Virus Taxonomy 1996 —
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Multiple Origins of Viral Capsid Proteins from Cellular Ancestors
Multiple origins of viral capsid proteins from PNAS PLUS cellular ancestors Mart Krupovica,1 and Eugene V. Kooninb,1 aInstitut Pasteur, Department of Microbiology, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015 Paris, France; and bNational Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894 Contributed by Eugene V. Koonin, February 3, 2017 (sent for review December 21, 2016; reviewed by C. Martin Lawrence and Kenneth Stedman) Viruses are the most abundant biological entities on earth and show genome replication. Understanding the origin of any virus group is remarkable diversity of genome sequences, replication and expres- possible only if the provenances of both components are elucidated sion strategies, and virion structures. Evolutionary genomics of (11). Given that viral replication proteins often have no closely viruses revealed many unexpected connections but the general related homologs in known cellular organisms (6, 12), it has been scenario(s) for the evolution of the virosphere remains a matter of suggested that many of these proteins evolved in the precellular intense debate among proponents of the cellular regression, escaped world (4, 6) or in primordial, now extinct, cellular lineages (5, 10, genes, and primordial virus world hypotheses. A comprehensive 13). The ability to transfer the genetic information encased within sequence and structure analysis of major virion proteins indicates capsids—the protective proteinaceous shells that comprise the that they evolved on about 20 independent occasions, and in some of cores of virus particles (virions)—is unique to bona fide viruses and these cases likely ancestors are identifiable among the proteins of distinguishes them from other types of selfish genetic elements cellular organisms. -
A Preliminary Study of Viral Metagenomics of French Bat Species in Contact with Humans: Identification of New Mammalian Viruses
A preliminary study of viral metagenomics of French bat species in contact with humans: identification of new mammalian viruses. Laurent Dacheux, Minerva Cervantes-Gonzalez, Ghislaine Guigon, Jean-Michel Thiberge, Mathias Vandenbogaert, Corinne Maufrais, Valérie Caro, Hervé Bourhy To cite this version: Laurent Dacheux, Minerva Cervantes-Gonzalez, Ghislaine Guigon, Jean-Michel Thiberge, Mathias Vandenbogaert, et al.. A preliminary study of viral metagenomics of French bat species in contact with humans: identification of new mammalian viruses.. PLoS ONE, Public Library of Science, 2014, 9 (1), pp.e87194. 10.1371/journal.pone.0087194.s006. pasteur-01430485 HAL Id: pasteur-01430485 https://hal-pasteur.archives-ouvertes.fr/pasteur-01430485 Submitted on 9 Jan 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License A Preliminary Study of Viral Metagenomics of French Bat Species in Contact with Humans: Identification of New Mammalian Viruses Laurent Dacheux1*, Minerva Cervantes-Gonzalez1, -
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. -
Diversity of Plant Virus Movement Proteins: What Do They Have in Common?
processes Review Diversity of Plant Virus Movement Proteins: What Do They Have in Common? Yuri L. Dorokhov 1,2,* , Ekaterina V. Sheshukova 1, Tatiana E. Byalik 3 and Tatiana V. Komarova 1,2 1 Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; [email protected] (E.V.S.); [email protected] (T.V.K.) 2 Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia 3 Department of Oncology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; [email protected] * Correspondence: [email protected] Received: 11 November 2020; Accepted: 24 November 2020; Published: 26 November 2020 Abstract: The modern view of the mechanism of intercellular movement of viruses is based largely on data from the study of the tobacco mosaic virus (TMV) 30-kDa movement protein (MP). The discovered properties and abilities of TMV MP, namely, (a) in vitro binding of single-stranded RNA in a non-sequence-specific manner, (b) participation in the intracellular trafficking of genomic RNA to the plasmodesmata (Pd), and (c) localization in Pd and enhancement of Pd permeability, have been used as a reference in the search and analysis of candidate proteins from other plant viruses. Nevertheless, although almost four decades have passed since the introduction of the term “movement protein” into scientific circulation, the mechanism underlying its function remains unclear. It is unclear why, despite the absence of homology, different MPs are able to functionally replace each other in trans-complementation tests. Here, we consider the complexity and contradictions of the approaches for assessment of the ability of plant viral proteins to perform their movement function. -
An Insect Nidovirus Emerging from a Primary Tropical Rainforest
RESEARCH ARTICLE An Insect Nidovirus Emerging from a Primary Tropical Rainforest Florian Zirkel,a,b,c Andreas Kurth,d Phenix-Lan Quan,b Thomas Briese,b Heinz Ellerbrok,d Georg Pauli,d Fabian H. Leendertz,c W. Ian Lipkin,b John Ziebuhr,e Christian Drosten,a and Sandra Junglena,c Institute of Virology, University of Bonn Medical Center, Bonn, Germanya; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USAb; Research Group Emerging Zoonosesc and Center for Biological Safety-1,d Robert Koch Institute, Berlin, Germany; and Institute of Medical Virology, Justus Liebig University Gießen, Gießen, Germanye ABSTRACT Tropical rainforests show the highest level of terrestrial biodiversity and may be an important contributor to micro- bial diversity. Exploitation of these ecosystems may foster the emergence of novel pathogens. We report the discovery of the first insect-associated nidovirus, tentatively named Cavally virus (CAVV). CAVV was found with a prevalence of 9.3% during a sur- vey of mosquito-associated viruses along an anthropogenic disturbance gradient in Côte d’Ivoire. Analysis of habitat-specific virus diversity and ancestral state reconstruction demonstrated an origin of CAVV in a pristine rainforest with subsequent spread into agriculture and human settlements. Virus extension from the forest was associated with a decrease in virus diversity (P < 0.01) and an increase in virus prevalence (P < 0.00001). CAVV is an enveloped virus with large surface projections. The RNA genome comprises 20,108 nucleotides with seven major open reading frames (ORFs). ORF1a and -1b encode two large pro- teins that share essential features with phylogenetically higher representatives of the order Nidovirales, including the families Coronavirinae and Torovirinae, but also with families in a basal phylogenetic relationship, including the families Roniviridae and Arteriviridae. -
Synthesis of Potato Virus X Rnas by Membrane- Containing Extracts
JOURNAL OF VIROLOGY, July 1996, p. 4795–4799 Vol. 70, No. 7 0022-538X/96/$04.0010 Copyright q 1996, American Society for Microbiology Synthesis of Potato Virus X RNAs by Membrane- Containing Extracts SERGEY V. DORONIN AND CYNTHIA HEMENWAY* Department of Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7622 Received 16 October 1995/Accepted 30 March 1996 Membrane-containing extracts isolated from tobacco plants infected with the plus-strand RNA virus, potato virus X (PVX), supported synthesis of four major, high-molecular-weight PVX RNA products (R1 to R4). Nuclease digestion and hybridization studies indicated that R1 and R2 are a mixture of partially single- stranded replicative intermediates and double-stranded replicative forms. R3 and R4 are double-stranded products containing sequences typical of the two major PVX subgenomic RNAs. The newly synthesized RNAs were demonstrated to have predominantly plus-strand polarity. Synthesis of these products was remarkably stable in the presence of ionic detergents. Potato virus X (PVX), the type member of the Potexvirus tracts were derived from Nicotiana tabacum leaves at 7 days genus, is a flexuous rod-shaped particle containing a single, postinoculation by a procedure similar to that described by genomic RNA of 6.4 kb that is capped and polyadenylated (21, Lurie and Hendrix (15). Inoculated and upper leaves (50 g) 27). Of the five open reading frames (ORFs), the first encodes were homogenized in 150 ml of buffer I (50 mM Tris-HCl [pH a 165-kDa protein (P1) that has homology to other known 7.5], 250 mM sucrose, 5 mM MgCl2, 1 mM EDTA, 10 mM RNA-dependent RNA polymerase (RdRp) proteins (23). -
Borna Disease Virus Infection in Animals and Humans
Synopses Borna Disease Virus Infection in Animals and Humans Jürgen A. Richt,* Isolde Pfeuffer,* Matthias Christ,* Knut Frese,† Karl Bechter,‡ and Sibylle Herzog* *Institut für Virologie, Giessen, Germany; †Institut für Veterinär-Pathologie, Giessen, Germany; and ‡Universität Ulm, Günzburg, Germany The geographic distribution and host range of Borna disease (BD), a fatal neuro- logic disease of horses and sheep, are larger than previously thought. The etiologic agent, Borna disease virus (BDV), has been identified as an enveloped nonsegmented negative-strand RNA virus with unique properties of replication. Data indicate a high degree of genetic stability of BDV in its natural host, the horse. Studies in the Lewis rat have shown that BDV replication does not directly influence vital functions; rather, the disease is caused by a virus-induced T-cell–mediated immune reaction. Because antibodies reactive with BDV have been found in the sera of patients with neuro- psychiatric disorders, this review examines the possible link between BDV and such disorders. Seroepidemiologic and cerebrospinal fluid investigations of psychiatric patients suggest a causal role of BDV infection in human psychiatric disorders. In diagnostically unselected psychiatric patients, the distribution of psychiatric disorders was found to be similar in BDV seropositive and seronegative patients. In addition, BDV-seropositive neurologic patients became ill with lymphocytic meningoencephali- tis. In contrast to others, we found no evidence is reported for BDV RNA, BDV antigens, or infectious BDV in peripheral blood cells of psychiatric patients. Borna disease (BD), first described more predilection for the gray matter of the cerebral than 200 years ago in southern Germany as a hemispheres and the brain stem (8,19). -
Module1: General Concepts
NPTEL – Biotechnology – General Virology Module1: General Concepts Lecture 1: Virus history The history of virology goes back to the late 19th century, when German anatomist Dr Jacob Henle (discoverer of Henle’s loop) hypothesized the existence of infectious agent that were too small to be observed under light microscope. This idea fails to be accepted by the present scientific community in the absence of any direct evidence. At the same time three landmark discoveries came together that formed the founding stone of what we call today as medical science. The first discovery came from Louis Pasture (1822-1895) who gave the spontaneous generation theory from his famous swan-neck flask experiment. The second discovery came from Robert Koch (1843-1910), a student of Jacob Henle, who showed for first time that the anthrax and tuberculosis is caused by a bacillus, and finally Joseph Lister (1827-1912) gave the concept of sterility during the surgery and isolation of new organism. The history of viruses and the field of virology are broadly divided into three phases, namely discovery, early and modern. The discovery phase (1886-1913) In 1879, Adolf Mayer, a German scientist first observed the dark and light spot on infected leaves of tobacco plant and named it tobacco mosaic disease. Although he failed to describe the disease, he showed the infectious nature of the disease after inoculating the juice extract of diseased plant to a healthy one. The next step was taken by a Russian scientist Dimitri Ivanovsky in 1890, who demonstrated that sap of the leaves infected with tobacco mosaic disease retains its infectious property even after its filtration through a Chamberland filter. -
Microbe Hunting W
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, Sept. 2010, p. 363–377 Vol. 74, No. 3 1092-2172/10/$12.00 doi:10.1128/MMBR.00007-10 Copyright © 2010, American Society for Microbiology. All Rights Reserved. Microbe Hunting W. Ian Lipkin* Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York INTRODUCTION .......................................................................................................................................................363 DIVERSITY OF THE MICROBIAL UNIVERSE...................................................................................................364 PROOF OF CAUSATION .........................................................................................................................................364 Possible Causal Relationship................................................................................................................................365 Probable Causal Relationship...............................................................................................................................365 Interventional evidence ......................................................................................................................................366 (i) Challenges ..................................................................................................................................................366 Prophylactic evidence .........................................................................................................................................367 -
Bornaviridae
1 Bornaviridae Taxonomy Riboviria › Orthornavirae › Negarnaviricota › Haploviricotina › Monjiviricetes › Mononegavirales › Born aviridae Derivation of name Borna refers to the city of Borna in Saxony, Germany, where many horses died in 1885 during an epidemic of a neurological disease, designated as Borna disease (BD), caused by the infectious agent presently known as Borna disease virus (BDV). Genus Bornavirus Type species Borna disease virus Virion properties Morphology Electron microscopy studies of negatively stained infectious particles of an isolate of Borna disease virus (BDV) have shown that virions have a spherical morphology with a diameter of 90±10 nm containing an internal electron-dense core (50–60 nm). Physicochemical and physical properties Virion Molecular weight not known. Virus infectivity is rapidly lost by heat treatment at 56 °C. Virions are relatively stable at 37 °C, and only minimal infectivity loss is observed after 24 hrs incubation at 37 °C in the presence of serum. Virions are inactivated below pH 5.0, as well as by treatment with organic solvents, detergents, and exposure to UV radiation. Infectivity is completely and rapidly destroyed by chlorine-containing disinfectants or formaldehyde treatment. Nucleic acid The genome consists of a single molecule of a linear, negative sense ssRNA about 8.9 kb in size and Mr of about 3×106). The RNA genome is not polyadenylated. Extracistronic sequences are found at the 3′ (leader) and 5′ (trailer) ends of the BDV genome. The ends of the BDV genome RNA exhibit partial Prepared By : Dr. Vandana Gupta 2 inverted complementarity. Full-length plus-strand (antigenomic) RNAs are present in infected cells and in viral ribonucleoproteins. -
FIG. 1 O Γ Fiber
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date Χ ft i ft 22 September 2011 (22.09.2011) 2011/116189 Al (51) International Patent Classification: (74) Agents: KOLOM, Melissa E. et al; LEYDIG, VOIT & A61K 39/235 (2006.01) A61K 39/385 (2006.01) MAYER, LTD., Two Prudential Plaza, Suite 4900, 180 N. Stetson Ave., Chicago, Illinois 60601-673 1 (US). (21) International Application Number: PCT/US201 1/028815 (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (22) International Filing Date: AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, 17 March 201 1 (17.03.201 1) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, (25) Filing Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (26) Publication Language: English KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (30) Priority Data: ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, 61/3 14,847 17 March 2010 (17.03.2010) NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, 61/373,704 13 August 2010 (13.08.2010) SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (71) Applicant (for all designated States except US): COR¬ NELL UNIVERSITY [US/US]; Cornell Center for (84) Designated States (unless otherwise indicated, for every Technology Enterprise and Commercialization kind of regional protection available): ARIPO (BW, GH, (("CCTEC"), 395 Pine Tree Road, Suite 310, Ithaca, New GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, York 14850 (US). -
Evolutionary Selection of the Nuclear Localization Signal in the Viral Nucleoprotein Leads to Host Adaptation of the Genus Orthobornavirus
viruses Article Evolutionary Selection of the Nuclear Localization Signal in the Viral Nucleoprotein Leads to Host Adaptation of the Genus Orthobornavirus Ryo Komorizono 1,2 , Yukiko Sassa 3, Masayuki Horie 1,4 , Akiko Makino 1,2,* and Keizo Tomonaga 1,2,5,* 1 Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; [email protected] (R.K.); [email protected] (M.H.) 2 Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan 3 Laboratory of Veterinary Infectious Disease, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan; [email protected] 4 Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8507, Japan 5 Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan * Correspondence: [email protected] (A.M.); [email protected] (K.T.) Received: 20 October 2020; Accepted: 10 November 2020; Published: 11 November 2020 Abstract: Adaptation of the viral life cycle to host cells is necessary for efficient viral infection and replication. This evolutionary process has contributed to the mechanism for determining the host range of viruses. Orthobornaviruses, members of the family Bornaviridae, are non-segmented, negative-strand RNA viruses, and several genotypes have been isolated from different vertebrate species. Previous studies revealed that some genotypes isolated from avian species can replicate in mammalian cell lines, suggesting the zoonotic potential of avian orthobornaviruses. However, the mechanism by which the host specificity of orthobornaviruses is determined has not yet been identified.