Reverse Genetics of RNA Viruses E-Book

Anne Bridgen

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 800

Veröffentlichungsjahr: 2012

Beschreibung

Reverse genetics, the genetic manipulation of RNA viruses to create a wild-type or modified virus, has led to important advances in our understanding of viral gene function and interaction with host cells. Since many severe viral human and animal pathogens are RNA viruses, including those responsible for polio, measles, rotaviral diarrhoea  and influenza infections, it is also an extremely powerful technique with important potential application for the prevention and control of a range of human and animal viral diseases.

Reverse Genetics of RNA Viruses provides a comprehensive account of the very latest developments in reverse genetics of RNA viruses through a wide range of applications within each of the core virus groups including; positive sense, negative sense and double stranded RNA viruses. Written by a team of international experts in the field, it provides a unique insight into how the field has developed, what problems are being addressed now and where applications may lead in the future. It will prove invaluable to bioscience, medical and veterinary students, those starting research in this area as well as other researchers and teachers needing to update their knowledge of this fast-moving field.

• An authoritative, comprehensive overview of reverse genetics in RNA Viruses.
• Includes numerous examples of cutting- edge applications of reverse genetics within each of the RNA viral groups. 
• Written by a team of international experts, including some of the leading researchers in the field.

Leseprobe

Contents

Cover

Title Page

Copyright

Dedication

List of Contributors

Acknowledgements

Chapter 1: Introduction

1.1 Background

1.2 Reverse genetics for different classes of genome

1.3 Methodology

1.4 Difficulties in establishing a reverse genetics system

1.5 Recent developments

1.6 Are there any boundaries for conducting reverse genetics?

Part I: Positive sense RNA viruses

Chapter 2: Coronavirus reverse genetics

2.1 The Coronavirinae

2.2 Infectious bronchitis

2.3 Coronavirus genome organisation

2.4 The coronavirus replication cycle

2.5 Development of reverse genetics system for coronaviruses including IBV

2.6 Reverse genetics system for IBV

2.7 Reverse genetics systems for the modification of coronavirus genomes

2.8 Using coronavirus reverse genetics systems for gene delivery

Acknowledgements

Chapter 3: Reverse genetic tools to study hepatitis C virus

3.1 Introduction: hepatitis C

3.2 Hepatitis C virus

3.3 Construction of infectious clones for hepatitis C virus

3.4 Study of HCV RNA replication in cell culture systems

3.5 Use of HCV replicons to study viral replication

3.6 Utility of replicons for drug screening

3.7 Development of the infectious cell culture systems for HCV

3.8 Construction of intergenotypic viral chimeras

3.9 Non-JFH1 derived genomes

3.10 Cell lines that support HCV replication

3.11 Study of HCV in physiologically more relevant cell culture systems

3.12 Animal models for HCV infection

3.13 Reverse genetics of clinically relevant HCV genotypes in vivo

3.14 Conclusion

Acknowledgments

Chapter 4: Calicivirus reverse genetics

4.1 Introduction

4.2 Feline calicivirus

4.3 Murine norovirus

4.4 Porcine enteric calicivirus

4.5 Rabbit haemorrhagic disease virus

4.6 Human norovirus

4.7 Conclusion

Acknowledgements

Part II: Negative sense RNA viruses

Chapter 5: Reverse genetics of rhabdoviruses

5.1 Introduction: the Rhabdoviridae family

5.2 Rhabdovirus reverse genetics

5.3 Applications and examples

5.4 Conclusion

Acknowledgements

Chapter 6: Modification of measles virus and application to pathogenesis studies

6.1 Introduction

6.2 Measles: the disease

6.3 Measles: the infectious agent

6.4 RNA synthesis: a tail of two processes

6.5 Transcription: starting, stopping, dropping off or starting again

6.6 From transcription to replication: the elusive switch

6.7 Getting in and getting out

6.8 Measles virus: reverse genetics

6.9 Future perspectives

Acknowledgements

Chapter 7: Bunyavirus reverse genetics and applications to studying interactions with host cells

7.1 Introduction: the family Bunyaviridae

7.2 Bunyavirus replication

7.3 History of bunyavirus reverse genetics

7.4 Minigenome systems for bunyaviruses

7.5 Virus-like particle production

7.6 Rescue systems for bunyaviruses

7.7 Application of reverse genetics to study bunyavirus replication

7.8 Outlook

Chapter 8: Using reverse genetics to improve influenza vaccines

8.1 Introduction

8.2 Influenza vaccines

8.3 The use of reverse genetics to generate recombinant influenza A, B and C viruses

8.4 Using reverse genetics technology for generation of pandemic virus vaccine

8.5 Other strategies for generating live attenuated vaccines based on viruses engineered by reverse genetics

8.6 Strategies to improve the safety or yield of influenza vaccines

8.7 Improvements to the PR8 high growth strain

8.8 Improving the immunogenicity by engineering recombinant viruses that express cytokine genes

8.9 Novel species-specific attenuation that takes advantage of microRNAs

8.10 Conclusion

Part III: Double-stranded RNA viruses

Chapter 9: Bluetongue virus reverse genetics

9.1 Introduction to Bluetongue virus

9.2 Bluetongue virus replication

9.3 Reverse genetics

9.4 Uses of reverse genetics in orbivirus research

9.5 Future perspectives

Chapter 10: Genetic modification in mammalian orthoreoviruses

10.1 Introduction

10.2 Forward-genetics in orthoreoviruses

10.3 Reovirus/cell interactions

10.4 Reverse-genetics in orthoreoviruses

10.5 Reovirus as an oncolytic agent

10.6 Conclusion

Part IV: Recent and future developments

Chapter 11: Reverse genetics and quasispecies

11.1 Definition of quasispecies and evidence

11.2 Reverse genetics and RNA virus population heterogeneity: consensus is always a compromise

11.3 Examples of the use of the theory to disable or manipulate the quasispecies under controlled environments

11.4 Future prospects of virus population genetics and reverse genetics

11.5 Conclusion

Chapter 12: Summary and perspectives

12.1 Introduction

12.2 Analysis of the role of specific non-coding sequence motifs involved in replication, transcription, polyadenylation and packaging

12.3 Analysis of the roles of viral proteins

12.4 Analysis of virus–host interactions at a global level

12.5 Understanding the basis of pathogenicity

12.6 Real-time virus imaging in vitro and in vivo

12.7 Structure-function analysis of viruses and viral domains

12.8 Vaccine generation

12.9 Drug development

12.10 Gene delivery and knock-out in plant cells including virus-induced gene silencing (VIGS)

12.11 Gene delivery in arthropod and mammalian cells

12.12 Development of oncolytic virus and adaptation to this purpose

12.13 Personal highlights and future directions

Plates

Index

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Library of Congress Cataloging-in-Publication Data

Reverse genetics of RNA viruses : applications and perspectives / [edited by] Anne Bridgen. p. ; cm. Includes bibliographical references and index. ISBN 978-0-470-97965-5 (cloth) I. Bridgen, Anne, 1961– [DNLM: 1. RNA Viruses–genetics. 2. Reverse Genetics–methods. 3. RNA, Viral–genetics. 4. Viral Proteins–genetics. 5. Viral Vaccines. QW 168] 579.2′5–dc23 2012016778

A catalogue record for this book is available from the British Library.

Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books.

Cover design: Gary Thompson

First Impression 2013

I would like to dedicate this book to Professor Sir Kenneth Murray, FRS, FRSE, for his mentoring during the course of my PhD and his introduction to the powerful world of molecular biology.

Ken, you were an inspiration in the way in which you searched out important issues in science and tackled them, no matter how insurmountable the obstacles. Your groundbreaking work on the manipulation of hepatitis B virus and early development of an effective and safe vaccine has been much of the inspiration to my work in this field, and I thank you for this.

List of Contributors

Maria Armesto, Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Newbury, UK

Wendy S. Barclay, Department of Medicine, Imperial College London, UK

Kirsten Bentley, Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Newbury, UK

Erica Bickerton, Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Newbury, UK

Antonio V. Borderia, Institut Pasteur, Paris, France

Mark Boyce, Institute for Animal Health, Pirbright Laboratory, Pirbright, UK

Anne Bridgen, Croft Dhu, Newtonmore, Inverness-shire, UK

Paul Britton, Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Newbury, UK

Karl-Klaus Conzelmann, Max von Pettenkofer Institute and Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany

Iris J.C. Dautzenberg, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands

W. Paul Duprex, Department of Microbiology, Boston University, School of Medicine and National Emerging Infectious Disease Laboratories, Boston, USA

Ruth A. Elderfield, Department of Medicine, Imperial College London, UK

Richard M. Elliott, Biomedical Sciences Research Complex, School of Biology, University of St Andrews, UK

Alexander Ghanem, Max von Pettenkofer Institute and Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany

Ian Goodfellow, Section of Virology, Department of Medicine, Imperial College London, UK

Lorian C.S. Hartgroves, Department of Medicine, Imperial College London, UK

Rob C. Hoeben, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands

Sarah Keep, Avian Viral Diseases, Institute for Animal Health, Compton Laboratory, Newbury, UK

Alexander Ploss, Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, USA

Linda J. Rennick, Department of Microbiology, Boston University, School of Medicine and National Emerging Infectious Disease Laboratories, Boston, USA

Peter A.E. Sillevis Smitt, Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands

Sanne K. van den Hengel, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden and Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands

Diana J.M. van den Wollenberg, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands

Marco Vignuzzin Institut Pasteur, Paris, France

Acknowledgements

I wish to thank all those who have participated in the planning and execution of this book. First and foremost to my publishing editor at Wiley, Nicky McGirr, for her support and encouragement in the planning stages of the book. Also to my writing editor Fiona Woods (Seymour) for her answering of endless questions and guidance along the way.

Thanks are due for the constructive criticism of those who refereed the book outline. Several suggestions made at this stage have been incorporated and have improved the final book.

Huge thanks are due to the chapter authors for giving their precious time to describe their viral system. This volume could not have been written without you so thanks indeed.

I also thank my many research colleagues in reverse genetics, most particularly Professor Richard Elliott in whose laboratory I first worked in reverse genetics and his group in Glasgow (now St Andrews), but also all those with whom I shared trials and tribulations, as well as successes, at meetings and seminars.

I thank my current colleagues and students, particularly Dr Michael Baron at the Institute of Animal Health, Pirbright and my doctoral student Mr Siddharth Bakshi at the University of Ulster for their patience while I was writing this book. And to Dr Michael Baron and Professor Rachel Fearns, Boston University School of Medicine, for proof reading my chapters (the introduction and perspectives chapters).

It has taken a lot longer and been a lot more work than I anticipated, and so I particularly thank my husband Dr Ian Bradbury for his support during the prolonged writing and editing, and his forbearance when I decided that writing in Chamonix was preferable to writing at home! Thank you, all of you.

1

Introduction

Anne Bridgen

Croft Dhu, Newtonmore, Inverness-shire, Scotland

1.1 Background

Viruses with ribonucleic acid (RNA) genomes make up many of our current most serious human pathogens. For example, influenza A virus, poliovirus, rotaviruses, dengue virus, hepatitis C virus, West Nile fever virus, yellow fever virus and measles virus are all RNA viruses, and are between them responsible for millions of human deaths each year. Rotaviruses alone are responsible for around 350,000–600,000 infant deaths each year from diarrhoea (Parashar et al., 2003). One of the features of RNA viruses is that the viral polymerase responsible for their replication is not very accurate as there is no proof-reading capacity. This low accuracy means that, in the presence of antiviral drugs, viral escape mutants soon arise which no longer respond to the drug. There are thus very few effective antivirals directed against RNA viruses. In addition, many of the new emerging viruses which arise through viral mutation, genome segment reassortment or host switching to suddenly enter the human population are RNA viruses. These include the coronavirus severe acute respiratory syndrome (SARS) virus, Ebola and Marburg filoviruses, and avian and swine flu, and are the viruses that tend to cause the highest mortality rates. There is thus a high requirement to be able to analyse these viruses and to develop effective vaccines and antivirals.

RNA viruses possess several different types of RNA genomes. Some have a non-segmented genome, or the genome can be split into a number of different segments, for example, 2 for arenaviruses, 3 for bunyaviruses, 7–8 for influenza viruses and 10–12 for reoviruses. In addition, they can comprise positive sense, negative sense or ambisense RNA, and be either single- or double-stranded. Positive sense RNAs can be translated directly into protein, while a negative sense RNA has first to be transcribed by the viral proteins to form positive stranded RNA that can be translated. Ambisense RNAs are those which contain genes running in both orientations within the same genome or genome segment. There are also retroviruses and hepadnaviruses which go through both RNA and deoxyribonucleic acid (DNA) phases via reverse transcription of their RNA. These last named groups of viruses, which include the human immunodeficiency viruses, will not be discussed in this volume despite their importance, as the amount of research in this area would easily require a separate volume.

In classical genetics, the specific genes in an organism were deduced from observations of the phenotype of the organism. Reverse genetics is a term coined to describe processes where information flows in the opposite direction, that is, the gene is determined or altered directly, and the resultant phenotype observed. In the context of virology, this then refers to changes introduced directly into the complementary DNA (cDNA) used to generate infectious RNA virus or virus-like particles, in order to study the function of specific gene sequences and proteins, and the term has come to be applied to the ability to go from a DNA copy of the viral genome to a new virus. Neumann and Kawaoka (2004) define reverse genetics as the generation of a virus entirely from cDNA. It is an incredibly powerful tool both for the generation of modified viruses, which can act as vaccines or vectors, and for the analysis of viral genes and non-coding sequences.

1.2 Reverse genetics for different classes of genome

One of the most definitive ways in which to study the roles of specific sequences in viral genomes is to modify them and to generate infectious virus, that is, to ‘rescue’ the virus, from these modified sequences. For DNA viruses this was relatively straightforward once molecular biological techniques became sufficiently sophisticated to allow this, as the DNA could be introduced directly into cells to generate infectious virus. Thus, infectious T2 bacteriophage was rescued from DNA as early as 1957 (Fraser et al., 1957). The first RNA virus to be rescued from its cDNA was the bacteriophage Qbeta rescued by Taniguchi et al. (1978), while the first mammalian plus stranded RNA virus to be rescued was poliovirus by Racaniello and Baltimore (1981). Researchers subsequently discovered that this process was more efficient if the RNA was transcribed in vitro and the nascent RNA transfected into cells (Boyer and Haenni, 1994); this process was then applied to many plus sense RNA viruses. Some difficulties were encountered with specific families of viruses, however, such as coronaviruses, as is discussed in Section 1.4.

Negative sense RNA viruses proved less amenable to such studies as the minimal infectious unit comprises the viral RNA encapsidated by the nucleocapsid and replication proteins to form a ribonucleoprotein (RNP) complex. It was not until 1994 that Schnell et al. (1994) succeeded in rescuing the first negative sense RNA virus, the rhabdovirus rabies virus, from cDNA. One of the main reasons for this breakthrough was the decision to transfect cells with cDNA plasmids encoding the viral antigenome rather than the genome. This meant that there was less negative sense RNA present in the cell which could hybridise to the positive sense viral mRNAs and thus induce host innate immune responses.

Figure 1.1 How rescue is achieved.

To add to the difficulties of rescuing negative sense RNA viruses from cDNA, many of them comprise segmented genomes, so, for their rescue, cells must be transfected with constructs for each of the genome segments as well as for the replication proteins. Early rescue experiments for the eight-segmented genome virus influenza A virus involved modification of single RNA segments and use of helper viruses (Luytjes ., 1989; Enami ., 1990). However, this is not an efficient process as only a small proportion of the helper viruses acquires the novel segment. The first segmented, negative sense RNA virus to be rescued entirely from cDNA was the tri-segmented bunyavirus Bunyamwera virus (Bridgen and Elliott, 1996). This used the approach initiated for the non-segmented rabies virus in using positive sense, antigenomic constructs for rescue. Rescue of influenza A virus entirely from cDNA followed later (Fodor ., 1999; Neumann ., 1999), in a procedure involving transfection of cells with 12 different plasmids. This original technique has been modified extensively and now rescue can be achieved using far fewer plasmids.