Viral Genomes – Molecular Structure, Diversity, Gene Expression Mechanisms and Host-Virus Interactions Edited by Maria Laura Garcia and Víctor Romanowski potx

VIRAL GENOMES –
MOLECULAR STRUCTURE,
DIVERSITY, GENE
EXPRESSION MECHANISMS
AND HOST-VIRUS
INTERACTIONS

Edited by Maria Laura Garcia
and Víctor Romanowski
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Viral Genomes – Molecular Structure, Diversity, Gene Expression Mechanisms and
Host-Virus Interactions
Edited by Maria Laura Garcia and Víctor Romanowski

Published by InTech
Janeza Trdine 9, 51000 Rijeka, Croatia

Copyright © 2012 InTech
All chapters are Open Access distributed under the Creative Commons Attribution 3.0
license, which allows users to download, copy and build upon published articles even for
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As for readers, this license allows users to download, copy and build upon published
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Notice
Statements and opinions expressed in the chapters are these of the individual contributors
and not necessarily those of the editors or publisher. No responsibility is accepted for the
accuracy of information contained in the published chapters. The publisher assumes no
responsibility for any damage or injury to persons or property arising out of the use of any
materials, instructions, methods or ideas contained in the book.

Publishing Process Manager Romina Krebel
Technical Editor Teodora Smiljanic
Cover Designer InTech Design Team

First published February, 2012
Printed in Croatia

A free online edition of this book is available at www.intechopen.com
Additional hard copies can be obtained from

Viral Genomes – Molecular Structure, Diversity, Gene Expression Mechanisms
and Host-Virus Interactions, Edited by Maria Laura Garcia and Víctor Romanowski
p. cm.
ISBN 978-953-51-0098-0

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Contents
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Preface IX
Part 1 Virus Genomes Organization and Functions 1
Chapter 1 The Baculoviral Genome 3
M. Leticia Ferrelli, Marcelo F. Berretta, Mariano N. Belaich,
P. Daniel Ghiringhelli, Alicia Sciocco-Cap and Víctor Romanowski
Chapter 2 Nudivirus Genomics and Phylogeny 33
Yongjie Wang, Olaf R.P. Bininda-Emonds, and Johannes A. Jehle
Chapter 3 Foot and Mouth Disease Virus Genome 53
Consuelo Carrillo
Chapter 4 Ophioviruses: State of the Art 69
Maria Laura Garcia
Part 2 Regulation of Viral Replication and Gene Expression 89
Chapter 5 Ribosomal Frameshift Signals in Viral Genomes 91
Ewan P. Plant
Chapter 6 Cis–Acting RNA Elements of
Human Immunodeficiency Virus 123
Mario P.S. Chin
Chapter 7 Hepatitis B Virus X Protein:
A Key Regulator of the Virus Life Cycle 141
Julie Lucifora and Ulrike Protzer

Part 3 Genomic Sequence Diversity and Evolution 155
Chapter 8 Application of a Microarray-Based Assay
for the Study of Genetic Diversity of West Nile Virus 157
Andriyan Grinev, Zhong Lu, Vladimir Chizhikov and Maria Rios
VI Contents

Chapter 9 Microarray Techniques for Evaluation of
Genetic Stability of Live Viral Vaccines 181
Majid Laassri, Elena Cherkasova, Mones S. Abu-Asab
and Konstantin Chumakov
Chapter 10 Inter- and Intra-Host Evolution of Dengue
Viruses and the Inference to the Pathogenesis 195
Day-Yu Chao
Part 4 Host-Virus Interactions 217
Chapter 11 Flavivirus Neurotropism, Neuroinvasion, Neurovirulence
and Neurosusceptibility: Clues to Understanding
Flavivirus- and Dengue-Induced Encephalitis 219
Myriam Lucia Velandia and Jaime E. Castellanos
Chapter 12 Vaccines and Antiviral Drugs for Diseases
Associated with the Epstein-Barr Virus 241
Limin Chen, Ning Li and Cheng Luo
Chapter 13 Identification of Aquatic Birnavirus VP3 Death Domain
and Its Dynamic Interaction Profiles in Early and
Middle Replication Stages in Fish Cells 261
Jiann-Ruey Hong and Jen-Leih Wu
Chapter 14 Molecular Virology and Pathogenicity
of Citrus tristeza virus 275
Maria R. Albiach-Marti

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Preface
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Viral genomes are diverse in size and molecular structure. The bacteriophage MS2
genome is one of the smallest known; it encodes just four genes: maturation protein
(A-protein), coat protein, replicase protein, and lysis. However, the expression of these
proteins depends upon a complex interplay between translation and RNA secondary
structure. It was the first fully sequenced viral genome (1): it took more than five years
to determine the 3,569 nucleotides long single-stranded RNA of MS2 phage (1976). A
year later the ΦX174 circular single-stranded DNA genome of 5,386 nucleotides,
encoding 11 proteins, was published (2). These two genomes were the first to be
determined in scientific history.
It has been a long way since these fabulous achievements of the early years molecular
biology. Long before the advent of recombinant DNA technology, viruses (having a
discrete number of genes) were indeed the first tools at hand to explore the
mechanisms of genome replication and gene expression.
Several leaps in sequencing strategies and technological advances (a blend of
chemistry, enzymology, robotics and computer sciences) have increased our potential
to molecularly describe new viral genomes in virtually no-time. Advances in
molecular cloning and cell biology have also had a great impact on our understanding
of virus infections and paved the way to new therapies.
This book compiles chapters written by experts on diferent aspects of selected viruses
with DNA and RNA genomes that are pathogens for humans, other animals and

plants. They represent just a sample of the smallest genomes (ranging from several
thousands to hundreds of thousands nucleotides) that “come to life” when they
succeed infecting a susceptible host cell. The molecular structures of viral genomes are
as diverse as the molecularly exquisite alternatives of interactions with their host
targets. The different chapters visit fundamental concepts of contemporary Virology.
Although many edges of viral biology touch upon several aspects in an intertwigned
manner (genomics, cell biology, pathogenesis, etc.), the chapters have been arranged in
sections according to the main issues raised in each of them.
Section 1 deals with the organization of large viral dsDNA genomes and also smaller
ssRNA (monopartite and segmented) genomes. Bioinformatic analyses shed light on
X Preface

the potential function of yet unknown gene products and the evolutionary history of
viral families. This information is complemented with experimental data on
morphology, gene expression, pathology and viral population structure (quasispecies).
Section 2 addresses mechanisms that affect regulation of replication and gene
expression in viral RNA and DNA genomes (translational frameshifting signals, RNA
structures that affect recombination, genome packaging, etc., protein-DNA
interactions that affect viral and cellular genes transcription).
A new generation sequencing technologies, enzymatic amplification of specific
nucleotide sequence targets, and nucleic acid hybridization analyses in diferent types
of platforms are some of the tools that revolutionized the study of fundamental
aspects of Virology and also yielded practical applications such as assessing live
attenuated virus vaccine stability. These issues are explored in Section 3.
Finally, Section 4 explores some aspects of virus-host interactions that impact on
tissue tropism, virulence, pathogenesis and the development of vaccines and
therapeutic strategies.
The editors wish to thank the authors for their contributions as well as the publishing
team for their expert work and dedication.

Profs. María Laura García and Víctor Romanowski
Instituto de Biotecnología y Biología Molecular
(IBBM, CONICET-UNLP)
Facultad de Ciencias Exactas
Universidad Nacional de La Plata
Argentina
References
[1] Fiers W, Contreras R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, Min Jou
W, Molemans F, Raeymaekers A, Van den Berghe A, Volckaert G, Ysebaert
M. (1976). Complete nucleotide sequence of bacteriophage MS2 RNA:
primary and secondary structure of the replicase gene. Nature 260 (5551):500-
507.
[2] Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA,
Slocombe PM, Smith M (1977). Nucleotide sequence of bacteriophage phi
X174 DNA. Nature 265 (5596): 687–695.




Part 1
Virus Genomes Organization and Functions