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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
# Springer Nature India Private Limited 2019This work is subject to copyright. All rights are reserved by the Publisher, whether the whole orpart of the material is concerned, specifically the rights of translation, reprinting, reuse ofillustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way,and transmission or information storage and retrieval, electronic adaptation, computer software, orby similar or dissimilar methodology now known or hereafter developed.The use of general descriptive names, registered names, trademarks, service marks, etc. in thispublication does not imply, even in the absence of a specific statement, that such names are exemptfrom the relevant protective laws and regulations and therefore free for general use.The publisher, the authors, and the editors are safe to assume that the advice and information in thisbook are believed to be true and accurate at the date of publication. Neither the publisher nor theauthors or the editors give a warranty, expressed or implied, with respect to the material containedherein or for any errors or omissions that may have been made. The publisher remains neutral withregard to jurisdictional claims in published maps and institutional affiliations.
This Springer imprint is published by the registered company Springer Nature India PrivateLimitedThe registered company address is: 7th Floor, Vijaya Building, 17 Barakhamba Road, New Delhi110 001, India
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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viii Foreword
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
ix
x Preface
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
entsFor 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: [email protected].
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.
xiii
xiv Introduction
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
Smith KM (1937) Text book of Plant Virus Diseases. P Blakiston’s Son and Company, PhiladelphiaSimmonds P (2015) Methods for virus classification and the challenge of incorporating metagenomic
sequence data. J Gen Virol 96:1193–1206
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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
Sutic DE, Ford RE, Tosic MT (1999) Handbook of plant virus diseases. CRC Press, pp 584Tsugita A, Gish DT, Young J, Fraenkel-Conrat H, Knight CA, StanleyWM (1960) The complete amino
acid sequence of the protein of tobacco mosaic virus. Proc Natl Acad Sci U S A 46:1463–1469Van Regenmortel MH (1989) Applying the species concept to plant viruses. Arch Virol 104:1–17Van Regenmortel MHV (1990) Virus species, a much overlooked but essential concept in virus
classification. Intervirol 31:241–254Van Regenmortel MHV (2001) Perspectives on binomial names for virus species. Arch Virol
146:1637–1640Van Regenmortel MHV (2016a) Only viruses, but not their genome sequences, can be classified into
hierarchical species and genus classes. Curr Top Virol 13:59–68Van Regenmortel MHV (2016b) “Classes, taxa and categories in hierarchical virusclassification: a
review of current debates on definitions and names of virus species” appeared in Bionomina.Dumerilia 10:1e20
Van Regenmortel MHV (2016c) Recent developments in the definition and official names of virusspecies. In: Genetics and Evolution of Infectious Diseases, pp 1–23. https://doi.org/10.1016/B978-0-12-799942-5.00001-9
Van Regenmortel MHV, Fauquet CM (2002) Only italicized species names of viruses have a taxonomicmeaning. Arch Virol 147:2247–2250
Van Regenmortel MHV, Bishop DHL, Fauquet CM,MayoMA,Maniloff J, Calisher CH (1997) Guide-lines to the demarcation of virus species. Arch Virol 142:1505–1518
Van Regenmortel MHV, Mayo MA, Fauquet CM, Maniloff J (2000a) Virus nomenclature: consensusversus chaos. Arch Virol 145:2227–2232
Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, Maniloff J,Mayo MA, McGeoch DJ, Pringle CR, Wickner RB (2000b) Virus taxonomy: Seventh report of theInternational Committee on Taxonomy of Viruses. Academic, San Diego
Wildy P (1971) Classification and nomenclature of viruses. First report of the International Committeeon Nomenclature of Viruses. Monog Virol 5:1–81
About the Au
thorsDr. 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.