Viruses Viruses Molecular Biology, Host Interactions, and Applications to Biotechnology Paula Tennant The University of the West Indies, Mona, Jamaica Gustavo Fermin Universidad de Los Andes, Me´rida, Venezuela Jerome E. Foster The University of the West Indies, St. Augustine, Trinidad Academic Press is an imprint of Elsevier 125 London Wall, London EC2Y 5AS, United Kingdom 525 B Street, Suite 1800, San Diego, CA 92101-4495, United States 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom Copyright r 2018 Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress ISBN: 978-0-12-811257-1 For Information on all Academic Press publications visit our website at https://www.elsevier.com/books-and-journals Publisher: John Fedor Acquisition Editor: Linda Versteeg-Buschman Editorial Project Manager: Pat Gonzalez Production Project Manager: Stalin Viswanathan Cover Designer: Mark Rogers Typeset by MPS Limited, Chennai, India Preface It is an exciting time to study virology! The world of viruses is much greater and more diverse than previously recognized. Discoveries such as the Mimivirus and its virophage, have stimulated new discussions on the defini- tion of viruses, their place in the current view of the tree of life, and their inherent and derived “interactomics” defined as the molecules and the pro- cesses by which virus gene products interact with themselves and with the host’s cellular gene products to bring about changes in phenotypes, and of their own evolution. Viruses are also facilitating the development and crea- tion of new materials and powerful tools for gene and genome engineering. However, viral diseases continue to plague us, our animals and crop plants; sadly, in the last decade, diseases such as SARS, H1N1 influenza, Nipah virus disease have wreaked havoc around the world as have Cassava Mosaic and Brown Streak virus diseases in Eastern and Southern Africa. Ebola, Chikungunya, and West Nile viruses have reemerged and the AIDS epidemic continues to sweep across sub-Saharan Africa and parts of Asia. This book explores several concepts fundamental to Virology. While most texts focus on the pathogenesis and clinical aspect of viral diseases or the molecular biology of viral replication, we present viruses not only as for- midable foes, but also as entities that can be beneficial to their hosts and humankind, and as entities that are helping to shape the Tree of Life. A com- plete overview of modern virology is intended, not a comprehensive or ency- clopedia treatment of these topics. It is hoped that this overview with sufficient documentation for more indepth study will be of value to anyone learning Virology at any stage; a novice trying to understand the basic prin- ciples for the first time, an intermediate student of Virology preparing to study more advanced areas in the discipline, or anyone who has ended their formal education, but has maintained an interest in the discipline. An ele- mentary knowledge of molecular biology is assumed, especially of the basic structures of nucleic acids and proteins, of the genetic code, and the pro- cesses involved in transcription and protein synthesis. The volume comprises 13 chapters. The first chapter provides a general introduction on the history of the discipline. Subsequent four chapters cover the basic aspects of virology including the structure of viruses, the organiza- tion of their genomes, and basic strategies in replication and expression. xv xvi Preface Principles are emphasized in these chapters, along with the diversity and ver- satility of viruses. The five chapters that follow examine virus examples, from a cross section of hosts, to illustrate the principles as well as the diver- sity of viruses, how they cause disease and how their hosts react to such dis- ease, exploring developments in the field of hostÀmicrobe interactions in recent years. We then explore the medical and agricultural importance of viruses and how viruses can be surprisingly beneficial to their hosts. The book is the product of a corporative effort. We wish to express our appreciation to all the contributing authors. We are especially grateful to members of the editorial team, Jill Leonard, Linda Versteeg-Buschman, Halima Williams, Joslyn Paguio, Pat Gonzalez, and Stalin Viswanathan, for providing support, feedback, and guidance during the process. Gratitude is extended to many of our colleagues for their advice and helpful discussions. Finally, we are indebted to all who have helped shape our careers over the years, especially our students. Paula Tennant, Gustavo Fermin, and Jerome E. Foster Chapter 1 Introduction: A Short History of Virology Gustavo Fermin1 and Paula Tennant2 1Universidad de Los Andes, Me´rida, Venezuela, 2The University of the West Indies, Mona, Jamaica [Physicists] feel that the field of bacterial viruses is a fine playground for seri- ous children who ask ambitious questions. Max Delbruck¨ As masterly expressed by the French microbiologist Andre´ Lwoff in his Nobel Lecture of 1965, “For the philosopher, order is the entirety of repeti- tions manifested, in the form of types or of laws, by perceived objects. Order is an intelligible relation. For the biologist, order is a sequence in space and time. However, according to Plato, all things arise out of their opposites. Order was born of the original disorder, and the long evolution responsible for the present biological order necessarily had to engender disorder. An organism is a molecular society, and biological order is a kind of social order. Social order is opposed to revolution, which is an abrupt change of order, and to anarchy, which is the absence of order. I am presenting here today both revolution and anarchy, for which I am fortunately not the only one responsible. However, anarchy cannot survive and prosper except in an ordered society, and revolution becomes sooner or later the new order. Viruses have not failed to follow the general law. They are strict parasites which, born of disorder, have created a very remarkable new order to ensure their own perpetuation.” In this introductory chapter, we present a short his- tory of the main breakthroughs in the history of virology along with some of the reasons why viruses are considered among the most intriguing and fasci- nating creations of nature. Viruses. DOI: https://doi.org/10.1016/B978-0-12-811257-1.00001-2 © 2018 Elsevier Inc. All rights reserved. 1 2 Viruses C332,652H492,388N98,245O131,196P7,501S2,340 The empirical formula, C332,652H492,388N98,245O131,196P7,501S2,340, represents the chemical composition of the poliovirus, a virus that has earned the rep- utation of being one of the world’s most feared pathogens. In most infec- tions this virus is limited to the alimentary tract but paralytic poliomyelitis occurs in less than 1% of cases when the virus enters the central nervous system and replicates in the motor neurons of the spinal cord. Describing the poliovirus as a formula portrays the virus as a chemical, a particle of high symmetry containing all the properties required for survival. Even so, one cannot recreate the virus by mixing all its components—even in exact amounts. At most, one could synthesize a template free, biologically mean- ingful array of logically ordered nucleotides based on prior knowledge— since a virus is more than a chemical entity, and an evolved product of biological information. Indeed viruses were first defined as simple entities, lacking the mechanisms necessary for metabolic function, consisting of a single type of nucleic acid encased in a protein coat. Since some virus par- ticles can form aggregates and bond to each other to form a crystal, viruses were considered as molecular, and not cellular, entities. Many defi- nitions of life, being based on the cellular theory, excluded viruses as liv- ing organisms. The recent discovery of a new group of virus species is, however, chal- lenging the classification of viruses as nonliving entities and has reignited debates on the definition of life. These viruses, designated as mimiviruses, were isolated in 1992 from a water sample collected in an air conditioning system during investigations of a pneumonia outbreak in England.