Encyclopedia of Plant Viruses and Viroids 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. 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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 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, including plant viruses and viroids We also dedicate this book to all the past and present research faculty and students of plant virology 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important and timely Encyclopedia as I have been involved in many similar earlier projects whose products are now sadly out of date: the CMI/AAB Descriptions of Plant Viruses, which Bryan Harrison and I started in 1970, and later the VIDE database, which morphed into the ICTVdB under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 pathogens and is also required for devising useful names for them. Note that virus and viroid species are man-made groupings, namely, “related strains/isolates, which are so similarthatitismostconvenienttoknow them by a single name.” Recent advances in molecular biology 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 plant virus and viroid diseases. 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 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 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 mosaic virus 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 human 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 disease 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 bacteria. 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 infections of related and unrelated viruses.