Genome Sequence Analysis of Csrv1: a Pathogenic Reovirus That Infects the Blue Crab Callinectes Sapidus Across Its Trans-Hemispheric Range
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Genome Sequencing by Random Priming Methods for Viral Identification
Genome sequencing by random priming methods for viral identification Rosseel Toon Dissertation submitted in fulfillment of the requirements for the degree of Doctor of Philosophy (PhD) in Veterinary Sciences, Faculty of Veterinary Medicine, Ghent University, 2015 Promotors: Dr. Steven Van Borm Prof. Dr. Hans Nauwynck “The real voyage of discovery consist not in seeking new landscapes, but in having new eyes” Marcel Proust, French writer, 1923 Table of contents Table of contents ....................................................................................................................... 1 List of abbreviations ................................................................................................................. 3 Chapter 1 General introduction ................................................................................................ 5 1. Viral diagnostics and genomics ....................................................................................... 7 2. The DNA sequencing revolution ................................................................................... 12 2.1. Classical Sanger sequencing .................................................................................. 12 2.2. Next-generation sequencing ................................................................................... 16 3. The viral metagenomic workflow ................................................................................. 24 3.1. Sample preparation ............................................................................................... -
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. -
Viral Gastroenteritis
viral gastroenteritis What causes viral gastroenteritis? y Rotaviruses y Caliciviruses y Astroviruses y SRV (Small Round Viruses) y Toroviruses y Adenoviruses 40 , 41 Diarrhea Causing Agents in World ROTAVIRUS Family Reoviridae Genus Segments Host Vector Orthoreovirus 10 Mammals None Orbivirus 11 Mammals Mosquitoes, flies Rotavirus 11 Mammals None Coltivirus 12 Mammals Ticks Seadornavirus 12 Mammals Ticks Aquareovirus 11 Fish None Idnoreovirus 10 Mammals None Cypovirus 10 Insect None Fijivirus 10 Plant Planthopper Phytoreovirus 12 Plant Leafhopper OiOryzavirus 10 Plan t Plan thopper Mycoreovirus 11 or 12 Fungi None? REOVIRUS y REO: respiratory enteric orphan, y early recognition that the viruses caused respiratory and enteric infections y incorrect belief they were not associated with disease, hence they were considered "orphan " viruses ROTAVIRUS‐ PROPERTIES y Virus is stable in the environment (months) y Relatively resistant to hand washing agents y Susceptible to disinfection with 95% ethanol, ‘Lyy,sol’, formalin STRUCTURAL FEATURES OF ROTAVIRUS y 60‐80nm in size y Non‐enveloped virus y EM appearance of a wheel with radiating spokes y Icosahedral symmetry y Double capsid y Double stranded (ds) RNA in 11 segments Rotavirus structure y The rotavirus genome consists of 11 segments of double- stranded RNA, which code for 6 structural viral proteins, VP1, VP2, VP3, VP4, VP6 and VP7 and 6 non-structural proteins, NSP1-NSP6 , where gene segment 11 encodes both NSP5 and 6. y Genome is encompassed by an inner core consisting of VP2, VP1 and VP3 proteins. Intermediate layer or inner capsid is made of VP6 determining group and subgroup specifici ti es. y The outer capsid layer is composed of two proteins, VP7 and VP4 eliciting neutralizing antibody responses. -
Physicochemical Properties of Double-Stranded RNA Used to Discover a Reo-Like Virus from Blue Crab Callinectes Sapidus
Vol. 93: 17–29, 2010 DISEASES OF AQUATIC ORGANISMS Published December 7 doi: 10.3354/dao02280 Dis Aquat Org OPENPEN ACCESSCCESS Physicochemical properties of double-stranded RNA used to discover a reo-like virus from blue crab Callinectes sapidus Holly A. Bowers1, Gretchen A. Messick2, Ammar Hanif1, Rosemary Jagus1, Lee Carrion3, Oded Zmora4, Eric J. Schott1,* 1Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland 21202, USA 2Center for Coastal Environmental Health & Biomolecular Research at Charleston USDOC/NOAA/NOS/NCCOS, Oxford, Maryland 21654, USA 3Coveside Crabs, Inc., Dundalk, Maryland 21222, USA 4Institute of Marine and Environmental Technology, University of Maryland Baltimore County, Baltimore, Maryland 21202, USA ABSTRACT: Mortality among blue crab Callinectes sapidus in soft shell production facilities is typi- cally 25% or greater. The harvest, handling, and husbandry practices of soft shell crab production have the potential to spread or exacerbate infectious crab diseases. To investigate the possible role of viruses in soft shell crab mortalities, we took advantage of the physicochemical properties of double- stranded RNA (dsRNA) to isolate a putative virus genome. Further characterization confirmed the presence of a reo-like virus that possesses 12 dsRNA genome segments. The virus was present in >50% of dead or dying soft shell crabs, but fewer than 5% of healthy hard crabs. Injection of the virus caused mortality and resulted in the appearance of viral RNA and virus inclusions in hemocytes. The genome of the virus was partially sequenced and the information used to develop a reverse transcrip- tion polymerase chain reaction (RT-PCR) assay that is able to detect the virus genome in as little as 7.5 pg of total RNA. -
Mgr. Marie Vilánková
www.novinky.cz www.rozhlas.cz VIRY Mgr. Marie Vilánková © ECC s.r.o. www.stefajir.cz Všechna práva vyhrazena Viry • Jejich zařazení do živé přírody • Virus jako informace • Jejich členění, • způsoby pronikání do lidského organismu, • nejčastější zdravotní problémy s nimi spojené • Možnosti řešení, včetně akutních infekcí, preparáty Joalis • Proč preparát Antivex je velmi důležitý © ECC s.r.o. Všechna práva vyhrazena Země • Životní prostředí – živé organismy - rostliny, živočichové… – tvořeny buňkami • Rostliny – počátek potravního řetězce, umí zachytávat sluneční energii a ukládat do chemických vazeb • Zvířata – zdroj potravy – rostliny nebo jiná zvířata • Houby a plísně – rozklad hmoty na základní prvky • Bakterie – také rozklad, velký význam v oběhu živin, prospěšné svazky s jinými organismy, mohou také škodit - Různé vztahy mezi organismy – boj o potravu, získání životního prostoru, přežití… © ECC s.r.o. Všechna práva vyhrazena Živé organismy • Živé organismy tvořeny buňkami – jednobuněčné (bakterie, prvoci, některé plísně), vícebuněčné • Buňka – tvořena ze specializovaných částí organel - cytoplasma, jádro, mitochondrie, endoplasmatické retikulum … • Buněčná membrána: dvojitá vrstva fosfolipidů s molekulami bílkovin – velmi důležité NENAsycené mastné kyseliny – VÝŽIVA!!! • Každá buňka – samostatný organismus – přijímá potravu, vylučuje, rozmnožuje se, reaguje na okolí, má nějakou fci -stavební produkuje stavební materiál (bílkoviny), transportní bariérová – přenáší částice přes bariéru, pohybová – natahuje a smršťuje se, signalizační © ECC s.r.o. Všechna práva vyhrazena Organismus = společnost buněk Soubor buněk = základní funkční jednotka • Propojeny pojivem – mezibuněčná hmota – produkt buněk vazivo, chrupavky, kosti, tekutiny • Tkáně: soubor buněk stejného typu (nervová, svalová, epitel...) • Orgány: skládají se z tkání, tvoří soustavy orgánů • Tělo: je složeno z buněk – 3,5 x 1013 buněk (lidí na Zemi 109) • Délka těla= 1,7 m, průměrná velikost buňky 10 - 20 mikrometru, měřítko 10-6 - člověk se dívá na svět z družice © ECC s.r.o. -
Marine Surface Microlayer As a Source of Enteric Viruses
MARINE SURFACE MICROLAYER AS A SOURCE OF ENTERIC VIRUSES Ana Catarina Bispo Prata Tese de Doutoramento em Ciências do Mar e do Ambiente 2014 Ana Catarina Bispo Prata MARINE SURFACE MICROLAYER AS A SOURCE OF ENTERIC VIRUSES Tese de Candidatura ao grau de Doutor em Ciências do Mar e do Ambiente Especialidade em Oceanografia e Ecossistemas Marinhos submetida ao Instituto de Ciências Biomédicas de Abel Salazar da Universidade do Porto. Programa Doutoral da Universidade do Porto (Instituto de Ciências Biomédicas de Abel Salazar e Faculdade de Ciências) e da Universidade de Aveiro. Orientador – Doutor Adelaide Almeida Categoria – Professora Auxiliar Afiliação – Departamento de Biologia da Universidade de Aveiro Co-orientador – Doutor Newton Carlos Marcial Gomes Categoria – Investigador Principal do CESAM Afiliação – Departamento de Biologia da Universidade de Aveiro LEGAL DETAILS In compliance with what is stated in the legislation in vigor, it is hereby declared that the author of this thesis participated in the creation and execution of the experimental work leading to the results here stated, as well as in their interpretation and writing of the respective manuscripts. This thesis includes one scientific paper published in an international journal and three articles in preparation originated from part of the results obtained in the experimental work referenced as: • Prata C, Ribeiro A, Cunha A , Gomes NCM, Almeida A, 2012, Ultracentrifugation as a direct method to concentrate viruses in environmental waters: virus-like particles enumeration as a new approach to determine the efficiency of recovery, Journal of Environmental Monitoring, 14 (1), 64-70. • Prata C, Cunha A, Gomes N, Almeida A, Surface Microlayer as a source of health relevant enteric viruses in Ria de Aveiro. -
Molecular and Biological Characterization of a Cypovirus from the Mosquito Culex Restuans
Journal of Invertebrate Pathology 91 (2006) 27–34 www.elsevier.com/locate/yjipa Molecular and biological characterization of a Cypovirus from the mosquito Culex restuans Terry B. Green a,¤, Alexandra Shapiro a, Susan White a, Shujing Rao b, Peter P.C. Mertens b, Gerry Carner c, James J. Becnel a a ARS, CMAVE, 1600-1700 S.W. 23rd Drive, Gainesville, FL 32608, USA b Pirbright Laboratory, Institute for Animal Health, Ash Road Pirbright, Woking, Surrey GU24 0NF, UK c Clemson University, 114 Long Hall, Clemson, SC 29634, USA Received 4 August 2005; accepted 11 October 2005 Abstract A cypovirus from the mosquito Culex restuans (named CrCPV) was isolated and its biology, morphology, and molecular characteris- tics were investigated. CrCPV is characterized by small (0.1–1.0 m), irregularly shaped inclusion bodies that are multiply embedded. Lab- oratory studies demonstrated that divalent cations inXuenced transmission of CrCPV to Culex quinquefasciatus larvae; magnesium enhanced CrCPV transmission by »30% while calcium inhibited transmission. CrCPV is the second cypovirus from a mosquito that has been conWrmed by using molecular analysis. CrCPV has a genome composed of 10 dsRNA segments with an electropherotype similar to the recently discovered UsCPV-17 from the mosquito Uranotaenia sapphirina, but distinct from the lepidopteran cypoviruses BmCPV-1 (Bombyx mori) and TnCPV-15 (Trichoplusia ni). Nucleotide and deduced amino acid sequence analysis of CrCPV segment 10 (polyhe- drin) suggests that CrCPV is closely related (83% nucleotide sequence identity and 87% amino acid sequence identity) to the newly char- acterized UsCPV-17 but is unrelated to the 16 remaining CPV species from lepidopteran hosts. -
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 Studies of Piscine Orthoreovirus Proteins
Piscine orthoreovirus Series of dissertations at the Norwegian University of Life Sciences Thesis number 79 Viruses, not lions, tigers or bears, sit masterfully above us on the food chain of life, occupying a role as alpha predators who prey on everything and are preyed upon by nothing Claus Wilke and Sara Sawyer, 2016 1.1. Background............................................................................................................................................... 1 1.2. Piscine orthoreovirus................................................................................................................................ 2 1.3. Replication of orthoreoviruses................................................................................................................ 10 1.4. Orthoreoviruses and effects on host cells ............................................................................................... 18 1.5. PRV distribution and disease associations ............................................................................................. 24 1.6. Vaccine against HSMI ............................................................................................................................ 29 4.1. The non ......................................................37 4.2. PRV causes an acute infection in blood cells ..........................................................................................40 4.3. DNA -
Diversity and Classification of Reoviruses in Crustaceans: a Proposal
Journal of Invertebrate Pathology 182 (2021) 107568 Contents lists available at ScienceDirect Journal of Invertebrate Pathology journal homepage: www.elsevier.com/locate/jip Diversity and classification of reoviruses in crustaceans: A proposal Mingli Zhao a, Camila Prestes dos Santos Tavares b, Eric J. Schott c,* a Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD 21202, USA b Integrated Group of Aquaculture and Environmental Studies, Federal University of Parana,´ Rua dos Funcionarios´ 1540, Curitiba, PR 80035-050, Brazil c Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA ARTICLE INFO ABSTRACT Keywords: A variety of reoviruses have been described in crustacean hosts, including shrimp, crayfish,prawn, and especially P virus in crabs. However, only one genus of crustacean reovirus - Cardoreovirus - has been formally recognized by ICTV CsRV1 (International Committee on Taxonomy of Viruses) and most crustacean reoviruses remain unclassified. This Cardoreovirus arises in part from ambiguous or incomplete information on which to categorize them. In recent years, increased Crabreovirus availability of crustacean reovirus genomic sequences is making the discovery and classification of crustacean Brachyuran Phylogenetic analysis reoviruses faster and more certain. This minireview describes the properties of the reoviruses infecting crusta ceans and suggests an overall classification of brachyuran crustacean reoviruses based on a combination of morphology, host, genome organization pattern and phylogenetic sequence analysis. 1. Introduction fish, crustaceans, marine protists, insects, ticks, arachnids, plants and fungi (Attoui et al., 2005; Shields et al., 2015). Host range and disease 1.1. Genera of Reoviridae family symptoms are also important indicators that help to identify viruses of different genera (Attoui et al., 2012). -
Origin and Evolution of Emerging Liaoning Virus(Genus Seadornavirus, Family Reoviridae)
Origin and Evolution of Emerging Liaoning Virusgenus Seadornavirus, family Reoviridae) Jun Zhang Shandong University of Technology Hong Liu ( [email protected] ) Shandong University of Technology https://orcid.org/0000-0002-5182-4750 Jiahui Wang Shandong University of Technology Jiheng Wang Shandong University of Technology Jianming Zhang Shandong University of Technology Jiayue Wang Shandong University of Technology Xin Zhang Shandong University of Technology Hongfang Ji Shandong University of Technology Zhongfen Ding Shandong University of Technology Han Xia Chinese Academy of Sciences Chunyang Zhang Shandong University of Technology Qian Zhao Shandong University of Technology Guodong Liang Chinese Center for Disease Control and Prevention Research Keywords: Liaoning virus, LNV, Seadornavirus, Evolution, Migration Posted Date: January 15th, 2020 DOI: https://doi.org/10.21203/rs.2.20915/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/13 Abstract Background:Liaoning virus(LNV) is a member of the genus Seadornavirus, family Reoviridae and has been isolated from kinds of sucking insects in Asia and Australia. However, there are no systematic studies describe the molecular genetic evolution and migration of LNVs isolated from different time, regions and vectors. Methods:Here, a phylogenetic analysis using Bayesian Markov chain Monte Carlo simulations was conducted on the LNVs isolated from a variety of vectors during 1990-2014,worldwide. Results:The phylogenetic analysis demonstrated that the LNV could be divided into 3 genotypes, of which genotype 1 mainly composed of LNVs isolated from Australia during 1990 to 2014 as well as the original LNV strain(LNV-NE97-31) isolated from Liaoning province in northern China in 1997,genotype 2 comprised of the isolates all from Xinjiang province in western China and genotype 3 consisted the isolates from Qinghai and Shanxi province of central China.