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Encyclopedia of and K. Subramanya Sastry • Bikash Mandal John Hammond • S. W. Scott R. W. Briddon

Encyclopedia of Plant Viruses and Viroids K. Subramanya Sastry Bikash Mandal Indian Council of Agricultural Indian Agricultural Research Institute Research, IIHR New Delhi, India Bengaluru, India Indian Council of Agricultural Research, IIOR and IIMR Hyderabad, India

John Hammond S. W. Scott USDA, Agricultural Research Service Clemson University Beltsville, MD, USA Clemson, SC, USA

R. W. Briddon John Innes Centre Norwich, 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 2019 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of , reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from 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 this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This Springer imprint is published by the registered company Springer Nature India Private Limited The registered company address is: 7th Floor, Vijaya Building, 17 Barakhamba Road, New Delhi 110 001, India DEDICATION

This book “Encyclopedia of Plant Viruses and Viroids” is dedicated to the International Committee on of Viruses (ICTV)

(past and present executive, study groups and other members) for its continuous hard work providing systematic in the taxonomy and of viruses, including plant viruses and viroids

We also dedicate this book to all the past and present research faculty and students of plant and allied subjects of the world for their rich research contributions and for advancing the study of plant viruses and viroids.

Authors K. Subramanya Sastry Bikash Mandal John Hammond S. W. Scott R. W. Briddon Foreword

It is a real pleasure to be invited to write a Foreword to this important and timely Encyclopedia as I have been involved in many similar earlier projects whose products are now sadly out of date: the CMI/AAB Descriptions 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 survivor of the first committee of the International Committee on Taxonomy of Viruses (ICTV). It was elected at the Moscow Congress in 1966 and initially called the Provisional Committee on Nomenclature of Viruses. So I bring blessings from that august heavenly band! All of these earlier efforts by hundreds of virologists were the antecedents of this magnificent Encyclopedia. The careful collation and presentation of biological information of individual viruses and viroids is as important as ever for a variety of purposes. It is required for identifying novel and is also required for devising useful names for them. Note that and are man-made groupings, namely, “related strains/isolates, which are so similarthatitismostconvenienttoknow them by a single name.” Recent advances in molecular allow the genomic sequences of all subcellular pathogens to be determined routinely, and although numerical relationships can be calculated from those sequences, and used to form arbitrary categories, phenotypic information is indispensable for interpreting that information to form the most useful groupings to be given single names. This is clearly recognized by the 2018 ICTV Code of Nomenclature which includes the recently modernized Rule 3.20 and states “A species is a monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria.” Arbitrary boundaries between taxa based on sequence similarity are not enough; biological (phenotypic) attributes are just as 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 and viroid . Appropriate integrated control programs must be based on accurate scientific information on the biology, mode of spread, etiology, and geography of pathogens. Finally, one must

vii 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 of identified 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 . 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 . Hence, there is a need for publications of multi-sourced and “digested information” like this Encyclopedia of Plant Viruses and Viroids, 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 1516 plant viruses and viroids, and the results of their Herculean endeavors are conveniently available both as hard copy and as an e-book.

Canberra, Australia Adrian Gibbs October 2019 Preface

The tropical, subtropical, and temperate environments harbor diverse plant pathogens. In almost all countries, a large number of plant pathogens cause substantial crop yield losses. Among them, plant viruses and viroids are significant plant pathogens that reduce plant vigor, yield, and quality of crop products. Since the discovery of tobacco at the end of the nineteenth century, numerous plant viruses and viroids have been discovered all over the world. At present, there are 1484 viruses and 32 viroids reported to affect plants. They are spread from plant to plant and from region to region by vectors, trade, and activity relating to agriculture. As a result, over time some are distributed globally, whereas others have restricted distributions. Pioneer studies have demonstrated the complexity and diversity of viruses, and their interactions with vectors in relation to epidemics and crop losses. In many countries, researchers have made some headway in developing virus-resistant planting material and have also developed cultural, chemical, and integrated approaches for combating virus diseases. In addition, recently developed molecular techniques, ELISA, PCR, rolling circle amplification, next-generation sequencing, siRNA deep sequencing, and metagenomic approaches, are being utilized for accurate virus and viroid diagnosis / identification, with nucleotide sequence analyses perhaps being the most reliable means to identify the viruses. As an increasing number of viruses are being discovered, nomenclature and classification has become an increasingly challenging subject in virology. In the early days of virology, researchers named viruses based on disease symptoms and the name of the plant species from which they were initially 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 and classification in all fields of virology, the International Committee on Taxonomy of Viruses (ICTV) was constituted 50 years ago. The formation of the ICTV was a unifying moment in the history of global research on viruses. The taxonomic information collated by the ICTV is published in the form of a consolidated report at about 5-year intervals. The first report was published in 1971 and the tenth report in 2017. In the initial reports, plant viruses were divided into groups unlike viruses infecting vertebrates or . The proposal and acceptance of the species concept for viruses was an important milestone in 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 fully implemented in the seventh report published in 1999 which marks the beginning of the modern era of virus taxonomy. In many instances, definite association of a specific virus with a disease is difficult to achieve due either to the induction of similar symptoms by different viruses or to the presence of mixed of related and unrelated viruses. The “Descriptions of Plant Viruses” were originally published by the Commonwealth Mycological Institute (CMI) and the Association of Applied (AAB) and then 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 to 1996. Subsequently, a large number of viruses and viroids have been identified, and the taxonomic positions of many previously known viruses have been revised. Currently, the ICTV provides the list of approved 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 the published literature on plant virology up to 2018. Sustained efforts over 5 years have resulted in the synthesis of this book, Encyclopedia of Plant Viruses and Viroids. It covers the description of 1516 plant viruses and viroids. Each of the viruses and viroids is described to the extent possible based on the available data, including taxonomic position, geographic distribution, symptoms, hosts, transmission, virion morphology, and genomic properties. Synonyms by which viruses have been reported previously are also included to aid in the interpretation of older reports in the literature. The unique aspect of this encyclopedia is that all viruses and viroids known to infect a plant species globally are described and the plant species are arranged in alphabetical order of the scientific name of the plant. Genomic features and the relationships of each virus are included in the description, which is one of the most important criteria for 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 plant viruses, the information available for these newly described viruses (the range, symptomatology, distribution, incidence, relationships, impact on plant yields, etc.) is limited. We hope that this encyclopedia will be of great help by serving as a ready-reference source for background information on host plants and viruses/viroids for researchers and academics.

November 2019 K. Subramanya Sastry Bikash Mandal John Hammond S. W. Scott R. W. Briddon Authors Acknowledgments

For the finalization of this reference book entitled Encyclopedia of Plant Viruses and Viroids, the authors have benefited immensely from critical and constructive suggestions made by a large number of plant virologists in both national and international scientific communities, viz., Professors M. J. Adams, M. H. V. Van Regenmortel, A. J. Gibbs, T. A. Zitter, the late G. Loebenstein, H. R. Pappu, Anupam Varma, 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 , the late J. M. Thresh, and the late M. V. Nayudu, and from other scholarly academicians, friends, and colleagues who provided their timely guidance and assistance during the finalization of this reference book, and the authors are highly grateful to them. We are also highly indebted to all of those contributing their expertise to the International Committee on Taxonomy 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. The authors 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 us to use partial information / descriptions of plant virus families, and species provided in the tenth ICTVonline while finalizing this reference book. If there are any inadvertent discrepancies between the taxonomic 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 scientific authorities of international organizations like the FAO, EPPO, APS, and CABI and various publishers for their prompt help in providing information and permissions. We express our sincere gratitude to Mr. C. Nagaraja for computerizing the book and for the secretarial 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 continuous support during the preparation of this book and also to his parents the late Kokkarachedu Panduranga Sastry 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 and support over the period of preparation of this Encyclopedia, and his colleagues, in particular Drs. Dimitre Mollov and Ramon Jordan, for the assistance with some sections. Dr. Bikash Mandal is highly thankful to his better half, Dr. Seema Mandal for her encouragement and support during the preparation of the Encyclopaedia. We thank Elsevier, CABI, Springer, Academic Press, and other publishers for providing permissions for using some of the information from their earlier publications. The authors gratefully appreciate and acknowledge the staff of Springer publishers particularly Dr. Mamta Kapila, Zuzana Bernhart, Tina

xi xii Acknowledgments

Shelton and Pavithra Balakrishnan for the continuous support and the meticulous care taken in bringing out this publication at an early date. We hope that this book will be of value and interest to many plant researchers particularly plant virologists, teachers, students of agriculture, companies, and researchers at quarantine stations, to serve as a comprehensive and accurate reference book for the plant virus and viroid diseases of all crops with some of the latest information on classification, transmission, genomic characters, and other 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 Sastry Bikash Mandal John Hammond S. W. Scott R. W. Briddon Authors Introduction

The Overview of Description of Plant Viruses and Viroids

Virology, a branch of biological science, developed after the discovery of in 1898. Viruses are known to infect all sorts of living , and those with host ranges known to be restricted within the plant are referred to as plant viruses. Although a few plant viruses are known to also infect their vectors, so far none of the plant viruses are known to infect higher including human beings. Plant viruses range in sizes from 16 to 2000 nm and are generally organized with nucleic acids and in either cubic or helical symmetry resulting in an isometric or rod-shaped architecture. A second of infectious agents previously presumed to be viruses, and typified by the agent of spindle tuber disease, was shown to consist of only a covalently closed circular strand of single-stranded ribonucleic acid, lacking any protein coat; these agents were referred to as viroids (Diener 1971) and were later shown to lack any protein-coding capacity (e.g., Flores et al. 1997). Plant viruses are an important constraint on world agriculture. Of all the phytopathogens, studies of plant 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 vector involved in its transmission. Numerous plant viruses are presently known globally, and almost all crop species are affected by one or more viruses. Over the last three decades, the application of molecular techniques has revolutionized our understanding of plant viruses. Viruses are simple biological entities that undergo continuous and rapid changes in their genetic makeup and thereby emerge as numerous variants that pose a challenge for their identification and classification. No single property of viruses is adequate 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 sequence and organization are used to describe a virus. The genome sequence is the ultimate feature in virus identification, which establishes genetic relationships and the evolutionary history of a virus. Therefore sequence information has become of paramount importance in viral taxonomy. However, genomic characteristics do not by themselves justify taxonomic allocations, and the wish to record phylogeny should 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 the lowest level in virus classification; unfortunately, many virologists (Pringle 1991) thought that this definition would provide them with guidelines for the establishment and demarcation of new virus species and allow decisions as to whether a virus was a member of a particular species. This led to a continuing debate about the presumed usefulness of a species definition for creating new species taxa and identifying their members.

xiii xiv Introduction

Frequently, the disease caused by a virus is difficult to understand due to the symptoms resulting from a mixed of viruses that may or may not be related. The reverse genetic approach to develop infectious clones of viruses provides an opportunity to determine the authentic disease symptoms caused by a virus. Epidemiology, biology, molecular biology, and interactions with vector and host are important areas of studies in plant virology with a goal of offering a solution to the problems imposed by plant viruses in sustainable agricultural production. The intensification of crop cultivation, environmental change, and international trade in agricultural products has resulted in more problems across the world. The application of molecular tools and techniques and genome sequence information has identified numerous new plant viruses. Over time, nomenclature and classification 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 from which the virus was first isolated, e.g., tobacco mosaic virus. However, with the discovery of greater numbers 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 different symptoms in different plant species and different viruses could cause the same symptoms in a single plant species and has led to the misidentification of plant viruses. The earliest classification of plant viruses was published by James Johnson in 1927. He used a system to differentiate the viruses by naming 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 period by 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 five characters: symptom, host, transmission, longevity in vitro, and thermal inactivation point. In the period from 1915 to 1940, several insect vectors, including , whiteflies, , planthoppers, and , were identified as being able to transmit plant viruses with extraordinary specificity, and this property was used as an important criterion for differentiation of viral disease from diseases caused by fungi and in the taxonomy of plant viruses. Fungi and were later discovered to be vectors of some plant viruses. During the years from 1935 to 1960, new technologies, such as electron microscopy, 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, protein symmetry, the presence or absence of an envelope, physical properties (buoyant density, molecular mass, sedimentation coefficient, virion stability), and chemical properties (type of [RNA or DNA], strandedness [single or double], topology [linear or circular], polarity [positive or negative] have been used as relevant physicochemical characters in the taxonomy of viruses. Another system proposed for virus classification was the use of cryptograms as an addition to the vernacular (common) name of the virus (Gibbs et al. 1966; Gibbs and Harrison 1968; Gibbs 1968). The cryptogram consisted of four pairs of symbols, which represented (i) the type, and strandedness of the genomic nucleic acid; (ii) the molecular weight of the nucleic acid, and the percentage of nucleic acid in the viral particle; (iii) the outline of the particle, and of the nucleocapsid; and (iv) the types of host, and types of vector. For example, the cryptogram of the group, as it was then described, is [R/1: 2.2/ 6: E/E: S/0] (RNA genome/single stranded: 2.2 Â 106 MW/6% nucleic acid): elongated particle/ nucleocapsid: seed plant hosts/spreads without a vector. The cryptogram system drew attention to the level 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 or bacterial virologists, despite the potential for applicability. Furthermore, the cryptogram system was not readily expanded to allow for the added complexities of the multipartite viruses then being identified, or for the variety of replication strategies including reverse , or negative and ambisense . 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 with the determination of the coat protein amino acid sequence of TMV (Tsugita et al. 1960). Protein sequencing was used to examine the phylogeny of many other organisms, establishing presumptive evolutionary using highly conserved (e.g., Dayhoff et al. 1978), and many of the methods used for comparing nucleotide 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 of viruses. However, there is no reason to assume that when virus species are demarcated only on the basis of 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 of a 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. Viral genome sequence was very useful in resolving the confusion over the synonymous identity of several plant viruses in the ninth report of the International Committee on Taxonomy of Viruses (ICTV) where the 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 approaches were articulated for virus nomenclature and classification, but none was adopted uniformly. It was increasingly felt that a uniform and internationally agreed system of nomenclature and classification was necessary to accommodate known and as yet unidentified viruses. In order to develop internationally agreed rules and regulations for nomenclature and classification of viruses, the “International Committee on Nomenclature of Viruses” (ICNV) was established during the ninth congress of the “International Association of Microbiological Societies” held in Moscow in 1966. Subsequently, the ICNV changed its name to ICTV in 1975 and became 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 viruses, the ICTValso 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 the members of the various subcommittees, national members, and 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 of taxonomy of viruses. So far the ICTV has published the virus taxonomy up to the ninth report in the form 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 the taxonomic report will no longer be published in the form of a hard copy book and the 2017 classification report will be available online as an open access resource at http://www.ictvonline.org/report (Adams et al. 2017). In the ninth report of the ICTV, 23 families and 114 genera and 1286 plant viruses were included. Even 30 viroids infecting plants are grouped by ninth ICTV report 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 in 26 families, 118 genera, and 1516 plant virus species. Even 32 viroids infecting plants are grouped in the tenth ICTV report into 8 genera and 2 families (Anon 2017). The current ICTV taxonomy can be found at talk. ictvonline.org/taxonomy. xvi Introduction

An important turning point in the development of plant virology was in 1960, when the amino acid sequence of the capsid protein of TMV was determined (Tsugita et al. 1960). Over the subsequent decades, viruses have been studied in greater detail, and the complete genome sequence of even the largest virus is now routinely determined. Each genome sequence provides the complete genetic character of an individual virus isolate. Much of the phenotypic information encoded by these sequences can be determined. Comparisons of the sequences and the proteins they encode provide estimates of phylogenetic relatedness and past evolutionary history, which are important types of information required in classification of viruses. Metagenomic data are changing our views on virus diversity and are therefore challenging the way in which we recognize and classify viruses (Simmonds 2015; Van Regenmortel 2016b). The viruses detected using metagenomic sequencing data can be described in three different ways: (1) known knowns, 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 or known viruses that have not been found previously in the surveyed environment; and (3) unknown unknowns, viruses that are completely novel and share little to no sequence similarity with other known viruses. Sequencing data for each instance can be analyzed differently based on the questions being addressed. The removal of non-viral sequences from the sample either before or after sequencing will, of course, increase the chances of identifying viruses within a metagenomic sequence dataset, so care should be taken in both sample preparation before sequencing and manipulation of sequence data after sequencing. For known knowns and unknown knowns, the screening of the sequence dataset for the presence of known viruses can drastically reduce the amount of time needed for analysis and as such, aid detection and identifi- cation of viruses (Stobbe et al. 2013). offers us a unique tool to elucidate the current state of viruses in plants and the roles different viruses play in virus: virus and virus: host interactions. It has been proposed that it should be possible to incorporate viral metagenomic sequences in the existing official virus classification system (Van Regenmortel 2016c). An important milestone of virus taxonomy is the recognition and adoption of the virus species concept. Van Regenmortel (1989) defined virus species as “A viral species is a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche,” which was accepted by the ICTV in 1991 and fully adopted in the seventh report published in 1999. Virus classification deals with the abstract classes of viruses. Avirus is an entity with distinct and independent existence, and it should not be confused with the virus species that is a conceptual construction of human minds and not real. Brandes and Wetter (1959), following the 1950 recommendation of the Virus Subcommittee of the International Nomenclature Committee for the first-listed and most important characteristic of the virus particles, “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 into 12 classes based on particle length and rigidity/flexibility and grouped these into 4 groups each containing 3 of the original 12, namely, (i) rigid rods of ~130 nm (barley stripe mosaic [hordei]virus and 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 ); (ii) flexible filaments of ~480 nm (white mosaic virus), ~515 nm (, cactus virus 1 = cactus virus X), an intermediate group with reported size overlapping the ~480 and ~515 nm classes (cymbidium mosaic virus), and ~580 nm (potato aucuba mosaic virus), all now recognized as ; (iii) rigid to slightly flexible particles of ~620 (Wisconsin streak virus) or ~650 nm (red clover vein mosaic virus, carnation latent virus, potato virus S, potato virus M, and cactus virus 2) transmitted by aphids, all currently definitive or tentative carlaviruses, and ~700 nm (wheat streak mosaic virus) transmitted by mites, now classified as a ; and (iv) flexible threads of ~730 nm (beet mosaic virus, potato virus A, , tobacco etch virus, and henbane mosaic virus – all ), ~750 nm (bean Introduction xvii common mosaic virus, bean yellow mosaic virus, pea mosaic virus, mosaic virus, turnip mosaic virus, cocksfoot [streak] mosaic virus, mosaic virus, and sorghum red stripe virus [= sugarcane mosaic virus] – also all potyviruses), and ~1250 nm ( – now recognized as a ). By the time of the first report of the ICTV (1971), potato virus X was recognized as the of the Potato virus X group, potato virus Yas type member of the Potato virus Y group, and carnation latent virus as a member of the Carnation latent virus group; in the second report (1976), these were, respectively, the Potexvirus group, group, and group; in 1993 the “groups” were elevated to genus status, with the genus Potyvirus also classified within the family .The genera Potexvirus and Carlavirus were included in the family in 2004 and divided in 2009 between the Alphaflexiviridae and Betaflexiviridae, respectively, of the order . Wheat streak mosaic virus was initially classified by the ICTV as a member of the genus , 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 of the 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 from new sequence information and phylogeny, and several previously recognized species have either been folded into other taxa as synonyms have been identified, or some species previously established only on biological information and lacking sequence information have been abolished as recognized species. 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 (a species, genus, subfamily, family, or order) or the name of a virus as a physical or genetic entity replicating in a host. Virologists have encountered problems in naming newly discovered viruses that differ 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 family . 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 the first letter capitalized. A virus name should never be italicized, even when it includes the name of a host species or genus, and should be written in lower case. This ensures that it is distinguishable from a species name, which otherwise might be identical. The first letters of words in a virus name, including the first word, should only begin with a capital when these words are proper nouns (including host genus names but not virus genus names) or start a sentence. Single letters in virus names, including alphanumerical strain designations, may be capitalized. In most texts, virus names are used much more frequently 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 the scientific name. The abbreviated version of the virus name is used in the form of a unique acronym (or almost unique; there are a few exceptions) for each virus isolate or strain. However, as a species includes a group of close variants (isolates/strain), the species name is never abbreviated. In a manuscript, often virus family, genus, and species names are used in singular and plural form without referring to the taxonomic terms. Under such informal usage, vernacular terms are used where they are neither italicized nor have the first letter capitalized, e.g., and isolates of curl New Delhi virus (Van Regenmortel and Fauquet 2002). xviii Introduction

Table 1 Order, family, genus and type species of plant viruses and viroids classification (Source: ICTV 2018b.v1) I. Plant viruses Nature of genome Order Family Genus Type species (+) sense ssRNA Viruses Tobacco ringspot virus Satsuma dwarf virus Parsnip yellow fleck virus Tomato torrado virus 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 Tymovirales Alphaflexiviridae Shallot virus X latent virus Indian citrus ringspot virus Platypuvirus Donkey orchid symptomless virus Potexvirus Potato virus X Tymovirales Betaflexiviridae Carlavirus Carnation latent virus stem pitting virus Robigovirus Cherry necrotic rusty mottle virus Unassigned Banana mild mosaic virus Unassigned Banana virus X Unassigned Sugarcane striate mosaic- associated virus Apple stem grooving virus Chordovirus Carrot Ch virus 1 Citrus leaf blotch virus Divavirus Diuris virus A Prunevirus Apricot vein clearing associated virus Potato virus T Apple chlorotic leaf spot virus Wamavirus Watermelon virus A Tymovirales Grapevine fleck virus Marafivirus rayado fino virus Turnip yellow mosaic virus Unassigned Poinsettia mosaic virus Unassigned Benyviridae Beet necrotic yellow vein virus Unassigned Botourmiaviridae Ourmia melon virus Unassigned Alfamovirus mosaic virus zonate spot virus mosaic virus Tobacco streak virus Olive latent virus 2 (continued) Introduction xix

Table 1 (continued) I. Plant viruses Nature of genome Order Family Genus Type species Unassigned Grapevine leafroll-associated virus 3 Closterovirus Beet yellows virus Lettuce infectious yellows virus Grapevine leafroll-associated virus 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-associated virus Unassigned Persimmon virus B Unassigned Kitaviridae Blunervirus Blueberry necrotic ring blotch virus Citrus leprosis virus C Hibiscus green spot virus 2 Unassigned Luteoviridae Pea enation mosaic virus 1 virus PAV Unassigned Barley yellow dwarf virus GPV Unassigned Barley yellow dwarf virus SGV Unassigned Chickpea stunt disease associated virus 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 Blackberry virus Y Barley yellow mosaic virus Sweet potato mild mottle virus Macluravirus Maclura mosaic virus 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-associated virus Unassigned Spartina mottle virus Unassigned Polemovirus Poinsettia latent virus Sobemovirus Southern bean mosaic virus Unassigned Carrot mottle virus Alphacarmovirus Carnation mottle virus Tobacco necrosis virus A (continued) xx Introduction

Table 1 (continued) I. Plant viruses Nature of genome Order Family Genus Type species Pothos latent virus Betacarmovirus Tobacco necrosis virus D Gallantivirus Galinsoga mosaic virus Gammacarmovirus Melon necrotic spot virus Macanavirus Furcraea necrotic streak virus Maize chlorotic mottle virus Pelarspovirus Pelargonium line pattern virus 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 Carnation ringspot virus Oat chlorotic stunt virus Unassigned Soil-borne wheat mosaic virus Goravirus Gentian ovary ringspot virus Barley stripe mosaic virus clump virus Potato mop-top virus Tobacco mosaic virus Unassigned Unassigned Raspberry bushy dwarf virus (-) sense Serpentovirales Ophiovirus Citrus psorosis ophiovirus ssRNA Lettuce necrotic yellows Viruses cytorhabdovirus Dichorhavirus Orchid fleck dichorhavirus Nucleorhabdovirus Potato yellow dwarf nucleorhabdovirus Lettuce big-vein associated varicosavirus Fimoviridae European mountain ash ringspot- associated emaravirus Bunyavirales Bunyavirales Unassigned Coguvirus Citrus coguvirus (+/-) sense Bunyavirales Tospoviridae Tomato spotted wilt tospovirus ssRNA viruses dsRNA viruses Unassigned Amalgavirus Southern tomato virus Unassigned Alphaendornavirus Oryza sativa alphaendornavirus Unassigned 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) Introduction xxi

Table 1 (continued) I. Plant viruses Nature of genome 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 temperate virus Unassigned White clover cryptic virus 3 Unassigned Wound tumor virus Rice ragged stunt virus (+) sense Unassigned ssDNA Viruses Subterranean clover stunt virus Unassigned foliar decay virus (+/-) sense Unassigned Geminiviridae Beet curly top Iran virus ssDNA Viruses Bean golden yellow mosaic virus Capulavirus Euphorbia caput-medusae latent virus Eragrostis curvula streak virus Grablovirus Grapevine red blotch virus Maize streak virus Tomato pseudo-curly top virus Turnip curly top virus Unassigned Citrus chlorotic dwarf associated virus Unassigned Mulberry mosaic dwarf associated virus dsDNA Commelina yellow mottle virus (Reverse Cauliflower mosaic virus transcribing Cassava vein mosaic virus viruses) Petunia vein clearing virus Rosadnavirus Rose yellow vein virus Tobacco vein clearing virus Soybean chlorotic mottle virus Rice tungro bacilliform virus II. Plant viroids Nature of genome Order Family Genus Type species (+) sense ssRNA Unassigned Avsunviroid sunblotch viroid Viroids Elaviroid latent viroid Pelamoviroid Peach latent mosaic viroid Unassigned Apscaviroid Apple scar skin viroid Cocadviroid Coconut cadang-cadang viroid Coleviroid Coleus blumei viroid 1 Potato spindle tuber viroid xxii Introduction

The form and orthography of official virus nomenclature has thus changed over the years and continues to evolve. Tomato spotted wilt disease, which was first described in Australia in 1915, was identified as a virus in 1930 and named as tomato spotted wilt virus (Best 1968) and was first recognized as a species by the ICTV in the first report (1971) under the name Tomato spotted wilt virus of the Tomato spotted wilt virus group. This was amended in 1990 to the genus Tospovirus, family Bunyaviridae, and then the species name modified to Tomato spotted wilt tospovirus (still genus Tospovirus, family Bunyaviridae) in 2015. During 2016, and susequently in 2018b.v1 the species name 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 the simple “virus” at the end of the species name, to immediately connect the species name with the appropriate genus. There are currently proposals to increase the number of taxonomic ranks to which viruses may be assigned, but there is a considerable range of opinion on this subject which may take years to resolve before a final decision is reached. Rather than describing the current and proposed rules of nomenclature and orthography here, the reader is therefore advised to refer for the current status and proposals, complete with current information on how to write a virus name, available at the ICTV website, https://talk.ictvonline.org/, which is the authoritative source of information on current virus taxonomy. 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 several viruses may infect a single plant species and the knowledge base of plant viruses is expanding constantly, efforts were made in the past to compile a global database of plant viruses. The Description 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 series comprises of excellent descriptions of over 354 individual plant viruses that were originally published as hard copy between 1970 and 1989. Each DPV was prepared by an expert and contained cryptogram (identifying feature), synonyms, main disease symptoms, geographical distribution, host range, strains, transmission, serology, stability in sap, purification, properties of particles, particle structure and composition, relation with cells and tissues, notes, references, and a plate depicting diagnostic symptoms and virions. Subsequently, an online version of DPV was developed that since 1998 has included detailed descriptions of plant viruses together with information on taxonomy and sequences. 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 about viruses, viroids, and satellites of plants, fungi, and (Adams and Antoniw 2005, 2006). In the early 1980s, the Virus Ecology Research Group of the Research School of Biological Sciences, Australian National University, initiated work compiling a database on viruses of legumes to test the use of the 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). The project was subsequently extended to create a data bank for plant viruses, which was known as the Virus Identification Data Exchange (VIDE) project. The international VIDE project, which uses the DELTA database system, assembled diagnostic information about plant viruses from all over the world. This resulted in the first computer database of plant virus descriptions (Boswell et al. 1986). In 1991, it became the first component of the Universal Virus Database of the International Committee on Taxonomy of Viruses (ICTVdB) (Büchen-Osmond and Dallwitz 1996). The directory of the ICTVdB contains a list of approved virus names linked to virus descriptions coded from information in the seventh report of the ICTV (van Regenmortel et al. 2000b) and includes updates subsequently approved by the ICTV. It also Introduction xxiii incorporates the plant virus database VIDEdB and is illustrated with EM pictures, diagrams, and images of symptoms contributed by virologists from around the world. The work of the ICTVdB, which was concluded in 2008, contained data on as many as 4949 virus species. Although the ICTV has discontinued the work on its database of virus descriptions, it has been suggested that the storage of metadata of viruses in public databases, such as Wikipedia (http://en.wikipedia.org) or the Encyclopedia of Life (http://www. eol.org) (Gibbs 2013), should be promoted. The VIDE database has been updated from time to time and is available 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: Descriptions and Lists from the VIDE Database (Brunt et al. 1996). The book, Viruses of Plants covered more than 900 viruses arranged alphabetically, with each described with characters related to the susceptibility of host 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 encyclopedia resource 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 Protection Organization 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, A Textbook of Plant Virus Diseases,byK.M.Smith, which described plant viruses, their properties, and associated diseases. The science of plant virology grew rapidly due to the development of techniques to study protein and nucleic acids, the two major constituents of viruses. As a result, numerous plant viruses were discovered in various parts of the world. Over time several 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; Rao et 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 important criterion for the identification and differentiation of plant viruses. As a result, the confusion over the synonymous identity of several plant viruses was resolved, and in the ninth report of the ICTV, definite plant virus species as well as tentative members of a genus were listed (King et al. 2012). However, a basic 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 have changed over time. In this Encyclopedia of Plant Viruses and Viroids, the natural infection of different viruses and viroids on nearly 1020 host plants are described based on the current international taxonomic criteria of the ICTV (Anon 2017). The book has been designed with the objective of providing a comprehensive 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 to date 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 to infect a particular plant species. All of the virus species that have been recognised by ICTV, have been included; in addition tentative species, which have recently been published or published previously but not yet recognised by ICTV for various reasons, have been included in this encyclopaedia. The virus name in this book appears as the major subtitle in each section of virus description. In order to differentiate the officially recognised and tentative virus species, they were presented as italic and non-italic subtitle. As the subtitle is a name of a virus which is necessary to refer to the subsequent text, it has been abbreviated for convenience, even though it is an official name (virus species). Each virus has been described with the following descriptors (to the extent that information is available): taxonomic position, geographical distribution, 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

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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 has served as scientist at different ICAR institutions, such as IIHR, Bengaluru; IIOR (DOR) Hyderabad; and IIMR (NRCS), Hyderabad (India). Prof. Sastry’s research has been primarily on epidemiology, manage- ment, and molecular and biotechnological approaches for characterization of viruses and virus-like diseases of crops of horticultural, oil , and millets. He has published 83 research articles and 5 reference books on 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 journal VirusDisease (Springer) and Virus Research News (Newsletter).

Dr. John Hammond is currently working as Research Plant Pathologist, United States Department of Agriculture, Agricultural Research Service, Floral and Nursery Plants Research Unit, Beltsville. His major 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 plants to 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 detection and identification.

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

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