Encyclopedia of Plant Viruses and Viroids

K. Subramanya Sastry • Bikash MandalJohn Hammond • S. W. ScottR. W. Briddon

Encyclopedia of PlantViruses and Viroids

K. Subramanya SastryIndian Council of AgriculturalResearch, IIHRBengaluru, India

Indian Council of AgriculturalResearch, IIOR and IIMRHyderabad, India

Bikash MandalIndian Agricultural Research InstituteNew Delhi, India

John HammondUSDA, Agricultural Research Service

Beltsville, MD, USA

S. W. ScottClemson University

Clemson, SC, USA

R. W. BriddonJohn Innes CentreNorwich, UK

ISBN 978-81-322-3911-6 ISBN 978-81-322-3912-3 (eBook)ISBN 978-81-322-3913-0 (print and electronic bundle)https://doi.org/10.1007/978-81-322-3912-3

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DEDICATION

This book “Encyclopedia of Plant Viruses and Viroids”is dedicated to

the International Committee on Taxonomy of Viruses (ICTV)

(past and present executive, study groups and other members)for its continuous hard work providing systematic order in the

taxonomy and nomenclature of viruses, includingplant viruses and viroids

We also dedicate this book to all the past and present researchfaculty and students of plant virology and allied subjects of theworld for their rich research contributions and for advancing the

study of plant viruses and viroids.

AuthorsK. Subramanya Sastry

Bikash MandalJohn Hammond

S. W. ScottR. W. Briddon

Foreword

It is a real pleasure to be invited to write a Foreword to this important and timely Encyclopedia as I havebeen involved in many similar earlier projects whose products are now sadly out of date: the CMI/AABDescriptions of Plant Viruses, which Bryan Harrison and I started in 1970, and later the VIDE database,which morphed into the ICTVdB under Cornelia Büchen-Osmond. Furthermore, I am the sole survivorof the first committee of the International Committee on Taxonomy of Viruses (ICTV). It was elected atthe Moscow Congress in 1966 and initially called the Provisional Committee on Nomenclature ofViruses. So I bring blessings from that august heavenly band! All of these earlier efforts by hundreds ofvirologists were the antecedents of this magnificent Encyclopedia.

The careful collation and presentation of biological information of individual viruses and viroids isas important as ever for a variety of purposes. It is required for identifying novel pathogens and is alsorequired for devising useful names for them. Note that virus and viroid species are man-madegroupings, namely, “related strains/isolates, which are so similar that it is most convenient to knowthem by a single name.” Recent advances in molecular biology allow the genomic sequences of allsubcellular pathogens to be determined routinely, and although numerical relationships can becalculated from those sequences, and used to form arbitrary categories, phenotypic information isindispensable for interpreting that information to form the most useful groupings to be given singlenames. This is clearly recognized by the 2018 ICTV Code of Nomenclature which includes therecently modernized Rule 3.20 and states “A species is a monophyletic group of viruses whoseproperties can be distinguished from those of other species by multiple criteria.”Arbitrary boundariesbetween taxa based on sequence similarity are not enough; biological (phenotypic) attributes are justas important.

Up-to-date well-ordered information is also required by field pathologists, researchers, and, espe-cially, those trying to devise control measures that minimize the economic damage caused by plant virusand viroid diseases. Appropriate integrated control programs must be based on accurate scientificinformation on the biology, mode of spread, etiology, and geography of pathogens. Finally, one must

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recognize the value of this Encyclopedia for the training of students, who are the scientists, pathologists,politicians, and administrators of the future.

The plant viruses and viroids listed by the ICTV are only the tip of the iceberg, as the number ofidentified plant pathogens, including viruses and viroids, is growing at an alarming rate as they“emerge” from wild and local hosts and spread worldwide in the ever-increasing global trade in plants.Primary reports appear in the traditional journals and in metadata, like the CABI Crop Compendium,but a few are also recorded in such open-access databases as Wikipedia. Hence, there is a need forpublications of multi-sourced and “digested information” like this Encyclopedia of Plant Viruses andViroids, which has been assembled by one of India’s most experienced senior plant virologists,Prof. K. Subramanya Sastry, and a team of associated authors, Dr. Bikash Mandal, Dr. John Hammond,Prof. S.W. Scott, and Prof. R.W. Briddon. In this Encyclopedia, the authors have included around 1516plant viruses and viroids, and the results of their Herculean endeavors are conveniently available both ashard copy and as an e-book.

Canberra, Australia Adrian GibbsOctober 2019

Preface

The tropical, subtropical, and temperate environments harbor diverse plant pathogens. In almost allcountries, a large number of plant pathogens cause substantial crop yield losses. Among them, plantviruses and viroids are significant plant pathogens that reduce plant vigor, yield, and quality of cropproducts. Since the discovery of tobacco mosaic virus at the end of the nineteenth century, numerousplant viruses and viroids have been discovered all over the world. At present, there are 1484 viruses and32 viroids reported to affect plants. They are spread from plant to plant and from region to region byvectors, trade, and human activity relating to agriculture. As a result, over time some are distributedglobally, whereas others have restricted distributions.

Pioneer studies have demonstrated the complexity and diversity of viruses, and their interactionswith vectors in relation to disease epidemics and crop losses. In many countries, researchers have madesome headway in developing virus-resistant planting material and have also developed cultural,chemical, and integrated approaches for combating virus diseases. In addition, recently developedmolecular techniques, ELISA, PCR, rolling circle amplification, next-generation sequencing, siRNAdeep sequencing, and metagenomic approaches, are being utilized for accurate virus and viroiddiagnosis / identification, with nucleotide sequence analyses perhaps being the most reliable meansto identify the viruses.

As an increasing number of viruses are being discovered, nomenclature and classification hasbecome an increasingly challenging subject in virology. In the early days of virology, researchersnamed viruses based on disease symptoms and the name of the plant species from which they wereinitially isolated. This resulted in the accumulation of multiple names for one virus in the literature,causing a great deal of confusion. To oversee the rules and regulations of virus nomenclature andclassification in all fields of virology, the International Committee on Taxonomy of Viruses (ICTV) wasconstituted 50 years ago. The formation of the ICTV was a unifying moment in the history of globalresearch on viruses. The taxonomic information collated by the ICTV is published in the form of aconsolidated report at about 5-year intervals. The first report was published in 1971 and the tenth reportin 2017. In the initial reports, plant viruses were divided into groups unlike viruses infecting vertebratesor bacteria. The proposal and acceptance of the species concept for viruses was an important milestonein virus classification that led to the formation of taxonomic structure for viruses as orders, families,genera, and species. The virus species concept was originally adopted in 1991 by the ICTV and fullyimplemented in the seventh report published in 1999 which marks the beginning of the modern era ofvirus taxonomy.

In many instances, definite association of a specific virus with a disease is difficult to achieve dueeither to the induction of similar symptoms by different viruses or to the presence of mixed infections ofrelated and unrelated viruses. The “Descriptions of Plant Viruses” were originally published by theCommonwealth Mycological Institute (CMI) and the Association of Applied Biologists (AAB) andthen by the Virus Identification Data Exchange (VIDE), International Committee on Taxonomy of

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Viruses Virus Database, and CAB International, and these publications included viruses described up to1996. Subsequently, a large number of viruses and viroids have been identified, and the taxonomicpositions of many previously known viruses have been revised. Currently, the ICTV provides the list ofapproved virus species but not their full description. However, a full description of ecological, physical,biological, and molecular properties is essential for the identification of each virus.

To develop a comprehensive description of the global plant viruses and viroids, we have covered thepublished literature on plant virology up to 2018. Sustained efforts over 5 years have resulted in thesynthesis of this book, Encyclopedia of Plant Viruses and Viroids. It covers the description of 1516plant viruses and viroids. Each of the viruses and viroids is described to the extent possible based on theavailable data, including taxonomic position, geographic distribution, symptoms, hosts, transmission,virion morphology, and genomic properties. Synonyms by which viruses have been reported previouslyare also included to aid in the interpretation of older reports in the literature. The unique aspect of thisencyclopedia is that all viruses and viroids known to infect a plant species globally are described and theplant species are arranged in alphabetical order of the scientific name of the plant. Genomic features andthe relationships of each virus are included in the description, which is one of the most important criteriafor virus or viroid species identification. It must be pointed out that although the widespread use of next-generation sequencing to identify and classify viruses is rapidly adding to the number of reported plantviruses, the information available for these newly described viruses (the host range, symptomatology,distribution, incidence, vector relationships, impact on plant yields, etc.) is limited. We hope that thisencyclopedia will be of great help by serving as a ready-reference source for background informationon host plants and viruses/viroids for researchers and academics.

November 2019 K. Subramanya SastryBikash MandalJohn Hammond

S. W. ScottR. W. Briddon

Authors

Acknowledgm

ents

For the finalization of this reference book entitled Encyclopedia of Plant Viruses and Viroids, theauthors have benefited immensely from critical and constructive suggestions made by a large number ofplant virologists in both national and international scientific communities, viz., ProfessorsM. J. Adams,M. H. V. Van Regenmortel, A. J. Gibbs, T. A. Zitter, the late G. Loebenstein, H. R. Pappu, AnupamVarma, P. Lavakumar, V. Muniyappa, M. Krishna Reddy, F. J. Morales, T. Sano, G. P. Rao,D. V. R. Saigopal, P. Sreenivasulu, P. Parvatha Reddy, B. L. Subba Rao, Kokkarachedu Sridhar,G. Nagaraja, R. A. Naidu, the late Karl Maramorosch, the late J. M. Thresh, and the late M. V. Nayudu,and from other scholarly academicians, friends, and colleagues who provided their timely guidance andassistance during the finalization of this reference book, and the authors are highly grateful to them. Weare also highly indebted to all of those contributing their expertise to the International Committee onTaxonomy of Viruses (ICTV) for their dedicated work in preparing the tenth report on Virus Taxonomy(2018), which we have utilized as the basis for plant virus and viroid classification in this book. Theauthors express their indebtedness to Prof. Andrew J. Davison (President); Prof. Elliot J. Lefkowitz(Editor-in-Chief ICTV Report); study group members and all other members of ICTV for facilitating usto use partial information / descriptions of plant virus families, genus and species provided in the tenthICTVonline while finalizing this reference book. If there are any inadvertent discrepancies between thetaxonomic classifications shown here and the ICTV tenth report, the authors defer to the ICTV.

The authors and the Springer publishers are highly thankful to all the administrative and scientificauthorities of international organizations like the FAO, EPPO, APS, and CABI and various publishersfor their prompt help in providing information and permissions.

We express our sincere gratitude to Mr. C. Nagaraja for computerizing the book and for thesecretarial assistance throughout the preparation of this reference book. We are also grateful to Miss.B. Pavithra of SPi Global, Pondicherry, for taking keen interest during the finalization of proofs. Prof.K. Subramanya Sastry expresses his gratitude to his wife Mrs. B. N. K. Kumari for her continuoussupport during the preparation of this book and also to his parents the late Kokkarachedu PandurangaSastry and the late K. Subhadramma for their eternal blessings. We thank Mokkapati Muralidhar,Mokkapati Padmavathi, and K. Sridhar for their co-operation during the completion of this book.

Dr. John Hammond gratefully recognizes his wife, Dr. Rosemarie Hammond, for her sacrifices andsupport over the period of preparation of this Encyclopedia, and his colleagues, in particularDrs. Dimitre Mollov and Ramon Jordan, for the assistance with some sections. Dr. Bikash Mandal ishighly thankful to his better half, Dr. Seema Mandal for her encouragement and support during thepreparation of the Encyclopaedia.

We thank Elsevier, CABI, Springer, Academic Press, and other publishers for providing permissionsfor using some of the information from their earlier publications. The authors gratefully appreciate andacknowledge the staff of Springer publishers particularly Dr. Mamta Kapila, Zuzana Bernhart, Tina

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xii Acknowledgments

Shelton and Pavithra Balakrishnan for the continuous support and the meticulous care taken in bringingout this publication at an early date.

We hope that this book will be of value and interest to many plant pathology researchers particularlyplant virologists, teachers, students of agriculture, seed companies, and researchers at quarantinestations, to serve as a comprehensive and accurate reference book for the plant virus and viroid diseasesof all crops with some of the latest information on classification, transmission, genomic characters, andother aspects.

We shall deem it an honor and reward if readers find this book is of great help by serving as a ready-reference source to obtain the background and latest information on the host plants and viruses/viroids.We welcome the submission of suggestions and comments for the improvement of this Encyclopedia/reference book in the future editions to e-mail: ksubramanyasastry1944@gmail.com.

K. Subramanya SastryBikash MandalJohn Hammond

S. W. ScottR. W. Briddon

Authors

Introduction

The Overview of Description of Plant Viruses and Viroids

Virology, a branch of biological science, developed after the discovery of tobacco mosaic virus in 1898.Viruses are known to infect all sorts of living organisms, and those with host ranges known to berestricted within the plant kingdom are referred to as plant viruses. Although a few plant viruses areknown to also infect their insect vectors, so far none of the plant viruses are known to infect higheranimals including human beings. Plant viruses range in sizes from 16 to 2000 nm and are generallyorganized with nucleic acids and protein in either cubic or helical symmetry resulting in an isometric orrod-shaped architecture. A second class of infectious agents previously presumed to be viruses, andtypified by the agent of potato spindle tuber disease, was shown to consist of only a covalently closedcircular strand of single-stranded ribonucleic acid, lacking any protein coat; these agents were referredto as viroids (Diener 1971) and were later shown to lack any protein-coding capacity (e.g., Floreset al. 1997).

Plant viruses are an important constraint on world agriculture. Of all the phytopathogens, studies ofplant viruses have received special attention as they cause significant losses to crop yield and quality,and the management of the diseases requires a knowledge of both the associated virus and any vectorinvolved in its transmission. Numerous plant viruses are presently known globally, and almost all cropspecies are affected by one or more viruses. Over the last three decades, the application of moleculartechniques has revolutionized our understanding of plant viruses. Viruses are simple biological entitiesthat undergo continuous and rapid changes in their genetic makeup and thereby emerge as numerousvariants that pose a challenge for their identification and classification. No single property of viruses isadequate to identify them. A set of characters such as the disease they incite, the host plants they infect,the mode of transmission, specific vector, virion morphology, and more recently genome sequence andorganization are used to describe a virus. The genome sequence is the ultimate feature in virusidentification, which establishes genetic relationships and the evolutionary history of a virus. Thereforesequence information has become of paramount importance in viral taxonomy. However, genomiccharacteristics do not by themselves justify taxonomic allocations, and the wish to record phylogenyshould not overshadow the importance of the other phenotypic and biological properties.

The definition of a species as a polythetic class was endorsed by the ICTV, and species became thelowest level in virus classification; unfortunately, many virologists (Pringle 1991) thought that thisdefinition would provide them with guidelines for the establishment and demarcation of new virusspecies and allow decisions as to whether a virus was a member of a particular species. This led to acontinuing debate about the presumed usefulness of a species definition for creating new species taxaand identifying their members.

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Frequently, the disease caused by a virus is difficult to understand due to the symptoms resultingfrom a mixed infection of viruses that may or may not be related. The reverse genetic approach todevelop infectious clones of viruses provides an opportunity to determine the authentic diseasesymptoms caused by a virus. Epidemiology, biology, molecular biology, and interactions with vectorand host are important areas of studies in plant virology with a goal of offering a solution to theproblems imposed by plant viruses in sustainable agricultural production. The intensification of cropcultivation, environmental change, and international trade in agricultural products has resulted in moreviral disease problems across the world. The application of molecular tools and techniques and genomesequence information has identified numerous new plant viruses. Over time, nomenclature andclassification of viruses have been emerged as a complex and intense area of study in virology.

Taxonomy of Plant Viruses

Plant viruses were initially identified based on the disease symptoms and the name of the host fromwhich the virus was first isolated, e.g., tobacco mosaic virus. However, with the discovery of greaternumbers of plant viruses, some of the recommended criteria were inadequate for classification. Further,more difficulties were encountered when it was shown that a particular virus could cause differentsymptoms in different plant species and different viruses could cause the same symptoms in a singleplant species and has led to the misidentification of plant viruses. The earliest classification of plantviruses was published by James Johnson in 1927. He used a system to differentiate the viruses bynaming them using the host name where the disease was first observed, the word “virus,” and a number(e.g., tobacco virus 1 for TMV). Other efforts for grouping plant viruses were made during this periodby Smith (1937) and Holmes (1939) with minor modifications of the system published by Johnson(1927). Johnson and Hoggan (1935) further revised and developed a classification system using fivecharacters: symptom, host, transmission, longevity in vitro, and thermal inactivation point. In the periodfrom 1915 to 1940, several insect vectors, including aphids, whiteflies, thrips, planthoppers, andleafhoppers, were identified as being able to transmit plant viruses with extraordinary specificity, andthis property was used as an important criterion for differentiation of viral disease from diseases causedby fungi and in the taxonomy of plant viruses. Fungi and nematodes were later discovered to be vectorsof some plant viruses. During the years from 1935 to 1960, new technologies, such as electronmicroscopy, centrifugation, electrophoresis, and methodologies such as negative staining, virus puri-fication, and crystallography were used to determine the physical and biochemical properties of viruses.Virion morphology, capsid protein symmetry, the presence or absence of an envelope, physicalproperties (buoyant density, molecular mass, sedimentation coefficient, virion stability), and chemicalproperties (type of nucleic acid [RNA or DNA], strandedness [single or double], topology [linear orcircular], polarity [positive or negative] have been used as relevant physicochemical characters in thetaxonomy of viruses.

Another system proposed for virus classification was the use of cryptograms as an addition to thevernacular (common) name of the virus (Gibbs et al. 1966; Gibbs and Harrison 1968; Gibbs 1968). Thecryptogram consisted of four pairs of symbols, which represented (i) the type, and strandedness of thegenomic nucleic acid; (ii) the molecular weight of the nucleic acid, and the percentage of nucleic acid inthe viral particle; (iii) the outline of the particle, and of the nucleocapsid; and (iv) the types of host, andtypes of vector. For example, the cryptogram of thePotexvirus group, as it was then described, is [R/1: 2.2/6: E/E: S/0] (RNA genome/single stranded: 2.2 � 106 MW/6% nucleic acid): elongated particle/nucleocapsid: seed plant hosts/spreads without a vector. The cryptogram system drew attention to thelevel of data required for adequate classification, but was not fully available for many known viruses;however, the usage was restricted almost entirely to the plant virus community, with negligible adoption

Introduction xv

by animal or bacterial virologists, despite the potential for applicability. Furthermore, the cryptogramsystemwas not readily expanded to allow for the added complexities of themultipartite viruses then beingidentified, or for the variety of replication strategies including reverse transcription, or negative andambisense genomes. The cryptogram system was never officially adopted by the ICTV but was none-theless used in ICTV reports for a few years, before being discontinued for any ICTV use after 1977.

Before any plant viral nucleotide sequences were determined, an important milestone was reached withthe determination of the coat protein amino acid sequence of TMV (Tsugita et al. 1960). Protein sequencingwas used to examine the phylogeny of many other organisms, establishing presumptive evolutionary treesusing highly conserved proteins (e.g., Dayhoff et al. 1978), and many of the methods used for comparingnucleotide sequences were derived from those developed for analysis of amino acid sequences.

The genomic sequence of a virus is considered the most important criterion in the classification ofviruses. However, there is no reason to assume that when virus species are demarcated only on the basisof genome sequences and a derived hypothetical phylogeny, this will necessarily produce a classifica-tion that is more correct, relevant, or useful than a classification based on all the phenotypic properties ofa virus (Calisher et al. 1995; Mahner and Bunge 1997). The generation of plant virus genome sequence,however, provides critical information for the identification and differentiation of plant viruses. Viralgenome sequence was very useful in resolving the confusion over the synonymous identity of severalplant viruses in the ninth report of the International Committee on Taxonomy of Viruses (ICTV) wherethe definite plant virus species as well as tentative members of a genus were listed (King et al. 2012).

During the formative phase of virus taxonomy, various systems or approacheswere articulated for virusnomenclature and classification, but none was adopted uniformly. It was increasingly felt that a uniformand internationally agreed system of nomenclature and classification was necessary to accommodateknown and as yet unidentified viruses. In order to develop internationally agreed rules and regulations fornomenclature and classification of viruses, the “International Committee on Nomenclature of Viruses”(ICNV) was established during the ninth congress of the “International Association of MicrobiologicalSocieties” held in Moscow in 1966. Subsequently, the ICNV changed its name to ICTV in 1975 andbecame a part of the “Virology Division” of the “International Union of Microbiological Societies”(IUMS). In addition to developing a universal taxonomy for all viruses, viroids, and satellite viruses, theICTValso performs an important role in communicating taxonomic decisions and maintenance of an up-to-date index of virus species (Van Regenmortel 1990; Van Regenmortel et al. 1997, 2000a, b).

The organizational structure of the ICTV is comprised of the executive committee, subcommittees,and study groups. New taxonomic proposals are scrutinized rigorously by members of the study group,subcommittee, and executive committee and finally accepted following ratification by a vote of themembers of the various subcommittees, national members, and life members. The ICTV report pro-vides taxonomic standards and official recognition of new viruses and approves creation of virus taxa.Every 5 years ICTV study groups revise the status of viruses and publish a consolidated report oftaxonomy of viruses. So far the ICTV has published the virus taxonomy up to the ninth report in theform of a hard copy book in 1971, 1976, 1979, 1982, 1991, 1995, 2000, 2005, and 2012 (Wildy 1971;Fenner 1976; Matthews 1979, 1982; Francki et al. 1991; Murphy et al. 1995; Van Regenmortel et al.2000a, b; Fauquet et al. 2005; King et al. 2012). It has now been decided by the ICTV that thetaxonomic report will no longer be published in the form of a hard copy book and the 2017 classificationreport will be available online as an open access resource at http://www.ictvonline.org/report (Adamset al. 2017). In the ninth report of the ICTV, 23 families and 114 genera and 1286 plant viruses wereincluded. Even 30 viroids infecting plants are grouped by ninth ICTVreport into 8 genera and 2 families(King et al. 2012). In the tenth ICTV report (2018b.v1), among the total viruses, the plant viruses are in26 families, 118 genera, and 1516 plant virus species. Even 32 viroids infecting plants are grouped inthe tenth ICTV report into 8 genera and 2 families (Anon 2017). The current ICTV taxonomy can befound at talk. ictvonline.org/taxonomy.

xvi Introduction

An important turning point in the development of plant virology was in 1960, when the amino acidsequence of the capsid protein of TMV was determined (Tsugita et al. 1960). Over the subsequentdecades, viruses have been studied in greater detail, and the complete genome sequence of even thelargest virus is now routinely determined. Each genome sequence provides the complete geneticcharacter of an individual virus isolate. Much of the phenotypic information encoded by thesesequences can be determined. Comparisons of the gene sequences and the proteins they encode provideestimates of phylogenetic relatedness and past evolutionary history, which are important types ofinformation required in classification of viruses.

Metagenomic data are changing our views on virus diversity and are therefore challenging the wayin which we recognize and classify viruses (Simmonds 2015; Van Regenmortel 2016b). The virusesdetected using metagenomic sequencing data can be described in three different ways: (1) knownknowns, virus species or isolates that are already known to be in the environment being surveyed;(2) unknown knowns, new virus species or isolates of a known family or known viruses that have notbeen found previously in the surveyed environment; and (3) unknown unknowns, viruses that arecompletely novel and share little to no sequence similarity with other known viruses. Sequencing datafor each instance can be analyzed differently based on the questions being addressed. The removal ofnon-viral sequences from the sample either before or after sequencing will, of course, increase thechances of identifying viruses within a metagenomic sequence dataset, so care should be taken in bothsample preparation before sequencing and manipulation of sequence data after sequencing. For knownknowns and unknown knowns, the screening of the sequence dataset for the presence of known virusescan drastically reduce the amount of time needed for analysis and as such, aid detection and identifi-cation of viruses (Stobbe et al. 2013). Metagenomics offers us a unique tool to elucidate the current stateof viruses in plants and the roles different viruses play in virus: virus and virus: host interactions. It hasbeen proposed that it should be possible to incorporate viral metagenomic sequences in the existingofficial virus classification system (Van Regenmortel 2016c).

An important milestone of virus taxonomy is the recognition and adoption of the virus speciesconcept. Van Regenmortel (1989) defined virus species as “A viral species is a polythetic class ofviruses that constitutes a replicating lineage and occupies a particular ecological niche,” which wasaccepted by the ICTV in 1991 and fully adopted in the seventh report published in 1999. Virusclassification deals with the abstract classes of viruses. Avirus is an entity with distinct and independentexistence, and it should not be confused with the virus species that is a conceptual construction ofhuman minds and not real.

Brandes and Wetter (1959), following the 1950 recommendation of the Virus Subcommittee of theInternational Nomenclature Committee for the first-listed and most important characteristic of the virusparticles, “morphology and methods of reproduction,” proposed a classification of rod- and flexuous-shaped plant viruses on the basis of morphological differences. They subdivided various viruses into12 classes based on particle length and rigidity/flexibility and grouped these into 4 groups eachcontaining 3 of the original 12, namely, (i) rigid rods of ~130 nm (barley stripe mosaic [hordei]virusand soil-borne wheat mosaic [furo]virus), ~180 nm (potato stem mottle virus = tobacco rattle [tobra]virus), and ~300 nm (tobacco mosaic virus and three other tobamoviruses); (ii) flexible filaments of~480 nm (white clover mosaic virus), ~515 nm (potato virus X, cactus virus 1 = cactus virus X), anintermediate group with reported size overlapping the ~480 and ~515 nm classes (cymbidium mosaicvirus), and ~580 nm (potato aucuba mosaic virus), all now recognized as potexviruses; (iii) rigid toslightly flexible particles of ~620 (Wisconsin pea streak virus) or ~650 nm (red clover vein mosaicvirus, carnation latent virus, potato virus S, potato virusM, and cactus virus 2) transmitted by aphids, allcurrently definitive or tentative carlaviruses, and ~700 nm (wheat streak mosaic virus) transmitted bymites, now classified as a tritimovirus; and (iv) flexible threads of ~730 nm (beet mosaic virus, potatovirus A, potato virus Y, tobacco etch virus, and henbane mosaic virus – all potyviruses), ~750 nm (bean

Introduction xvii

common mosaic virus, bean yellow mosaic virus, pea mosaic virus, soybean mosaic virus, turnipmosaic virus, cocksfoot [streak] mosaic virus, lettuce mosaic virus, and sorghum red stripe virus [=sugarcane mosaic virus] – also all potyviruses), and ~1250 nm (beet yellows virus – now recognized asa closterovirus).

By the time of the first report of the ICTV (1971), potato virus X was recognized as the type speciesof the Potato virus X group, potato virus Yas type member of the Potato virus Y group, and carnationlatent virus as a member of the Carnation latent virus group; in the second report (1976), these were,respectively, the Potexvirus group, Potyvirus group, andCarlavirus group; in 1993 the “groups”wereelevated to genus status, with the genus Potyvirus also classified within the family Potyviridae. Thegenera Potexvirus and Carlavirus were included in the family Flexiviridae in 2004 and divided in2009 between the Alphaflexiviridae and Betaflexiviridae, respectively, of the order Tymovirales.Wheat streak mosaic virus was initially classified by the ICTVas a member of the genus Rymovirus,family Potyviridae, but transferred to the new genus Tritimovirus (still Potyviridae) in 1998.These examples show the general stability of plant virus classification throughout the history ofthe ICTV, with addition of further levels of discrimination as more information becomes available;most of the new information leading to updated taxonomic placement has come directly fromnew sequence information and phylogeny, and several previously recognized species have eitherbeen folded into other taxa as synonyms have been identified, or some species previously establishedonly on biological information and lacking sequence information have been abolished as recognizedspecies.

The latest plant virus and viroid classification is provided in Table 1.

Nomenclature of Viruses

In deciding how to write a virus name, it is important to know whether it is the name of a virus taxon(a species, genus, subfamily, family, or order) or the name of a virus as a physical or genetic entityreplicating in a host. Virologists have encountered problems in naming newly discovered viruses thatdiffer by genome organization or sequence identity from those which induce similar disease symptoms.This situation is frequently encountered while naming members of the genus of the familyGeminiviridae. The ICTV provides a stable and uniform nomenclature system of the virus species,genus, family, and order. The orthography rules are available at https://talk.ictvonline.org/information/w/faq/386. The ICTV-recognized taxa (order, family, genus, and species) are written in italic with thefirst letter capitalized. Avirus name should never be italicized, even when it includes the name of a hostspecies or genus, and should be written in lower case. This ensures that it is distinguishable from aspecies name, which otherwise might be identical. The first letters of words in a virus name, includingthe first word, should only begin with a capital when these words are proper nouns (including hostgenus names but not virus genus names) or start a sentence. Single letters in virus names, includingalphanumerical strain designations, may be capitalized. In most texts, virus names are used much morefrequently than species names and may, therefore, be abbreviated. In the case of virus strain and isolate,the name is neither italicized nor is the first letter capitalized, unless it is a proper noun or part of thescientific name. The abbreviated version of the virus name is used in the form of a unique acronym (oralmost unique; there are a few exceptions) for each virus isolate or strain. However, as a speciesincludes a group of close variants (isolates/strain), the species name is never abbreviated. In amanuscript, often virus family, genus, and species names are used in singular and plural form withoutreferring to the taxonomic terms. Under such informal usage, vernacular terms are used where they areneither italicized nor have the first letter capitalized, e.g., begomoviruses and isolates of tomato leaf curlNew Delhi virus (Van Regenmortel and Fauquet 2002).

Table 1 Order, family, genus and type species of plant viruses and viroids classification (Source: ICTV 2018b.v1)

I. Plant viruses

Nature ofgenome Order Family Genus Type species

(+) sensessRNAViruses

Picornavirales Secoviridae Comovirus Cowpea mosaic virus

Fabavirus Broad bean wilt virus 1

Nepovirus Tobacco ringspot virus

Cheravirus Cherry rasp leaf virus

Sadwavirus Satsuma dwarf virus

Sequivirus Parsnip yellow fleck virus

Torradovirus Tomato torrado virus

Waikavirus Rice tungro spherical virus

Unassigned Black raspberry necrosis virus

Unassigned Chocolate lily virus A

Unassigned Dioscorea mosaic associated virus

Unassigned Strawberry latent ringspot virus

Unassigned Strawberry mottle virus

Tymovirales Alphaflexiviridae Allexivirus Shallot virus X

Lolavirus Lolium latent virus

Mandarivirus Indian citrus ringspot virus

Platypuvirus Donkey orchid symptomless virus

Potexvirus Potato virus X

Tymovirales Betaflexiviridae Carlavirus Carnation latent virus

Foveavirus Apple stem pitting virus

Robigovirus Cherry necrotic rusty mottle virus

Unassigned Banana mild mosaic virus

Unassigned Banana virus X

Unassigned Sugarcane striate mosaic-associated virus

Capillovirus Apple stem grooving virus

Chordovirus Carrot Ch virus 1

Citrivirus Citrus leaf blotch virus

Divavirus Diuris virus A

Prunevirus Apricot vein clearing associatedvirus

Tepovirus Potato virus T

Trichovirus Apple chlorotic leaf spot virus

Vitivirus Grapevine virus A

Wamavirus Watermelon virus A

Tymovirales Tymoviridae Maculavirus Grapevine fleck virus

Marafivirus Maize rayado fino virus

Tymovirus Turnip yellow mosaic virus

Unassigned Poinsettia mosaic virus

Unassigned Benyviridae Benyvirus Beet necrotic yellow vein virus

Unassigned Botourmiaviridae Ourmiavirus Ourmia melon virus

Unassigned Bromoviridae Alfamovirus Alfalfa mosaic virus

Anulavirus Pelargonium zonate spot virus

Bromovirus Brome mosaic virus

Cucumovirus Cucumber mosaic virus

Ilarvirus Tobacco streak virus

Oleavirus Olive latent virus 2

(continued)

xviii Introduction

Table 1 (continued)

I. Plant viruses

Nature ofgenome Order Family Genus Type species

Unassigned Closteroviridae Ampelovirus Grapevine leafroll-associatedvirus 3

Closterovirus Beet yellows virus

Crinivirus Lettuce infectious yellows virus

Velarivirus Grapevine leafroll-associatedvirus 7

Unassigned Actinidia virus 1

Unassigned Alligatorweed stunting virus

Unassigned Blueberry virus A

Unassigned Megakepasma mosaic virus

Unassigned Mint vein banding-associated virus

Unassigned Olive leaf yellowing-associatedvirus

Unassigned Persimmon virus B

Unassigned Kitaviridae Blunervirus Blueberry necrotic ring blotchvirus

Cilevirus Citrus leprosis virus C

Higrevirus Hibiscus green spot virus 2

Unassigned Luteoviridae Enamovirus Pea enation mosaic virus 1

Luteovirus Barley yellow dwarf virus PAV

Polerovirus Potato leafroll virus

Unassigned Barley yellow dwarf virus GPV

Unassigned Barley yellow dwarf virus SGV

Unassigned Chickpea stunt disease associatedvirus

Unassigned Groundnut rosette assistor virus

Unassigned Indonesian soybean dwarf virus

Unassigned Sweet potato leaf speckling virus

Unassigned Tobacco necrotic dwarf virus

Unassigned Potyviridae Bevemovirus Bellflower veinal mottle virus

Brambyvirus Blackberry virus Y

Bymovirus Barley yellow mosaic virus

Ipomovirus Sweet potato mild mottle virus

Macluravirus Maclura mosaic virus

Poacevirus Triticum mosaic virus

Potyvirus Potato virus Y

Roymovirus Rose yellow mosaic virus

Rymovirus Ryegrass mosaic virus

Tritimovirus Wheat streak mosaic virus

Unassigned Common reed chlorotic stripe virus

Unassigned Longan witches broom-associatedvirus

Unassigned Spartina mottle virus

Unassigned Solemoviridae Polemovirus Poinsettia latent virus

Sobemovirus Southern bean mosaic virus

Unassigned Tombusviridae Umbravirus Carrot mottle virus

Alphacarmovirus Carnation mottle virus

Alphanecrovirus Tobacco necrosis virus A

(continued)

Introduction xix

Table 1 (continued)

I. Plant viruses

Nature ofgenome Order Family Genus Type species

Aureusvirus Pothos latent virus

Betacarmovirus Turnip crinkle virus

Betanecrovirus Tobacco necrosis virus D

Gallantivirus Galinsoga mosaic virus

Gammacarmovirus Melon necrotic spot virus

Macanavirus Furcraea necrotic streak virus

Machlomovirus Maize chlorotic mottle virus

Panicovirus Panicum mosaic virus

Pelarspovirus Pelargonium line pattern virus

Tombusvirus Tomato bushy stunt virus

Zeavirus Maize necrotic streak virus

Unassigned Bean mild mosaic virus

Unassigned Chenopodium necrosis virus

Unassigned Cucumber soil-borne virus

Unassigned Trailing lespedeza virus 1

Dianthovirus Carnation ringspot virus

Avenavirus Oat chlorotic stunt virus

Unassigned Virgaviridae Furovirus Soil-borne wheat mosaic virus

Goravirus Gentian ovary ringspot virus

Hordeivirus Barley stripe mosaic virus

Pecluvirus Peanut clump virus

Pomovirus Potato mop-top virus

Tobamovirus Tobacco mosaic virus

Tobravirus Tobacco rattle virus

Unassigned Unassigned Idaeovirus Raspberry bushy dwarf virus

(-) sensessRNAViruses

Serpentovirales Aspiviridae Ophiovirus Citrus psorosis ophiovirus

Mononegavirales Rhabdoviridae Cytorhabdovirus Lettuce necrotic yellowscytorhabdovirus

Dichorhavirus Orchid fleck dichorhavirus

Nucleorhabdovirus Potato yellow dwarfnucleorhabdovirus

Varicosavirus Lettuce big-vein associatedvaricosavirus

Bunyavirales Fimoviridae Emaravirus European mountain ash ringspot-associated emaravirus

Bunyavirales Phenuiviridae Tenuivirus Rice stripe tenuivirus

Bunyavirales Unassigned Coguvirus Citrus coguvirus

(+/-) sensessRNAviruses

Bunyavirales Tospoviridae Orthotospovirus Tomato spotted wilt tospovirus

dsRNA viruses Unassigned Amalgaviridae Amalgavirus Southern tomato virus

Unassigned Endornaviridae Alphaendornavirus Oryza sativa alphaendornavirus

Unassigned Partitiviridae Alphapartitivirus White clover cryptic virus 1

Betapartitivirus Atkinsonella hypoxylon virus

Deltapartitivirus Pepper cryptic virus 1

Unassigned Alfalfa cryptic virus 1

Unassigned Carnation cryptic virus 1

Unassigned Carrot temperate virus 1

(continued)

xx Introduction

Table 1 (continued)

I. Plant viruses

Nature ofgenome Order Family Genus Type species

Unassigned Carrot temperate virus 2

Unassigned Carrot temperate virus 3

Unassigned Carrot temperate virus 4

Unassigned Hop trefoil cryptic virus 1

Unassigned Hop trefoil cryptic virus 3

Unassigned Radish yellow edge virus

Unassigned Ryegrass cryptic virus

Unassigned Spinach temperate virus

Unassigned White clover cryptic virus 3

Unassigned Reoviridae Phytoreovirus Wound tumor virus

Fijivirus Fiji disease virus

Oryzavirus Rice ragged stunt virus

(+) sensessDNAViruses

Unassigned Nanoviridae Babuvirus Banana bunchy top virus

Nanovirus Subterranean clover stunt virus

Unassigned Coconut foliar decay virus

(+/-) sensessDNAViruses

Unassigned Geminiviridae Becurtovirus Beet curly top Iran virus

Begomovirus Bean golden yellow mosaic virus

Capulavirus Euphorbia caput-medusae latentvirus

Curtovirus Beet curly top virus

Eragrovirus Eragrostis curvula streak virus

Grablovirus Grapevine red blotch virus

Mastrevirus Maize streak virus

Topocuvirus Tomato pseudo-curly top virus

Turncurtovirus Turnip curly top virus

Unassigned Citrus chlorotic dwarf associatedvirus

Unassigned Mulberry mosaic dwarf associatedvirus

dsDNA(Reversetranscribingviruses)

Ortervirales Caulimoviridae Badnavirus Commelina yellow mottle virus

Caulimovirus Cauliflower mosaic virus

Cavemovirus Cassava vein mosaic virus

Petuvirus Petunia vein clearing virus

Rosadnavirus Rose yellow vein virus

Solendovirus Tobacco vein clearing virus

Soymovirus Soybean chlorotic mottle virus

Tungrovirus Rice tungro bacilliform virus

II. Plant viroids

Nature ofgenome Order Family Genus Type species

(+) sense ssRNAViroids

Unassigned Avsunviroidae Avsunviroid Avocado sunblotch viroid

Elaviroid Eggplant latent viroid

Pelamoviroid Peach latent mosaic viroid

Unassigned Pospiviroidae Apscaviroid Apple scar skin viroid

Cocadviroid Coconut cadang-cadang viroid

Coleviroid Coleus blumei viroid 1

Hostuviroid Hop stunt viroid

Pospiviroid Potato spindle tuber viroid

Introduction xxi

xxii Introduction

The form and orthography of official virus nomenclature has thus changed over the years andcontinues to evolve. Tomato spotted wilt disease, which was first described in Australia in 1915, wasidentified as a virus in 1930 and named as tomato spotted wilt virus (Best 1968) and was first recognizedas a species by the ICTV in the first report (1971) under the name Tomato spotted wilt virus of theTomato spotted wilt virus group. This was amended in 1990 to the genus Tospovirus, familyBunyaviridae, and then the species name modified to Tomato spotted wilt tospovirus (still genusTospovirus, family Bunyaviridae) in 2015. During 2016, and susequently in 2018b.v1 the speciesname changed to Tomato spotted wilt orthotospovirus, genus Orthotospovirus, family Tospoviridae,order Bunyavirales. The names of other viral species are also revised, with the genus name replacing thesimple “virus” at the end of the species name, to immediately connect the species name with theappropriate genus. There are currently proposals to increase the number of taxonomic ranks to whichviruses may be assigned, but there is a considerable range of opinion on this subject which may takeyears to resolve before a final decision is reached. Rather than describing the current and proposed rulesof nomenclature and orthography here, the reader is therefore advised to refer for the current status andproposals, complete with current information on how to write a virus name, available at the ICTVwebsite, https://talk.ictvonline.org/, which is the authoritative source of information on current virustaxonomy. Van Regenmortel (2001) has discussed the perspectives of binomial names for virus species.

Plant Viral Database

It is necessary to have descriptions of the major parameters that identify a particular virus. As severalviruses may infect a single plant species and the knowledge base of plant viruses is expandingconstantly, efforts were made in the past to compile a global database of plant viruses. TheDescription of Plant Viruses (DPV) was originally published jointly by the Commonwealth Myco-logical Institute (CMI) and the Association of Applied Biologists (AAB), UK. The DPV seriescomprises of excellent descriptions of over 354 individual plant viruses that were originallypublished as hard copy between 1970 and 1989. Each DPV was prepared by an expert and containedcryptogram (identifying feature), synonyms, main disease symptoms, geographical distribution, hostrange, strains, transmission, serology, stability in sap, purification, properties of particles, particlestructure and composition, relation with cells and tissues, notes, references, and a plate depictingdiagnostic symptoms and virions. Subsequently, an online version of DPV was developed that since1998 has included detailed descriptions of plant viruses together with information on taxonomy andsequences. It provides a comprehensive resource that is widely used for teaching, disease manage-ment, and research. The DPVweb (http://www.dpvweb.net) provides a source of information aboutviruses, viroids, and satellites of plants, fungi, and protozoa (Adams and Antoniw 2005, 2006).

In the early 1980s, the Virus Ecology Research Group of the Research School of Biological Sciences,AustralianNational University, initiatedwork compiling a database on viruses of legumes to test the use ofthe computer-based Description Language for Taxonomy (DELTA) system (http://delta-intkey.com/www/refs.htm) for storing and manipulating taxonomic descriptions (Boswell and Gibbs 1983). Theproject was subsequently extended to create a data bank for plant viruses, which was known as the VirusIdentification Data Exchange (VIDE) project. The international VIDE project, which uses the DELTAdatabase system, assembled diagnostic information about plant viruses from all over the world. Thisresulted in the first computer database of plant virus descriptions (Boswell et al. 1986). In 1991, it becamethe first component of the Universal Virus Database of the International Committee on Taxonomy ofViruses (ICTVdB) (Büchen-Osmond and Dallwitz 1996). The directory of the ICTVdB contains a list ofapproved virus names linked to virus descriptions coded from information in the seventh report of theICTV (van Regenmortel et al. 2000b) and includes updates subsequently approved by the ICTV. It also

Introduction xxiii

incorporates the plant virus databaseVIDEdB and is illustratedwith EMpictures, diagrams, and images ofsymptoms contributed by virologists from around the world. The work of the ICTVdB, which wasconcluded in 2008, contained data on asmany as 4949 virus species. Although the ICTVhas discontinuedthe work on its database of virus descriptions, it has been suggested that the storage of metadata of virusesin public databases, such asWikipedia (http://en.wikipedia.org) or the Encyclopedia of Life (http://www.eol.org) (Gibbs 2013), should be promoted. TheVIDE database has been updated from time to time and isavailable online (http://pvo.bio-mirror.cn/refs.htm) (Brunt et al. 1996).

The VIDE database became an important resource for plant viruses and was subsequently consol-idated and published in the form of books by the CAB International: Viruses of Tropical Plants:Descriptions and Lists from the VIDE Database (Brunt et al. 1990) and Viruses of Plants: Descriptionsand Lists from the VIDE Database (Brunt et al. 1996). The book, Viruses of Plants covered more than900 viruses arranged alphabetically, with each described with characters related to the susceptibility ofhost plants and properties for virus identification.

Detailed information on selected plant viruses, their images, maps, biology, distribution, impact,diagnosis, molecular biology, management, and bibliography are available online in the encyclopediaresource Invasive Species Compendium (http://www.cabi.org/isc) and Crop Protection Compendium(http://www.cabi.org/cpc) by CAB International. The European and Mediterranean Plant ProtectionOrganization also provides datasheet information about plant viruses (https://www.eppo.int).

Books on Description of Plant Viruses

The first book on plant viruses was published in 1937,ATextbook of Plant VirusDiseases, byK.M. Smith,which described plant viruses, their properties, and associated diseases. The science of plant virology grewrapidly due to the development of techniques to study protein and nucleic acids, the twomajor constituentsof viruses. As a result, numerous plant viruses were discovered in various parts of the world. Over timeseveral textbooks on plant viruses were written (Smith 1937; Gibbs and Harrison 1976; Matthews 1981;Sutic et al. 1999; Hull 2002; Loebenstein and Thottappilly 2003; Mahy and Van Regenmortel 2008; Raoet al. 2008, 2012; Subramanya Sastry 2013a, b; Subramanya Sastry and Zitter 2014; Mandal et al. 2017).Books on individual virus description were written during the 1990s: Viruses of Tropical Plants:Descriptions and Lists from the VIDE Database and Viruses of Plants (Brunt et al. 1990, 1996).

The generation of plant virus genome sequence information provided the single most importantcriterion for the identification and differentiation of plant viruses. As a result, the confusion over thesynonymous identity of several plant viruses was resolved, and in the ninth report of the ICTV, definiteplant virus species as well as tentative members of a genus were listed (King et al. 2012). However, abasic description of the officially recognized plant viruses is not available.

The Design and Objectives of the Book

The available books that describe plant viruses were published 20 years ago. During the last two decades,numerous plant viruses and viroids have been discovered, and their nomenclature and classifications havechanged over time. In this Encyclopedia of Plant Viruses and Viroids, the natural infection of differentviruses and viroids on nearly 1020 host plants are described based on the current international taxonomiccriteria of the ICTV (Anon 2017). The book has been designed with the objective of providing acomprehensive description of plant viruses and viroids known to infect a specific plant species globally;entries are arranged by the alphabetical order of plant species, and all the viruses and viroids characterized todate have been included under each plant species.Most of the previously published books described viruses

xxiv Introduction

in alphabetical order, which did not provide a ready reference of the number of viruses or viroids known toinfect a particular plant species. All of the virus species that have been recognised by ICTV, have beenincluded; in addition tentative species, which have recently been published or published previously but notyet recognised by ICTV for various reasons, have been included in this encyclopaedia. The virus name inthis book appears as the major subtitle in each section of virus description. In order to differentiate theofficially recognised and tentative virus species, they were presented as italic and non-italic subtitle. As thesubtitle is a name of a virus which is necessary to refer to the subsequent text, it has been abbreviated forconvenience, even though it is an official name (virus species). Each virus has been described with thefollowing descriptors (to the extent that information is available): taxonomic position, geographicaldistribution, symptoms and host range, transmission, virion properties, and genome properties. A consol-idated list of references cited in the text has been provided at the end of the virus descriptions under each host.

References

Adams MJ, Antoniw JF (2005) DPVweb: an open access internet resource on plant viruses and virusdiseases. Outlook Pest Manag 16:268–270

AdamsMJ, Antoniw JF (2006) DPVweb: a comprehensive database of plant and fungal virus genes andgenomes. Nucleic Acids Res 34(Database issue):D382–D385

Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ, Kropinski AM,Krupovic M, Kuhn JH, Mushegian AR, Nibert ML, Sabanadzovic S, Sanfaçon H, Siddell SG,Simmonds P, Varsani A, Zerbini FM, Orton RJ, Smith DB, Gorbalenya AE, Davison AJ(2017) 50 Years of the International Committee on Taxonomy of Viruses: progress and prospects.Arch Virol 162:1441–1446

Anon (2017) Virus taxonomy: the classification and nomenclature of viruses. The online (10th) reportof the ICTV. https://talk.ictvonline.org/ictv-reports/ictv_online_report/

Best RJ (1968) Tomato spotted wilt virus. In: KM Smith and MA Lauffer (eds). Advances in VirusResearch, Vol. 13. Academic Press, New York. pp 66–146

Boswell KF, Gibbs AJ (eds) (1983) Viruses of legumes 1983 – Descriptions and keys from VIDE.Australian National University, Canberra, 139 pp

Boswell KF, Dallwitz MJ, Gibbs AJ, Watson L (1986) The VIDE (Virus Identification Data Exchange)project: a data bank for plant viruses. Rev Plant Pathol 65:221–231

Brandes J, Wetter C (1959) Classification of elongated plant viruses on the basis of particle morphol-ogy. Virology 8:99–115

Brunt A, Crabtree K, Gibbs A (1990) Viruses of tropical plants: Descriptions and lists from the VIDEdatabase. CAB International, Wallingford, 707 pp

Brunt AA, Crabtree K, Dallwitz MJ, Gibbs AJ, Watson L (1996) Viruses of plants. Descriptions andlists from the VIDE database. CAB International, Wallingford, 1484 pp

Büchen-Osmond C, Dallwitz M (1996) Towards a universal virus database – progress in the ICTVdB.Arch Virol 141:392–399

Calisher CH, Horzinek M, Mayo MA, Ackermann HW, Maniloff (1995) Sequence analyses andunifying system of virus taxonomy: consensus via consent. Arch Virol 140:2093–2099

Diener TO (1971) Potato spindle tuber ‘virus’. IV. A replicating, low molecular weight RNA. Virology45:411–428

Fauquet C, MayoMA,Maniloff J, Desselberger U, Ball LA (eds) (2005) Virus taxonomy: eighth reportof the International Committee on Taxonomy of Viruses. Elsevier/Academic, Amsterdam

Introduction xxv

Fenner F (1976) Classification and nomenclature of viruses. Second report of the InternationalCommittee on Taxonomy of Viruses. Intervirol 7:1–115

Flores R, Di Serio F, Hernandez C (1997) Viroids: the non-encoding genomes. Seminars Virol 8:65–73Francki RIB, Fauquet CM, Knudson DL, Brown F (1991) Classification and nomenclature of viruses.

Fifth report of the International Committee on Taxonomy of Viruses. Arch Virol Suppl. 2. Springer,Vienna

Gibbs AJ (1968) Cryptograms. In: Martyn EB (ed). Plant Virus Names. Commonwealth Mycol InstKew, Surrey, pp 135–149

Gibbs AJ (2013) Viral taxonomy needs a spring clean; its exploration era is over. Virology J 10:254Gibbs AJ, Harrison BD (1968) Realistic approach to virus classification and nomenclature. Nature 218:

927–929Gibbs A, Harrison BD (1976) Plant Virology: The Principles. Edward Arnold, London (UK). ISBN:

071312508X, 292 pp.Gibbs AJ, Harrison BD, Watson DH, Wildy P (1966) What's in a virus name? Nature 209:450–454Holmes FO (1939) Proposal for extension of the binomial system of nomenclature to include viruses.

Phytopathology 29:431–436Hull R (2002) Matthews’ Plant Virology, 4th edn, New York, NY: Academic Press. 1056 p, ISBN: 978-

0-12-361160-4Johnson J (1927) The classification of plant viruses. Res Bull Wis Agric Exp Stn 76:1–16Johnson J, Hoggan IA (1935) A descriptive key for plant viruses. Phytopathology 25:328–343King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (2012) Virus taxonomy: classification and

nomenclature of viruses. Ninth report of the International Committee on Taxonomy of Viruses.Elsevier Academic Press, San Diego

Loebenstein G, Thottappilly G (2003) Virus and virus-like diseases of major crops in developingcountries. Springer Publishers, Netherlands. https://doi.org/10.1007/978-94-007-0791-7

Mahner M, Bunge M (1997) Foundations of biophilosophy. Springer, BerlinMahy BWJ, Van Regenmortel MHV (2008) Desk encyclopaedia of plant and fungal virology. Elsevier

PublishersMandal B, Rao GP, Baranwal VK, Jain RK (2017) A century of plant virology in India. Springer

Publishers, p 805Matthews RE (1979) Third report of the International Committee on Taxonomy of Viruses. Classifi-

cation and nomenclature of viruses. Intervirol 12:129–296Matthews REF (1981) Plant Virology, 2nd edn. Academic Press, ISBN: 9781483258669, pp 916Matthews REF (1982) Classification and nomenclature of viruses. Fourth report of the international

committee on taxonomy of viruses. Intervirol 17:1–199Murphy FA, Fauquet CM, Bishop DHL, Ghabrial SA, Jarvis AW, Martelli GP, Mayo MA, Summers

MD (1995) Virus taxonomy. Sixth report of the International Committee on Taxonomy of Viruses.Springer, Vienna

Pringle CR (1991) The 20th meeting of the executive committee of the ICTV. Virus species, highertaxa, a universal database and other matters. Arch Virol 119:303e4.5

Rao GP, Kumar PL, Holguin-Pena RJ (2008) Characterization, diagnosis and management of plantviruses. Vegetable and pulse crops, vol III. Studium Press, LLS, Houstan, 408 p

Rao GP, Baranwal VK, Mandal B, Rishi N (2012) Recent trends in plant virology. Studium Press LLC,USA, 493 p

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Stobbe AH, Daniels J, Espindola AS, Verma R, Melcher U, Ochoa-Corona F et al (2013) E-probediagnostic nucleic acid analysis (EDNA): a theoretical approach for handling of next generationsequencing data for diagnostics. J Mirobiol Methods 94:356–366

Subramanya Sastry K (2013a) Seed-borne plant virus diseases. Springer Publishers, p 327Subramanya Sastry K (2013b) Plant virus and viroid diseases in the tropics. Introduction of plant

viruses and sub-viral agents, classification, assessment of loss, transmission and diagnosis,vol 1. Springer Publishers, 361 p

Subramanya Sastry K, Zitter TA (2014) Plant virus and viroid diseases in the tropics. Epidemiology andmanagement of plant viruses, vol 2. Springer Publishers, 489 p

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About the Au

thors

Dr. K. Subramanya Sastry a retired Principal Scientist from Indian Council of Agricultural Research(ICAR), India, has carried out research in plant virology for over 28 years. During his service period, he hasserved as scientist at different ICAR institutions, such as IIHR, Bengaluru; IIOR (DOR) Hyderabad; andIIMR (NRCS), Hyderabad (India). Prof. Sastry’s research has been primarily on epidemiology, manage-ment, andmolecular and biotechnological approaches for characterization of viruses and virus-like diseasesof crops of horticultural, oil seeds, and millets. He has published 83 research articles and 5 reference bookson plant virology, and 3 of them are through Springer Publishers. Dr. K. Subramanya Sastry is the editor-in-chief of this present reference book entitled Encyclopedia of Plant Viruses and Viroids.

Dr. Bikash Mandal is currently working as Principal Scientist in Advanced Center for Plant Virology,Indian Agricultural Research Institute (IARI), New Delhi. His research and teaching area is plant

xxvii

xxviii About the Authors

virology. He has totally 153 publications that include 2 books, 8 book chapters, 72 research papers,5 popular technical articles, and 65 conference abstracts. He is the editor-in-chief of the journalVirusDisease (Springer) and Virus Research News (Newsletter).

Dr. John Hammond is currently working as Research Plant Pathologist, United States Department ofAgriculture, Agricultural Research Service, Floral and Nursery Plants Research Unit, Beltsville. Hismajor areas of research are viruses affecting ornamental crops, with emphasis on potyvirus, potexvirus,and carlavirus detection, differentiation, and methods of introducing resistance, use of transgenic plantsto examine virus resistance and infectious viral clones to determine factors affecting host range,symptom induction, and systemic movement, and development of microarrays for plant virus detectionand identification.

Dr. Simon W. Scott has recently retired from Clemson University as a Professor Emeritus in PlantPathology. His major areas of research were viruses and virus-like agents affecting woody deciduousspecies with an emphasis on viruses that affect the dominant fruit crop in South Carolina (peaches). Hehas established a program to index large blocks of peach trees in the southeastern USA prior topropagation as part of the USDA/APHIS National Clean Plant Network. In addition, he has producedextensive sequence data for a number of Ilarviruses, allowing long-standing taxonomic anomalies to becorrected.

About the Authors xxix

Dr. Robert William Briddon has worked as Principle Investigator in Agricultural BiotechnologyDivision, National Institute of Biotechnology and Genetic Engineering (funded by United StatesDepartment of Agriculture (USDA) through the International Center for Agricultural Research in theDry Areas (ICARDA, Islamabad Office). His research area is in study of vector transmission of plantinfecting viruses, particularly the interactions involved between virus and insect vector of circulativelyand propagatively transmitted viruses and the evolution thereof. He has totally 135 publications in ISIWeb of knowledge. He is also a member of British Society for Plant Pathology, European WhiteflyStudy Network, and International Committee on Taxonomy of Viruses.