Genetic Characterization, Molecular Epidemiology, and Phylogenetic MARK Relationships of Insect-Specific Viruses in the Taxon Negevirus
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Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses
viruses Article Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses Thanuja Thekke-Veetil 1, Doris Lagos-Kutz 2 , Nancy K. McCoppin 2, Glen L. Hartman 2 , Hye-Kyoung Ju 3, Hyoun-Sub Lim 3 and Leslie. L. Domier 2,* 1 Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; [email protected] 2 Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; [email protected] (D.L.-K.); [email protected] (N.K.M.); [email protected] (G.L.H.) 3 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 300-010, Korea; [email protected] (H.-K.J.); [email protected] (H.-S.L.) * Correspondence: [email protected]; Tel.: +1-217-333-0510 Academic Editor: Eugene V. Ryabov and Robert L. Harrison Received: 5 November 2020; Accepted: 29 November 2020; Published: 1 December 2020 Abstract: Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. -
Small Hydrophobic Viral Proteins Involved in Intercellular Movement of Diverse Plant Virus Genomes Sergey Y
AIMS Microbiology, 6(3): 305–329. DOI: 10.3934/microbiol.2020019 Received: 23 July 2020 Accepted: 13 September 2020 Published: 21 September 2020 http://www.aimspress.com/journal/microbiology Review Small hydrophobic viral proteins involved in intercellular movement of diverse plant virus genomes Sergey Y. Morozov1,2,* and Andrey G. Solovyev1,2,3 1 A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia 2 Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia 3 Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia * Correspondence: E-mail: [email protected]; Tel: +74959393198. Abstract: Most plant viruses code for movement proteins (MPs) targeting plasmodesmata to enable cell-to-cell and systemic spread in infected plants. Small membrane-embedded MPs have been first identified in two viral transport gene modules, triple gene block (TGB) coding for an RNA-binding helicase TGB1 and two small hydrophobic proteins TGB2 and TGB3 and double gene block (DGB) encoding two small polypeptides representing an RNA-binding protein and a membrane protein. These findings indicated that movement gene modules composed of two or more cistrons may encode the nucleic acid-binding protein and at least one membrane-bound movement protein. The same rule was revealed for small DNA-containing plant viruses, namely, viruses belonging to genus Mastrevirus (family Geminiviridae) and the family Nanoviridae. In multi-component transport modules the nucleic acid-binding MP can be viral capsid protein(s), as in RNA-containing viruses of the families Closteroviridae and Potyviridae. However, membrane proteins are always found among MPs of these multicomponent viral transport systems. -
Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID-19 Pandemic: a Repo
Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. November 2020 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University November 30th, 2020 1 Contents Page Introduction 3 Project goal and specific objectives 3 Methods used to identify and include relevant literature 4 Report structure 5 Summary of update report 5 Report results a) Which patients are at greater risk of the consequences of COVID-19 and so 7 consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that oral health professionals 9 should screen for prior to providing in-person health care? c) What evidence exists to support patient scheduling, waiting and other non- treatment management measures for in-person oral health care? 10 d) What evidence exists to support the use of various forms of personal protective equipment (PPE) while providing in-person oral health care? 13 e) What evidence exists to support the decontamination and re-use of PPE? 15 f) What evidence exists concerning the provision of aerosol-generating 16 procedures (AGP) as part of in-person -
Multipartite Viruses: Organization, Emergence and Evolution
UNIVERSIDAD AUTÓNOMA DE MADRID FACULTAD DE CIENCIAS DEPARTAMENTO DE BIOLOGÍA MOLECULAR MULTIPARTITE VIRUSES: ORGANIZATION, EMERGENCE AND EVOLUTION TESIS DOCTORAL Adriana Lucía Sanz García Madrid, 2019 MULTIPARTITE VIRUSES Organization, emergence and evolution TESIS DOCTORAL Memoria presentada por Adriana Luc´ıa Sanz Garc´ıa Licenciada en Bioqu´ımica por la Universidad Autonoma´ de Madrid Supervisada por Dra. Susanna Manrubia Cuevas Centro Nacional de Biotecnolog´ıa (CSIC) Memoria presentada para optar al grado de Doctor en Biociencias Moleculares Facultad de Ciencias Departamento de Biolog´ıa Molecular Universidad Autonoma´ de Madrid Madrid, 2019 Tesis doctoral Multipartite viruses: Organization, emergence and evolution, 2019, Madrid, Espana. Memoria presentada por Adriana Luc´ıa-Sanz, licenciada en Bioqumica´ y con un master´ en Biof´ısica en la Universidad Autonoma´ de Madrid para optar al grado de doctor en Biociencias Moleculares del departamento de Biolog´ıa Molecular en la facultad de Ciencias de la Universidad Autonoma´ de Madrid Supervisora de tesis: Dr. Susanna Manrubia Cuevas. Investigadora Cient´ıfica en el Centro Nacional de Biotecnolog´ıa (CSIC), C/ Darwin 3, 28049 Madrid, Espana. to the reader CONTENTS Acknowledgments xi Resumen xiii Abstract xv Introduction xvii I.1 What is a virus? xvii I.2 What is a multipartite virus? xix I.3 The multipartite lifecycle xx I.4 Overview of this thesis xxv PART I OBJECTIVES PART II METHODOLOGY 0.5 Database management for constructing the multipartite and segmented datasets 3 0.6 Analytical -
Evolutionary Continuum Between Small Rna and Dna Viruses
EVOLUTIONARY CONTINUUM BETWEEN SMALL RNA AND DNA VIRUSES Mart Krupovic Institut Pasteur [email protected] 03.07.2014 100 nm 20 nm 100 nm Giant viruses versus tiny ones Mimivirus Porcine circovirus 1 Capsid diameter: ~400 nm Capsid diameter: ~17 nm Genome size: 1,181,404 bp Genome size: 1,758 nt # of genes: 1,018 # of genes: 2 2000 nm 100 nm Courtesy Prof D. Raoult Courtesy Prof S. McNulty The (described) virosphere: 120 distinct taxa Adenoviridae, Alloherpesviridae, Alphaflexiviridae, Alphatetraviridae, Alvernaviridae, Amalgaviridae, Ampullaviridae, Anelloviridae, Arenaviridae, Arteriviridae, Ascoviridae, Asfarviridae, Astroviridae, Bacilladnavirus, Bacillarnavirus, Baculoviridae, Barnaviridae, Benyviridae, Betaflexiviridae, Bicaudaviridae, Bidnaviridae, Birnaviridae, Bornaviridae, Bromoviridae, Bunyaviridae, Caliciviridae, Carmotetraviridae, Caulimoviridae, Chrysoviridae, Cilevirus, Circoviridae, Clavaviridae, Closteroviridae, Coronaviridae, Corticoviridae, Cystoviridae, Deltavirus, Dicistroviridae, Dinodnavirus, Emaravirus, Endornaviridae, Filoviridae, Flaviviridae, Fuselloviridae, Gammaflexiviridae, Geminiviridae, ‘Gemycircularvirus’, Globuloviridae, Guttaviridae, Hepadnaviridae, Hepeviridae, Herpesviridae, Higrevirus, Hypoviridae, Hytrosaviridae, Idaeovirus, Iflaviridae, Inoviridae, Iridoviridae, Labyrnavirus, Leviviridae, Lipothrixviridae, Luteoviridae, Malacoherpesviridae, Marnaviridae, Marseilleviridae, Megabirnaviridae, Mesoniviridae, Metaviridae, Microviridae, Mimiviridae, Myoviridae, Nanoviridae, Narnaviridae, Nimaviridae, -
Edna-Host: Detection of Global Plant Viromes Using High Throughput Sequencing
EDNA-HOST: DETECTION OF GLOBAL PLANT VIROMES USING HIGH THROUGHPUT SEQUENCING By LIZBETH DANIELA PENA-ZUNIGA Bachelor of Science in Biotechnology Escuela Politecnica de las Fuerzas Armadas (ESPE) Sangolqui, Ecuador 2014 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY May 2020 EDNA-HOST: DETECTION OF GLOBAL PLANT VIROMES USING HIGH THROUGHPUT SEQUENCING Dissertation Approved: Francisco Ochoa-Corona, Ph.D. Dissertation Adviser Committee member Akhtar, Ali, Ph.D. Committee member Hassan Melouk, Ph.D. Committee member Andres Espindola, Ph.D. Outside Committee Member Daren Hagen, Ph.D. ii ACKNOWLEDGEMENTS I would like to express sincere thanks to my major adviser Dr. Francisco Ochoa –Corona for his guidance from the beginning of my journey believing and trust that I am capable of developing a career as a scientist. I am thankful for his support and encouragement during hard times in research as well as in personal life. I truly appreciate the helpfulness of my advisory committee for their constructive input and guidance, thanks to: Dr. Akhtar Ali for his support in this research project and his kindness all the time, Dr. Hassan Melouk for his assistance, encouragement and his helpfulness in this study, Dr. Andres Espindola, developer of EDNA MiFi™, he was extremely helpful in every step of EDNA research, and for his willingness to give his time and advise; to Dr. Darren Hagen for his support and advise with bioinformatics and for his encouragement to develop a new set of research skills. I deeply appreciate Dr. -
A Novel Insect-Infecting Virga/Nege-Like Virus Group and Its Pervasive Endogenization
Kondo et al., 1 Virus Research (special issue: “Integrated Viral Sequence”). A novel insect-infecting virga/nege-like virus group and its pervasive endogenization into insect genomes Hideki Kondo a *, Sotaro Chiba b, c, Kazuyuki Maruyama a, Ida Bagus Andika a, Nobuhiro Suzuki a a Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan b Asian Satellite Campuses Institute, Nagoya University, Nagoya 464-8601, Japan. c Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan. *Corresponding author Hideki Kondo Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan E-mail: [email protected] Tel. +81(86) 434-1232 / Fax. +81(86) 434-1232 MS information: Abstract, 241 words; Main text, 6187 words; Figures, 5; Supplemental tables, 3; Supplemental figures, 7. Kondo et al., 2 Abstract Insects are the host and vector of diverse viruses including those that infect vertebrates, plants, and fungi. Recent wide-scale transcriptomic analyses have uncovered the existence of a number of novel insect viruses belonging to an alphavirus-like superfamily (virgavirus/negevirus- related lineage). In this study, through an in silico search using publicly available insect transcriptomic data, we found numerous virus-like sequences related to insect virga/nege-like viruses. Phylogenetic analysis showed that these novel viruses and related virus-like sequences fill the major phylogenetic gaps between insect and plant virga/negevirus lineages. Interestingly, one of the phylogenetic clades represents a unique insect-infecting virus group. Its members encode putative coat proteins which contained a conserved domain similar to that usually found in the coat protein of plant viruses in the family Virgaviridae. -
Plant Health 2019 Abstracts of Presentations
Plant Health 2019 Abstracts of Presentations Abstracts submitted for presentation at the APS Plant Health 2019 Annual Meeting in Cleveland, Ohio, U.S.A., August 3–7, 2019 (including abstracts submitted for presentation at the 2019 APS North Central Division meeting). The recommended format for citing annual meeting abstracts, using the first abstract below as an example, is as follows: Chen, Y., Badillo-Vargas, I. E., Martin, K., Rotenberg, D., and Whitfield, A. E. 2019. Characterization of novel thrips vector proteins that bind to tomato spotted wilt virus. (Abstr.) Phytopathology 109:S2.1. https://doi.org/10.1094/PHYTO-109-10-S2.1 The abstracts are published as a supplement to Phytopathology for citation purposes. They were not reviewed by the Phytopathology Editorial Board and were not edited by the APS editorial staff. https://doi.org/10.1094/PHYTO-109-10-S2.1 © 2019 The American Phytopathological Society Characterization of novel thrips vector proteins that bind to tomato spotted wilt virus Y. CHEN (1), I. E. Badillo-Vargas (2), K. Martin (1), D. Rotenberg (1), A. E. Whitfield (1), (1) North Carolina State University, Raleigh, NC, USA; (2) Texas A&M AgriLife Research, Weslaco, TX, USA Tomato spotted wilt virus (TSWV) is transmitted by thrips species in a persistent, propagative manner. Frankliniella occidentalis is the most efficient vector, but at least six other thrips species are competent vectors. The TSWV structural glycoprotein (GN) plays an important role in viral attachment and possibly entry into insect host cells. However, the insect molecules that interact with GN during infection and dissemination in thrips vector are still largely unknown. -
Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA)
viruses Review Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA) Vsevolod L. Popov 1,2,3,4,5,*, Robert B. Tesh 1,2,3,4,5, Scott C. Weaver 2,3,4,5,6 and Nikos Vasilakis 1,2,3,4,5,* 1 Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA; [email protected] 2 Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA; [email protected] 3 Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA 4 Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA 5 World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA 6 Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA * Correspondence: [email protected] (V.L.P.); [email protected] (N.V.); Tel.: +1-409-747-2423 (V.L.P.); +1-409-747-0650 (N.V.) Received: 30 April 2019; Accepted: 24 May 2019; Published: 25 May 2019 Abstract: Since the beginning of modern virology in the 1950s, transmission electron microscopy (TEM) has been an important and widely used technique for discovery, identification and characterization of new viruses. Using TEM, viruses can be differentiated by their ultrastructure: shape, size, intracellular location and for some viruses, by the ultrastructural cytopathic effects and/or specific structures forming in the host cell during their replication. -
Plant Virus RNA Replication
eLS Plant Virus RNA Replication Alberto Carbonell*, Juan Antonio García, Carmen Simón-Mateo and Carmen Hernández *Corresponding author: Alberto Carbonell ([email protected]) A22338 Author Names and Affiliations Alberto Carbonell, Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Campus UPV, Valencia, Spain Juan Antonio García, Centro Nacional de Biotecnología (CSIC), Madrid, Spain Carmen Simón-Mateo, Centro Nacional de Biotecnología (CSIC), Madrid, Spain Carmen Hernández, Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Campus UPV, Valencia, Spain *Advanced article Article Contents • Introduction • Replication cycles and sites of replication of plant RNA viruses • Structure and dynamics of viral replication complexes • Viral proteins involved in plant virus RNA replication • Host proteins involved in plant virus RNA replication • Functions of viral RNA in genome replication • Concluding remarks Abstract Plant RNA viruses are obligate intracellular parasites with single-stranded (ss) or double- stranded RNA genome(s) generally encapsidated but rarely enveloped. For viruses with ssRNA genomes, the polarity of the infectious RNA (positive or negative) and the presence of one or more genomic RNA segments are the features that mostly determine the molecular mechanisms governing the replication process. RNA viruses cannot penetrate plant cell walls unaided, and must enter the cellular cytoplasm through mechanically-induced wounds or assisted by a 1 biological vector. After desencapsidation, their genome remains in the cytoplasm where it is translated, replicated, and encapsidated in a coupled manner. Replication occurs in large viral replication complexes (VRCs), tethered to modified membranes of cellular organelles and composed by the viral RNA templates and by viral and host proteins. -
Expansion of Microbial Virology by Impetus of the Reduction of Viral Dark Matter Siddharth Ravindran Krishnamurthy Washington University in St
Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Summer 8-15-2017 Expansion of Microbial Virology by Impetus of the Reduction of Viral Dark Matter Siddharth Ravindran Krishnamurthy Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Part of the Allergy and Immunology Commons, Immunology and Infectious Disease Commons, Medical Immunology Commons, and the Virology Commons Recommended Citation Krishnamurthy, Siddharth Ravindran, "Expansion of Microbial Virology by Impetus of the Reduction of Viral Dark Matter" (2017). Arts & Sciences Electronic Theses and Dissertations. 1221. https://openscholarship.wustl.edu/art_sci_etds/1221 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Immunology Dissertation Examination Committee: David Wang, Chair Gaya Amarasinghe Gautam Dantas Michael Diamond Daved Fremont S Josh Swamidass The Reduction of Viral Dark Matter by Expanding of Viral Diversity by Siddharth Ravindran Krishnamurthy A dissertation presented to The Graduate School of Washington University in partial fulfillment -
Evidence to Support Safe Return to Clinical Practice
Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University July 31st, 2020 1 Contents Page Foreword 4 Background 5 Project goal and specific objectives 5 Methods used to identify and include relevant literature 6 Report structure 7 Report summary 7 Report results a) Which patients are at greater risk of the consequences of COVID-19 9 and so consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that dental 10 professionals should screen for prior to providing in-person oral health care? c) What evidence exists to support patient scheduling, waiting and 11 other non-treatment management measures for in-person oral health care? d) What evidence exists to support the use of various forms of 13 personal protective equipment (PPE) while providing in-person oral health care? e) What evidence exists to support the decontamination and re-use of 14 PPE? f) What evidence exists concerning the provision of aerosol- 14 generating procedures (AGP) as part of in-person oral health care? g) What