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Using Cell Lines to Study Factors Affecting Transmission of Fish Viruses
Using cell lines to study factors affecting transmission of fish viruses by Phuc Hoang Pham A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy in Biology Waterloo, Ontario, Canada, 2014 ©Phuc Hoang Pham 2014 AUTHOR'S DECLARATION I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii ABSTRACT Factors that can influence the transmission of aquatic viruses in fish production facilities and natural environment are the immune defense of host species, the ability of viruses to infect host cells, and the environmental persistence of viruses. In this thesis, fish cell lines were used to study different aspects of these factors. Five viruses were used in this study: viral hemorrhagic septicemia virus (VHSV) from the Rhabdoviridae family; chum salmon reovirus (CSV) from the Reoviridae family; infectious pancreatic necrosis virus (IPNV) from the Birnaviridae family; and grouper iridovirus (GIV) and frog virus-3 (FV3) from the Iridoviridae family. The first factor affecting the transmission of fish viruses examined in this thesis is the immune defense of host species. In this work, infections of marine VHSV-IVa and freshwater VHSV-IVb were studied in two rainbow trout cell lines, RTgill-W1 from the gill epithelium, and RTS11 from spleen macrophages. RTgill-W1 produced infectious progeny of both VHSV-IVa and -IVb. However, VHSV-IVa was more infectious than IVb toward RTgill-W1: IVa caused cytopathic effects (CPE) at a lower viral titre, elicited CPE earlier, and yielded higher titres. -
Grapevine Virus Diseases: Economic Impact and Current Advances in Viral Prospection and Management1
1/22 ISSN 0100-2945 http://dx.doi.org/10.1590/0100-29452017411 GRAPEVINE VIRUS DISEASES: ECONOMIC IMPACT AND CURRENT ADVANCES IN VIRAL PROSPECTION AND MANAGEMENT1 MARCOS FERNANDO BASSO2, THOR VINÍCIUS MArtins FAJARDO3, PASQUALE SALDARELLI4 ABSTRACT-Grapevine (Vitis spp.) is a major vegetative propagated fruit crop with high socioeconomic importance worldwide. It is susceptible to several graft-transmitted agents that cause several diseases and substantial crop losses, reducing fruit quality and plant vigor, and shorten the longevity of vines. The vegetative propagation and frequent exchanges of propagative material among countries contribute to spread these pathogens, favoring the emergence of complex diseases. Its perennial life cycle further accelerates the mixing and introduction of several viral agents into a single plant. Currently, approximately 65 viruses belonging to different families have been reported infecting grapevines, but not all cause economically relevant diseases. The grapevine leafroll, rugose wood complex, leaf degeneration and fleck diseases are the four main disorders having worldwide economic importance. In addition, new viral species and strains have been identified and associated with economically important constraints to grape production. In Brazilian vineyards, eighteen viruses, three viroids and two virus-like diseases had already their occurrence reported and were molecularly characterized. Here, we review the current knowledge of these viruses, report advances in their diagnosis and prospection of new species, and give indications about the management of the associated grapevine diseases. Index terms: Vegetative propagation, plant viruses, crop losses, berry quality, next-generation sequencing. VIROSES EM VIDEIRAS: IMPACTO ECONÔMICO E RECENTES AVANÇOS NA PROSPECÇÃO DE VÍRUS E MANEJO DAS DOENÇAS DE ORIGEM VIRAL RESUMO-A videira (Vitis spp.) é propagada vegetativamente e considerada uma das principais culturas frutíferas por sua importância socioeconômica mundial. -
THE ERIOPHYID MITES of CALIFORNIA (Acarina: Eriophyidae) by H
BULLETIN OF THE CALIFORNIA INSECT SURVEY VOLUME 2, NO. 1 THE ERIOPHYID MITES OF CALIFORNIA (Acarina: Eriophyidae) BY H. H. KEIFER (California Scare Department of Agriculture) UNIVERSITY OF CALIFORNIA PRESS BERKELEY AND LOS ANGELES 1352 BULLETIN OF THE CALIFORNIA INSECT SURVEY Editors: E. 0. Essig, S. B. Freeborn, E. G. Linsley, R. L. Usinger Volume 2, No. 1, pp. 1-128, plates 1-39 Submitted by Editors, May 6, 1952 Issued December 12, 1952 Price $2.00 UNIVERSITY OF CALIFORNIA PRESS BERKELEY AND LOS ANGELES CALIFORNIA CAMBRIDGE UNIVERSITY PRESS LONDON, ENGLAND PRINTED BY OFFSET IN THE UNITED STATBS OF AMERICA Contents Page Introduction .......................... 1 Hostlist ........................... 5 Keys to Genera. Species. and higher Groups ...........11 Discussion of Species ..................... 20 Bib 1iography .......................... 62 Host index ........................... 64 List of comn names ...................... 67 Index to mites. Genera. Species. etc .............. 08 Plate symbols ......................... 71 List of plates ......................... 72 Plates ............................. 74 THE ERIOPHYID MITES OF CALIFORNIA Introduction ’IhisBulletin is the result of fifteen years would classify these mites at the present, faces of intermittent exploration of California for the prospect of a growing number of species in the Friophyid mites. hhen the work began in 1937 the large genera, and of broad revisions to come. But principal species recognized were the relatively I believe the average type of Eriophyid to have al- few economic species. ‘Ihis situation not only left ready been pretty well defined, since these mites an opportunity to discover and describe new spe- are widespread, and ancient in origin. cies, it also demanded that as many new Eriophyids As we now know these tiny creatures, they con- as possible be put in print in order to erect a stitute a closed group, structurally pointing to taxonomic framework. -
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 -
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. -
Data-Driven Identification of Potential Zika Virus Vectors Michelle V Evans1,2*, Tad a Dallas1,3, Barbara a Han4, Courtney C Murdock1,2,5,6,7,8, John M Drake1,2,8
RESEARCH ARTICLE Data-driven identification of potential Zika virus vectors Michelle V Evans1,2*, Tad A Dallas1,3, Barbara A Han4, Courtney C Murdock1,2,5,6,7,8, John M Drake1,2,8 1Odum School of Ecology, University of Georgia, Athens, United States; 2Center for the Ecology of Infectious Diseases, University of Georgia, Athens, United States; 3Department of Environmental Science and Policy, University of California-Davis, Davis, United States; 4Cary Institute of Ecosystem Studies, Millbrook, United States; 5Department of Infectious Disease, University of Georgia, Athens, United States; 6Center for Tropical Emerging Global Diseases, University of Georgia, Athens, United States; 7Center for Vaccines and Immunology, University of Georgia, Athens, United States; 8River Basin Center, University of Georgia, Athens, United States Abstract Zika is an emerging virus whose rapid spread is of great public health concern. Knowledge about transmission remains incomplete, especially concerning potential transmission in geographic areas in which it has not yet been introduced. To identify unknown vectors of Zika, we developed a data-driven model linking vector species and the Zika virus via vector-virus trait combinations that confer a propensity toward associations in an ecological network connecting flaviviruses and their mosquito vectors. Our model predicts that thirty-five species may be able to transmit the virus, seven of which are found in the continental United States, including Culex quinquefasciatus and Cx. pipiens. We suggest that empirical studies prioritize these species to confirm predictions of vector competence, enabling the correct identification of populations at risk for transmission within the United States. *For correspondence: mvevans@ DOI: 10.7554/eLife.22053.001 uga.edu Competing interests: The authors declare that no competing interests exist. -
ARTHROPOD MONITORING: Mosquito Studies
64 ARTHROPOD MONITORING: Mosquito Studies - Greenwoods, Summer 1995 Wi~~iam L. Butts Expanded sampling of the area inunediately adj acent to the large bog ("Cranberry Bog") for anthrophilic mosquitoes was the main focus of studies at Greenwoods. Initial plans to conduct biting/alighting sampling from a boat at selected sites around the margin of the impoundment were abandoned due to logistical difficulties. Emergent and submerged obstructions made it impossible to move about by boat at a rate that would allow for sampling at a sufficient number of sites within the hours of feeding activity. It was also evident that repeated sampling by boat would cause an unacceptable level of disruption to aquatic vegetation. A series of eight sampling sites marked with bicolored streamers was established along the west side of the bog from the point of access to the main dam northward. A similar series was laid out along the east side with three sampling stations south of the one at the dock site and four stations north of it. Biting/alighting collections were made by the author sitting for 20 minutes at each site with one forearm exposed. Mosquitoes alighting upon that arm or at other points on the body within reach of the other arm were collected by inverting a small killing vial over the mosquitoes. Sampling series were begun at approximately first light and in late evening beginning at a time estimated to terminate the series when unaided visual observation became difficult. In most instances one side of the bog was sampled in the evening and the other side the following morning. -
The Mosquitoes of Minnesota
Technical Bulletin 228 April 1958 The Mosquitoes of Minnesota (Diptera : Culicidae : Culicinae) A. RALPH BARR University of Minnesota Agricultural Experiment Station ~2 Technirnl Rull!'lin :z2g 1-,he Mosquitoes of J\ilinnesota (Diptera: Culicidae: Culicinae) A. llALPII R\lm University of Minnesota Agricultural Experiment Station CONTENTS I. Introduction JI. Historical Ill. Biology of mosquitoes ................................ Zoogeography Oviposition ......................................... Breeding places of larvae ................................... I) Larrnl p;rowth ....................................... Ill ,\atural factors in the control of larvae .................. JI The pupal stage ............................................... 12 .\lating .................................... _ ..... 12 Feeding of adults ......................................... 12 Hibernation 11 Seasonal distribution II I\ . Techniques Equipment Eggs ............................... · .... · · · · · · · · · · · · · · · · · · · · · · · · · · · · · Larvae Pupae Adults Colonization and rearing . IB \. Systematic treatment Keys to genera Adult females . l'J \fale terminalia . 19 Pupae ······················································· .... ········ 2.'i Larvae ····················································· ..... ········ 2S :-n Anopheles ········································· ··························· Anopheles (Anopheles) barberi .................... · · · · · · · · · · · · · · · · · · · · · · · · earlei ...•......................... · · · · · -
Detection and Characterization of a Novel Marine Birnavirus Isolated from Asian Seabass in Singapore
Chen et al. Virology Journal (2019) 16:71 https://doi.org/10.1186/s12985-019-1174-0 RESEARCH Open Access Detection and characterization of a novel marine birnavirus isolated from Asian seabass in Singapore Jing Chen1†, Xinyu Toh1†, Jasmine Ong1, Yahui Wang1, Xuan-Hui Teo1, Bernett Lee2, Pui-San Wong3, Denyse Khor1, Shin-Min Chong1, Diana Chee1, Alvin Wee1, Yifan Wang1, Mee-Keun Ng1, Boon-Huan Tan3 and Taoqi Huangfu1* Abstract Background: Lates calcarifer, known as seabass in Asia and barramundi in Australia, is a widely farmed species internationally and in Southeast Asia and any disease outbreak will have a great economic impact on the aquaculture industry. Through disease investigation of Asian seabass from a coastal fish farm in 2015 in Singapore, a novel birnavirus named Lates calcarifer Birnavirus (LCBV) was detected and we sought to isolate and characterize the virus through molecular and biochemical methods. Methods: In order to propagate the novel birnavirus LCBV, the virus was inoculated into the Bluegill Fry (BF-2) cell line and similar clinical signs of disease were reproduced in an experimental fish challenge study using the virus isolate. Virus morphology was visualized using transmission electron microscopy (TEM). Biochemical analysis using chloroform and 5-Bromo-2′-deoxyuridine (BUDR) sensitivity assays were employed to characterize the virus. Next-Generation Sequencing (NGS) was also used to obtain the virus genome for genetic and phylogenetic analyses. Results: The LCBV-infected BF-2 cell line showed cytopathic effects such as rounding and granulation of cells, localized cell death and detachment of cells observed at 3 to 5 days’ post-infection. -
Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies
viruses Review Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies Varvara I. Maliogka 1,* ID , Angelantonio Minafra 2 ID , Pasquale Saldarelli 2, Ana B. Ruiz-García 3, Miroslav Glasa 4 ID , Nikolaos Katis 1 and Antonio Olmos 3 ID 1 Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; [email protected] 2 Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy; [email protected] (A.M.); [email protected] (P.S.) 3 Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain; [email protected] (A.B.R.-G.); [email protected] (A.O.) 4 Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic; [email protected] * Correspondence: [email protected]; Tel.: +30-2310-998716 Received: 23 July 2018; Accepted: 13 August 2018; Published: 17 August 2018 Abstract: Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. -
NDP 39 Hazelnut Big Bud Mite
NDP ## V# - National Diagnostic Protocol for Phytoptus avellanae National Diagnostic Protocol Phytoptus avellanae Nalepa Hazelnut big bud mite NDP 39 V1 NDP 39 V1 - National Diagnostic Protocol for Phytoptus avellanae © Commonwealth of Australia Ownership of intellectual property rights Unless otherwise noted, copyright (and any other intellectual property rights, if any) in this publication is owned by the Commonwealth of Australia (referred to as the Commonwealth). Creative Commons licence All material in this publication is licensed under a Creative Commons Attribution 3.0 Australia Licence, save for content supplied by third parties, logos and the Commonwealth Coat of Arms. Creative Commons Attribution 3.0 Australia Licence is a standard form licence agreement that allows you to copy, distribute, transmit and adapt this publication provided you attribute the work. A summary of the licence terms is available from http://creativecommons.org/licenses/by/3.0/au/deed.en. The full licence terms are available from https://creativecommons.org/licenses/by/3.0/au/legalcode. This publication (and any material sourced from it) should be attributed as: Subcommittee on Plant Health Diagnostics (2017). National Diagnostic Protocol for Phytoptus avellanae – NDP39 V1. (Eds. Subcommittee on Plant Health Diagnostics) Author Davies, J; Reviewer Knihinicki, D. ISBN 978-0-9945113-9-3 CC BY 3.0. Cataloguing data Subcommittee on Plant Health Diagnostics (2017). National Diagnostic Protocol for Phytoptus avellanae NDP39 V1. (Eds. Subcommittee on Plant Health -
Rapid Protein Sequence Evolution Via Compensatory Frameshift Is Widespread in RNA Virus Genomes
Park and Hahn BMC Bioinformatics (2021) 22:251 https://doi.org/10.1186/s12859-021-04182-9 RESEARCH Open Access Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes Dongbin Park and Yoonsoo Hahn* *Correspondence: [email protected] Abstract Department of Life Science, Background: RNA viruses possess remarkable evolutionary versatility driven by the Chung-Ang University, Seoul 06794, South Korea high mutability of their genomes. Frameshifting nucleotide insertions or deletions (indels), which cause the premature termination of proteins, are frequently observed in the coding sequences of various viral genomes. When a secondary indel occurs near the primary indel site, the open reading frame can be restored to produce functional proteins, a phenomenon known as the compensatory frameshift. Results: In this study, we systematically analyzed publicly available viral genome sequences and identifed compensatory frameshift events in hundreds of viral protein- coding sequences. Compensatory frameshift events resulted in large-scale amino acid diferences between the compensatory frameshift form and the wild type even though their nucleotide sequences were almost identical. Phylogenetic analyses revealed that the evolutionary distance between proteins with and without a compensatory frameshift were signifcantly overestimated because amino acid mismatches caused by compensatory frameshifts were counted as substitutions. Further, this could cause compensatory frameshift forms to branch in diferent locations in the protein and nucleotide trees, which may obscure the correct interpretation of phylogenetic rela- tionships between variant viruses. Conclusions: Our results imply that the compensatory frameshift is one of the mecha- nisms driving the rapid protein evolution of RNA viruses and potentially assisting their host-range expansion and adaptation.