Tai Lieu Chat Luong Principles and Applications Contents Preface to Second Edition Preface to First Edition Abbreviations Used in This Book Greek Letters Used i n This Book Color Coding for Molecules Chapter 1: Viruses and Their Importance Viruses are Ubiquitous on Earth 1.2 Reasons for Studying Viruses 1.3 The Nature of V iruses 1.4 The Remainder of the Book Learning Outcomes Sources of Further Information Chapter 2: Methods Used in Virology 2.1 Introduction to Methods Used in Virology 2.2 Cultivation of Viruses 2.3 Isolation of Viruses 2.4 Centrifugation 2.5 Structural Investigations of Cells and Virions 2.6 Electrophoretic Techniques 2.7 Detection of Viruses and Virus Components 2.8 Infectivity Assays Virus Genetics 2.10 Investigation of ProteinslJ"Protein Interactions Learning Outcomes Sources of Further Information Chapter 3: Virus Structure Introduction to Virus Structure 3.2 Virus Genomes 3.3 Virus Proteins 3.4 Capsids 3.5 Virion Membranes 3.6 Occlusion Bodies 3.7 Other Virion Components Learning Outcomes Sources of Further Information Chapter 4: Virus Transmission Introduction to Virus Transmission 4.2 Transmission of Plant Viruses 4.3 Transmission of Vertebrate Viruses 4.4 Transmission of Invertebrate Viruses 4.5 Permissive Cells Learning Outcomes Sources of Further Information Chapter : Attachment and Entry of Viruses into Cells 5.1 Overview of Virus Replication 5.2 Animal Viruses 5.3 Bacteriophages Learning Outcomes Sources of Further Information Chapter 6: Transcription, Translation, and Transport Introduction to Transcription, Translation, and Transport 6.2 Transcription of Virus Genomes 6.3 Transcription in Eukaryotes 6.4 Translation in Eukaryotes 6.5 Transport of Molecules in Eukaryotic Cells 6.6 Transcription and Translation in Bacteria Learning Outcomes Sources of Further Information Chapter : Virus Genome Replication Overview of Virus Genome Replication 7.2 Locations of Virus Genome Replication in Eu karyotic Cells Initiation of Genome Replication Polymerases 7.5 DNA Replication Double-Stranded RNA Replication 7.7 Single-Stranded RNA Replication 7.8 Reverse Transcription Learning Outcomes Sources of Further Information Chapter : Assembly and Exit of Virions from Cells Introduction to Assembly and Exit of Virions from Cells 8.2 Nucleocapsid Assembly 8.3 Formation of Virion Membranes 8.4 Virion Exit From the Infected Cell Learning Outcomes Sources of Further Information Chapter : Outcomes of Infection for the Host Introduction to Outcomes of Infection for the Host 9.2 Factors Affecting Outcomes of Infection 9.3 Non-Productive Infections 9.4 Productive Infections Learning Outcomes Sources of Further Information Chapter 10: Classification andl Nomenclature of Viruses 10 Hi story of Virus Classification and Nomenclature 10.2 Modern Virus Classification and Nomenclature 10.3 Baltimore Classification of Viruses Learning Outcomes Sources of Further Information Chapter 11: Herpesviruses (and Other dsDNA Viruses) 1 Introduction to Herpesviruses 1 The Human Herpesviruses 1 The Herpesvirus Virion 11.4 HSV-1 Genome Organization 1 HSV-1 RepI ication 1 Latent Herpesvirus Infection 11.7 Other dsDNA Viruses Learning Outcomes Sources of Further Information Chapter 12: Parvoviruses (and Other ssDNA Viruses) 12.1 Introduction to Parvoviruses 12.2 Examples of Parvoviruses 12.3 Parvovirus Virion 12.4 Parvovirus Replication 12.5 Other ssDNA Vi ruses Learning Outcomes Sources of Further Information Chapter 13: Reoviruses (and Other dsRNA Viruses) 13.l Introduction to Reoviruses 13.2 Rotavirus Virion 13.3 Rotavirus Repl ication 13.4 Other dsRNA Viruses Learning Outcomes Sources of Further Information Chapter 14: Picornaviruses (and Other Plus-Strand RNA Viruses) 14 Introduction to Picornavi ruses 14.2 Some Important Picornaviruses 14.3 Picornavirus Virion 14.4 Picornavirus Replication 14.5 Picornavirus Recombination 14.6 Picornavirus Experimental Systems 14.7 Other Plus-Strand RNA Vi ruses Learning Outcomes Sources of Further Information Chapter 15: Rhabdoviruses (and Other Minus-Strand RNA Viruses) 15 Introduction to Rhabdoviruses 15.2 Some Important Rhabdoviruses 15.3 The Rhabdovirus Virion and Genome Organization 15.4 Rhabdovirus Replication 15.5 Other Minus-Strand RNA Viruses and Viruses with Ambisense Genomes 15.6 Reverse Genetics Learning Outcomes Sources of Further Information Chapter 16: Influenza Virus 16.1 Introduction to Influenza Viruses 16.2 The Influenza Virion 16.3 Influenza A Virus Replication 16.4 Importance of Influenza Viruses 16.5 Reverse Genetics Learning Outcomes Sources of Further Information Chapter 17: Retroviruses 17 Introduction to Retrovi ruses 17.2 Retrovirus Virion 17.3 Retrovirus Replication 17.4 Examples of Retroviruses 17.5 Retroviruses as Gene Vectors 17 Endogenous Retroviruses Learning Outcomes Sources of Further Information Chapter 18: Human Immunodeficiency Viruses 18.1 Introduction to HIV 18.2 HIV Virion 18.3 HIV Genome 18.4 HIV-1 Replication 18.5 HIV-1 Variability 18.6 Progression of HIV Infection 18.7 Prevention of HIV Transmission Learning Outcomes Sources of Further Information Chapter 19: Hepadnaviruses (and Other Reverse-Tra nscribing DNA Viruses) 19.1 Introduction to Hepadnaviruses 19.2 Importance of HBV 19.3 HBV Virion 19.4 Non-Infectious Particles 19.5 Soluble Virus Protein 19.6 HBV Genome 19.7 HBV Genetic Groups 19.8 HBV Replication 19.9 Prevention and Treatment of HBV Infection 19.10 Other Reverse-Tra nscri bing DNA Viruses Learn ing Outcomes Sources of Further Information Chapter 20: Bacterial Viruses 20.1 Introduction to Bacterial Viruses ( Bacteriophages) 20.2 Single-Stranded RNA Phages 20.3 Double-Stranded RNA Phages 20.4 Single-Stranded DNA Phages 20.5 Double-Stranded DNA Phages Learning Outcomes Sources of Further Information Chapter : Origins and Evolution of Viruses Introduction to Origins and Evolution of Viruses 21.2 Origins of Viruses 21.3 Evolution of Viruses Learning Outcomes Sources of Further Information Chapter 22: Emerging Viruses 22.1 Introduction to Emerging Viruses 22.2 Viruses in New Host Species 22.3 Viruses in New Areas 22.4 Viruses in New Host Species and in New Areas 22.5 New viruses 22.6 Recently Discovered Viruses 22 Re-Emerging Viruses 22.8 Virus Surveil lance 22.9 Dealing with Outbreaks Learning Outcomes Sources of Further Information Chapter 23: Viruses and Cancer 23 Introduction to Viruses and Cancer 23.2 Papillomavi rus-Linked Cancers 23.3 Polyomavirus-Linked Cancers 23.4 Epsteinsl.>"Barr Virus-Linked Cancers 23.5 Kaposisl.>™s Sarcoma 23.6 Adult T Cell Leukemia 23.7 Hepatocellular Carcinoma 23.8 Virus-Associated Cancers in Animals 23.9 Cell Lines Derived From Virus-Associated Cancers 23 How Do Viruses Cause Cancer? 23 1 Prevention of Virus-Induced Cancers Learning Outcomes Sources of Further Information Chapter 24: Survival of Infectivity 24.1 Preservation of Virus Infectivity 24.2 Destruction of Virus Infectivity 24.3 Inactivation Targets in Virions 24.4 Inactivation Kinetics 24 Agents that Inactivate Virus Infectivity Learning Outcomes Sources of Further Information Chapter 25: Virus Vaccines 25 Introduction to Virus Vaccines 25.2 Live Attenuated Virus Vaccines 25.3 Inactivated Virus Vaccines 25.4 Virion Subunit Vaccines 25.5 Live Recombinant Virus Vaccines 25.6 Mass-Production of Viruses for Vaccines 25.7 Virus-Like Particles 25.8 Synthetic Peptide Vaccines 25.9 DNA Vaccines 25 10 Storage and Transport of Vaccines Learning Outcomes Sources of Further Information Chapter 26: Anti-viral Drugs 26.1 Introduction to Anti-viral Drugs 26.2 Development of Anti-viral Drugs 26.3 Examples of Anti-viral Drugs 26.4 Drug Resistance 26.5 Anti-vi l Drug Research Lea rn i ng Outcomes Sou rces of Fu rther Information Chapter 27: Pri ons 27 l Introd uction to Prions 27.2 Tra nsm issi ble Spongiform Encephal opathies 27 The Nature of Prions 27.4 Pri on Di seases 27.5 Pri on Stra i ns 27 Pri on Tra nsm i ssion 27 The Protei n-Only Hypothesis Lea rn i ng Outcomes Sou rces of Fu rther Informati on Vi rologistss1> Vocabulary TM Index VIROLOGY PRINCIPLES AND APPLICATIONS John B Carter and Venelia A Saunders [S ormRG] ET I h33 KATI TPB I y This edition first published 2013 by John Wiley & Sons Ltd Copyright © 2013, 2007 John Wiley & Sons Ltd Cover image: Glass Sculpture of HIV virus courtesy of Wellcome Images All effo rt has been made to trace and acknowledge ownership of copyright The publisher would be glad to hear from any copyright holders whom it has not been possible to contact Registered office John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, P019 8SQ, United Kingdom For details of our global editorial offices, for customer services, and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com The rights of John Carter and Venetia Saunders to be identified as the authors of this work has been asserted in accordance with the U K Copyright, Designs and Patents Act 1988 All rights reserved No part of this publication may be reprod uced, stored in a retrieval syste m , or transm itted, in any form o r by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher Wiley publishes in a variety of print and electronic formats and by print-on-demand Some material included with standard print versions of this book may not be included i n e-books or in print-on-demand If this book refers to media such as a CD or DVD that is not included in the version you purchased, you may download this material at http ://books upport.wiley.com For more information about Wiley products, visit www.wiley.com Designations used by companies to distinguish their products are often claimed as trademarks All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners The publisher is not associated with any product or vendor mentioned in this book This p u blication is designed to provide accurate and authoritative information in regard to the subject matter covered It is sold on the understanding that the publisher is not engaged in rendering professional services If professional advice or other expert assistance is req u i red, the services of a com petent professiional should be sought Library of Congress Catalog ing-in-Pu blication Data Carter, John B., 1944Virology : principles and applications / John Carter, Venetia Saunders - 2nd ed p.; cm Includes bibliographical references and index ISBN 978-1-119-99 143-4 (cloth) - ISBN 978- 1-1 19-99142-7 (pbk.) human Merkel cell monkey structure polyphage polyprotein HIV picornavirus retrovirus polypurine tract, retrovirus HIV polyribonucleotidyl transferase porcine circovirus portal herpesvi rus positive effector of transcription positive-strand RNA viruses, see plus-strand RNA viruses post-transcriptional gene silencing, see RNA silencing post-translational modification of proteins hepatitis B virus influenza virus picornavirus retrovirus rhabdovirus rotavirus post-transplant lymphoproliferative disorder potato virus X potato virus Y transmission potato yellow dwarf virus Potyviridae potyvirus, helper-component proteinase Poxviridae poxvirus capping enzymes envelope formation PPT, see polypurine tract prairie dog pRb pre-integration complex, retrovirus HIV pregenome, hepadnavirus Pribnow box primary effusion lymphoma primase primer hepatitis B virus influenza virus picornavirus retrovirus primer binding site prions protein-only hypothesis replication species barrier strain transmission PRNP gene probe, DNA procapsid herpesvi rus parvovirus picornavirus processivity factor productive infection programmed cell death prohead promoter bacterial eukaryote hepatitis B virus phage T4 phage O» retrovirus proofreading prophage protease cell HIV picornavirus retrovirus protease inhibitor protein-only hypothesis proteins, virus nomenclature proto-oncogene provirus, retrovirus HIV Pr Pc PrPres PrPSc Prusiner, Stanley pseudoknot Pteropus quasi-equivalence theory quasispecies quaternary ammonium compound rabies vaccine rabies virus M protein transmission raltegravir re-emerging viruses read-th rough protein real-time PCR reassortant influenza virus rotavirus reassortment receptor recombinant picornavirus vaccinia virus recombination phage T2 picornavirus template switching mechanism Reed, Walter Reed-Muench method Reoviridae genera phylogenetic tree reoviruses repeat sequences herpes simplex virus replicase replication compartments replication complex, picornavi rus replication origin replicative form replicative intermediate picornavirus rhabdovirus single-stranded RNA phage reservoir Marburg and Ebola viruses rabies virus resistance to anti-viral drugs respiratory syncytial virus treatment of infection vaccines restriction system retinobl astoma protein, see pRB retrotra nsposi ti on retrotransposon Retroviridae retrovirus assembly budding capsid (CA) protein endogenous env gene gag gene gene vectors genome genome replication matrix (MA) protein nucleocapsid ( NC) protein oncogene packaging signal pol gene recombination replication structure surface (SU) prote in transcription translation transmembrane (TM) protein Rev response element reverse genetics influenza virus minus-strand RNA viruses plus-strand RNA vi ruses vaccine reverse transcriptase hepatitis B virus inhibitors molecular biology applications retrotra nsposon retrovirus reverse transcription error rate hepatitis B virus HIV retrotransposon retrovirus reverse transcription complex, retrovirus HIV reverse transcription-polymerase chain reaction, see RT-PCR RF, see replicative form Rhabdoviridae rhabdovirus assembly budding fish genome genome replication glycoprotein (G) host gene inhibition intergenic sequence large protein (L) matrix protein (M) nucleoprotein (N) phosphoprotein (P) plant replication replicative intermediate RNA polymerase structure transcription translation rhinovirus caps id receptors serotypes rho factor RI, see replicative intermediate ribavirin ribonuclease H hepatitis B virus retrovirus ribosomal frameshift HIV retroviruses ribosomal subunits eukaryotic prokaryotic ribozyme rice dwarf virus, transmission rice tungro bacilliform virus rinderpest RISC ritonavir RNA in DNA viruses RNA interference ( RNAi) RNA phage RNA polymerase see also DNA-dependent RNA polymerase see also RNA-dependent RNA polymerase RNA polymerase II RNA replication picornavirus rhabdovirus rotavirus single-stranded RNA phages RNA silencing RNA triphosphatase RNA-dependent RNA polymerase influenza virus picornavirus rhabdovirus rotavirus RNA-induced silencing complex RNase H, see ribonuclease H rolling circle DNA replication herpesvirus DNA phages rolling hairpin DNA replication rooted phylogenetic tree rotavirus disease double-layered particle replication RNA polymerase stability structure transcription translation triple-layered particle vaccines Rous sarcoma virus oncogene Rous, Peyton RRE RT-PCR SARS coronavirus West Nile virus rubella virus transmission ryegrass mosaic virus, transmission Sabin, Albert Salk, Jonas Sanger, Fred sarcoma SARS SARS coronavirus genome satellite tobacco mosaic virus, capsid satellite tobacco necrosis virus satellite virus dependovirus scaffolding protein herpesvi rus phage T4 phage ntX174 scrapie atyp ical SDS-PAGE rotavirus RNA secondary structure of nucleic acid Secoviridae seed-transmitted viruses segmented genome ambisense RNA viruses bunyavi ruses influenza virus us-strand RNA viruses plus-strand RNA vi ruses reassortment reoviruses tobacco rattle virus selectivity index self-assembly of virion self-priming of DNA replication semi -conservative replication double-stranded DNA double-stranded RNA Semliki Forest virus sequencing genomes SARS coronavirus serotype severe acute respiratory syndrome sex pilus sexual transmission Shiga toxin Shine-Dalgarno sequence shingles sialic acid sigma factor sigma replication of DNA sign of disease signal sequence simian foamy virus simian immunodeficiency virus phylogenetic tree simian virus endocytosis T antigen simple retroviruses Sin Nom bre virus single-stranded DNA binding protein single-stranded DNA phage single-stranded RNA phage Min Jou (MJ) interaction replicase replication cycle van Duin (VD) interaction single-stranded RNA replication Siphoviridae SIV, see simian immunodeficiency virus slippery sequence smallpox vaccination virus Soc Southern blotting species (taxonomic group) spike, envelope herpesvi rus influenza virus HIV rhabdovirus spliced transcript HIV influenza A virus parvovirus retrovirus split gene Spongospora subterranea spraing Spumavirus squamous cell carcinoma steps in virus replication sterilization stomatitis storage of viruses structure of viruses subclinical infection subfamily (taxonomic group) subgenomic messenger RNAs superinfection immunity suppressor transfer RNA surveillance of virus disease swine flu SV40, see simian virus symmetry helical icosahedral symptom, definition syncytium T even phage T lymphocyte (T cell) HIV infection T7 DNA polymerase Tl RNA polymerase tailed phage TAR element TATA box Tax protein taxonomic groups TCIDSO tectivirus DNA replication genome tegument temperate phage Tenuivirus term inally redundant terminase tetherin theta replication of DNA thymidine kinase cell herpesvi rus thymine dimer tick-borne encephalitis virus tick vectors tobacco necrosis satellite virus, genome tobacco mosaic virus assembly genome structure transport through plasmodesmata tobacco rattle virus Tobamovirus Tobravirus tobravirus transmission Togaviridae Toll-like receptor tomato mosaic virus tomato yellow leaf curl virus, transmission Tombusviridae tombusvirus P19 protein torque teno virus transactivation response element transcriptase see also reverse transcriptase transcription bacterial eukaryotic hepatitis B virus herpesvi rus HIV influenza virus initiation parvovirus phage T4 phage T7 picornavirus retrovirus rhabdovirus rotavirus termination transcription factor transcription factor IID (TFIID) transduction transfection transfer RNA in retrovirus virion transformation transgenic mice translation bacterial eu karyotic hepatitis B virus herpesvi rus HIV influenza virus initiation parvovirus picornavirus retrovirus rhabdovirus rotavirus translational coupling transmissible spongiform encephalopathy transmission electron microscope transmission of prions transmission of viruses bluetongue virus chikungunya virus filoviruses Hendra virus hepatitis B virus HIV invertebrate viruses Nipah virus plant vi ruses vertebrate viruses West Nile virus transovarial transmission transport of proteins in cells influenza virus transposition transposon Trichodoridae triple-layered particle, rotavirus turnip crinkle virus, capsid turnip yellow mosaic virus Twort, Frederick U3 sequence US sequence ultraviolet radiation, effect on i nfectivity uncoating unrooted phylogenetic tree uridylylation of poliovirus VPg vaccination wild mammals vaccines contamination DNA hepatitis B virus HIV human papillomavirus inactivated influenza live, attenuated Mareksn™s disease virus MMR peptide poliovirus preservation quality control recombinant subunit virus-like particle virus production vaccinia virus recombinant variant Creutzfeldt-Jakob disease (vOD) varicella varicella-zoster virus variola virus vector transmission of viruses see also cloning vector see also gene vector Vero cells vertical transmission plant vi ruses vertebrate viruses invertebrate viruses vesicular stomatitis virus budding phosphoprotei n Vesiculovirus viremia HIV see also blood, virus in virion assembly definition detection size structure virological synapse viroplasm virulence virulence factor, bacterial vi rul ent phage vi rus defi n ition vi rus replication, overview vi rus- l i ke particle VPg (vi rus p rotei n, genome l i n ked ) wal leye dermal sarcoma vi rus wart water treatment Watson, James West N i l e virus western blotti ng white clover cryptic vi rus whitefly vectors wi nter vom iting disease woodchuck hepatitis vi rus Worl d H ealth Organization X-linked severe com b i ned i m m unodeficiency (X-SCID) X-ray crystal llog raphy yeast two-hybrid system yel low fever virus buddi ng structure transmission vacci ne zidovud ine zinc fi nger Zi nder, N orton zoster