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Changes to Virus Taxonomy 2004
Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales -
Topics in Viral Immunology Bruce Campell Supervisory Patent Examiner Art Unit 1648 IS THIS METHOD OBVIOUS?
Topics in Viral Immunology Bruce Campell Supervisory Patent Examiner Art Unit 1648 IS THIS METHOD OBVIOUS? Claim: A method of vaccinating against CPV-1 by… Prior art: A method of vaccinating against CPV-2 by [same method as claimed]. 2 HOW ARE VIRUSES CLASSIFIED? Source: Seventh Report of the International Committee on Taxonomy of Viruses (2000) Edited By M.H.V. van Regenmortel, C.M. Fauquet, D.H.L. Bishop, E.B. Carstens, M.K. Estes, S.M. Lemon, J. Maniloff, M.A. Mayo, D. J. McGeoch, C.R. Pringle, R.B. Wickner Virology Division International Union of Microbiological Sciences 3 TAXONOMY - HOW ARE VIRUSES CLASSIFIED? Example: Potyvirus family (Potyviridae) Example: Herpesvirus family (Herpesviridae) 4 Potyviruses Plant viruses Filamentous particles, 650-900 nm + sense, linear ssRNA genome Genome expressed as polyprotein 5 Potyvirus Taxonomy - Traditional Host range Transmission (fungi, aphids, mites, etc.) Symptoms Particle morphology Serology (antibody cross reactivity) 6 Potyviridae Genera Bymovirus – bipartite genome, fungi Rymovirus – monopartite genome, mites Tritimovirus – monopartite genome, mites, wheat Potyvirus – monopartite genome, aphids Ipomovirus – monopartite genome, whiteflies Macluravirus – monopartite genome, aphids, bulbs 7 Potyvirus Taxonomy - Molecular Polyprotein cleavage sites % similarity of coat protein sequences Genomic sequences – many complete genomic sequences, >200 coat protein sequences now available for comparison 8 Coat Protein Sequence Comparison (RNA) 9 Potyviridae Species Bymovirus – 6 species Rymovirus – 4-5 species Tritimovirus – 2 species Potyvirus – 85 – 173 species Ipomovirus – 1-2 species Macluravirus – 2 species 10 Higher Order Virus Taxonomy Nature of genome: RNA or DNA; ds or ss (+/-); linear, circular (supercoiled?) or segmented (number of segments?) Genome size – 11-383 kb Presence of envelope Morphology: spherical, filamentous, isometric, rod, bacilliform, etc. -
Using Transfer Learning for Image-Based Cassava Disease
Using Transfer Learning for Image-Based Cassava Disease Detection Amanda Ramcharan 1, Kelsee Baranowski 1, Peter McCloskey 2,Babuali Ahmed 3, James Legg 3, and David Hughes 1;4;5∗ 1Department of Entomology, College of Agricultural Sciences, Penn State University, State College, PA, USA 2Department of Computer Science, Pittsburgh University,Pittsburgh, PA, USA 3International Institute for Tropical Agriculture, Dar el Salaam, Tanzania 4Department of Biology, Eberly College of Sciences, Penn State University, State College, PA, USA 5Center for Infectious Disease Dynamics, Huck Institutes of Life Sciences, Penn State University, State College, PA, USA Correspondence*: David Hughes [email protected] ABSTRACT Cassava is the third largest source of carbohydrates for human food in the world but is vulnerable to virus diseases, which threaten to destabilize food security in sub-Saharan Africa. Novel methods of cassava disease detection are needed to support improved control which will prevent this crisis. Image recognition offers both a cost effective and scalable technology for disease detection. New transfer learning methods offer an avenue for this technology to be easily deployed on mobile devices. Using a dataset of cassava disease images taken in the field in Tanzania, we applied transfer learning to train a deep convolutional neural network to identify three diseases and two types of pest damage (or lack thereof). The best trained model accuracies were 98% for brown leaf spot (BLS), 96% for red mite damage (RMD), 95% for green mite damage (GMD), 98% for cassava brown streak disease (CBSD), and 96% for cassava mosaic disease (CMD). The best model achieved an overall accuracy of 93% for data not used in the training process. -
Discrimination and Trancriptional Response
DISCRIMINATION AND TRANCRIPTIONAL RESPONSE ANALYSIS OF HEMIPTERAN PHYTOPATHOGEN VECTORS By SHARON ANDREASON Bachelor of Science in Biology University of Texas at Tyler Tyler, Texas 2009 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 July, 2016 DISCRIMINATION AND TRANSCRIPTIONAL RESPONSE ANALYSIS OF HEMIPTERAN PHYTOPATHOGEN VECTORS Dissertation Approved: Astri Wayadande, Ph.D. Dissertation Adviser Jacqueline Fletcher, Ph.D. Francisco Ochoa-Corona, Ph.D. Ulrich Melcher, Ph.D. ii ACKNOWLEDGEMENTS I would first like to extend my deepest thanks to my advisor, Dr. Astri Wayadande, for all of her years of support. Always full of positivity, encouragement, and advice, her enthusiasm for research and effort devoted to others are attributes that I aspire to cultivate in my future career. I am forever grateful for her guidance throughout earning my degree. I would also like to thank my committee members, Drs. Jacqueline Fletcher, Francisco Ochoa-Corona, and Ulrich Melcher, each of whom have not only offered me thoughtful advice through my research, but have also educated and inspired me in unique and invaluable ways. I am deeply appreciative of their guidance over the years. I want to thank Dr. Judith Brown, without whom I would not have had the opportunity to work on such an important vector system. I am sincerely grateful to Dr. Mohammad Arif, who provided exceptional expertise and advice through my whitefly projects. I would also like to extend my thanks to Dr. Trenna Blagden for all her help and guidance on my projects, particularly during my work with EDNA, as well as for the professional advice she has provided. -
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 -
Molecular Analysis of Vanilla Mosaic Virus from the Cook Islands
Molecular Analysis of Vanilla mosaic virus from the Cook Islands Christopher Puli’uvea A thesis submitted to Auckland University of Technology in partial fulfilment of the requirements for the degree of Master of Science (MSc) 2017 School of Science I Abstract Vanilla was first introduced to French Polynesia in 1848 and from 1899-1966 was a major export for French Polynesia who then produced an average of 158 tonnes of cured Vanilla tahitensis beans annually. In 1967, vanilla production declined rapidly to a low of 0.6 tonnes by 1981, which prompted a nation-wide investigation with the aim of restoring vanilla production to its former levels. As a result, a mosaic-inducing virus was discovered infecting V. tahitensis that was distinct from Cymbidium mosaic virus (CyMV) and Odontoglossum ringspot virus (ORSV) but serologically related to dasheen mosaic virus (DsMV). The potyvirus was subsequently named vanilla mosaic virus (VanMV) and was later reported to infect V. tahitensis in the Cook Islands and V. planifolia in Fiji and Vanuatu. Attempts were made to mechanically inoculate VanMV to a number of plants that are susceptible to DsMV, but with no success. Based on a partial sequence analysis, VanMV-FP (French Polynesian isolate) and VanMV-CI (Cook Islands isolate) were later characterised as strains of DsMV exclusively infecting vanilla. Since its discovery, little information is known about how VanMV-CI acquired the ability to exclusively infect vanilla and lose its ability to infect natural hosts of DsMV or vice versa. The aims of this research were to characterise the VanMV genome and attempt to determine the molecular basis for host range specificity of VanMV-CI. -
RNA Viral Metagenome of Whiteflies Leads to the Discovery and Characterization of a Whitefly- Transmitted Carlavirus in North America
University of South Florida Scholar Commons Marine Science Faculty Publications College of Marine Science 1-21-2014 RNA Viral Metagenome of Whiteflies Leads ot the Discovery and Characterization of a Whitefly-Transmitted Carlavirus in North America Karyna Rosario University of South Florida, [email protected] Heather Capobianco University of Florida Terry Fei Fan Ng University of South Florida Mya Breitbart University of South Florida, [email protected] Jane E. Polston University of Florida Follow this and additional works at: https://scholarcommons.usf.edu/msc_facpub Part of the Marine Biology Commons Scholar Commons Citation Rosario, Karyna; Capobianco, Heather; Ng, Terry Fei Fan; Breitbart, Mya; and Polston, Jane E., "RNA Viral Metagenome of Whiteflies Leads ot the Discovery and Characterization of a Whitefly-Transmitted Carlavirus in North America" (2014). Marine Science Faculty Publications. 229. https://scholarcommons.usf.edu/msc_facpub/229 This Article is brought to you for free and open access by the College of Marine Science at Scholar Commons. It has been accepted for inclusion in Marine Science Faculty Publications by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. RNA Viral Metagenome of Whiteflies Leads to the Discovery and Characterization of a Whitefly- Transmitted Carlavirus in North America Karyna Rosario1*, Heather Capobianco2, Terry Fei Fan Ng1¤, Mya Breitbart1, Jane E. Polston2 1 College of Marine Science, University of South Florida, Saint Petersburg, Florida, United States of America, 2 Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America Abstract Whiteflies from the Bemisia tabaci species complex have the ability to transmit a large number of plant viruses and are some of the most detrimental pests in agriculture. -
Viroze Biljaka 2010
VIROZE BILJAKA Ferenc Bagi Stevan Jasnić Dragana Budakov Univerzitet u Novom Sadu, Poljoprivredni fakultet Novi Sad, 2016 EDICIJA OSNOVNI UDŽBENIK Osnivač i izdavač edicije Univerzitet u Novom Sadu, Poljoprivredni fakultet Trg Dositeja Obradovića 8, 21000 Novi Sad Godina osnivanja 1954. Glavni i odgovorni urednik edicije Dr Nedeljko Tica, redovni profesor Dekan Poljoprivrednog fakulteta Članovi komisije za izdavačku delatnost Dr Ljiljana Nešić, vanredni profesor – predsednik Dr Branislav Vlahović, redovni profesor – član Dr Milica Rajić, redovni profesor – član Dr Nada Plavša, vanredni profesor – član Autori dr Ferenc Bagi, vanredni profesor dr Stevan Jasnić, redovni profesor dr Dragana Budakov, docent Glavni i odgovorni urednik Dr Nedeljko Tica, redovni profesor Dekan Poljoprivrednog fakulteta u Novom Sadu Urednik Dr Vera Stojšin, redovni profesor Direktor departmana za fitomedicinu i zaštitu životne sredine Recenzenti Dr Vera Stojšin, redovni profesor, Univerzitet u Novom Sadu, Poljoprivredni fakultet Dr Mira Starović, naučni savetnik, Institut za zaštitu bilja i životnu sredinu, Beograd Grafički dizajn korice Lea Bagi Izdavač Univerzitet u Novom Sadu, Poljoprivredni fakultet, Novi Sad Zabranjeno preštampavanje i fotokopiranje. Sva prava zadržava izdavač. ISBN 978-86-7520-372-8 Štampanje ovog udžbenika odobrilo je Nastavno-naučno veće Poljoprivrednog fakulteta u Novom Sadu na sednici od 11. 07. 2016.godine. Broj odluke 1000/0102-797/9/1 Tiraž: 20 Mesto i godina štampanja: Novi Sad, 2016. CIP - Ʉɚɬɚɥɨɝɢɡɚɰɢʁɚɭɩɭɛɥɢɤɚɰɢʁɢ ȻɢɛɥɢɨɬɟɤɚɆɚɬɢɰɟɫɪɩɫɤɟɇɨɜɢɋɚɞ -
Template for Taxonomic Proposal to the ICTV Executive Committee to Create a New Genus Unassigned to a Family
Template for Taxonomic Proposal to the ICTV Executive Committee To create a new Genus unassigned to a Family Code† 2007.039P To create a new unassigned genus † Code 2007.040P To name the new genus* Torradovirus Code† To create and designate the species 2007.041P Tomato torrado virus As the type species of the new genus* † Code 2007.042P To create the following as additional species of the new genus*: Tomato marchitez virus † Assigned by ICTV officers * repeat these lines and the corresponding arguments for each genus created in the family Author(s) with email address(es) of the Taxonomic Proposal Helene Sanfacon ([email protected]) Rene van der Vlugt ([email protected]) Olivier Le Gall ([email protected]) Joan Wellink ([email protected]) Alexander V. Karasev ([email protected]) Thierry Wetzel ([email protected]) Old Taxonomic Order Order Family Genus Type Species Species in the Genus Unassigned Species in the Genus Unassigned Species in the family New Taxonomic Order Order Picornavirales Family Secoviridae (proposed new family, see 2007 proposal) Genus Torradovirus Type Species Tomato torrado virus Species in the Genus Tomato marchitez virus ICTV-EC comments and response of the SG Argumentation to choose the type species in the genus Tomato torrado virus (ToTV) was the first virus for which the entire sequence is known. The 3 CPs have been characterized and the nature of the CPs has been confirmed experimentally by mass spectrometry analysis (Verbeek, 2007a). The sequence of Tomato marchitez virus (ToMarV) was recently elucidated (Verbeek, 2007b). Three CPs have been detected but have not been sequenced. -
A Mosaic of Submicroscopic Entities Causing Big Problems in Cassava in Brazil
27 a 30 de Agosto de 2019 Recife-PE A mosaic of submicroscopic entities causing big problems in cassava in Brazil (Um mosaico de entidades submicroscópicas causando grandes problemas à mandioca no Brasil) ANDRADE, E.C. Embrapa Mandioca e Fruticultura, CNPMF, CEP 44380-000, Cruz das Almas, BA. E-mail: [email protected] Cassava (Manihot esculenta Crantz) is the third most important source of calories for human nutrition in the world. It is mainly propagated by stem cuttings and this practice led to dissemination of viruses and other systemic pathogens. In Brazil, at least three viruses were reported causing economic losses in cassava. Cassava vein mosaic virus (CsVMV; Caulimoviridade/ Cavemovirus) is widespread in the northeast semi-arid environment. CsVMV induces initial stunning on germinated stems, and as plant grows, leaves display a range of symptoms that includes a chlorosis along the veins, leaf distortion and epinasty of the young leaves. Cassava common mosaic virus (CsCMV; Alphaflexiviridae/Potexvirus), is widespread in Latin America, and in Brazil is prevalent in the southern/southeast regions. CsCMC infection interferes with the photosynthesis of plants and consequently with its development, and thus cause serious losses in root yield and the quality of the propagation material. Cassava frog skin disease (CFSD), was initially restricted to the Amazon region, but nowadays has been causing serious losses in southern plantations. Plants infected with this disease usually have no symptoms on the aerial part, while the tuberous root exhibited a woody appearance, thickened cork-like peel with opaque aspect, and coalescent lip-like slits in a honeycomb pattern. -
Libro De Abstract
SPECIAL THANKS EMPRESAS COLABORADORAS SEV VI R O L O G Í A Publicación Oficial de la Sociedad Española de Virología 13th Spanish National Congress Of Virology Madrid 2015 CONGRESO NACIONAL DE Volumen 18 Número 1/2015 EXTRAORDINARIO VIROLOGÍA . PUBLICACIÓN OFICIAL DE LA SOCIEDAD ESPAÑOLA DE VIROLOGÍA 13th Spanish National Congress Of Virology Madrid 2015 Del 7 al 10 de junio de 2015 Auditorio de la Fábrica Nacional de Moneda y Timbre Real Casa de la Moneda de Madrid Volumen 18 Madrid 2015 Número 1/2015 EXTRAORDINARIO Edición y Coordinación: M Angeles Muñoz-Fernández &M. Dolores García-Alonso Diseño y Maquetación: DM&VCH.events.S.L. Diseño Portada: M. Dolores García-Alonso Impresión: Fragma: Servicios de impresión digital en Madrid ISSN (versión digital): 2172-6523 SEV – Sociedad Española de Virología Centro de Biología Molecular “Severo Ochoa” C/ Nicolás Cabrera, 1 28049 Cantoblanco – Madrid [email protected] Página web del congreso: www.congresonacionalvirologia2015.com La responsabilidad del contenido de las colaboraciones publicadas corresponderá a sus autores, quienes autorizan la reproducción de sus artículos a la SEV exclusivamente para esta edición. La SEV no hace necesariamente suyas las opiniones o los criterios expresados por sus colaboradores. Virología. Publicación Oficial de la Sociedad Española de Virología XIII CONGRESO NACIONAL DE VIROLOGÍA B I E N V E N I D A El Comité Organizador del XIII Congreso Nacional de Virología (XIII CNV) tiene el placer de comunicaros que éste se celebrará en Madrid, del 7 al 10 de junio de 2015. En el XIII CNV participan conjuntamente la Sociedad Española de Virología (SEV) y la Sociedad Italiana de Virología (SIV), y estará abierto13th a Spanish la participación National de virólogos de Latinoamérica. -
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