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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 -
And Giant Guitarfish (Rhynchobatus Djiddensis)
VIRAL DISCOVERY IN BLUEGILL SUNFISH (LEPOMIS MACROCHIRUS) AND GIANT GUITARFISH (RHYNCHOBATUS DJIDDENSIS) BY HISTOPATHOLOGY EVALUATION, METAGENOMIC ANALYSIS AND NEXT GENERATION SEQUENCING by JENNIFER ANNE DILL (Under the Direction of Alvin Camus) ABSTRACT The rapid growth of aquaculture production and international trade in live fish has led to the emergence of many new diseases. The introduction of novel disease agents can result in significant economic losses, as well as threats to vulnerable wild fish populations. Losses are often exacerbated by a lack of agent identification, delay in the development of diagnostic tools and poor knowledge of host range and susceptibility. Examples in bluegill sunfish (Lepomis macrochirus) and the giant guitarfish (Rhynchobatus djiddensis) will be discussed here. Bluegill are popular freshwater game fish, native to eastern North America, living in shallow lakes, ponds, and slow moving waterways. Bluegill experiencing epizootics of proliferative lip and skin lesions, characterized by epidermal hyperplasia, papillomas, and rarely squamous cell carcinoma, were investigated in two isolated poopulations. Next generation genomic sequencing revealed partial DNA sequences of an endogenous retrovirus and the entire circular genome of a novel hepadnavirus. Giant Guitarfish, a rajiform elasmobranch listed as ‘vulnerable’ on the IUCN Red List, are found in the tropical Western Indian Ocean. Proliferative skin lesions were observed on the ventrum and caudal fin of a juvenile male quarantined at a public aquarium following international shipment. Histologically, lesions consisted of papillomatous epidermal hyperplasia with myriad large, amphophilic, intranuclear inclusions. Deep sequencing and metagenomic analysis produced the complete genomes of two novel DNA viruses, a typical polyomavirus and a second unclassified virus with a 20 kb genome tentatively named Colossomavirus. -
The Discovery, Distribution and Diversity of DNA Viruses Associated with Drosophila Melanogaster in Europe
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.16.342956; this version posted March 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Title: The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe Running title: DNA viruses of European Drosophila Key Words: DNA virus, Endogenous viral element, Drosophila, Nudivirus, Galbut virus, Filamentous virus, Adintovirus, Densovirus, Bidnavirus Authors: Megan A. Wallace 1,2 [email protected] 0000-0001-5367-420X Kelsey A. Coffman 3 [email protected] 0000-0002-7609-6286 Clément Gilbert 1,4 [email protected] 0000-0002-2131-7467 Sanjana Ravindran 2 [email protected] 0000-0003-0996-0262 Gregory F. Albery 5 [email protected] 0000-0001-6260-2662 Jessica Abbott 1,6 [email protected] 0000-0002-8743-2089 Eliza Argyridou 1,7 [email protected] 0000-0002-6890-4642 Paola Bellosta 1,8,9 [email protected] 0000-0003-1913-5661 Andrea J. Betancourt 1,10 [email protected] 0000-0001-9351-1413 Hervé Colinet 1,11 [email protected] 0000-0002-8806-3107 Katarina Eric 1,12 [email protected] 0000-0002-3456-2576 Amanda Glaser-Schmitt 1,7 [email protected] 0000-0002-1322-1000 Sonja Grath 1,7 [email protected] 0000-0003-3621-736X Mihailo Jelic 1,13 [email protected] 0000-0002-1637-0933 Maaria Kankare 1,14 [email protected] 0000-0003-1541-9050 Iryna Kozeretska 1,15 [email protected] 0000-0002-6485-1408 Volker Loeschcke 1,16 [email protected] 0000-0003-1450-0754 Catherine Montchamp-Moreau 1,4 [email protected] 0000-0002-5044-9709 Lino Ometto 1,17 [email protected] 0000-0002-2679-625X Banu Sebnem Onder 1,18 [email protected] 0000-0002-3003-248X Dorcas J. -
And Γ- Cytoplasmic Actin in Vaccinia Virus Infection
Lights, Camera, Actin: Divergent roles of β- and γ- cytoplasmic actin in vaccinia virus infection NOORUL BISHARA MARZOOK A thesis submitted in fulfillment of requirements for the degree of Doctor of Philosophy FACULTY OF SCIENCE SCHOOL OF MOLECULAR BIOSCIENCE UNIVERSITY OF SYDNEY 2017 i TABLE OF CONTENTS Table of Contents ........................................................................................................... ii Acknowledgements ....................................................................................................... v Declaration ................................................................................................................... vii Abstract ....................................................................................................................... viii List of Figures ................................................................................................................ x List of Publications Arising From This Work.............................................................. xi Abbreviations Used ..................................................................................................... xii Chapter 1: Introduction ............................................................................................... 1 1.1 The Cytoskeleton ............................................................................................................ 2 1.1.1 The Eukaryotic Cytoskeleton ..................................................................................... -
Lepidoptera: Tortricidae: Tortricinae) and Evolutionary Correlates of Novel Secondary Sexual Structures
Zootaxa 3729 (1): 001–062 ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Monograph ZOOTAXA Copyright © 2013 Magnolia Press ISSN 1175-5334 (online edition) http://dx.doi.org/10.11646/zootaxa.3729.1.1 http://zoobank.org/urn:lsid:zoobank.org:pub:CA0C1355-FF3E-4C67-8F48-544B2166AF2A ZOOTAXA 3729 Phylogeny of the tribe Archipini (Lepidoptera: Tortricidae: Tortricinae) and evolutionary correlates of novel secondary sexual structures JASON J. DOMBROSKIE1,2,3 & FELIX A. H. SPERLING2 1Cornell University, Comstock Hall, Department of Entomology, Ithaca, NY, USA, 14853-2601. E-mail: [email protected] 2Department of Biological Sciences, University of Alberta, Edmonton, Canada, T6G 2E9 3Corresponding author Magnolia Press Auckland, New Zealand Accepted by J. Brown: 2 Sept. 2013; published: 25 Oct. 2013 Licensed under a Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0 JASON J. DOMBROSKIE & FELIX A. H. SPERLING Phylogeny of the tribe Archipini (Lepidoptera: Tortricidae: Tortricinae) and evolutionary correlates of novel secondary sexual structures (Zootaxa 3729) 62 pp.; 30 cm. 25 Oct. 2013 ISBN 978-1-77557-288-6 (paperback) ISBN 978-1-77557-289-3 (Online edition) FIRST PUBLISHED IN 2013 BY Magnolia Press P.O. Box 41-383 Auckland 1346 New Zealand e-mail: [email protected] http://www.mapress.com/zootaxa/ © 2013 Magnolia Press 2 · Zootaxa 3729 (1) © 2013 Magnolia Press DOMBROSKIE & SPERLING Table of contents Abstract . 3 Material and methods . 6 Results . 18 Discussion . 23 Conclusions . 33 Acknowledgements . 33 Literature cited . 34 APPENDIX 1. 38 APPENDIX 2. 44 Additional References for Appendices 1 & 2 . 49 APPENDIX 3. 51 APPENDIX 4. 52 APPENDIX 5. -
Lycorma Delicatula (Hemiptera: Auchenorrhyncha: Fulgoridae: Aphaeninae) Finally, but Suddenly Arrived in Korea
Entomological Research 38 (2008) 281–286 RESEARCHBlackwell Publishing Ltd PAPER Lycorma delicatula (Hemiptera: Auchenorrhyncha: Fulgoridae: Aphaeninae) finally, but suddenly arrived in Korea Jung Min HAN1, Hyojoong KIM2, Eun Ji LIM1, Seunghwan LEE2, Yong-Jung KWON3 and Soowon CHO1 1 Department of Plant Medicine, Chungbuk National University, Cheongju, Korea 2 School of Agricultural Biotechnology, Seoul National University, Seoul, Korea 3 Division of Applied Biology and Chemistry, Kyungpook National University, Daegu, Korea Correspondence Abstract Soowon Cho, Department of Plant Medicine, Chungbuk National University, A history of name changes in two fulgorid species – Lycorma delicatula and Limois Cheongju 361-763, Korea. emelianovi – is reviewed. Lycorma delicatula was once mistakenly reported to Email: [email protected] occur in Korea. Now, it has suddenly become common in western Korea, creating the suspicion that it has recently arrived from China and settled in Korea. A brief Received 6 April 2008; accepted 26 August morphological and biological description of L. delicatula is provided, and its 2008. original Korean name, “ggot-mae-mi”, is revalidated. Limois emelianovi, sometimes considered a synonym of emeljanovi, is the correct name for this species, doi: 10.1111/j.1748-5967.2008.00188.x as emeljanovi is simply another transliteration of the personal name Emelianov, Emeljanov or Emel’yanov. The name emelianovi stands correct based on the International Code of Zoological Nomenclature code 32.5.1, because there is no internal evidence of an inadvertent error, and an incorrect transliteration is not considered an inadvertent error. The cytochrome oxidase I (COI) barcoding regions of both species were sequenced and compared for future reference. -
Sex Pheromones and Reproductive Isolation of Three Species in Genus Adoxophyes
J Chem Ecol (2009) 35:342–348 DOI 10.1007/s10886-009-9602-z Sex Pheromones and Reproductive Isolation of Three Species in Genus Adoxophyes Chang Yeol Yang & Kyeung Sik Han & Kyung Saeng Boo Received: 9 September 2008 /Revised: 29 December 2008 /Accepted: 18 January 2009 /Published online: 17 February 2009 # Springer Science + Business Media, LLC 2009 Abstract We tested differences in female pheromone to the binary blends increased attraction of male A. orana production and male response in three species of the but not A. honmai and Adoxophyes sp. males, suggesting genus Adoxophyes in Korea. Females of all three species that these minor components, in addition to the relative produced mixtures of (Z)-9-tetradecenyl acetate (Z9–14: ratios of the two major components, play an important role OAc) and (Z)-11-tetradecenyl acetate (Z11–14:OAc) as in reproductive isolation between Adoxophyes species in major components but in quite different ratios. The ratio the southern and midwestern Korea where these species of Z9–14:OAc and Z11–14:OAc in pheromone gland occur sympatrically. extracts was estimated to be ca. 100:200 for Adoxophyes honmai, 100:25 for Adoxophyes orana, and 100:4,000 for Keywords Adoxophyes . (Z)-9-tetradecenyl acetate . Adoxophyes sp. Field tests showed that males of each (Z)-11-tetradecenyl acetate . Lepidoptera . Tortricidae . species were preferentially attracted to the two-component Reproductive isolation blends of Z9–14:OAc and Z11–14:OAc mimicking the blends found in pheromone gland extracts of conspecific females. The effects of minor components identified in Introduction gland extracts on trap catches varied with species. -
Diversity of Large DNA Viruses of Invertebrates ⇑ Trevor Williams A, Max Bergoin B, Monique M
Journal of Invertebrate Pathology 147 (2017) 4–22 Contents lists available at ScienceDirect Journal of Invertebrate Pathology journal homepage: www.elsevier.com/locate/jip Diversity of large DNA viruses of invertebrates ⇑ Trevor Williams a, Max Bergoin b, Monique M. van Oers c, a Instituto de Ecología AC, Xalapa, Veracruz 91070, Mexico b Laboratoire de Pathologie Comparée, Faculté des Sciences, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier, France c Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands article info abstract Article history: In this review we provide an overview of the diversity of large DNA viruses known to be pathogenic for Received 22 June 2016 invertebrates. We present their taxonomical classification and describe the evolutionary relationships Revised 3 August 2016 among various groups of invertebrate-infecting viruses. We also indicate the relationships of the Accepted 4 August 2016 invertebrate viruses to viruses infecting mammals or other vertebrates. The shared characteristics of Available online 31 August 2016 the viruses within the various families are described, including the structure of the virus particle, genome properties, and gene expression strategies. Finally, we explain the transmission and mode of infection of Keywords: the most important viruses in these families and indicate, which orders of invertebrates are susceptible to Entomopoxvirus these pathogens. Iridovirus Ó Ascovirus 2016 Elsevier Inc. All rights reserved. Nudivirus Hytrosavirus Filamentous viruses of hymenopterans Mollusk-infecting herpesviruses 1. Introduction in the cytoplasm. This group comprises viruses in the families Poxviridae (subfamily Entomopoxvirinae) and Iridoviridae. The Invertebrate DNA viruses span several virus families, some of viruses in the family Ascoviridae are also discussed as part of which also include members that infect vertebrates, whereas other this group as their replication starts in the nucleus, which families are restricted to invertebrates. -
University of Florida Thesis Or Dissertation Formatting
THE ROLE OF CELL SIGNALING IN POXVIRUS TROPISM: THE CASE OF THE M-T5 HOST-RANGE PROTEIN OF MYXOMA VIRUS By STEVEN JAMES WERDEN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2009 1 © 2009 Steven James Werden 2 To my family 3 ACKNOWLEDGMENTS I would like to thank Dr. Grant McFadden for continuous support, encouragement and advice during the course of my PhD. I am truly grateful for all the time and energy he has spent training me to become a better scientist and critical thinker. Without his guidance and persistent help this dissertation would not have been possible. In addition, I am appreciative to my committee members, Drs. Richard Condit, Greg Schultz and Dave Bloom for their encouraging words, fruitful discussion and most importantly, their commitment to helping me succeed. During the past five years, I have had the opportunity and privilege to work with many talented individuals. I would like to acknowledge all members of the McFadden laboratory, both past and present, for creating a work environment that fostered creativity. Special thanks go to Drs.Gen Wang, Steve Nazarian, Marianne Stanford and Fuan Wang for providing technical training. Dr. John Barrett deserves a special mention for his continued mentorship and support. I must not forget to thank those who attended the weekly “Poxaholics” meetings, for providing constructive criticism and a wonderful atmosphere to present data. Thanks go out to Doug Smith for assistance with the confocal microscope and to all who contributed reagents that were used in this dissertation. -
ICTV Code Assigned: 2011.001Ag Officers)
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . -
Whole-Proteome Phylogeny of Large Dsdna Viruses and Parvoviruses
Yu et al. BMC Evolutionary Biology 2010, 10:192 http://www.biomedcentral.com/1471-2148/10/192 RESEARCH ARTICLE Open Access Whole-proteomeResearch article phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model Zu-Guo Yu1,2, Ka Hou Chu*3, Chi Pang Li3, Vo Anh1, Li-Qian Zhou2 and Roger Wei Wang4 Abstract Background: The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results: In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions: The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size. -
Giovanny Fagua González
Phylogeny, evolution and speciation of Choristoneura and Tortricidae (Lepidoptera) by Giovanny Fagua González A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Systematics and Evolution Department of Biological Sciences University of Alberta © Giovanny Fagua González, 2017 Abstract Leafrollers moths are one of the most ecologically and economically important groups of herbivorous insects. These Lepidoptera are an ideal model for exploring the drivers that modulate the processes of diversification over time. This thesis analyzes the evolution of Choristoneura Lederer, a well known genus because of its pest species, in the general context of the evolution of Tortricidae. It takes an inductive view, starting with analysis of phylogenetic, biogeographic and diversification processes in the family Tortricidae, which gives context for studying these processes in the genus Choristoneura. Tectonic dynamics and niche availability play intertwined roles in determining patterns of diversification; such drivers explain the current distribution of many clades, whereas events like the rise of angiosperms can have more specific impacts, such as on the diversification rates of herbivores. Tortricidae are a diverse group suited for testing the effects of these determinants on the diversification of herbivorous clades. To estimate ancestral areas and diversification patterns in Tortricidae, a complete tribal-level dated tree was inferred using molecular markers and calibrated using fossil constraints. The time-calibrated phylogeny estimated that Tortricidae diverged ca. 120 million years ago (Mya) and diversified ca. 97 Mya, a timeframe synchronous with the rise of angiosperms in the Early-Mid Cretaceous. Ancestral areas analysis supports a Gondwanan origin of Tortricidae in the South American plate.