Next Generation Sequencing Technologies for Insect Virus Discovery
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Virology Journal Biomed Central
Virology Journal BioMed Central Research Open Access The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities Alexander I Culley1, Andrew S Lang2 and Curtis A Suttle*1,3 Address: 1University of British Columbia, Department of Botany, 3529-6270 University Blvd, Vancouver, B.C. V6T 1Z4, Canada, 2Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada and 3University of British Columbia, Department of Earth and Ocean Sciences, Department of Microbiology and Immunology, 1461-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada Email: Alexander I Culley - [email protected]; Andrew S Lang - [email protected]; Curtis A Suttle* - [email protected] * Corresponding author Published: 6 July 2007 Received: 10 May 2007 Accepted: 6 July 2007 Virology Journal 2007, 4:69 doi:10.1186/1743-422X-4-69 This article is available from: http://www.virologyj.com/content/4/1/69 © 2007 Culley et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: RNA viruses have been isolated that infect marine organisms ranging from bacteria to whales, but little is known about the composition and population structure of the in situ marine RNA virus community. In a recent study, the majority of three genomes of previously unknown positive-sense single-stranded (ss) RNA viruses were assembled from reverse-transcribed whole- genome shotgun libraries. -
Virus Particle Structures
Virus Particle Structures Virus Particle Structures Palmenberg, A.C. and Sgro, J.-Y. COLOR PLATE LEGENDS These color plates depict the relative sizes and comparative virion structures of multiple types of viruses. The renderings are based on data from published atomic coordinates as determined by X-ray crystallography. The international online repository for 3D coordinates is the Protein Databank (www.rcsb.org/pdb/), maintained by the Research Collaboratory for Structural Bioinformatics (RCSB). The VIPER web site (mmtsb.scripps.edu/viper), maintains a parallel collection of PDB coordinates for icosahedral viruses and additionally offers a version of each data file permuted into the same relative 3D orientation (Reddy, V., Natarajan, P., Okerberg, B., Li, K., Damodaran, K., Morton, R., Brooks, C. and Johnson, J. (2001). J. Virol., 75, 11943-11947). VIPER also contains an excellent repository of instructional materials pertaining to icosahedral symmetry and viral structures. All images presented here, except for the filamentous viruses, used the standard VIPER orientation along the icosahedral 2-fold axis. With the exception of Plate 3 as described below, these images were generated from their atomic coordinates using a novel radial depth-cue colorization technique and the program Rasmol (Sayle, R.A., Milner-White, E.J. (1995). RASMOL: biomolecular graphics for all. Trends Biochem Sci., 20, 374-376). First, the Temperature Factor column for every atom in a PDB coordinate file was edited to record a measure of the radial distance from the virion center. The files were rendered using the Rasmol spacefill menu, with specular and shadow options according to the Van de Waals radius of each atom. -
Tibet Orbivirus, a Novel Orbivirus Species Isolated from Anopheles
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2014 Tibet Orbivirus, a novel Orbivirus species isolated from Anopheles maculatus mosquitoes in Tibet, China Minghua Li Chinese Center for Disease Control and Prevention, Beijing Yayun Zheng Chinese Center for Disease Control and Prevention, Beijing Guoyan Zhao Washington University School of Medicine in St. Louis Shihong Fu Chinese Center for Disease Control and Prevention, Beijing David Wang Washington University School of Medicine in St. Louis See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Li, Minghua; Zheng, Yayun; Zhao, Guoyan; Fu, Shihong; Wang, David; Wang, Zhiyu; and Liang, Guodong, ,"Tibet Orbivirus, a novel Orbivirus species isolated from Anopheles maculatus mosquitoes in Tibet, China." PLoS One.9,2. e88738. (2014). https://digitalcommons.wustl.edu/open_access_pubs/3048 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Minghua Li, Yayun Zheng, Guoyan Zhao, Shihong Fu, David Wang, Zhiyu Wang, and Guodong Liang This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/3048 Tibet Orbivirus, a Novel Orbivirus Species Isolated from Anopheles maculatus Mosquitoes in Tibet, China Minghua Li1., Yayun Zheng1,2., Guoyan Zhao3, Shihong Fu1, David Wang3, Zhiyu Wang2, Guodong Liang1,2* 1 State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, 2 School of Public Health, Shandong University, Jinan, Shandong Province, China, 3 Washington University, St. -
Molecular Characterization of a New Monopartite Dsrna Mycovirus from Mycorrhizal Thelephora Terrestris
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Virology 489 (2016) 12–19 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/yviro Molecular characterization of a new monopartite dsRNA mycovirus from mycorrhizal Thelephora terrestris (Ehrh.) and its detection in soil oribatid mites (Acari: Oribatida) Karel Petrzik a,n, Tatiana Sarkisova a, Josef Starý b, Igor Koloniuk a, Lenka Hrabáková a,c, Olga Kubešová a a Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic b Institute of Soil Biology, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05 České Budějovice, Czech Republic c Department of Genetics, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31a, 370 05 České Budějovice, Czech Republic article info abstract Article history: A novel dsRNA virus was identified in the mycorrhizal fungus Thelephora terrestris (Ehrh.) and sequenced. Received 28 July 2015 This virus, named Thelephora terrestris virus 1 (TtV1), contains two reading frames in different frames Returned to author for revisions but with the possibility that ORF2 could be translated as a fusion polyprotein after ribosomal -1 fra- 4 November 2015 meshifting. Picornavirus 2A-like motif, nudix hydrolase, phytoreovirus S7, and RdRp domains were found Accepted 10 November 2015 in a unique arrangement on the polyprotein. A new genus named Phlegivirus and containing TtV1, PgLV1, Available online 14 December 2015 RfV1 and LeV is therefore proposed. Twenty species of oribatid mites were identified in soil material in Keywords: the vicinity of T. -
RNA Silencing-Based Improvement of Antiviral Plant Immunity
viruses Review Catch Me If You Can! RNA Silencing-Based Improvement of Antiviral Plant Immunity Fatima Yousif Gaffar and Aline Koch * Centre for BioSystems, Institute of Phytopathology, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, D-35392 Giessen, Germany * Correspondence: [email protected] Received: 4 April 2019; Accepted: 17 July 2019; Published: 23 July 2019 Abstract: Viruses are obligate parasites which cause a range of severe plant diseases that affect farm productivity around the world, resulting in immense annual losses of yield. Therefore, control of viral pathogens continues to be an agronomic and scientific challenge requiring innovative and ground-breaking strategies to meet the demands of a growing world population. Over the last decade, RNA silencing has been employed to develop plants with an improved resistance to biotic stresses based on their function to provide protection from invasion by foreign nucleic acids, such as viruses. This natural phenomenon can be exploited to control agronomically relevant plant diseases. Recent evidence argues that this biotechnological method, called host-induced gene silencing, is effective against sucking insects, nematodes, and pathogenic fungi, as well as bacteria and viruses on their plant hosts. Here, we review recent studies which reveal the enormous potential that RNA-silencing strategies hold for providing an environmentally friendly mechanism to protect crop plants from viral diseases. Keywords: RNA silencing; Host-induced gene silencing; Spray-induced gene silencing; virus control; RNA silencing-based crop protection; GMO crops 1. Introduction Antiviral Plant Defence Responses Plant viruses are submicroscopic spherical, rod-shaped or filamentous particles which contain different kinds of genomes. -
Interactions Among Multiple Structural Proteins
Hypothesis on particle structure and assembly of rice dwarf phytoreovirus: interactions among multiple structural Title proteins Author(s) Ueda, Shigenori; Masuta, Chikara; Uyeda, Ichiro Journal of General Virology, 78, 3135-3140 Citation https://doi.org/10.1099/0022-1317-78-12-3135 Issue Date 1997 Doc URL http://hdl.handle.net/2115/5819 Type article File Information JGV78.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Journal of General Virology (1997), 78, 3135–3140. Printed in Great Britain ...............................................................................................................................................................................................................SHORT COMMUNICATION Hypothesis on particle structure and assembly of rice dwarf phytoreovirus: interactions among multiple structural proteins Shigenori Ueda, Chikara Masuta and Ichiro Uyeda Laboratory of Plant Virology and Mycology, Department of Agrobiology and Bioresources, Faculty of Agriculture, Hokkaido University, Sapporo 060, Japan and has non-specific nucleic acid-binding activity (Ueda & To study the morphogenesis and packaging of rice Uyeda, 1997). dwarf phytoreovirus (RDV), the interactions among Little is known about the replication and assembly process multiple structural proteins were analysed using of RDV or about interactions among multiple structural both the yeast two-hybrid system and far-Western proteins in viral particles. Therefore, in this study, we blotting analysis. The -
Viral Metagenomics of Aphids Present in Bean and Maize Plots on Mixed
Wamonje et al. Virology Journal (2017) 14:188 DOI 10.1186/s12985-017-0854-x RESEARCH Open Access Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus Francis O. Wamonje1, George N. Michuki2,4, Luke A. Braidwood1, Joyce N. Njuguna3, J. Musembi Mutuku3, Appolinaire Djikeng3,5, Jagger J. W. Harvey3,6 and John P. Carr1* Abstract Background: Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farmers to provide fixed nitrogen for cultivation of starch crops such as maize. We used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples. Samples were collected from farms in Kenya in a range of agro-ecological zones. Results: Cytochrome oxidase 1 (CO1) gene sequencing showed that Aphis fabae was the sole aphid species present in bean plots in the farms visited. Sequencing of total RNA from aphids using the Illumina platform detected three dicistroviruses. Maize leaf RNA was also analysed. Identification of Aphid lethal paralysis virus (ALPV), Rhopalosiphum padi virus (RhPV), and a novel Big Sioux River virus (BSRV)-like dicistrovirus in aphid and maize samples was confirmed using reverse transcription-polymerase chain reactions and sequencing of amplified DNA products. -
Genome Sequence Analysis of Csrv1: a Pathogenic Reovirus That Infects the Blue Crab Callinectes Sapidus Across Its Trans-Hemispheric Range
fmicb-07-00126 February 8, 2016 Time: 17:51 # 1 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 10 February 2016 doi: 10.3389/fmicb.2016.00126 Genome Sequence Analysis of CsRV1: A Pathogenic Reovirus that Infects the Blue Crab Callinectes sapidus Across Its Trans-Hemispheric Range Emily M. Flowers1,2, Tsvetan R. Bachvaroff1, Janet V. Warg3, John D. Neill4, Mary L. Killian3, Anapaula S. Vinagre5, Shanai Brown6, Andréa Santos e Almeida1 and Eric J. Schott1* 1 Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA, 2 University of Maryland School of Medicine, Baltimore, MD, USA, 3 National Veterinary Services Laboratories, Animal and Plant Health Inspection Service , United States Department of Agriculture, Ames, IA, USA, 4 National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA, 5 Departamento de Fisiologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil, 6 Department of Biology, Morgan State University, Baltimore, MD, USA The blue crab, Callinectes sapidus Rathbun, 1896, which is a commercially important Edited by: Ian Hewson, trophic link in coastal ecosystems of the western Atlantic, is infected in both North Cornell University, USA and South America by C. sapidus Reovirus 1 (CsRV1), a double stranded RNA virus. Reviewed by: The 12 genome segments of a North American strain of CsRV1 were sequenced Hélène Montanié, Université de la Rochelle, France using Ion Torrent technology. Putative functions could be assigned for 3 of the 13 Thierry Work, proteins encoded in the genome, based on their similarity to proteins encoded in other United States Geological Survey, USA reovirus genomes. -
I CHARACTERIZATION of ORTHOREOVIRUSES ISOLATED from AMERICAN CROW (CORVUS BRACHYRHYNCHOS) WINTER MORTALITY EVENTS in EASTERN CA
CHARACTERIZATION OF ORTHOREOVIRUSES ISOLATED FROM AMERICAN CROW (CORVUS BRACHYRHYNCHOS) WINTER MORTALITY EVENTS IN EASTERN CANADA A Thesis Submitted to the Graduate Faculty in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY In the Department of Pathology and Microbiology Faculty of Veterinary Medicine University of Prince Edward Island Anil Wasantha Kalupahana Charlottetown, P.E.I. July 12, 2017 ©2017, A.W. Kalupahana i THESIS/DISSERTATION NON-EXCLUSIVE LICENSE Family Name: Kalupahana Given Name, Middle Name (if applicable): Anil Wasantha Full Name of University: Atlantic Veterinary Collage at the University of Prince Edward Island Faculty, Department, School: Department of Pathology and Microbiology Degree for which thesis/dissertation was Date Degree Awarded: July 12, 2017 presented: PhD DOCTORThesis/dissertation OF PHILOSOPHY Title: Characterization of orthoreoviruses isolated from American crow (Corvus brachyrhynchos) winter mortality events in eastern Canada Date of Birth. December 25, 1966 In consideration of my University making my thesis/dissertation available to interested persons, I, Anil Wasantha Kalupahana, hereby grant a non-exclusive, for the full term of copyright protection, license to my University, the Atlantic Veterinary Collage at the University of Prince Edward Island: (a) to archive, preserve, produce, reproduce, publish, communicate, convert into any format, and to make available in print or online by telecommunication to the public for non-commercial purposes; (b) to sub-license to Library and Archives Canada any of the acts mentioned in paragraph (a). I undertake to submit my thesis/dissertation, through my University, to Library and Archives Canada. Any abstract submitted with the thesis/dissertation will be considered to form part of the thesis/dissertation. -
Sequence Analysis and GTP-Binding Ability of the Minor Core Protein P5 of Rice Gall Dwarf Virus
JARQ 36 (2), 83 – 87 (2002) http://www.jircas.affrc.go.jp GTP-Binding Ability of P5 of RGDV Sequence Analysis and GTP-Binding Ability of the Minor Core Protein P5 of Rice Gall Dwarf Virus Kenzaburo ICHIMI1, Akira KIKUCHI2, Yusuke MORIYASU3, Boxiong ZHONG4, Kyoji HAGIWARA5, Hiroshi KAMIUNTEN6 and Toshihiro OMURA5* 1,2,3,4,5 National Agricultural Research Center (Tsukuba, Ibaraki 305–8666, Japan) 6 Faculty of Agriculture, Miyazaki University (1–1 Gakuenkihanadai Nishi, Miyazaki 889–2155, Japan) Abstract Analysis of the nucleotide sequence of the genome segment S5 of Rice gall dwarf virus (RGDV), which belongs to the genus Phytoreovirus, revealed that this segment encodes a putative protein of approximately 91 kDa. Antiserum raised against the protein reacted with a minor structural protein of similar size in RGDV, demonstrating that S5 encodes the structural protein of RGDV. The protein named P5 appeared to be a component of viral core particles. Although no overall homology was found to any other proteins, including those of animal-infecting reoviruses, P5 of RGDV exhibited a significant homology to P5 of Rice dwarf virus (50%), which might be a guanylyltransferase, and to P5 of Wound tumor virus (55%). These results, together with the observation that P5 bound guanosine triphosphate suggest that P5 of RGDV shows a guanylyltransferase activity and, moreover, that plant- infecting reoviruses have a similar functional and/or structural organization to that of animal-infecting reoviruses. Discipline: Plant disease Additional key words: RGDV, Phytoreovirus animal reoviruses5, 18, 26. In RDV, the P5 protein encoded Introduction by the S5 segment of the dsRNA genome binds GTP covalently, suggesting that P5 of RDV can be a One of the notable properties of the viruses in the guanylyltransferase29. -
The Reoviridae the VIRUSES
The Reoviridae THE VIRUSES Series Editors HEINZ FRAENKEL-CONRAT, University of California Berkeley, California ROBERT R. WAGNER, University of Virginia School of Medicine Charlottesville, Virginia THE HERPESVIRUSES, Volumes I, 2, 3, and 4 Edited by Bernard Roizman THE REOVIRIDAE Edited by Wolfgang K. Joklik THE PARVOVIRUSES Edited by Kenneth I. Berns The Reoviridae Edited by WOLFGANG K. JOKLIK Duke University Medical Center Durham, North Carolina Springer Science+Business Media, LLC Library of Congress Cataloging in Publication Data Main entry under title: The Reoviridae. (Viruses) Includes bibliographical references and index. 1. Reoviruses. L Joklik, Wolfgang K. II. Series. QR414.R46 1983 576/.64 83-6276 ISBN 978-1-4899-0582-6 ISBN 978-1-4899-0582-6 ISBN 978-1-4899-0580-2 (eBook) DOI 10.1007/978-1-4899-0580-2 © Springer Science+Business Media New York 1983 Originally published by Plenum Press, New York in 1983 Softcover reprint of the hardcover 1st edition 1983 All rights reserved No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher Con tribu tors Guido 'Boccardo, Istituto di Fitovirologia Applicata del C.N.R., 10135 To rino, Italy Bernard N. Fields, Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115; and Depart ment of Medicine, Brigham and Women's Hospital, Boston, Massa chusetts 02115 R. I. B. Fran'cki, Department of Plant Pathology, Waite Agricultural Re search Institute, The University of Adelaide, Adelaide 5064, South Australia Barry M. -
REOVIRUS.Pdf
REOVIRUS MAMMALIAN ORTHOREOVIRUS 1 (ATCC VR-230) REOVIRUS TYPE 2 (ATCC VR-231) REOVIRUS 3 (ATCC VR-824) PATHOGEN SAFETY DATA SHEET / INFECTIOUS SUBSTANCES INFECTIOUS AGENT NAME: Reovirus GENERAL: Reoviridae is a family of viruses that can affect the gastrointestinal system and respiratory tract. Viruses in the family Reoviridae have genomes consisting of segmented, double-stranded RNA (dsRNA). The name "Reoviridae" is derived from respiratory enteric orphan viruses. The term "orphan virus" means that a virus is not associated with any known disease. Even though viruses in the Reoviridae family have more recently been identified with various diseases, the original name is still used. Reovirus infection occurs often in humans, but most cases are mild or subclinical. Rotavirus, however, can cause severe diarrhea and intestinal distress in children. Reovirus can be readily detected in feces, and may also be recovered from pharyngeal or nasal secretions, urine, cerebrospinal fluid, and blood. Despite the ease of finding reovirus in clinical specimens, their role in human disease or treatment is still uncertain. The reovirus has been demonstrated to have oncolytic (cancer-killing) properties and has encouraged the development of reovirus-based therapies for cancer treatment. Reolysin is a formulation of reovirus that is currently in clinical trials for the treatment of various cancers. Some viruses of this family infect plants. Examples are Phytoreovirus and Oryzavirus. CHARACTERISTICS: Reoviruses are non-enveloped and have an icosahedral capsid (T-13) composed of an outer and inner protein shell. The genomes of viruses in Reoviridae contain 10-12 segments which are grouped into three categories corresponding to their size: L (large), M (medium) and S (small).