binding and transcytosis 2377.5.2 Circulative virus receptors 2387.6 Circulative, propagative virus binding and entry 2397.6.1 Circulative, propagative viruses binding and entry 2397.6.2 Receptors in vectors of circulative, propagative viruses 2417.6.3 Vertical transmission of propagative, circulative viruses 2427.7 Virus transmission morphs for non-circulative viruses 2437.8 “Omics” tools for studying virus–arthropod interactions 2437.9 Vector innate immunity in response to viruses 2477.10 Host and vector manipulation by plant viruses 2507.10.1 Indirect (plant-mediated) manipulation of insect vectors by plant viruses 2507.10.2 Direct manipulation of insect vectors by plant viruses 2607.10.3 Mode of transmission and virus manipulation of plant hosts leading to enhanced vector transmission 2627.11 Summary points 2637.12 Acknowledgments 2647.13 References 265Chapter 8 Evolution and Origin of Human Viruses 289Rachele CAGLIANI, Alessandra MOZZI, Chiara PONTREMOLI, Manuela SIRONI8.1 Introduction 2898.2 Origin and ancient evolutionary history of human viruses 2908.2.1 Origin and ancient evolutionary history of human-infecting RNA viruses 2908.2.2 Origin and ancient evolutionary history of human-infecting reverse-transcribing viruses 2958.2.3 Origin and ancient evolutionary history of human-infecting DNA viruses 2988.3 Sources of viral genetic diversity 3038.4 Viral evolution and host range 3078.5 Recent evolution of human RNA viruses – selected examples 3138.6 Conclusion 3198.7 References 320List of Authors 341Index 345

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 xiMaría-Carla SALEH and Félix AUGUSTO REYChapter 1 DNA Viruses 1Lindsey M COSTANTINI and Blossom DAMANIA1.1 Introduction to DNA viruses 11.1.1 What are the most abundant DNA viruses? 21.1.2 Human DNA viruses 41.2 Taxonomy and structure 61.2.1 Small DNA tumor virus, e.g human papillomavirus 71.2.2 Large DNA tumor virus, e.g Kaposi’s sarcoma-associated herpesvirus 71.3 Genomes 81.3.1 HPV, a small DNA tumor virus genome 91.3.2 KSHV, a large DNA tumor virus genome 101.4 Gene expression and regulation 101.4.1 Small DNA tumor virus gene expression, the HPV example 121.4.2 Large DNA tumor virus gene expression, the KSHV example 131.4.3 DNA virus inhibition of cellular gene expression 141.5 Infectious cycle 151.5.1 Small DNA tumor virus life cycle, the HPV example 161.5.2 Large DNA tumor virus life cycle, the KSHV example 181.6 Viral-induced cellular survival 201.6.1 Small DNA tumor virus enhancement of cell survival, e.g HPV 211.6.2 Large DNA tumor virus enhancement of cell survival, e.g KSHV 211.7 Disease prevalence and prevention 221.7.1 HPV, a small tumor DNA virus and disease associations 221.7.2 KSHV, a large DNA tumor virus and disease associations 241.8 Conclusion 251.9 References 26Chapter 2 Double-stranded RNA Viruses 33Michelle M. ARNOLD, Albie VAN DIJK and Susana LÓPE2.1 Introduction 332.2 Rotaviruses 372.2.1 Virion structure 372.2.2 Genome 382.2.3 Virus entry 392.2.4 Transcription, replication and genome segment sorting 402.2.5 Host cell interactions: protein synthesis 412.2.6 Innate immune evasion 422.3 Reoviruses 432.3.1 The use of reovirus as an anti-cancer agent 432.3.2 Virion structure 432.3.3 Genome 442.3.4 Virus entry 442.3.5 Transcription and protein synthesis 452.3.6 RNA packaging and virion assembly 462.3.7 Innate immune evasion 482.4 Orbiviruses 492.4.1 Virion structure 512.4.2 Genome 512.4.3 Replication cycle 512.4.4 Virus entry 522.4.5 Transcription, (+)ssRNA selection and packaging, replication 522.4.6 Innate immune evasion 542.5 Concluding remarks and future challenges to understand dsRNA virus biology 552.6 References 56Chapter 3 Negative-strand RNA Viruses 69Rachel FEARNS3.1 Introduction 693.2 Replication cycles of negative-strand RNA viruses 703.2.1 The order Mononegavirales 703.2.2 The order Bunyavirales 733.2.3 The order Articulavirales 773.2.4 The genus Deltavirus 783.2.5 Summary of viral replication cycles 803.3 The transcription and replication machinery of the negative-strand RNA viruses 803.3.1 Overview of the different negative-strand RNA virus polymerases 803.3.2 Orthomyxovirus polymerases and their transcription and replication mechanisms 813.3.3 The bunyavirus polymerase 853.3.4 The mononegavirus polymerases and their transcription and replication mechanisms 863.3.5 Concluding remarks 903.4 References 91Chapter 4 Viral Epitranscriptomics 105Rachel NETZBAND and Cara T PAGER4.1 Introduction 1054.1.1 What are epitranscriptomic marks? 1054.1.2 How are epitranscriptomic marks installed? 1064.2 The tools of RNA modification discovery 1064.2.1 Chromatography and mass spectrometry 1074.2.2 Sequencing methods for PTM detection 1094.3 RNA modifications deposited by viral enzymes 1134.3.1 Capping of 5’ end of viral RNA by viral methyltransferases 1134.3.2 2’O-methylation of viral RNA 1144.4 Editing of viral RNA by cellular enzymes 1204.4.1 Editing of uridine-to-pseudouridine (Ψ) 1214.4.2 Editing of adenosine-to-inosine 1234.5 Deposition of RNA modifications on viral RNA by cellular enzymes 1294.5.1 Role of N6-methyladenosine (m6A) on viral gene expression 1294.5.2 Role of 5-methylcytosine (m5C) in viral gene expression 1364.5.3 The viral epitranscriptome 1394.6 Conclusion 1404.7 References 141Chapter 5 Defective Viral Particles 159Carolina B LÓPEZ5.1 Introduction 1595.2 Discovery of defective viral genomes and early research 1605.3 Classes of defective viral genomes 1665.3.1 Mutations and frame shifts 1685.3.2 Deletion DVGs 1685.3.3 Copy-back and snap-back DVGs 1695.3.4 Others 1695.4 Impacts on the virus–host interaction 1705.4.1 Interference with virus replication 1705.4.2 Stimulation of the immune response 1715.4.3 Antivirals and vaccines 1735.4.4 Establishment of virus persistence 1745.4.5 Impact on virus spread 1755.5 Host factors affecting DVG accumulation and activity 1755.6 Conclusion 1765.7 References 176Chapter 6 Enteric Viruses and the Intestinal Microbiota 197Matthew PHILLIPS, Bria F DUNLAP, Megan T BALDRIDGE and Stephanie M KARST6.1 Introduction 1976.2 Enteric picornaviruses 1986.2.1 Intestinal microbiota enhance poliovirus stability 2006.2.2 Bacterial glycans facilitate virion attachment to target cells 2006.2.3 Intestinal microbiota promote poliovirus recombination 2006.3 Mouse mammary tumor virus 2016.3.1 MMTV binds LPS, which in turn promotes a tolerogenic immune environment conducive to viral persistence 2026.3.2 MMTV incorporates host LPS-binding proteins into its envelope 2026.4 Reoviruses 2046.4.1 Intestinal microbiota enhance reovirus stability 2046.4.2 Immunostimulatory properties of bacterial flagellin inhibit rotavirus infection 2066.4.3 Segmented filamentous bacteria have direct and indirect antiviral activity against rotavirus 2076.4.4 How to reconcile the seemingly contradictory observations of bacterial enhancement and bacterial suppression of rotavirus infection 2076.5 Noroviruses 2086.5.1 Intestinal microbiota can promote norovirus infection 2096.5.2 Intestinal microbiota can trigger antiviral immune responses during norovirus infection 2116.6 Astroviruses 2136.6.1 Host interferon responses reduce astrovirus replication and infection 2146.6.2 Dysbiosis can occur after AstV infection 2146.6.3 In vivo and in vitro culture systems for AstV pathogenesis studies 2156.7 Overall conclusion 2166.8 References 217Chapter 7 Plant–Virus–Vector Interactions 227Swapna Priya RAJARAPU, Diane E ULLMAN, Marilyne UZEST, Dorith ROTENBERG, Norma A ORDAZ and Anna E WHITFIELD7.1 Introduction 2277.2 Non-circulative virus transmission 2287.2.1 Vectors of non-circulative viruses 2307.2.2 Virus–vector interactions are highly specific 2317.2.3 Capsid strategy 2327.2.4 Helper strategy 2327.3 Circulative virus transmission 2347.3.1 Vectors of circulative viruses 2347.4 Receptors in vectors of non-circulative viruses 2357.4.1 Receptors in aphid stylets 2367.4.2 Receptors in vector foreguts 2377.5 Receptors in vectors of circulative viruses 2377.5.1 Circulative virus binding and transcytosis 2377.5.2 Circulative virus receptors 2387.6 Circulative, propagative virus binding and entry 2397.6.1 Circulative, propagative viruses binding and entry 2397.6.2 Receptors in vectors of circulative, propagative viruses 2417.6.3 Vertical transmission of propagative, circulative viruses 2427.7 Virus transmission morphs for non-circulative viruses 2437.8 “Omics” tools for studying virus–arthropod interactions 2437.9 Vector innate immunity in response to viruses 2477.10 Host and vector manipulation by plant viruses 2507.10.1 Indirect (plant-mediated) manipulation of insect vectors by plant viruses 2507.10.2 Direct manipulation of insect vectors by plant viruses 2607.10.3 Mode of transmission and virus manipulation of plant hosts leading to enhanced vector transmission 2627.11 Summary points 2637.12 Acknowledgments 2647.13 References 265Chapter 8 Evolution and Origin of Human Viruses 289Rachele CAGLIANI, Alessandra MOZZI, Chiara PONTREMOLI, Manuela SIRONI8.1 Introduction 2898.2 Origin and ancient evolutionary history of human viruses 2908.2.1 Origin and ancient evolutionary history of human-infecting RNA viruses 2908.2.2 Origin and ancient evolutionary history of human-infecting reverse-transcribing viruses 2958.2.3 Origin and ancient evolutionary history of human-infecting DNA viruses 2988.3 Sources of viral genetic diversity 3038.4 Viral evolution and host range 3078.5 Recent evolution of human RNA viruses – selected examples 3138.6 Conclusion 3198.7 References 320List of Authors 341Index 345

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 xiMaría-Carla SALEH and Félix AUGUSTO REYChapter 1 DNA Viruses 1Lindsey M COSTANTINI and Blossom DAMANIA1.1 Introduction to DNA viruses 11.1.1 What are the most abundant DNA viruses? 21.1.2 Human DNA viruses 41.2 Taxonomy and structure 61.2.1 Small DNA tumor virus, e.g human papillomavirus 71.2.2 Large DNA tumor virus, e.g Kaposi’s sarcoma-associated herpesvirus 71.3 Genomes 81.3.1 HPV, a small DNA tumor virus genome 91.3.2 KSHV, a large DNA tumor virus genome 101.4 Gene expression and regulation 101.4.1 Small DNA tumor virus gene expression, the HPV example 121.4.2 Large DNA tumor virus gene expression, the KSHV example 131.4.3 DNA virus inhibition of cellular gene expression 141.5 Infectious cycle 151.5.1 Small DNA tumor virus life cycle, the HPV example 161.5.2 Large DNA tumor virus life cycle, the KSHV example 181.6 Viral-induced cellular survival 201.6.1 Small DNA tumor virus enhancement of cell survival, e.g HPV 211.6.2 Large DNA tumor virus enhancement of cell survival, e.g KSHV 211.7 Disease prevalence and prevention 221.7.1 HPV, a small tumor DNA virus and disease associations 221.7.2 KSHV, a large DNA tumor virus and disease associations 241.8 Conclusion 251.9 References 26Chapter 2 Double-stranded RNA Viruses 33Michelle M. ARNOLD, Albie VAN DIJK and Susana LÓPE2.1 Introduction 332.2 Rotaviruses 372.2.1 Virion structure 372.2.2 Genome 382.2.3 Virus entry 392.2.4 Transcription, replication and genome segment sorting 402.2.5 Host cell interactions: protein synthesis 412.2.6 Innate immune evasion 422.3 Reoviruses 432.3.1 The use of reovirus as an anti-cancer agent 432.3.2 Virion structure 432.3.3 Genome 442.3.4 Virus entry 442.3.5 Transcription and protein synthesis 452.3.6 RNA packaging and virion assembly 462.3.7 Innate immune evasion 482.4 Orbiviruses 492.4.1 Virion structure 512.4.2 Genome 512.4.3 Replication cycle 512.4.4 Virus entry 522.4.5 Transcription, (+)ssRNA selection and packaging, replication 522.4.6 Innate immune evasion 542.5 Concluding remarks and future challenges to understand dsRNA virus biology 552.6 References 56Chapter 3 Negative-strand RNA Viruses 69Rachel FEARNS3.1 Introduction 693.2 Replication cycles of negative-strand RNA viruses 703.2.1 The order Mononegavirales 703.2.2 The order Bunyavirales 733.2.3 The order Articulavirales 773.2.4 The genus Deltavirus 783.2.5 Summary of viral replication cycles 803.3 The transcription and replication machinery of the negative-strand RNA viruses 803.3.1 Overview of the different negative-strand RNA virus polymerases 803.3.2 Orthomyxovirus polymerases and their transcription and replication mechanisms 813.3.3 The bunyavirus polymerase 853.3.4 The mononegavirus polymerases and their transcription and replication mechanisms 863.3.5 Concluding remarks 903.4 References 91Chapter 4 Viral Epitranscriptomics 105Rachel NETZBAND and Cara T PAGER4.1 Introduction 1054.1.1 What are epitranscriptomic marks? 1054.1.2 How are epitranscriptomic marks installed? 1064.2 The tools of RNA modification discovery 1064.2.1 Chromatography and mass spectrometry 1074.2.2 Sequencing methods for PTM detection 1094.3 RNA modifications deposited by viral enzymes 1134.3.1 Capping of 5’ end of viral RNA by viral methyltransferases 1134.3.2 2’O-methylation of viral RNA 1144.4 Editing of viral RNA by cellular enzymes 1204.4.1 Editing of uridine-to-pseudouridine (Ψ) 1214.4.2 Editing of adenosine-to-inosine 1234.5 Deposition of RNA modifications on viral RNA by cellular enzymes 1294.5.1 Role of N6-methyladenosine (m6A) on viral gene expression 1294.5.2 Role of 5-methylcytosine (m5C) in viral gene expression 1364.5.3 The viral epitranscriptome 1394.6 Conclusion 1404.7 References 141Chapter 5 Defective Viral Particles 159Carolina B LÓPEZ5.1 Introduction 1595.2 Discovery of defective viral genomes and early research 1605.3 Classes of defective viral genomes 1665.3.1 Mutations and frame shifts 1685.3.2 Deletion DVGs 1685.3.3 Copy-back and snap-back DVGs 1695.3.4 Others 1695.4 Impacts on the virus–host interaction 1705.4.1 Interference with virus replication 1705.4.2 Stimulation of the immune response 1715.4.3 Antivirals and vaccines 1735.4.4 Establishment of virus persistence 1745.4.5 Impact on virus spread 1755.5 Host factors affecting DVG accumulation and activity 1755.6 Conclusion 1765.7 References 176Chapter 6 Enteric Viruses and the Intestinal Microbiota 197Matthew PHILLIPS, Bria F DUNLAP, Megan T BALDRIDGE and Stephanie M KARST6.1 Introduction 1976.2 Enteric picornaviruses 1986.2.1 Intestinal microbiota enhance poliovirus stability 2006.2.2 Bacterial glycans facilitate virion attachment to target cells 2006.2.3 Intestinal microbiota promote poliovirus recombination 2006.3 Mouse mammary tumor virus 2016.3.1 MMTV binds LPS, which in turn promotes a tolerogenic immune environment conducive to viral persistence 2026.3.2 MMTV incorporates host LPS-binding proteins into its envelope 2026.4 Reoviruses 2046.4.1 Intestinal microbiota enhance reovirus stability 2046.4.2 Immunostimulatory properties of bacterial flagellin inhibit rotavirus infection 2066.4.3 Segmented filamentous bacteria have direct and indirect antiviral activity against rotavirus 2076.4.4 How to reconcile the seemingly contradictory observations of bacterial enhancement and bacterial suppression of rotavirus infection 2076.5 Noroviruses 2086.5.1 Intestinal microbiota can promote norovirus infection 2096.5.2 Intestinal microbiota can trigger antiviral immune responses during norovirus infection 2116.6 Astroviruses 2136.6.1 Host interferon responses reduce astrovirus replication and infection 2146.6.2 Dysbiosis can occur after AstV infection 2146.6.3 In vivo and in vitro culture systems for AstV pathogenesis studies 2156.7 Overall conclusion 2166.8 References 217Chapter 7 Plant–Virus–Vector Interactions 227Swapna Priya RAJARAPU, Diane E ULLMAN, Marilyne UZEST, Dorith ROTENBERG, Norma A ORDAZ and Anna E WHITFIELD7.1 Introduction 2277.2 Non-circulative virus transmission 2287.2.1 Vectors of non-circulative viruses 2307.2.2 Virus–vector interactions are highly specific 2317.2.3 Capsid strategy 2327.2.4 Helper strategy 2327.3 Circulative virus transmission 2347.3.1 Vectors of circulative viruses 2347.4 Receptors in vectors of non-circulative viruses 2357.4.1 Receptors in aphid stylets 2367.4.2 Receptors in vector foreguts 2377.5 Receptors in vectors of circulative viruses 2377.5.1 Circulative virus binding and transcytosis 2377.5.2 Circulative virus receptors 2387.6 Circulative, propagative virus binding and entry 2397.6.1 Circulative, propagative viruses binding and entry 2397.6.2 Receptors in vectors of circulative, propagative viruses 2417.6.3 Vertical transmission of propagative, circulative viruses 2427.7 Virus transmission morphs for non-circulative viruses 2437.8 “Omics” tools for studying virus–arthropod interactions 2437.9 Vector innate immunity in response to viruses 2477.10 Host and vector manipulation by plant viruses 2507.10.1 Indirect (plant-mediated) manipulation of insect vectors by plant viruses 2507.10.2 Direct manipulation of insect vectors by plant viruses 2607.10.3 Mode of transmission and virus manipulation of plant hosts leading to enhanced vector transmission 2627.11 Summary points 2637.12 Acknowledgments 2647.13 References 265Chapter 8 Evolution and Origin of Human Viruses 289Rachele CAGLIANI, Alessandra MOZZI, Chiara PONTREMOLI, Manuela SIRONI8.1 Introduction 2898.2 Origin and ancient evolutionary history of human viruses 2908.2.1 Origin and ancient evolutionary history of human-infecting RNA viruses 2908.2.2 Origin and ancient evolutionary history of human-infecting reverse-transcribing viruses 2958.2.3 Origin and ancient evolutionary history of human-infecting DNA viruses 2988.3 Sources of viral genetic diversity 3038.4 Viral evolution and host range 3078.5 Recent evolution of human RNA viruses – selected examples 3138.6 Conclusion 3198.7 References 320List of Authors 341Index 345