The Origin and Evolution of Viruses
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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. -
Use of Cell Culture in Virology for Developing Countries in the South-East Asia Region © World Health Organization 2017
USE OF CELL C USE OF CELL U LT U RE IN VIROLOGY FOR DE RE IN VIROLOGY V ELOPING C O U NTRIES IN THE NTRIES IN S O U TH- E AST USE OF CELL CULTURE A SIA IN VIROLOGY FOR R EGION ISBN: 978-92-9022-600-0 DEVELOPING COUNTRIES IN THE SOUTH-EAST ASIA REGION World Health House Indraprastha Estate, Mahatma Gandhi Marg, New Delhi-110002, India Website: www.searo.who.int USE OF CELL CULTURE IN VIROLOGY FOR DEVELOPING COUNTRIES IN THE SOUTH-EAST ASIA REGION © World Health Organization 2017 Some rights reserved. This work is available under the Creative Commons Attribution-NonCommercial- ShareAlike 3.0 IGO licence (CC BY-NC-SA 3.0 IGO; https://creativecommons.org/licenses/by-nc-sa/3.0/igo). Under the terms of this licence, you may copy, redistribute and adapt the work for non-commercial purposes, provided the work is appropriately cited, as indicated below. In any use of this work, there should be no suggestion that WHO endorses any specific organization, products or services. The use of the WHO logo is not permitted. If you adapt the work, then you must license your work under the same or equivalent Creative Commons licence. If you create a translation of this work, you should add the following disclaimer along with the suggested citation: “This translation was not created by the World Health Organization (WHO). WHO is not responsible for the content or accuracy of this translation. The original English edition shall be the binding and authentic edition.” Any mediation relating to disputes arising under the licence shall be conducted in accordance with the mediation rules of the World Intellectual Property Organization. -
Technical Glossary
WBVGL 6/28/03 12:00 AM Page 409 Technical Glossary abortive infection: Infection of a cell where there is no net increase in the production of infectious virus. abortive transformation: See transitory (transient or abortive) transformation. acid blob activator: A regulatory protein that acts in trans to alter gene expression and whose activity depends on a region of an amino acid sequence containing acidic or phosphorylated residues. acquired immune deficiency syndrome (AIDS): A disease characterized by loss of cell-mediated and humoral immunity as the result of infection with human immunodeficiency virus (HIV). acute infection: An infection marked by a sudden onset of detectable symptoms usually followed by complete or apparent recovery. adaptive immunity (acquired immunity): See immunity. adjuvant: Something added to a drug to increase the effectiveness of that drug. With respect to the immune system, an adjuvant increases the response of the system to a particular antigen. agnogene: A region of a genome that contains an open reading frame of unknown function; origi- nally used to describe a 67- to 71-amino acid product from the late region of SV40. AIDS: See acquired immune deficiency syndrome. aliquot: One of a number of replicate samples of known size. a-TIF: The alpha trans-inducing factor protein of HSV; a structural (virion) protein that functions as an acid blob transcriptional activator. Its specificity requires interaction with certain host cel- lular proteins (such as Oct1) that bind to immediate-early promoter enhancers. ambisense genome: An RNA genome that contains sequence information in both the positive and negative senses. The S genomic segment of the Arenaviridae and of certain genera of the Bunyaviridae have this characteristic. -
How Influenza Virus Uses Host Cell Pathways During Uncoating
cells Review How Influenza Virus Uses Host Cell Pathways during Uncoating Etori Aguiar Moreira 1 , Yohei Yamauchi 2 and Patrick Matthias 1,3,* 1 Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; [email protected] 2 Faculty of Life Sciences, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; [email protected] 3 Faculty of Sciences, University of Basel, 4031 Basel, Switzerland * Correspondence: [email protected] Abstract: Influenza is a zoonotic respiratory disease of major public health interest due to its pan- demic potential, and a threat to animals and the human population. The influenza A virus genome consists of eight single-stranded RNA segments sequestered within a protein capsid and a lipid bilayer envelope. During host cell entry, cellular cues contribute to viral conformational changes that promote critical events such as fusion with late endosomes, capsid uncoating and viral genome release into the cytosol. In this focused review, we concisely describe the virus infection cycle and highlight the recent findings of host cell pathways and cytosolic proteins that assist influenza uncoating during host cell entry. Keywords: influenza; capsid uncoating; HDAC6; ubiquitin; EPS8; TNPO1; pandemic; M1; virus– host interaction Citation: Moreira, E.A.; Yamauchi, Y.; Matthias, P. How Influenza Virus Uses Host Cell Pathways during 1. Introduction Uncoating. Cells 2021, 10, 1722. Viruses are microscopic parasites that, unable to self-replicate, subvert a host cell https://doi.org/10.3390/ for their replication and propagation. Despite their apparent simplicity, they can cause cells10071722 severe diseases and even pose pandemic threats [1–3]. -
Geve: a Genome-Based Endogenous Viral Element Database Provides
Database, 2016, 1–8 doi: 10.1093/database/baw087 Original article Original article Downloaded from https://academic.oup.com/database/article-abstract/doi/10.1093/database/baw087/2630466 by guest on 24 July 2019 gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes So Nakagawa1,2,* and Mahoko Ueda Takahashi2 1Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan and 2Micro/Nano Technology Center, Tokai University, 411 Kitakaname, Hiratsuka, Kanagawa, 259-1292, Japan *Corresponding author: Tel: þ81 463 93 1121 ext. 2661; Fax: þ81 463 93 5418; Email: [email protected] Citation details: Nakagawa,S. and Ueda Takahashi,M. gEVE: a genome-based endogenous viral element database pro- vides comprehensive viral protein-coding sequences in mammalian genomes. Database (2016) Vol. 2016: article ID baw087; doi:10.1093/database/baw087 Received 15 December 2015; Revised 15 April 2016; Accepted 4 May 2016 Abstract In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). -
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. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
Journal of Virology
JOURNAL OF VIROLOGY VOLUME 37 0 NUMBER 1 0 JANUARY 1981 EDITORIAL BOARD Robert R. Wagner, Editor-in-Chief (1982) University of Virginia School of Medicine, Charlottesville Dwight L. Anderson, Editor (1983) Haold S. Ginsberg, Editor (1984) School ofDentistry, Columbia University University of Minnesota, New York, N. Y. Minneapolis David T. Denhardt, Editor (1982) Edward M. Scolnick, Editor (1982) University of Western Ontario National Cancer Institute London, Ontario, Canada Bethesda, Md. David Baltimore (1981) Calderon Howe (1982) Dan S. Ray (1983) Amiya K. Banerjee (1982) Alice S. Huang (1981) M. E. Reichmann (1982) Kenneth I. Berns (1982) Tony Hunter (1983) Bernard E. Reilly (1983) David H. L. Bishop (1982) D. C. Kelly (1982) Wiliam S. Robinson (1983) David Botstein (1982) Thomas J. Kelly, Jr. (1982) Bernard Roizman (1982) Dennis T. Brown (1981) George Khoury (1981) Roland R. Rueckert (1982) Ahmad 1. Bukhari (1981) Jonathan A. King (1981) Norman P. Salzman (1981) Purnell Cboppin (1983) David W. Kingsbury (1982) Joseph Sambrook (1982) John M. Coffin (1983) Daniel Kolakofsky (1983) PrisciUa A. Schaffer (1981) Richard W. Compans (1982) Lloyd M. Kozboff (1982) Sondra Schlesinger (1983) Geoffrey M. Cooper (1981) Robert M. Krug (1983) June R. Scott (1983) Clive Dickson (1981) Robert A. Lazzarini 1981) Phillip A. Sharp (1982) Walter Doerfler (1983) Richard A. Lerner (1981) Aaron J. Shatkin (1982) Harrison Echols (1981) Myron Levine (1982) Saul J. Sllverstein (1982) Elvera Ehrenfeld (1983) Tomas Lindahl (1981) Lee D. Simon (1981) Robert N. Eisenman (1982) Douglas R. Lowy (1983) Kai Simons (1981) Suzanne U. Emerson (1983) Ronald B. Luftig (1981) Patrcia G. Spear (1981) Lynn Enquist (1981) Robert Martin (1981) Mark F. -
Capsid Structures, Variation and Flexibility. This Project Brings Together the Skills of Laboratories at Cornell University
Principal Investigator/Program Director (Last, first, middle): Parrish, Colin, R. Capsid structures, variation and flexibility. This project brings together the skills of laboratories at Cornell University and at Pennsylvania State University Medical Center to provide a detailed understanding of the roles of structural variation and flexibility in the parvoviral capsid, and their effects on receptor and antibody binding and the controls of cell infection and host range. These are fundamental problems that apply to all animal viruses, where the capsid must protect the genome in the environment, interact with host molecules including cell receptors and antibodies, and undergo a series of regulated structural transitions during cell entry to eventually release the genome for replication. Viral capsid binding to host receptors and antibodies can have varying and often unpredictable effects on infection, and those interactions also control many other replication steps. Where these virus-host interactions are specific they can control the viral host ranges. A model for understanding virus cell infection and host range control through differential receptor binding. We study two viruses that differ in host range due to 3 or 4 capsid protein mutations that control specific receptor binding. Canine parvovirus (CPV) arose around 1976 as a variant of feline panleukopenia virus (FPV), and caused a pandemic of disease during 1978 and 1979. That virus has continued to circulate worldwide as a serious canine pathogen, and has also evolved new antigenic, receptor binding, and host range variants. FPV and CPV both can bind the feline transferrin receptor 1 (TfR) to infect cat cells, and CPV gained the host range for dogs by gaining the ability to bind the canine TfR. -
Historical Overview 1
Historical Overview 1 Contents 1.1 Since When Have We Known of Viruses? ................................................ 3 1.2 What Technical Advances Have Contributed to the Development of Modern Virology? .......................................................................... 4 1.2.1 Animal Experiments Have Provided Important Insights into the Pathogenesis of Viral Diseases .................................................... 5 1.2.2 Cell Culture Systems Are an Indispensable Basis for Virus Research ........... 6 1.2.3 Modern Molecular Biology Is also a Child of Virus Research ................... 8 1.3 What Is the Importance of the Henle–Koch Postulates? .................................. 9 1.4 What Is the Interrelationship Between Virus Research, Cancer Research, Neurobiology and Immunology? .......................................................... 10 1.4.1 Viruses are Able to Transform Cells and Cause Cancer .......................... 10 1.4.2 Central Nervous System Disorders Emerge as Late Sequelae of Slow Viral Infections ........................................................................... 12 1.4.3 Interferons Stimulate the Immune Defence Against Viral Infections . .. .. .. .. 12 1.5 What Strategies Underlie the Development of Antiviral Chemotherapeutic Agents? . 13 1.6 What Challenges Must Modern Virology Face in the Future? .. ... ... ... ... ... ... ... ... 13 Further Reading ................................................................................... 14 1.1 Since When Have We Known of Viruses? “Poisons” were -
RNA Viruses of Amblyomma Variegatum and Rhipicephalus Microplus and Cattle Susceptibility in the French Antilles
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 12 December 2019 doi:10.20944/preprints201912.0172.v1 Peer-reviewed version available at Viruses 2020, 12, 144; doi:10.3390/v12020144 Article RNA viruses of Amblyomma variegatum and Rhipicephalus microplus and cattle susceptibility in the French Antilles Mathilde Gondard 1,2,#, Sarah Temmam 3,#, Elodie Devillers 1, Valérie Pinarello 2,4, Thomas Bigot 3,5, Delphine Chrétien 3, Rosalie Aprelon 2,4, Muriel Vayssier-Taussat 1, Emmanuel Albina 2,4, Marc Eloit 3,6* and Sara Moutailler 1* 1 UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, Maisons-Alfort, France; [email protected]; [email protected]; [email protected]; [email protected] 2 CIRAD, UMR ASTRE, F-97170 Petit-Bourg, Guadeloupe, France; [email protected]; [email protected]; [email protected] 3 Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, Paris, France; [email protected] ; [email protected] ; [email protected] ; [email protected] 4 ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France; [email protected]; [email protected]; [email protected] 5 Institut Pasteur – Bioinformatics and Biostatistics Hub – Computational Biology Department, Institut Pasteur, USR 3756 CNRS, Paris, France. 6 National Veterinary School of Alfort, Paris-Est University, Maisons-Alfort, 94704 Cedex, France. [email protected] # These authors contributed equally. * Correspondence: [email protected]; Tel.: +33 1 49 77 46 50; [email protected]; Tel.: +33 1 44 38 92 16 Abstract: Ticks transmit a wide variety of pathogens including bacteria, parasites and viruses. -
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.