Applied Plant Virology: Advances, Detection, and Antiviral Strategies

Cover
Applied Plant Virology: Advances, Detection, and Antiviral Strategies
Copyright
Dedication
Contents
List of Contributors
About the Editor
Foreword
Preface
Acknowledgments
Part 1: Important landmarks in the history of virology
1 Major advances in the history of plant virology
	1.1 Introduction
	1.2 Introduction of tobacco plants to Europe from the Americas
	1.3 A tobacco disease in Europe that led to the beginning of virology
	1.4 Discovery of plant DNA viruses, satellites, and viroids in the 20th century
		1.4.1 DNA virus discovery
		1.4.2 Viral satellites discovery
		1.4.3 Viroid discovery
	1.5 Virus-infected plant biology, the early years (1903–52)
	1.6 Virus transmission
		1.6.1 Nonvector transmission
		1.6.2 Vector transmission
		1.6.3 Viral protein involvement in aphid or nematode vector transmission
		1.6.4 Propagative transmission
		1.6.5 Transmission involving helper viruses
		1.6.6 Circulative nonpropagative transmission
	1.7 The beginning and rise of molecular virology with tobacco mosaic virus as a model system (1935–60)
	1.8 The development of biophysical virology with tobacco mosaic virus as a model system (1937–89)
	1.9 Replication
		1.9.1 Replication of RNA viruses
		1.9.2 Replication of DNA viruses
		1.9.3 Viroid replication
	1.10 Methods
		1.10.1 Serology
		1.10.2 Electron microscopy
		1.10.3 Confocal microscopy
		1.10.4 Analytical and preparative ultracentrifugation
		1.10.5 Density gradient ultracentrifugation
		1.10.6 Gel electrophoresis
		1.10.7 Protoplast systems
		1.10.8 A model plant susceptible to many viruses
		1.10.9 Chemotherapy
		1.10.10 Hybridization
		1.10.11 Polymerase chain reaction
		1.10.12 Microarrays
		1.10.13 Genetic engineering
		1.10.14 First-generation RNA sequencing
		1.10.15 First-generation DNA sequencing
		1.10.16 Next-generation sequencing
		1.10.17 Next-generation sequencing of ancient viruses
	1.11 Resistance to virus infection
		1.11.1 Pathogen-derived resistance in transgenic plants
		1.11.2 RNA silencing
		1.11.3 Genome editing
		1.11.4 CRISPR-Cas system editing confers resistance to plant viruses
	1.12 Control by exclusion
	References
Part 2: Techniques for assay detection and diagnosis of plant viruses
2 Recent advances of virus diagnostics in horticultural crops
	References
3 Advance methods for the isolation and characterization of plant viruses infecting crops
	3.1 Introduction
	3.2 History
	3.3 Methods based on biology of the virus
		3.3.1 Bioassay/indicator hosts/virus indexing
		3.3.2 Methods of transmission
		3.3.3 Cytological studies of diseased host-plants
	3.4 Methods depending on physical properties of virus particles
		3.4.1 Stability and physicochemical properties
		3.4.2 Electron microscopy
	3.5 Methods depending on properties of viral proteins
		3.5.1 ELISA-based procedures
		3.5.2 Serologically specific electron microscopy
		3.5.3 Immunoblotting techniques
		3.5.4 Immunosensors
	3.6 Methods involving properties of the viral nucleic acid
		3.6.1 Polymerase chain reaction, its variants and nucleotide sequencing
		3.6.2 Hybridization-based procedures
		3.6.3 DNA microarray
	3.7 Conclusions
	References
4 Diagnosis of the casual viruses of crop plants
	4.1 Detection and identification assays based on biological properties
		4.1.1 Virus inoculation and symptomatology (biological indexing)
	4.2 Detection and identification assays based on physical properties
		4.2.1 Stability and physicochemical properties of virus
		4.2.2 Structural properties of virus: electron microscopy techniques
	4.3 Detection and identification assays based on biochemical properties of plants
	4.4 Detection and identification assays based on serology
		4.4.1 Precipitation and agglutination tests
		4.4.2 Enzyme-linked immunosorbent assay
		4.4.3 Immunosorbent electron microscopy
	4.5 Detection and identification assays based on virus nucleic acid
		4.5.1 Nucleic acid spot hybridization
		4.5.2 Nucleic acid amplification methods
			4.5.2.1 Polymerase chain reaction
			4.5.2.2 Reverse transcription–polymerase chain reaction
			4.5.2.3 Cooperational polymerase chain reaction
			4.5.2.4 Simultaneous detection of multiple infections: multiplex polymerase chain reaction
			4.5.2.5 Multiplex nested reverse transcription–polymerase chain reaction
			4.5.2.6 Real-time polymerase chain reaction
	4.6 Detection and identification assays based on isothermal amplification
		4.6.1 Nucleic acid sequence–based amplification
		4.6.2 Self-sustained sequence replication
		4.6.3 Rolling-circle amplification
		4.6.4 Loop-mediated isothermal amplification
	4.7 Advanced and developing methods
		4.7.1 Assays based on microarray systems
		4.7.2 Assays based on biosensors
		4.7.3 Assays based on high-throughput sequencing
	4.8 Conclusion
	References
5 Modern technologies for the diagnosis and assay of plants viruses
	5.1 Introduction
	5.2 Diagnostics for detection of viruses
		5.2.1 Conventional techniques
			5.2.1.1 Biological
				5.2.1.1.1 Growing-on tests
				5.2.1.1.2 Infectivity assays
			5.2.1.2 Biochemical (staining of inclusion bodies)
			5.2.1.3 Physical (electron microscopy)
		5.2.2 Modern techniques
			5.2.2.1 Serological tests/immunoassays
				5.2.2.1.1 Enzyme-linked immunosorbent assay
				5.2.2.1.2 Dotimmunobinding assay
				5.2.2.1.3 Tissue blotting immunoassay/tissue print immunoassay/tissue print immunoblotting
				5.2.2.1.4 Lateral flow strip method
			5.2.2.2 Nucleic acid–based methods
				5.2.2.2.1 Polymerase chain reaction
					Multiplex polymerase chain reaction
					Variants of polymerase chain reaction
						Reverse transcription–polymerase chain reaction
						Immunocapture polymerase chain reaction
						Real-time polymerase chain reaction/real-time reverse transcription–polymerase chain reaction
				5.2.2.2.2 Nucleic acid hybridization assays
				5.2.2.2.3 Double-stranded RNA analysis
				5.2.2.2.4 Microarrays
				5.2.2.2.5 Loop-mediated isothermal amplification
				5.2.2.2.6 Helicase-dependent amplification
				5.2.2.2.7 Recombinase polymerase amplification
				5.2.2.2.8 Next-generation sequencing
	5.3 Conclusion
	References
6 Diagnosis of plant virus diseases
	6.1 Introduction
	6.2 Evolution of serodiagnosis of plant virus diseases
		6.2.1 Serodiagnosis during the pre–enzyme-linked immunosorbent assay period
			6.2.1.1 Chloroplast agglutination and tube-precipitin tests
			6.2.1.2 Agar-gel double diffusion tests
		6.2.2 Serodiagnosis by enzyme-linked immunosorbent assay
			6.2.2.1 Double antibody sandwich enzyme-linked immunosorbent assay
			6.2.2.2 Other commonly used forms of enzyme-linked immunosorbent assay
			6.2.2.3 Affirmer protein–based enzyme-linked immunosorbent assay
			6.2.2.4 Dot blot, tissue blot and lateral flow immunoassays
	6.3 Electron microscopy
		6.3.1 Immunosorbent electron microscopy
	6.4 Nucleodiagnosis
		6.4.1 Polymerase chain reaction
			6.4.1.1 Nested polymerase chain reaction
			6.4.1.2 Multiplex polymerase chain reaction
		6.4.2 Isothermal amplification
		6.4.3 Rolling-circle amplification
			6.4.3.1 Microarray and next-generation sequencing
	6.5 Emerging technologies based on physicochemical changes
	6.6 Conclusion
	Acknowledgements
	References
7 Advances in protein-based diagnostic tools of plant viruses
	7.1 Introduction
	7.2 Methods based on properties of viral proteins
	7.3 Serology-based detection
		7.3.1 Enzyme-linked immunosorbent assay
		7.3.2 Immunoblotting
			7.3.2.1 Dot immunoblotting assay
			7.3.2.2 Tissue immunoblotting assay
			7.3.2.3 Immunosorbent electron microscopy
		7.3.3 Lateral-flow immunochromatographic assay
		7.3.4 Immunocapture assay
			7.3.4.1 Immunocapture polymerase chain reaction
			7.3.4.2 Immunocapture loop-mediated isothermal amplification
		7.3.5 Fluorescence polarization immunoassay
		7.3.6 Microparticle enzyme immunoassay
		7.3.7 Chemiluminescent immunoassay
		7.3.8 Radioimmunoassay
		7.3.9 Protein fingerprinting: a novel virus identification system
		7.3.10 Applications of gold nanoparticles in virus detection
		7.3.11 Quartz crystal microbalance immunosensors
	7.4 Limitations
	7.5 Conclusion
	References
	Further reading
8 Rapid detection of plant viruses and viroids
	8.1 Plant viral diseases and rapid diagnosis
	8.2 Rapid detection methods for plant viruses and viroids
		8.2.1 Enzyme-linked immunosorbent assay
		8.2.2 Immunochromatographic assay
		8.2.3 Thermal cycling–based amplification–polymerase chain reaction
		8.2.4 Isothermal nucleic acid amplification
		8.2.5 Other rapid detection methods
	8.3 Recombinase polymerase amplification — a rapid detection tool
		8.3.1 Recombinase polymerase amplification basics
			8.3.1.1 Recombinant polymerase amplification proteins and enzymes
			8.3.1.2 Recombinant polymerase amplification primers and probes
			8.3.1.3 Recombinant polymerase amplification reaction conditions
			8.3.1.4 Amplicon detection
		8.3.2 Recombinant polymerase amplification performance
		8.3.3 Rapid detection of viruses and viroids in plants via recombinant polymerase amplification
			8.3.3.1 Detection of plant RNA viruses
			8.3.3.2 Detection of plant DNA viruses
			8.3.3.3 Detection of viroids
		8.3.4 Pros, cons, and potential applications of recombinant polymerase amplification
	8.4 Rapid detection and plant viral disease control
		8.4.1 Considerations in choosing rapid detection methods
		8.4.2 Importance and potential application of rapid detection technologies
	Acknowledgment
	References
Part 3: Architecture of important viruses
9 Architecture of important plant viruses: the role of capsid protein—its assembly and architecture
	9.1 Introduction
	9.2 Methods for structure determination
	9.3 Arrangement of capsid proteins
	9.4 Icosahedral symmetry
	9.5 Quasi-equivalence and other structure theories
	9.6 The structure of capsid proteins
	9.7 Bacilliform particles
	9.8 Helical symmetry
	9.9 Rod-shaped and flexuous filamentous viruses
		9.9.1 Strong intersubunit interactions in tobamovirus virions
		9.9.2 Flexible intersubunit contacts in potexviruses
	9.10 Architecture and assembly of capsid proteins
	9.11 Intrinsically disordered domain
	9.12 Conclusion
	Acknowledgment
	References
Part 4: Plant molecular virology
10 Next-generation sequencing technologies and plant molecular virology: a practical perspective
	10.1 Introduction
	10.2 Next-generation sequencing
		10.2.1 Genesis of platforms available for next-generation sequencing
			10.2.1.1 First-generation sequencing technology
			10.2.1.2 Second-generation sequencing technologies
			10.2.1.3 Third-generation sequencing technologies
	10.3 Discovery of novel viruses
	10.4 Identification of virus-specific noncoding RNAs
	10.5 Viral diagnostics
	10.6 Metagenomics of viruses (metaviromics)
	10.7 Concluding remarks
	References
11 Molecular responses of plants to viruses with emphasis on small RNAs
	11.1 Plant immune response
	11.2 Plant–virus interactions
	11.3 Endogenous small RNAs in plant–virus interactions
		11.3.1 sRNA biogenesis and action
		11.3.2 Short RNA regulation in PTI
		11.3.3 Small RNA regulation in effector-triggered immunity
		11.3.4 Role of small RNAs in epigenetic responses
		11.3.5 Small RNAs in plant–virus interactions
	11.4 Conclusion
	References
12 Protein preparation from virus-infected plants for protoplast–chloroplast proteomics
	12.1 Introduction
	12.2 Materials
		12.2.1 Plant growth
		12.2.2 Virus infection
		12.2.3 Protoplast isolation
		12.2.4 Chloroplast isolation
		12.2.5 Protein extraction
	12.3 Methods
		12.3.1 Plant growth
		12.3.2 Virus inoculation
		12.3.3 Protoplast isolation
		12.3.4 Chloroplast isolation
		12.3.5 Protein extraction
	Acknowledgments
	References
Part 5: Replication of plant viruses
13 DNA plant viruses: biochemistry, replication, and molecular genetics
	13.1 Introduction
		13.1.1 Plant viruses
			13.1.1.1 Geminiviruses
		13.1.2 Gemini viruses classification
			13.1.2.1 Begomoviruses
		13.1.3 Bipartite Begomoviruses
		13.1.4 Potential functions of begomovirus-encoded proteins
		13.1.5 Monopartite begomoviruses and associated complexes
		13.1.6 Betasatellite
		13.1.7 Deltasatellite
		13.1.8 Alphasatellite
			13.1.8.1 Capulavirus
			13.1.8.2 Curtovirus
			13.1.8.3 Eragrovirus
			13.1.8.4 Becurtovirus
			13.1.8.5 Grablovirus
			13.1.8.6 Mastrevirus
			13.1.8.7 Topocuvirus
			13.1.8.8 Turncurtovirus
	13.2 Family Caulimoviridae (dsDNA viruses)
		13.2.1 Structure of virus particle
		13.2.2 Replication and biosynthesis of viral proteins
		13.2.3 Caulimovirus
		13.2.4 Petuvirus
		13.2.5 Cavemovirus
		13.2.6 Soymovirus
		13.2.7 Badnavirus
		13.2.8 Tungrovirus
	References
14 RNA plant viruses: biochemistry, replication and molecular genetics
	14.1 Introduction
	14.2 RNA replication and translation of plant viruses
		14.2.1 Initial infection
	14.3 A case study of tobamovirus replication
	14.4 Cellular mechanisms involved in viral replication complex formation
		14.4.1 Recruitment of red clover necrotic mosaic virus movement protein to viral replication complexes organized by a repli...
		14.4.2 Formation of viral replication complex and potato virus X movement protein
		14.4.3 Replication and movement of turnip mosaic virus
	14.5 Virus interaction with plant cytoskeleton
	14.6 Positive-sense single-stranded RNA virus replication: role of host factors
		14.6.1 Host proteins regulate viral genome replication in chloroplasts
	14.7 How is replication of virus affected by host silencing?
	14.8 Molecular approaches to study host factors and virus replication
	14.9 Conclusion
	References
Part 6: Physiology of virus infected hosts
15 Physiology of virus-infected plants
	15.1 Introduction
	15.2 Changes in photosynthetic activity in virus-infected hosts
	15.3 Chlorophyll content
	15.4 The rate of photosynthesis
	15.5 Changes in starch metabolism in virus-infected plants
	15.6 Changes in respiration in virus-infected plants
	15.7 Changes in nitrogen metabolism and proteins in virus-infected plants
	15.8 Changes in water content and transpiration of virus-infected plants
	15.9 Changes in hormone metabolism of virus-infected plants
	15.10 Conclusion
	References
Part 7: Viroids
16 Viroids: small entities with a mean punch
	16.1 Introduction
	16.2 Structure and taxonomy
		16.2.1 Family Pospiviroidae
		16.2.2 Family Avsunviroidae
	16.3 Replication of viroids
	16.4 Movement of viroids
	16.5 Symptoms and host–pathogen interaction
	16.6 Transmission of viroids
	16.7 Detection of viroids
	16.8 Control of viroids
	References
	Further reading
Part 8: Viruses of cryptogamic plants
17 Fungal viruses: an unlikely ally
	17.1 Introduction
	17.2 The birth of mycovirology
	17.3 Symptoms of mycoviruses
	17.4 Natural and experimental transmission of mycoviruses
	17.5 Classification of mycoviruses
	17.6 Double-stranded RNA mycoviruses
		17.6.1 Floating genus: Botybirnavirus
	17.7 Positive-sense single-stranded RNA mycoviruses
	17.8 Reverse-transcribing positive-sense RNA mycoviruses
	17.9 Negative-sense RNA mycoviruses
	17.10 Single-stranded DNA (ssDNA) mycoviruses
	17.11 Hypovirulence of mycoviruses
	17.12 Conclusions
	Acknowledgments
	References
	Further reading
18 Algal viruses
	18.1 The diversity of algal viruses
	18.2 Applications of algal viruses in advancement of molecular biology and for enhancement of biofuel production
	18.3 Environmental factors affecting growth and development of algae and viruses
		18.3.1 Temperature
		18.3.2 Salinity
		18.3.3 Ultraviolet radiation
		18.3.4 Photosynthetic active radiation
		18.3.5 Nutrients
		18.3.6 Inorganic particles
		18.3.7 Organic particles
		18.3.8 Carbon dioxide concentration
		18.3.9 pH
	References
Part 9: Transmission of plant viruses
19 The role of heat-shock proteins, in vector-virus transmission
	19.1 Introduction
	19.2 Endosymbionts
	19.3 GroEL-homologue protein
		19.3.1 GroEL-homologue protein specificity
	19.4 Virus coat protein
	19.5 Other heat-shock proteins
	References
	Further reading
Part 10: Vectors of plant viruses/virus, vector relationship
20 Mite (Acari Acarina) vectors involved in transmission of plant viruses
	20.1 Introduction
	20.2 Virus transmissions
	20.3 Mites-borne plant viruses
		20.3.1 Tetranychoidea (Raphignathina) mites
			20.3.1.1 Tenuipalpidae mites
			20.3.1.2 Brevipalpus mites
				20.3.1.2.1 Red and black flat mite Brevipalpus phoenicis (Geijskes)
		20.3.2 Tetranychidae mites
			20.3.2.1 Two-spotted spider mite Tetranychus urticae Koch
			20.3.2.2 Brown wheat mite Petrobia latens (Muller)
		20.3.3 Eriophyidae mites
			20.3.3.1 Dry-bulb mite Aceria tulipae (Keifer)
			20.3.3.2 Phyllocoptes fructiphilus Keifer
			20.3.3.3 Wheat curl mite Aceria tosichella (Keifer)
		20.3.4 Tarsonemid mites
			20.3.4.1 Broad mite Polyphagotarsonemus latus (Banks)
	20.4 Management of mite-vectored viruses
	20.5 Conclusions
	References
	Further reading
21 Different nematodes and plasmodiophorids as vectors of plant viruses
	21.1 Introduction
	21.2 Nematodes
		21.2.1 Feeding behavior of nematodes
		21.2.2 Virus ingestion activity of nematodes
		21.2.3 Virus retention and transmission by nematodes
		21.2.4 Plant viruses vectored by nematodes
			21.2.4.1 Stubby-root nematode Paratrichodorus minor
			21.2.4.2 Needle Nematode Paralongidorus maximus (Butschli)
		21.2.5 Management of nematode-transmitted viruses
			21.2.5.1 Detection and identification
			21.2.5.2 Exclusion
			21.2.5.3 Natural resistance to vector nematodes and their viruses
			21.2.5.4 Cultural control
			21.2.5.5 Transgenic resistance
			21.2.5.6 Chemical products
	21.3 Plasmodiophorids
		21.3.1 Plasmodiophorid-transmitted viruses
		21.3.2 Polymyxa graminis Ledingham
		21.3.3 Diseases caused by plasmodiophorid-transmitted viruses
		21.3.4 Mechanisms of virus acquisition and transmission
		21.3.5 Controlling of plasmodiophorid-transmitted viruses
	21.4 Conclusion
	References
22 Transmission of plant viruses through soil-inhabiting nematode vectors
	22.1 Introduction
	22.2 Transmission through nematodes
		22.2.1 Transmission of nepoviruses
		22.2.2 Transmission of tobraviruses
	22.3 Virus-nematode–vector relationship
		22.3.1 Ingestion
		22.3.2 Acquisition
		22.3.3 Adsorption
		22.3.4 Retention
		22.3.5 Release
		22.3.6 Transfer and establishment
	22.4 Transmission efficiency
	22.5 Mode of virus transmission by nematode
	References
23 New advances in insect vector biology and virus epidemiology
	23.1 Introduction
	23.2 Insect vector biology
	23.3 Elucidating complex interactions between viruses and vectors
		23.3.1 Virus impacts on biology and behavior of vector
		23.3.2 Using basic research in insect biology to fight disease
			23.3.2.1 Genetic control of insects
				23.3.2.1.1 Genetic suppression of the vectors ability to transmit pathogens
				23.3.2.1.2 Genetic suppression of insect populations
			23.3.2.2 New avenues for the behavioral manipulation of disease vector
	23.4 Viral epidemiology
	23.5 Integrated control measures against viruses and their vectors
	23.6 Conclusion
	References
24 Transmission of plant viruses in fields through various vectors
	24.1 Introduction
	24.2 Pathway of plant-virus transmission
		24.2.1 Horizontal transmission
		24.2.2 Vertical transmission
	24.3 Methods of transmission
		24.3.1 Noninsect transmission
			24.3.1.1 Transmission by sap inoculation or mechanical transmission
			24.3.1.2 Factors affecting mechanical transmission
				24.3.1.2.1 Effect of source of inoculum
				24.3.1.2.2 Effect of concentration of inoculum
				24.3.1.2.3 Effect of extraction medium
				24.3.1.2.4 Effect of metal ions and ionic strength
				24.3.1.2.5 Effect of substances protecting against phenolics
				24.3.1.2.6 Effect of charcoal
				24.3.1.2.7 Effect of enzymes
				24.3.1.2.8 Effect of detergents
			24.3.1.3 Transmission through seed
			24.3.1.4 Transmission through vegetative propagation
			24.3.1.5 Transmission by dodder
			24.3.1.6 Transmission through fungi
			24.3.1.7 Transmission through nematodes
			24.3.1.8 Nepoviruses
			24.3.1.9 Tobraviruses
			24.3.1.10 Virus–nematode relationships
		24.3.2 Insect transmission
			24.3.2.1 Virus–vector relationships
				24.3.2.1.1 Nonpersistent transmission
				24.3.2.1.2 Noncirculative, semipersistent transmission
				24.3.2.1.3 Circulative, nonpropagative transmission
				24.3.2.1.4 Circulative, propagative transmission
			24.3.2.2 Insect vectors of plant viruses
				24.3.2.2.1 Transmission through aphids
				24.3.2.2.2 Transmission by whiteflies
				24.3.2.2.3 Transmission through leafhopper/planthopper
				24.3.2.2.4 Transmission by mite
				24.3.2.2.5 Transmission thrips
				24.3.2.2.6 Transmission by beetle
	References
	Further reading
25 Bemisia tabaci (Gennadius) as vector of plant viruses
	25.1 Introduction
	25.2 Economic importance
	25.3 Biology
	25.4 Biotypes
	25.5 Host plant–vector–virus interaction
	25.6 Vector–virus
	25.7 Effect of ICMV on vector
	25.8 Management
	25.9 Virus–vector interactions and designing management tactics for plant viruses—future strategies and research needs
		25.9.1 Transmission research
		25.9.2 Strategic vector research
	References
26 Arthropod vectors of plant viruses
	26.1 Introduction
	26.2 Nonpersistent transmission
	26.3 Family Potyviridae (genera Potyvirus and Macluravirus)
	26.4 Family Bromoviridae (genera Alfamovirus and Cucumovirus)
	26.5 Family Betaflexiviridae (genus Carlavirus)
	26.6 Family Secoviridae (genus Fabavirus)
	26.7 Semipersistent transmission
	26.8 Family Closteroviridae (genera Ampelovirus, Closterovirus, and Crinivirus)
	26.9 Family Potyviridae (genus Ipomovirus)
	26.10 Family Secoviridae (genera Sequivirus, Torradovirus, and Waikavirus)
	26.11 Family Betaflexiviridae (genera Trichovirus and Vitivirus)
	26.12 Family Caulimoviridae (genera Badnavirus and Caulimovirus)
	26.13 Persistent-circulative transmission
	26.14 Family Geminiviridae (genera Becurtovirus, Begomovirus, Capulavirus, Curtovirus, Eragrovirus, Grablovirus, Mastreviru...
	26.15 Family Luteoviridae (genera Enamovirus, Luteovirus and Polerovirus)
	26.16 Family Nanoviridae (genera Babuvirus and Nanovirus)
	26.17 Persistent-propagative transmission
	26.18 Family Tospoviridae (genus Orthotospovirus)
	26.19 Family Phenuiviridae (genus Tenuivirus)
	26.20 Family Rhabdoviridae (genera Cytorhabdovirus and Nucleorhabdovirus)
	26.21 Family Tymoviridae (genus Marafivirus)
	26.22 Family Reoviridae (genera Phytoreovirus, Fijivirus, and Oryzavirus)
	26.23 Beetle transmission
	26.24 Unassigned family (genus Sobemovirus)
	26.25 Family Tombusviridae (genera Machlomovirus, Betacarmovirus, and Gammacarmovirus)
	26.26 Family Tymoviridae (genus Tymovirus)
	26.27 Family Secoviridae (genus Comovirus)
	26.28 Family Bromoviridae (genus Bromovirus)
	26.29 Mite transmission
	26.30 Aceria mites
	26.31 Potyviridae (genera Poacevirus, Rymovirus and Tritimovirus)
	26.32 Fimoviridae (genus Emaravirus)
	26.33 Alphaflexiviridae (genus Allexivirus)
	26.34 Secoviridae (genus Nepovirus)
	26.35 Betaflexiviridae (genus Trichovirus)
	26.36 Brevipalpus mites
	26.37 Family Rhabdoviridae (genus Dichorhavirus)
	26.38 Unassigned family (genus Cilevirus)
	26.39 Pollenborne insect-aided transmission
	26.40 Family Bromoviridae (genus Ilarvirus)
	26.41 Family Tombusviridae (genus Alphacarmovirus)
	26.42 Unassigned family (genus Sobemovirus)
	26.43 Conclusions
	References
27 Insects as transport devices of plant viruses
	27.1 Introduction
	27.2 Plant pathogen spread by vectors
	27.3 Types of virus transmission
	27.4 Categories of vectors
	27.5 Insect-transmitted plant-virus diseases
		27.5.1 Homoptera
			27.5.1.1 Aphids (Homoptera: Aphididae)
			27.5.1.2 Whiteflies (Homoptera: Aleyrodidae)
			27.5.1.3 Leafhoppers, planthoppers, and treehoppers (Homoptera)
				27.5.1.3.1 Planthoppers (Homoptera: Delphacidae)
				27.5.1.3.2 Leafhoppers (Homoptera: Cicadellidae)
				27.5.1.3.3 Treehoppers (Homoptera: Membracidae)
			27.5.1.4 Mealybugs and soft scales (Homoptera)
		27.5.2 Hemiptera
		27.5.3 Thrips (Thysanoptera: Thripidae)
		27.5.4 Diptera
		27.5.5 Coleoptera
		27.5.6 Orthoptera
		27.5.7 Lepidoptera
		27.5.8 Dermaptera
	27.6 Virus control
		27.6.1 Virus control by interfering vectors and transmission
			27.6.1.1 Reducing vector populations
			27.6.1.2 Reducing virus sources
			27.6.1.3 Interference with vector landing on crops
			27.6.1.4 Interference with the transmission process
		27.6.2 Host-plant resistance
		27.6.3 Cultural control
		27.6.4 Biological control
		27.6.5 Chemical control
		27.6.6 Regulatory measures
		27.6.7 Integrated management
	27.7 Conclusion
	References
Part 11: Epidemiology and evolution of viruses
28 Epidemiology and evolution of poytviruses infecting cucurbits
	28.1 Cucurbits
	28.2 Viruses of cucurbits
	28.3 Papaya ring spot virus
	28.4 Watermelon mosaic virus
	28.5 Zucchini yellow mosaic virus
	28.6 Zucchini tigre mosaic virus
	28.7 Evolution of papaya ringspot virus type W, watermelon mosaic virus, zucchini yellow mosaic virus, and zucchini tigre m...
		28.1.1 Natural variation
		28.1.2 Recombination
	Conclusions
	Acknowledgments
	References
	Further reading
Part 12: Nomenclature and classification of plant viruses
29 Plant virus taxonomy
	29.1 Introduction
	29.2 Plant viruses
	29.3 The diversity and classification of viruses
	29.4 International committee on taxonomy of viruses taxonomy
		29.4.1 The taxa of viruses
	29.5 Database and website
		29.5.1 Virus classification
		29.5.2 Virus taxonomy
		29.5.3 The International Committee on Taxonomy of Viruses database of virus taxonomy
	29.6 Nomenclature and classification of plant viruses
		29.6.1 Use of virus names
		29.6.2 Baltimore system of virus classification
			29.6.2.1 Latest classification
	29.7 The international code of nomenclature
		29.7.1 Names
		29.7.2 Name stems
		29.7.3 Derivation of species names
		29.7.4 Typography
		29.7.5 Virus names and the biocode
	29.8 Principles of virus taxonomy
		29.8.1 Stability
		29.8.2 Utility
		29.8.3 Acceptability
		29.8.4 Flexibility
	29.9 Plant virus biodiversity
	29.10 Current taxonomy of viruses
	29.11 Conclusions
	References
	Further reading
Part 13: Viral diseases of crops
30 Interspecific and intraspecific interactions among plant viruses in mixed infections
	30.1 Introduction
	30.2 General overview of interactions among viruses
	30.3 Interspecific interactions
		30.3.1 Most famous synergy
		30.3.2 Another couples in a synergistic marriage
		30.3.3 Genes involved in synergistic interactions
		30.3.4 Synergy as a driving force in the spread of viral diseases
	30.4 Intraspecific interactions
		30.4.1 Superinfection exclusion: viruses on a war footing
		30.4.2 Why exclusion?
		30.4.3 The extraordinary case of Citrus tristeza virus
		30.4.4 Spatial separation: move over, and leave room for others
	30.5 Interspecific and intraspecific helper dependence
		30.5.1 Get neighborly help
		30.5.2 Transport media used by potyviruses
		30.5.3 Transport media used by umbraviruses
	30.6 Implications of interspecific and intraspecific interactions
		30.6.1 Recombination: give a part of yourself to others
		30.6.2 Helper-dependent vector transmission: a multicomponent process
	30.7 Conclusion
	References
31 Begomovirus research in Oman: a critical appraisal and the way ahead
	31.1 Introduction
	31.2 Begomovirus research in Oman
	31.3 Conclusion
	References
	Further reading
32 Papaya ringspot virus–Carica papaya pathosystem
	32.1 Introduction
		32.1.1 Origin, taxonomy, and distribution of papaya
		32.1.2 Papaya genome
		32.1.3 Global production
		32.1.4 Papaya ringspot virus
			32.1.4.1 Taxonomy
			32.1.4.2 Symptom description
			32.1.4.3 Epidemiology
				32.1.4.3.1 Host plants
				32.1.4.3.2 Transmission
					Host selection by aphids
			32.1.4.4 Detection methods
			32.1.4.5 Genetic diversity
			32.1.4.6 Origin and dispersal
			32.1.4.7 Disease management
		32.1.5 Conclusion
	References
33 Viral diseases of crops: a critical review
	References
34 Molecular diversity of begomoviruses and DNA satellite molecules infecting ornamental plants in India
	34.1 Introduction
	34.2 Indian begomoviruses and satellite molecules in ornamental plants
	34.3 Phylogenetics and recombinations among the viruses and satellites
	34.4 Conclusion
	Acknowledgments
	References
35 Recent advances in begomovirus research in India
	35.1 Introduction
	35.2 Detection of begomoviruses
		35.2.1 Enzyme-linked immunosorbent assay
		35.2.2 Dot-immunobinding assay
		35.2.3 Nucleic acid hybridization method
		35.2.4 Dot-blot hybridization (nucleic acid spot hybridization)
		35.2.5 Southern blot
		35.2.6 Polymerase chain reaction–based assay
			35.2.6.1 Polymerase chain reaction detection of geminivirus using degenerate primer
			35.2.6.2 Reverse transcription–polymerase chain reaction
			35.2.6.3 Real-time polymerase chain reaction
			35.2.6.4 Rolling-circle amplification–polymerase chain reaction assay
		35.2.7 Rolling-circle amplification
		35.2.8 Microarray/DNA chip
	35.3 Molecular characterization of begomoviruses
		35.3.1 Mung bean yellow mosaic virus
		35.3.2 Black gram yellow mosaic virus
		35.3.3 Bhendi yellow vein mosaic virus
		35.3.4 Chilli leaf curl virus
		35.3.5 Cotton leaf curl virus
		35.3.6 Pumpkin yellow vein mosaic virus
		35.3.7 Tomato leaf curl New Delhi virus
		35.3.8 Tobacco leaf curl virus
		35.3.9 Tomato yellow leaf curl virus
		35.3.10 Papaya leaf curl virus
	35.4 Management of begomoviruses
		35.4.1 Pathogen-derived resistance
		35.4.2 RNA interference–mediated resistance
		35.4.3 Ribozyme-mediated resistance
		35.4.4 Small interfering RNA–mediated
		35.4.5 Artificial trans-acting short, interfering RNA
	References
36 Begomovirus research in Saudi Arabia: current status and future prospects
	36.1 Introduction
	36.2 Begomovirus infection in Saudi Arabia
		36.2.1 Amaranthus
		36.2.2 Beans
		36.2.3 Cucumber
		36.2.4 Corchorus
		36.2.5 Okra
		36.2.6 Ridge gourd
		36.2.7 Squash
		36.2.8 Tomato
	36.3 Conclusion
	Acknowledgements
	References
37 Beet curly top virus transmission, epidemiology, and management
	37.1 Beet curly top virus strains
	37.2 Leafhopper transmission of beet curly top virus
	37.3 Beet curley top virus epidemiology
	37.4 Management of curly top
	37.5 Conclusion
	References
Part 14: Economic losses due to infection by plant viruses
38 Overview of yield losses due to plant viruses
	38.1 Introduction
	38.2 Yield losses in different crops
	38.3 Cereals and millets
		38.3.1 Rice
		38.3.2 Wheat
		38.3.3 Barley
		38.3.4 Maize
	38.4 Sorghum and pearl millet
		38.4.1 Oats
	38.5 Legumes
		38.5.1 Common bean (Phaseolus vulgaris)
		38.5.2 Pea
		38.5.3 Chickpea
		38.5.4 Cowpea
		38.5.5 Greengram/mung bean
		38.5.6 Blackgram/urdbean
		38.5.7 Broad bean/faba bean
		38.5.8 Redgram/pigeonpea
		38.5.9 Lentil
	38.6 Vegetables
		38.6.1 Potato
		38.6.2 Tomato
		38.6.3 Chilli/pepper
		38.6.4 Eggplant/brinjal
		38.6.5 Ladies finger (bhendi)
		38.6.6 Cucurbits
		38.6.7 Carrot
		38.6.8 Crucifers
		38.6.9 Lettuce
		38.6.10 Tuber crops
		38.6.11 Sweet potato
		38.6.12 Cassava
		38.6.13 Aroids
		38.6.14 Yam and elephant foot yam
	38.7 Fruit crops
		38.7.1 Citrus
		38.7.2 Banana
		38.7.3 Grapes
		38.7.4 Papaya
		38.7.5 Watermelon
	38.8 Stone fruits (Prunus spp.)
	38.9 Pome fruits
		38.9.1 Apple
		38.9.2 Strawberry
		38.9.3 Pineapple
	38.10 Industrial crops
		38.10.1 Sugarcane
		38.10.2 Sugar beet
		38.10.3 Cotton
		38.10.4 Tobacco
		38.10.5 Cacao
		38.10.6 Jatropha
	38.11 Edible oil seed crops
		38.11.1 Groundnut/peanut
		38.11.2 Soybean
		38.11.3 Brassicas
		38.11.4 Sunflower
	38.12 Spice crops
		38.12.1 Onion and garlic
		38.12.2 Cardamoms
		38.12.3 Pepper
	38.13 Conclusion
	References
Part 15: Human disorders caused by ssRNA plant viruses and DNA green algal virus
39 Plant and green microalgae viruses in human diseases
	39.1 Introduction
	39.2 Plant RNA viruses in human diseases
		39.2.1 Tobacco mosaic virus
		39.2.2 Cowpea mosaic virus
		39.2.3 Pepper mild mottle virus
	39.3 Green microalgae DNA viruses in human diseases
		39.3.1 Acanthocystis turfacea chlorella virus 1
		39.3.2 Viruses of the green microalgae Tetraselmis viridis, Phaeodactylum tricornutum, and Dunaliella viridis
		39.3.3 Virus of the green algae Tetraselmis striata
	39.4 Perspective
	References
Part 16: Strategies for the management of viral diseases of crops
Section I: Antiviral agents
40 Management of viral diseases of crops
	40.1 Introduction
	40.2 Virus-induced disease management, the need of the hour
	40.3 Conventional measures
	40.4 Culture control
	40.5 Quarantine control
	40.6 Pest control, monitoring of host–vector populations
	40.7 Breeding for resistance
	40.8 Nonconventional measures
	40.9 Pathogen-derived resistance
	40.10 Coat protein–mediated resistance strategy
	40.11 Coat protein–mediated resistance strategy for RNA viruses
	40.12 Coat protein–mediated resistance strategy for DNA viruses
	40.13 Movement protein–mediated resistance
	40.14 Satellite RNA
	40.15 Replicase-mediated resistance
	40.16 Short, interfering RNA-mediated
	40.17 MicroRNA-mediated resistance
	40.18 Artificial microRNA-mediated
	40.19 Ribozyme-mediated virus resistance
	40.20 Artificial trans-acting short, interfering RNA–mediated virus resistance
	40.21 Virus-derived hairpin RNA transgene-mediated resistance
	40.22 Dual viral resistance
	40.23 Resistance against cucumber mosaic cucumovirus and tomato leaf curl begomovirus
	40.24 Resistance against tobacco etch potyvirus and tobacco mosaic tobamovirus
	40.25 Non–pathogen-derived resistance
	40.26 Tectaria macrodonta protein–mediated resistance
	40.27 Zinc finger nuclease–based plant-virus control
	40.28 Transcription activator-like effector nucleases–based plant-virus control
	40.29 Clustered regularly interspaced, short palindromic repeats–Cas9–mediated plant-virus resistance
	40.30 Conclusion
	References
41 Prevention and control of viral diseases of crops
	41.1 Introduction
	41.2 Healthy or virus-free seed
		41.2.1 Seed certification and quarantine control
	41.3 Virus-free vegetative planting material
	41.4 Cultural practices
		41.4.1 Alternate plant hosts of viruses
		41.4.2 Rouging and eradication of infected plants
		41.4.3 Planting and harvesting procedures
			41.4.3.1 Sowing
			41.4.3.2 Spacing
			41.4.3.3 Quarantine
	41.5 Vector movement, avoidance, or control
		41.5.1 Insecticidal control
		41.5.2 Biological control
		41.5.3 Nonchemical method of vector control
		41.5.4 Barrier crops
	41.6 Plant resistance to vectors
	41.7 Soilborne vectors
		41.7.1 Nematodes
		41.7.2 Fungi
		41.7.3 Antiviral chemicals
	41.8 Resistance to plant viruses
		41.8.1 Transgenic resistance to plant viruses
	Conclusion
	References
	Further reading
Section II: Systemic induced resistance
42 Systemic resistance inducers from plants—an ecofriendly approach for the management of viral diseases of crops
	42.1 Introduction
	42.2 Types of induced resistance
		42.2.1 Systemic acquired resistance
		42.2.2 Herbivore-induced resistance
		42.2.3 Induced systemic resistance
	42.3 Phenomenon of induced systemic resistance
	42.4 Agents that induce resistance
		42.4.1 Plant extracts
		42.4.2 Microorganism
	42.5 Biochemical and physiological changes in induced plants
	References
	Further reading
43 Mechanisms of systemic induced resistance
	43.1 Introduction
	43.2 Mechanisms of systemic induced resistance
	43.3 Immunity
	43.4 Resistance
	43.5 Induced resistance
	43.6 Localized induced resistance
	43.7 Systemic induced resistance
	43.8 Plant immune system against viruses
	43.9 Dominant resistance
	43.10 Recessive resistance
	43.11 RNA interference–mediated resistance
	43.12 Plant hormone–mediated resistance
	43.13 Plant innate immunity
	43.14 RNA silencing
		43.14.1 Duel resistance in systemically induced viruses
	Conclusion
	References
	Further reading
44 Clustered regularly interspaced short palindromic repeats- (CRISPR)–Cas9 system for engineering resistance to plant viruses
	44.1 History of development of virus resistance
	44.2 Methods for development of plant resistance to viruses
	44.3 Pathogen-derived resistance
	44.4 Small RNA-mediated resistance
	44.5 Induced systemic resistance
	44.6 Incarnation of clustered regularly interspaced short palindromic repeats–Cas9 technology
	44.7 Applications of CRISPR-Cas 9 technology
	44.8 DNA virus resistance
	44.9 RNA virus resistance
	44.10 Conclusion
	References
45 Molecular tools for engineering resistance in hosts against plant viruses
	45.1 Introduction
	45.2 Clustered regularly interspaced short palindromic repeats–Cas genome editing
		45.2.1 Cas9: type II nuclease for genome editing
		45.2.2 Cpf1/Cas12a: type V nuclease for genome editing
		45.2.3 Cas13: type VI nuclease for genome editing
	45.3 Genome editing by double-stranded DNA breaks
		45.3.1 Nonhomologous end joining
		45.3.2 Homology-directed repair
	45.4 Genome editing beyond double-stranded DNA breaks
	45.5 Plant immunity
		45.5.1 Dominant resistance
		45.5.2 Recessive resistance
	45.6 Resistance versus susceptibility: durability and ease
	45.7 CRISPR-Cas off-targeting concerns
	45.8 Conclusion
	References
46 CRISPR-Cas system-a promising tool for engineering resistance to plant viruses
	46.1 Introduction to genome editing technologies
	46.2 CRISPR-Cas based genome editing
	46.3 Application of CRISPR-Cas9 technology for plant-virus control
		46.3.1 Control of plant DNA viruses
		46.3.2 Control of plant RNA viruses
	46.4 Advantages and challenges of CRISPR-Cas for plant-virus control
	46.5 Web resources for CRISPR/Cas technology
	Glossary
	References
47 Plant translation factors and virus resistance
	47.1 Introduction
	47.2 Dominant versus recessive resistant gene of host cells
		47.2.1 Characteristics of dominant resistance genes
		47.2.2 Characteristics of recessive resistance genes
		47.2.3 Recessive resistance
			47.2.3.1 Curbing the infection with recessive resistance genes
		47.2.4 Translational defense against viruses
	47.3 Translation of cellular messenger RNAs in plants
		47.3.1 How do mutations in eIF4E and eIFiso4E affect plant–virus interactions?
		47.3.2 Virus-protein genome
		47.3.3 Cap-independent viral messenger RNA translation
			47.3.3.1 Cap-independent translation enhancer
			47.3.3.2 Internal ribosome entry sites
	47.4 A case study of translation of potyviridae
		47.4.1 Additional roles for translation factors in enhancing the virus-infection cycle
	47.5 Differences between a viral RNA and cellular RNA strategies in translation
		47.5.1 A brief note on role of elongation factors
			47.5.1.1 eEF1A and viral replication complex
	47.6 Virus strategy to enhance virulence
		47.6.1 A strategy used by caulimoviruses
	47.7 Plant host resistance against viruses
		47.7.1 Role of argonaute in translational repression of viral messenger RNA
		47.7.2 Passive resistance
		47.7.3 Engineering pants for virus resistance
			47.7.3.1 eIF4 factors in plants (most important of all PTFs)
			47.7.3.2 Clustered regularly interspaced short palindromic repeats–Cas9 technology
			47.7.3.3 Generation of resistance crops by introduction of resistance genes
				47.7.3.3.1 Classical breeding
				47.7.3.3.2 Targeting induced local lesions in genomes approach
				47.7.3.3.3 The transgenic approach
				47.7.3.3.4 RNA silencing
	47.8 Conclusion
	References
48 Identification and manipulation of host factors for the control of plant viruses
	48.1 Introduction
	48.2 Host factors in the virus life cycle
		48.2.1 Virion disassembly
		48.2.2 Viral genome translation
			48.2.2.1 eIF4F/eIF(iso)4F components
			48.2.2.2 eIF4A
			48.2.2.3 Other translational apparatus components
		48.2.3 Viral genome replication
			48.2.3.1 Host factors involved in membrane remodeling
			48.2.3.2 Host factors binding to viral RNA
			48.2.3.3 Heat-shock proteins and proteins involved in stress responses
			48.2.3.4 Modification of viral proteins by host factors
		48.2.4 Viral movement
			48.2.4.1 Cell-to-cell movement
				48.2.4.1.1 Host factors associated with endomembrane system, early secretory pathways, or cytoskeleton network
				48.2.4.1.2 Host factors that affect viral cell-to-cell movement through regulating plasmodesmata aperture
		48.2.5 Long-distance movement
	48.3 Antiviral strategies targeting host factors
		48.3.1 Natural recessive resistance
		48.3.2 Strategies in generating eIF4-based resistance
			48.3.2.1 Traditional breeding
			48.3.2.2 TILLING and EcoTILLING
			48.3.2.3 Genetic engineering approach
			48.3.2.4 Targeted genome editing
	48.4 Conclusion
	Acknowledgement
	References
	Further reading
49 Mechanisms of natural and genetically engineered resistance against viruses
	49.1 Introduction
	49.2 Virus genome as source of plant symptoms and impact of molecular virology
	49.3 Challenge for a high-quality plant
	49.4 Occurrence of the natural resistance against viruses
	49.5 Nonhost perennials and resistance against viruses
	49.6 Promising and sustainable approach to improve plants
	49.7 Innovative and supportive role of silencing
	49.8 Successful safe use of viral genes
	49.9 Conclusion
	References
Section III: Integrated management of viral diseases of crops
50 Integrated management of vectored viral diseases of plants
	50.1 Introduction
	50.2 Detection of plant viruses
	50.3 Management of vectored viral diseases
		50.3.1 Habitat and environmental control
		50.3.2 Reducing contact
		50.3.3 Soil solarization
		50.3.4 Chemical control
		50.3.5 Legislation
		50.3.6 Biological control
		50.3.7 Prevention of virus diseases
		50.3.8 Planting of virus-free materials
		50.3.9 Exclusion
		50.3.10 Extending of information to farmers
		50.3.11 Host resistance
		50.3.12 Promotion of biological control
		50.3.13 Need for epidemiological information
		50.3.14 Cultural control
		50.3.15 Heat therapy and certification
		50.3.16 Need for entomologists
		50.3.17 Choice of management strategies
	50.4 Integrated management scenarios for key vectors
	50.5 Conclusion
	References
	Further reading
51 Status of orchid viruses in India and management strategies for them
	51.1 Introduction
	51.2 Important viruses of orchids
		51.2.1 Cymbidium mosaic virus
			51.2.1.1 Virus structure and genetic diversity
		51.2.2 Odontoglossum ringspot virus
			51.2.2.1 Virus structure and genetic diversity
	51.3 Orchid fleck virus
		51.3.1 Virus structure and genetic diversity
	51.4 Cymbidium ringspot virus
		51.4.1 Virus structure and genetic diversity
	51.5 Potyviruses
	51.6 Cucumber mosaic virus
		51.6.1 Virus structure and genetic diversity
	51.7 Calanthe mild mosaic virus
	51.8 Tomato spotted wilt virus (tospovirus)
		51.8.1 Virus structure and genetic diversity
		51.8.2 Tospovirus on Phalaenopsis
		51.8.3 Groundnut Bud Necrosis Virus
	51.9 Detection of Orchid Viruses
		51.9.1 Biodiagnosis
		51.9.2 Electron Microscopy
	51.10 Serological Methods
		51.10.1 Enzyme-linked immunosorbent assay
		51.10.2 Immunosorbent electron microscopy
		51.10.3 Dot immunobinding assay and rapid immunofilter paper assay
		51.10.4 Tissue blot immunoassay
		51.10.5 Coat protein–specific peptides
		51.10.6 Matrix-assisted laser desorption–ionization
		51.10.7 Optical coherence tomography
		51.10.8 Quartz crystal microbalance
			51.10.8.1 Immunosensors
			51.10.8.2 Immunocapillary zone electrophoresis
	51.11 Nucleic acid–hybridization-based methods
		51.11.1 Tissue-print hybridization
		51.11.2 Slot blot hybridization
		51.11.3 Molecular beacons
		51.11.4 DNA-based biosensors
		51.11.5 Polymerase chain reaction–based techniques
			51.11.5.1 Reverse transcription–polymerase chain reaction
			51.11.5.2 Immunocapture polymerase chain reaction
			51.11.5.3 Multiplex reverse transcription–polymerase chain reaction
			51.11.5.4 TaqMan real-time reverse transcription–polymerase chain reaction
	51.12 Management of orchid viruses
		51.12.1 Sanitation
		51.12.2 Meristem culture
		51.12.3 Transgenic resistance
			51.12.3.1 Coat-protein–mediated resistance
			51.12.3.2 Replicase-mediated resistance
	Conclusion
	References
Part 17: Exclusion of plant viruses by certification and quarantine
52 Elimination of plant viruses by certification and quarantine for ensuring biosecurity
	52.1 Introduction
	52.2 Elimination of plant viruses through certification of planting material
		52.2.1 Seed certification
			52.2.1.1 Methodology for quality control of seeds
			52.2.1.2 Group testing of seeds for quality control of seed-transmitted viruses
			52.2.1.3 Seed Health Certification in India
			52.2.1.4 A case study of developing certification norms for seed-transmitted viruses of grain legumes
		52.2.2 National certification system for tissue culture plants
	52.3 Elimination of plant viruses through quarantine
		52.3.1 International framework for excluding transboundary movement of plant viruses
		52.3.2 National scenario for excluding transboundary movement of plant viruses
			52.3.2.1 Import quarantine
			52.3.2.2 Export quarantine
			52.3.2.3 Domestic quarantine
			52.3.2.4 The agricultural biosecurity bill of 2013
	52.4 Technical challenges in ensuring biosecurity
		52.4.1 Pest risk analysis
		52.4.2 Applicability of appropriate virus detection techniques
		52.4.3 Sample size
		52.4.4 Detecting an unknown/exotic virus
		52.4.5 Urgency of clearance of the sample
		52.4.6 Maintaining genebanks free from exotic viruses
	52.5 Conclusion
	References
53 Exclusion of plant viruses by certification and quarantine programs
	53.1 Introduction
	53.2 Certification programs
		53.2.1 Quarantine programs as a component of certification programs
		53.2.2 Clean stock programs
			53.2.2.1 How to obtain pathogen-tested germplasm
		53.2.3 Certification programs
		53.2.4 Seed production
		53.2.5 Considerations for certification programs
		53.2.6 Voluntary or mandatory certification program?
	53.3 Quarantine programs
		53.3.1 Pest-management districts
		53.3.2 Quarantine program for the eradication of Plum Pox Virus causing sharka disease
		53.3.3 Case study of the quarantine program to eradicate Asian strain of citrus canker in Florida
		53.3.4 Strains of Citrus canker
		53.3.5 History of quarantine programs to eradicate citrus canker in Florida
		53.3.6 Lessons and considerations for quarantine programs
	References
Part 18: Evolution of plant viruses
54 Hypotheses of virus origin and evolutionary patterns of plant viruses
	54.1 Introduction
	54.2 Virus origin hypothesis
		54.2.1 Cell-first model
			54.2.1.1 Degenerative hypothesis
			54.2.1.2 Progressive or escape hypothesis
		54.2.2 Virus-first model
			54.2.2.1 “Virus-first” hypothesis
			54.2.2.2 Precellular RNA hypothesis
	54.3 Evolution of plant viruses
		54.3.1 Evolution of RNA viruses in plant
			54.3.1.1 Evolution of positive-sense RNA viruses
			54.3.1.2 Evolution of double-stranded RNA viruses
			54.3.1.3 Evolution of negative-sense RNA viruses
		54.3.2 Evolution of double-stranded DNA of viruses
		54.3.3 Evolution of single-stranded DNA viruses
	54.4 Evolution of plant virus on a spatiotemporal scale
		54.4.1 Short-term evolution of plant viruses
		54.4.2 Long-term evolution of plant viruses
	54.5 Conclusion
	References
Index
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