Supplementary Table 1. Virus-Like Sequences Assembled From
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Insect-Transmitted Viruses and Their Management in Vegetables
Insect-transmitted viruses and their Management in vegetables Rajagopalbabu Srinivasan Bhabesh Dutta Tim Coolong UGA PIs UGA PIs UGA PIs In this webinar.. § Introduction to vectors, viruses, transmission § Insect-transmitted viruses in tomato and squash § OREI trials Prominence of insect-borne viruses Bacteria, fungi, and phytoplasmas 70% Viruses & viroids transmitted by vectors - Power, A. G. 2000. Current Opinion in Plant Biology 3: 336-340. - Hohn, T. 2007. PNAS 17905-17906. Insects as vectors of phytoviruses 400 80000 Total species described vector species viruses transmitted 300 60000 40000 200 20000 100 0 0 Homoptera Coleoptera Thysanoptera Homoptera Coleoptera Thysanoptera Thrips Larvae § Sucking mouthparts § Epidermal punctures Frankliniella fusca Pupae Adults PP virus transmission - Nagata and Peters. 2001. Virus-Insect-Plant- Interactions, pp 51-67, AP. - Whitfield et al. 2005. Annu. Rev. Phytopathol. 43:459–89. -Thrips photographs by G. Mortiz Thrips-transmitted tomato spotted wilt orthotospovirus in tomato Bemisia tabaci cryptic species - de Moya et al. 2019. Diversity Piercing and sucking mode of feeding § Key to transmission- secrete two types of saliva (watery saliva & gelling saliva) - Dixon 1973 Virus transmission Kliot et al. 2013 Viruses. 5(6):1516-35 Semi-persistent transmission Persistent circulative transmission Tomato yellow leaf curl virus (TYLCV) • DNA virus • Genus Begomovirus, Family Geminiviridae Marchant -unpublished Tomato chlorosis virus (ToCV) • RNA virus • Genus Crinivirus, Family Closteroviridae Squash -
A Novel Species of RNA Virus Associated with Root Lesion Nematode Pratylenchus Penetrans
SHORT COMMUNICATION Vieira and Nemchinov, Journal of General Virology 2019;100:704–708 DOI 10.1099/jgv.0.001246 A novel species of RNA virus associated with root lesion nematode Pratylenchus penetrans Paulo Vieira1,2 and Lev G. Nemchinov1,* Abstract The root lesion nematode Pratylenchus penetrans is a migratory species that attacks a broad range of plants. While analysing transcriptomic datasets of P. penetrans, we have identified a full-length genome of an unknown positive-sense single- stranded RNA virus, provisionally named root lesion nematode virus 1 (RLNV1). The 8614-nucleotide genome sequence encodes a single large polyprotein with conserved domains characteristic for the families Picornaviridae, Iflaviridae and Secoviridae of the order Picornavirales. Phylogenetic, BLAST and domain search analyses showed that RLNV1 is a novel species, most closely related to the recently identified sugar beet cyst nematode virus 1 and potato cyst nematode picorna- like virus. In situ hybridization with a DIG-labelled DNA probe confirmed the presence of the virus within the nematodes. A negative-strand-specific RT-PCR assay detected RLNV1 RNA in nematode total RNA samples, thus indicating that viral replication occurs in P. penetrans. To the best of our knowledge, RLNV1 is the first virus identified in Pratylenchus spp. In recent years, several new viruses infecting plant-parasitic assembly from high-throughput sequence data was supple- nematodes have been described [1–5]. Thus far, the viruses mented by sequencing of the 5¢ RACE-amplified cDNA have been identified in sedentary nematode species, such as ends of the virus. 5¢RACE reactions were performed with the soybean cyst nematode (SCN; Heterodera glycines), two the virus-specific primers GSP1, GSP2 and LN715 potato cyst nematode (PCN) species, Globodera pallida and (Table S1, available in the online version of this article) in G. -
2020 Taxonomic Update for Phylum Negarnaviricota (Riboviria: Orthornavirae), Including the Large Orders Bunyavirales and Mononegavirales
Archives of Virology https://doi.org/10.1007/s00705-020-04731-2 VIROLOGY DIVISION NEWS 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales Jens H. Kuhn1 · Scott Adkins2 · Daniela Alioto3 · Sergey V. Alkhovsky4 · Gaya K. Amarasinghe5 · Simon J. Anthony6,7 · Tatjana Avšič‑Županc8 · María A. Ayllón9,10 · Justin Bahl11 · Anne Balkema‑Buschmann12 · Matthew J. Ballinger13 · Tomáš Bartonička14 · Christopher Basler15 · Sina Bavari16 · Martin Beer17 · Dennis A. Bente18 · Éric Bergeron19 · Brian H. Bird20 · Carol Blair21 · Kim R. Blasdell22 · Steven B. Bradfute23 · Rachel Breyta24 · Thomas Briese25 · Paul A. Brown26 · Ursula J. Buchholz27 · Michael J. Buchmeier28 · Alexander Bukreyev18,29 · Felicity Burt30 · Nihal Buzkan31 · Charles H. Calisher32 · Mengji Cao33,34 · Inmaculada Casas35 · John Chamberlain36 · Kartik Chandran37 · Rémi N. Charrel38 · Biao Chen39 · Michela Chiumenti40 · Il‑Ryong Choi41 · J. Christopher S. Clegg42 · Ian Crozier43 · John V. da Graça44 · Elena Dal Bó45 · Alberto M. R. Dávila46 · Juan Carlos de la Torre47 · Xavier de Lamballerie38 · Rik L. de Swart48 · Patrick L. Di Bello49 · Nicholas Di Paola50 · Francesco Di Serio40 · Ralf G. Dietzgen51 · Michele Digiaro52 · Valerian V. Dolja53 · Olga Dolnik54 · Michael A. Drebot55 · Jan Felix Drexler56 · Ralf Dürrwald57 · Lucie Dufkova58 · William G. Dundon59 · W. Paul Duprex60 · John M. Dye50 · Andrew J. Easton61 · Hideki Ebihara62 · Toufc Elbeaino63 · Koray Ergünay64 · Jorlan Fernandes195 · Anthony R. Fooks65 · Pierre B. H. Formenty66 · Leonie F. Forth17 · Ron A. M. Fouchier48 · Juliana Freitas‑Astúa67 · Selma Gago‑Zachert68,69 · George Fú Gāo70 · María Laura García71 · Adolfo García‑Sastre72 · Aura R. Garrison50 · Aiah Gbakima73 · Tracey Goldstein74 · Jean‑Paul J. Gonzalez75,76 · Anthony Grifths77 · Martin H. Groschup12 · Stephan Günther78 · Alexandro Guterres195 · Roy A. -
82078843.Pdf
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Virology 489 (2016) 158–164 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/yviro Brief Communication Molecular characterization of Botrytis ourmia-like virus, a mycovirus close to the plant pathogenic genus Ourmiavirus Livia Donaire a, Julio Rozas b, María A. Ayllón a,n a Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223 Madrid, Spain b Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain article info abstract Article history: The molecular characterization of a novel single-stranded RNA virus, obtained by next generation Received 22 October 2015 sequencing using Illumina platform, in a field grapevine isolate of the plant pathogenic fungus Botrytis,is Returned to author for revisions reported in this work. The sequence comparison of this virus against the NCBI database showed a strong 20 November 2015 identity with RNA dependent RNA polymerases (RdRps) of plant pathogenic viruses belonging to the Accepted 25 November 2015 genus Ourmiavirus, therefore, this novel virus was named Botrytis ourmia-like virus (BOLV). BOLV has Available online 5 January 2016 one open reading frame of 2169 nucleotides, which encodes a protein of 722 amino acids showing Keywords: conserved domains of plant RNA viruses RdRps such as the most conserved GDD active domain. Our Botrytis analyses showed that BOLV is phylogenetically closer to the fungal Narnavirus and the plant Ourmiavirus Ourmiavirus than to Mitovirus of the family Narnaviridae. -
Studies on Interspecies and Intraspecies Transmission of Influenza a Viruses
STUDIES ON INTERSPECIES AND INTRASPECIES TRANSMISSION OF INFLUENZA A VIRUSES DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Hadi M. Yassine, M.Sc. ***** The Ohio State University 2009 Dissertation Committee: Professor Y.M. Saif, Adviser Professor D.J. Jackwood Approved by Professor J. Lejeune Assistant Professor C.W. Lee ______________________ Adviser Graduate Program in Veterinary Preventive Medicine i Copyright HAdi M. Yassine 2009 ii ABSTRACT Influenza A viruses are enveloped viruses belonging to the family Orthomyxoviradae that encompasses four more genera: Influenza B, Influenza C, Isavirus and Thogotovirus. Type A is the only genus that is highly infectious to variety of animal species, including human, pigs, wild and domestic birds, horses, cats, dogs, ferrets, seals, whales, and others. Avian viruses are generally thought to preferentially bind the N-acetylneuraminic acid- α2,3-galactose (NeuAcα2,3Gal) form of sialic acid receptors and human viruses preferentially bind to NeuAcα2,6Gal sialic acid receptors. Pigs express substantial amount of both forms of sialic acids on their upper respiratory epithelial cells, and it is believed that both avian and human influenza viruses can attach to the appropriate receptors and infect pigs. Hence, pigs have been postulated to serve as a “mixing vessels” in which two or more influenza viruses can co-infect and undergo reassortment with potential for development of new viruses that can transmit to and infect other species. An H1N1 influenza A virus, A/swine/Ohio/24366/07, was isolated from pigs in an Ohio County fair. -
How Influenza Virus Uses Host Cell Pathways During Uncoating
cells Review How Influenza Virus Uses Host Cell Pathways during Uncoating Etori Aguiar Moreira 1 , Yohei Yamauchi 2 and Patrick Matthias 1,3,* 1 Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; [email protected] 2 Faculty of Life Sciences, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; [email protected] 3 Faculty of Sciences, University of Basel, 4031 Basel, Switzerland * Correspondence: [email protected] Abstract: Influenza is a zoonotic respiratory disease of major public health interest due to its pan- demic potential, and a threat to animals and the human population. The influenza A virus genome consists of eight single-stranded RNA segments sequestered within a protein capsid and a lipid bilayer envelope. During host cell entry, cellular cues contribute to viral conformational changes that promote critical events such as fusion with late endosomes, capsid uncoating and viral genome release into the cytosol. In this focused review, we concisely describe the virus infection cycle and highlight the recent findings of host cell pathways and cytosolic proteins that assist influenza uncoating during host cell entry. Keywords: influenza; capsid uncoating; HDAC6; ubiquitin; EPS8; TNPO1; pandemic; M1; virus– host interaction Citation: Moreira, E.A.; Yamauchi, Y.; Matthias, P. How Influenza Virus Uses Host Cell Pathways during 1. Introduction Uncoating. Cells 2021, 10, 1722. Viruses are microscopic parasites that, unable to self-replicate, subvert a host cell https://doi.org/10.3390/ for their replication and propagation. Despite their apparent simplicity, they can cause cells10071722 severe diseases and even pose pandemic threats [1–3]. -
Characterization of P1 Leader Proteases of the Potyviridae Family
Characterization of P1 leader proteases of the Potyviridae family and identification of the host factors involved in their proteolytic activity during viral infection Hongying Shan Ph.D. Dissertation Madrid 2018 UNIVERSIDAD AUTONOMA DE MADRID Facultad de Ciencias Departamento de Biología Molecular Characterization of P1 leader proteases of the Potyviridae family and identification of the host factors involved in their proteolytic activity during viral infection Hongying Shan This thesis is performed in Departamento de Genética Molecular de Plantas of Centro Nacional de Biotecnología (CNB-CSIC) under the supervision of Dr. Juan Antonio García and Dr. Bernardo Rodamilans Ramos Madrid 2018 Acknowledgements First of all, I want to express my appreciation to thesis supervisors Bernardo Rodamilans and Juan Antonio García, who gave the dedicated guidance to this thesis. I also want to say thanks to Carmen Simón-Mateo, Fabio Pasin, Raquel Piqueras, Beatriz García, Mingmin, Zhengnan, Wenli, Linlin, Ruiqiang, Runhong and Yuwei, who helped me and provided interesting suggestions for the thesis as well as technical support. Thanks to the people in the greenhouse (Tomás Heras, Alejandro Barrasa and Esperanza Parrilla), in vitro plant culture facility (María Luisa Peinado and Beatriz Casal), advanced light microscopy (Sylvia Gutiérrez and Ana Oña), photography service (Inés Poveda) and proteomics facility (Sergio Ciordia and María Carmen Mena). Thanks a lot to all the assistance from lab313 colleagues. Thanks a lot to the whole CNB. Thanks a lot to the Chinese Scholarship Council. Thanks a lot to all my friends. Thanks a lot to my family. Madrid 20/03/2018 Index I CONTENTS Abbreviations………………………………………….……………………….……...VII Viruses cited…………………………………………………………………..……...XIII Summary…………………………………………………………………...….…….XVII Resumen…………………………………………………………......…...…………..XXI I. -
Tomato Spotted Wilt Virus
-- CALIFORNIA D EP ARTM ENT OF cdfaFOOD & AGRICULTURE ~ California Pest Rating Proposal for Tomato spotted wilt virus Current Pest Rating: C Proposed Pest Rating: C Kingdom: Viruses and viroids, Category: Riboviria Phylum: Negarnaviricota, Subphylum: Polyploviricotina Class: Ellioviricetes, Order: Bunyavirales Family: Tospoviridae, Genus: Orthotospovirus Comment Period: 6/30/2020 through 8/14/2020 Initiating Event: On August 9, 2019, USDA-APHIS published a list of “Native and Naturalized Plant Pests Permitted by Regulation”. Interstate movement of these plant pests is no longer federally regulated within the 48 contiguous United States. There are 49 plant pathogens (bacteria, fungi, viruses, and nematodes) on this list. California may choose to continue to regulate movement of some or all these pathogens into and within the state. In order to assess the needs and potential requirements to issue a state permit, a formal risk analysis for Tomato spotted wilt virus (TSWV) is given herein and a permanent pest rating is proposed. History & Status: Background: Named after Tomato spotted wilt virus, the family Tospoviridae includes species able to infect both insect vector, thrips (family Thripidae), and plant hosts. In plant pathology, viruses are often named after the first host they are described on and the most significant symptom they cause. "Spotted wilt" disease of tomato was first described in Australia in 1915. TSWV was the only member of the genus Tospovirus (now Orthotospovirus) until closely related Impatiens necrotic spot virus was characterized and added (Law and Moyer, 1990). The genus Orthotospovirus now contains TSWV as the type member and more than thirty distinct virus species. Most of them are more host specific than TSWV, and they can be separated by serological and molecular techniques (Agrios, 2005; Sherwood et al., 2003). -
Planta Daninha
AGUIAR, R.W.S. et al. Evaluation of weeds as virus reservoirs in watermelon crops 1 151103-PD-2016 PLANTA (9 páginas) DANINHAPROVA GRÁFICA SOCIEDADE BRASILEIRA DA CIÊNCIA DAS PLANTAS DANINHAS ISSN 0100-8358 (print) <http://www.sbcpd.org> 1806-9681 (online) Article EVALUATION OF WEEDS AS VIRUS RESERVOIRS IN WATERMELON CROPS Avaliação de Plantas Daninhas como Reservatórios de Vírus na Cultura da 1 AGUIAR, R.W.S. * Melancia ALVES, G.B.1 QUEIROZ, A.P.1 ABSTRACT - Watermelon is one of the most important vegetable crops in Brazil, which is grouped among the greatest producers worldwide. Viruses stand out among NASCIMENTO, I.R.1 the most damaging disease agents, which can drastically reduce fruit production. In LIMA, M.F.2 this context, weeds present in the field can also interfere in crop production, acting as reservoirs for viruses. Thus, this study aimed to investigate virus occurrence in weeds at the main watermelon-growing regions in the State of Tocantins. Viruses identification (e.g. potyviruses: Watermelon mosaic virus - WMV; Papaya ring spot virus – type watermelon -PRSV-W; Zucchini yellow mosaic virus- ZYMV; the cucumovirus Cucumber mosaic virus - CMV, and the orthotospovirus Zucchini lethal chlorosis virus - ZLCV) infecting weeds was performed by serology and confirmed by RT-PCR tests. Serological and molecular test results indicate that Amaranthus spinosus, Nicandra physaloides, Physalis angulata and Heliotropium indicum were infected by at least one virus species. The highest infection rate was represented by ZYMV (52.7%), followed by PRSV-W (22.2%); CMV, WMV, and ZLCV that showed the same infection rate (8.3%) each. -
Viruses Virus Diseases Poaceae(Gramineae)
Viruses and virus diseases of Poaceae (Gramineae) Viruses The Poaceae are one of the most important plant families in terms of the number of species, worldwide distribution, ecosystems and as ingredients of human and animal food. It is not surprising that they support many parasites including and more than 100 severely pathogenic virus species, of which new ones are being virus diseases regularly described. This book results from the contributions of 150 well-known specialists and presents of for the first time an in-depth look at all the viruses (including the retrotransposons) Poaceae(Gramineae) infesting one plant family. Ta xonomic and agronomic descriptions of the Poaceae are presented, followed by data on molecular and biological characteristics of the viruses and descriptions up to species level. Virus diseases of field grasses (barley, maize, rice, rye, sorghum, sugarcane, triticale and wheats), forage, ornamental, aromatic, wild and lawn Gramineae are largely described and illustrated (32 colour plates). A detailed index Sciences de la vie e) of viruses and taxonomic lists will help readers in their search for information. Foreworded by Marc Van Regenmortel, this book is essential for anyone with an interest in plant pathology especially plant virology, entomology, breeding minea and forecasting. Agronomists will also find this book invaluable. ra The book was coordinated by Hervé Lapierre, previously a researcher at the Institut H. Lapierre, P.-A. Signoret, editors National de la Recherche Agronomique (Versailles-France) and Pierre A. Signoret emeritus eae (G professor and formerly head of the plant pathology department at Ecole Nationale Supérieure ac Agronomique (Montpellier-France). Both have worked from the late 1960’s on virus diseases Po of Poaceae . -
Origins and Evolution of the Global RNA Virome
bioRxiv preprint doi: https://doi.org/10.1101/451740; this version posted October 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Origins and Evolution of the Global RNA Virome 2 Yuri I. Wolfa, Darius Kazlauskasb,c, Jaime Iranzoa, Adriana Lucía-Sanza,d, Jens H. 3 Kuhne, Mart Krupovicc, Valerian V. Doljaf,#, Eugene V. Koonina 4 aNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA 5 b Vilniaus universitetas biotechnologijos institutas, Vilnius, Lithuania 6 c Département de Microbiologie, Institut Pasteur, Paris, France 7 dCentro Nacional de Biotecnología, Madrid, Spain 8 eIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious 9 Diseases, National Institutes of Health, Frederick, Maryland, USA 10 fDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA 11 12 #Address correspondence to Valerian V. Dolja, [email protected] 13 14 Running title: Global RNA Virome 15 16 KEYWORDS 17 virus evolution, RNA virome, RNA-dependent RNA polymerase, phylogenomics, horizontal 18 virus transfer, virus classification, virus taxonomy 1 bioRxiv preprint doi: https://doi.org/10.1101/451740; this version posted October 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 ABSTRACT 20 Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in 21 animals and plants. The recent advances of metaviromics prompted us to perform a detailed 22 phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280