Information about http://media.wiley.com/product_data/excerpt/12/04713515/0471351512.pdf
ftoc.qxd 9/19/06 8:13 AM Page xiii …
Tags: cell surface, classification system, host cell, life on earth, messenger rnas, nature of viruses, protein coat, qxd, replication cycle, study of viruses, system 13, viral genes, viral genome, viral genomes, viral proteins, virion, virus genomes, virus particles, virus replication, virus structure,Pages: 10
Language: english
Created: Tue Sep 19 08:31:51 2006
Display cached document
Page 1
Page 2
Page 3
Page 4
Page 5
Page 6
Page 7
Page 8
Page 9
Page 10
ftoc.qxd 9/19/06 8:13 AM Page xiii
Contents
I. INTRODUCTION STEPS IN THE VIRUS REPLICATION CYCLE 12
1. Virions bind to receptors on the cell surface 12
1. Introduction to Virology 1 2. The virion (or the viral genome) enters the cell 12
3. Early viral genes are expressed: the Baltimore classification
THE NATURE OF VIRUSES 2 of viruses 13
Viruses consist of a nucleic acid genome packaged in a The six groups in the Baltimore classification system 13
protein coat 2 4. Early viral proteins direct replication of viral genomes 14
Viruses are dependent on living cells for their replication 2 5. Late messenger RNAs are made from newly-replicated
Virus particles break down and release their genomes inside genomes 15
the cell 2 6. Late viral proteins package viral genomes and assemble
Virus genomes are either RNA or DNA, but not both 2 virions 15
WHY STUDY VIRUSES? 3 7. Progeny virions are released from the host cell 15
Viruses are important disease-causing agents 3
Viruses can infect all forms of life 3
Viruses are the most abundant form of life on Earth 4 2. Virus Structure 17
The study of viruses has led to numerous discoveries in The molecular structure of virus particles 17
molecular and cell biology 4 How virus structure is studied: viruses come in a variety of
A BRIEF HISTORY OF VIROLOGY: THE STUDY OF sizes and shapes 18
VIRUSES 5 Small viruses come in simple, symmetrical packages 18
The scientific study of viruses is very recent 5 Many virus capsids have icosahedral symmetry 18
Viruses were first distinguished from other microorganisms Some examples of virions with icosahedral symmetry 21
by filtration 5 The concept of quasi equivalence 21
The crystallization of tobacco mosaic virus challenged How many subunits can be accomodated on the capsid
conventional notions about genes and the nature of living surface? 22
organisms 5 Other structures, large and small, display icosahedral
The "phage group" stimulated studies of bacteriophages and symmetry 23
helped found the field of molecular biology 7 Many virus capsids are organized as helical tubes 23
Study of tumor viruses led to discoveries in molecular Larger viruses come in more complex packages 24
biology and understanding of the nature of cancer 7 Specific packaging signals direct incorporation of viral
genomes into virions 25
DETECTION AND TITRATION OF VIRUSES 8 Core proteins may accompany the viral genome inside the
Most viruses were first detected and studied by infection of capsid 25
intact organisms 8 Scaffolding proteins help in virion assembly but are not
The plaque assay arose from work with bacteriophages 8 incorporated into the mature virion 25
Eukaryotic cells cultured in vitro have been adapted for Viral envelopes are made from lipid bilayer membranes 26
plaque assays 8 Viral glycoproteins are inserted into the lipid membrane to
Hemagglutination is a convenient and rapid assay for many form the envelope 26
viruses 9 Budding is driven by interactions between viral proteins 27
Virus particles can be seen and counted by electron Assembly and disassembly of virions: the importance of an
microscopy 10 irreversible step 27
The ratio of physical virus particles to infectious particles can
be much greater than 1 10
3. Virus Classification: The World of
THE VIRUS REPLICATION CYCLE:
Viruses 30
AN OVERVIEW 10
The single-cycle virus replication experiment 10 VIRUS CLASSIFICATION 30
An example of a virus replication cycle: mouse Many viruses, infecting virtually all known life forms, have
polyomavirus 11 been discovered 30
Analysis of viral macromolecules reveals the detailed Virus classification is based on molecular architecture,
pathways of virus replication 12 genetic relatedness, and host organism 31
xiii
ftoc.qxd 9/19/06 8:13 AM Page xiv
xiv Contents
Viruses are grouped into species, genera, and families 31 Virions and capsids are transported within the cell in vesicles
Distinct naming conventions and classification schemes have or on microtubules 49
developed in different domains of virology 32 Import of viral genomes into the nucleus 50
The many ways in which viral genomes are uncoated and
MAJOR VIRUS GROUPS 32
released 50
Study of the major groups of viruses leads to understanding
of shared characteristics and replication pathways 32
Viruses with single-stranded DNA genomes are small and 5. Single-Stranded RNA Bacteriophages 53
have few genes 33
The discovery of RNA phages stimulated research into
Viruses with double-stranded DNA genomes include the
messenger RNA function and RNA replication 53
largest known viruses 34
RNA phages are among the simplest known organisms 54
Most plant viruses and many viruses of vertebrates have
Two genera of RNA phages have subtle differences 54
positive-strand RNA genomes 35
RNA phages bind to the F-pilus and use it to insert their
All viruses with negative-strand RNA genomes have helical
RNA into the cell 55
nucleocapsids and some have fragmented genomes 36
Phage RNA is translated and replicated in a regulated
Viruses with double-stranded RNA genomes have
fashion 55
fragmented genomes packaged in capsids with icosahedral
RNA secondary structure controls translation of lysis and
symmetry 37
replicase genes 56
Viruses with a reverse transcription step in their replication
Ribosomes translating the coat gene disrupt secondary
cycle can have either RNA or DNA genomes 38
structure, allowing replicase translation 57
Satellite viruses and satellite nucleic acids require a helper
Ribosomes terminating coat translation can reinitiate at the
virus to replicate 39
lysis gene start site 57
Viroids do not code for proteins, but replicate independently
Replication versus translation: competition for the same
of other viruses 39
RNA template 58
THE EVOLUTIONARY ORIGIN OF VIRUSES 40 Genome replication requires four host cell proteins plus the
The first steps in the development of life on earth: the RNA replicase 58
world 40 A host ribosomal protein directs polymerase to the coat start
Viroids and RNA viruses may have originated in the RNA site 59
world 40 Polymerase skips the first A residue but adds a terminal A to
The transition to the DNA-based world 40 the minus strand copy 59
Small and medium-sized DNA viruses could have arisen Synthesis of plus strands is less complex and more efficient
as independently-replicating genetic elements than that of minus strands 59
in cells 41 The start site for synthesis of maturation protein is normally
Large DNA viruses could have evolved from cells that inaccessible to ribosomes 61
became obligatory intracellular parasites 41 Synthesis of maturation protein is controlled by delayed
RNA folding 61
Assembly and release of virions 62
4. Virus Entry 43
How do virions get into eukaryotic cells? 43
6. Bacteriophage X 174 63
Enveloped and nonenveloped viruses have distinct
penetration strategies 44 X174: a tiny virus with a big impact 63
Some viruses can pass directly from cell to cell 44 Overlapping reading frames allow efficient use of a small
A variety of cell surface proteins can serve as specific virus genome 64
receptors 45 X174 binds to glucose residues in lipopolysaccharide on the
Receptors interact with viral glycoproteins, surface cell surface 65
protrusions, or `canyons' in the surface of the virion 45 X174 delivers its genome into the cell through spikes on the
Many viruses enter the cell via receptor-mediated capsid surface 66
endocytosis 45 Stage I DNA replication generates double-stranded
Passage from endosomes to the cytosol is often triggered by replicative form DNA 66
low pH 47 Gene expression is controlled by the strength of promoters
Membrane fusion is mediated by specific viral "fusion and transcriptional terminators 66
proteins" 47 Replicative form DNAs are amplified via a rolling circle
Fusion proteins undergo major conformational changes that mechanism 67
lead to membrane fusion 48 Summary of viral DNA replication mechanisms 67
Nonenveloped viruses penetrate by membrane lysis or pore Procapsids are assembled by the use of scaffolding proteins
formation 49 67
ftoc.qxd 9/19/06 8:13 AM Page xv
Contents xv
Scaffolding proteins have a flexible structure 68 DNA is inserted into preformed proheads by an ATP-
Single-stranded genomes are packaged into procapsids as dependent mechanism 87
they are synthesized 68 Host cell lysis 88
Role of the J protein in DNA packaging 69
Cell lysis caused by E protein leads to release of phage 69
9. Parvoviruses 89
Did all icosahedral ssDNA virus families evolve from a
common ancestor? 69 Parvoviruses have very small virions and a linear, single-
stranded DNA genome 89
Parvoviruses replicate in cells that are going through the cell
7. Bacteriophage T7 71
cycle 90
T7: a model phage for DNA replication, transcription, and Discovery of mammalian parvoviruses 90
RNA processing 71 Parvoviruses have one of the simplest known virion
T7 genes are organized into three groups based on structures 91
transcription and gene function 72 Parvoviruses have very few genes 91
Entry of T7 DNA into the cytoplasm is powered by Single-stranded parvovirus DNAs have unusual terminal
transcription 73 structures 92
Transcription of class II and III genes requires a novel Uncoating of parvovirus virions takes place in the nucleus
T7-coded RNA polymerase 73 and is cell-specific 92
Class II genes code for enzymes involved in T7 DNA DNA replication begins by extension of the 3 end of the
replication 74 terminal hairpin 93
T7 RNAs are cleaved by host cell ribonuclease III to smaller, The DNA "end replication" problem 93
stable mRNAs 74 Steps in DNA replication 93
Regulation of class III gene expression 74 Non-structural proteins are multifunctional 95
DNA replication starts at a unique internal origin and is Adenovirus functions that help AAV replication 96
primed by T7 RNA polymerase 75 In the absence of helper virus, AAV DNA can integrate into
Large DNA concatemers are formed during replication 76 the cell genome 96
Concatemers are processed and packaged into preformed Parvovirus pathogenesis: the example of B19 virus 96
proheads 76
Special features of the T7 family of phages 76
10. Polyomaviruses 98
Mouse polyomavirus was discovered as a tumor-producing
8. Bacteriophage Lambda: A Piņata of
infectious agent 98
Paradigms 79
Simian virus 40 was found as a contaminant of Salk
In the beginning . . . 80 poliovirus vaccine 99
Uptake of DNA depends on cellular proteins involved in Polyomaviruses are models for studying DNA virus
sugar transport 80 replication and tumorigenesis 99
The lytic transcription program is controlled by Polyomavirus capsids are constructed from pentamers of the
termination and antitermination of RNA synthesis at major capsid protein 99
specific sites on the genome 81 The circular DNA genome is packaged with cellular
The CI repressor blocks expression of the lytic program by histones 100
regulating three nearby promoters: PL, PR, and PRM 82 Circular DNA becomes supercoiled upon removal of
Cleavage of CI repressor in cells with damaged DNA leads to histones 100
prophage induction 83 Supercoiled DNA can be separated from relaxed or linear
The Cro repressor suppresses CI synthesis and regulates DNA molecules 101
early gene transcription 83 Polyomavirus genes are organized in two divergent
Making the decision: Go lytic or lysogenize? 83 transcription units 102
A quick review 85 Virions enter cells in caveolae and are transported to the
Breaking and entering: The insertion of DNA into the nucleus 102
bacterial chromosome 85 The viral minichromosome is transcribed by cellular RNA
The great escape: The liberation of DNA from the polymerase II 103
bacterial chromosome 86 Four early mRNAs are made by differential splicing of a
Int synthesis is controlled by retroregulation 86 common transcript 104
DNA Replication is directed by O and P, but carried out T antigens share common N-terminal sequences but have
by host cell proteins 87 different C-terminal sequences 105
Assembly of heads involves chaperone and scaffolding T antigens bring resting cells into the DNA synthesis (S)
proteins 87 phase of the cell cycle 105
ftoc.qxd 9/19/06 8:13 AM Page xvi
xvi Contents
Small T antigen inhibits protein phosphatase 2A and induces E1A proteins bind to the retinoblastoma protein and activate
cell cycling 105 E2F, a cellular transcription factor 127
Middle T antigen stimulates protein tyrosine kinases that E1A proteins also activate other cellular transcription
signal cell proliferation and division 105 factors 128
Large T antigen activates or suppresses transcription of E1A proteins indirectly induce apoptosis by activation of
cellular genes by binding to a number of important cellular cellular p53 protein 128
regulatory proteins 107 E1B proteins suppress E1A-induced apoptosis, allowing viral
Large T antigen hexamers bind to the origin of DNA replication to proceed 128
replication and locally unwind the two DNA strands 108 The preterminal protein primes DNA synthesis carried out
Large T antigen hexamers assemble cellular DNA synthesis by viral DNA polymerase 129
machinery to initiate viral DNA replication 110 Single-stranded DNA is circularized via the inverted
High levels of late transcripts are made after DNA terminal repeat 130
replication begins 111 The major late promoter is activated after DNA replication
Three late mRNAs are made by alternative splicing 112 begins 131
How do polyomaviruses transform cells in vitro and cause Five different poly(A) sites and alternative splicing generate
tumors in vivo? 112 multiple late mRNAs 131
The tripartite leader ensures efficient transport of late
mRNAs to the cytoplasm 132
11. Papillomaviruses 114
The tripartite leader directs efficient translation of late
Papillomaviruses cause warts and other skin and mucosal adenovirus proteins 132
lesions 114 Adenoviruses kill cells by apoptosis, aiding virus release 132
Oncogenic human papillomaviruses are a major cause of Cell transformation and oncogenesis by human
genital tract cancers 115 adenoviruses 132
Papillomaviruses are not easily grown in cell culture 115
Papillomavirus genomes are circular, double-stranded
13. Herpes Simplex Virus 134
DNA 116
The infectious cycle follows differentiation of epithelial Herpesviruses are important human pathogens 135
cells 116 Most herpesviruses can establish latent infections 135
Viral mRNAs are made from two promoters and two Herpes simplex virus genomes contain both unique and
polyadenylation signals 117 repeated sequence elements 135
Viral E1 and E2 proteins bind to the replication origin and Nomenclature of herpes simplex virus genes and
direct initiation of DNA replication 118 proteins 137
Viral E7 protein interacts with cell cycle regulatory proteins, The icosahedral capsid is enclosed in an envelope along with
particularly Rb 118 tegument proteins 137
Viral E6 protein controls the level of cellular p53 Entry by fusion is mediated by envelope glycoproteins
protein 120 and may occur at the plasma membrane or in
Synergism between E6 and E7 and the predisposition to endosomes 138
cancer 121 Viral genes are sequentially expressed during the replication
Cells transformed by papillomaviruses express E6 and E7 cycle 138
gene products from integrated viral DNA 121 Tegument proteins interact with cellular machinery to
Future prospects for diagnosis and treatment of diseases activate viral gene expression and to degrade cellular
caused by papillomaviruses 121 messenger RNAs 139
Immediate early ( ) genes regulate expression of other
herpesvirus genes 140
12. Adenoviruses 123
gene products set the stage for viral DNA replication 140
Adenoviruses cause respiratory and enteric infections in Herpesvirus begins with bidirectional DNA replication 141
humans 124 Rolling-circle replication subsequently produces multimeric
Adenoviruses can be oncogenic, but not in humans 124 concatemers of viral DNA 141
Virions have icosahedral symmetry and are studded with DNA replication leads to activation of 1 and 2 genes 142
knobbed fibers 124 Viral nucleocapsids are assembled on a scaffold in the
Fibers make contact with cellular receptor proteins to initiate nucleus 143
infection 124 Envelopment and egress: three possible routes 143
Expression of adenovirus genes is controlled at the level of Many viral genes are involved in blocking host responses to
transcription 126 infection 143
E1A proteins are the kingpins of the adenovirus growth The establishment and maintenance of virus latency 145
cycle 127 Latency-associated transcripts include stable introns 145
ftoc.qxd 9/19/06 8:13 AM Page xvii
Contents xvii
14. Baculoviruses 147 Picornavirus virions bind to cellular receptors via depressions
or loop regions on their surface 171
Insect viruses were first discovered as pathogens of Genome RNA may pass through pores formed in cell
silkworms 148 membranes by capsid proteins 171
Baculoviruses are used for pest control and to express Translation initiates on picornavirus RNAs by a novel
eukaryotic proteins 148 internal ribosome entry mechanism 172
Baculoviruses produce two kinds of particles: "budded" and Essential features of picornavirus IRES elements 173
"occlusion-derived" virions 149 Interaction of picornavirus IRES elements with host cell
Baculoviruses have large, circular DNA genomes and encode proteins 175
many proteins 150 Picornavirus proteins are made as a single precursor polyprotein
Insects are infected by ingesting occlusion bodies; infection that is autocatalytically cleaved by viral proteinases 176
spreads within the insect via budded virions 151 Picornaviruses make a variety of proteinases that cleave the
Viral proteins are expressed in a timed cascade regulated at polyprotein and some cellular proteins 176
the transcription level 152 Replication of picornavirus RNAs is initiated in a
Immediate early gene products control expression of early multiprotein complex bound to proliferated cellular
genes 152 vesicles 176
Early gene products regulate DNA replication, late RNA synthesis is primed by VPg covalently bound to uridine
transcription, and apoptosis 153 residues 177
Late genes are transcribed by a novel virus-coded RNA Virion assembly involves cleavage of VP0 to VP2 plus
polymerase 153 VP4 178
Baculoviruses are widely used to express foreign Inhibition of host cell macromolecular functions 179
proteins 156
17. Flaviviruses 181
15. Poxviruses 157
Flaviviruses cause several important human diseases 182
Smallpox was a debilitating and fatal worldwide disease 158 Yellow fever is a devastating human disease transmitted by
Variolation led to vaccination, which has eradicated smallpox mosquitoes 182
worldwide 158 A live, attenuated yellow fever virus vaccine is available and
Poxviruses remain a subject of intense research interest 159 widely used 183
Linear vaccinia virus genomes have covalently sealed hairpin Hepatitis C virus: a recently discovered member of the
ends and lack introns 159 Flaviviridae 183
Two forms of vaccinia virions have different roles in The flavivirus virion contains an icosahedral nucleocapsid
spreading infection 160 wrapped in a tightly fitted envelope 183
Poxviruses replicate in the cytoplasm 162 Flavivirus E protein directs both binding to receptors and
Poxvirus genes are expressed in a regulated transcriptional membrane fusion 184
cascade controlled by viral transcription factors 162 Flaviviruses enter the cell by pH-dependent fusion 185
Virus-coded enzymes packaged in the core carry out early Flavivirus genome organization resembles that of
RNA synthesis and processing 162 picornaviruses 185
Enzymes that direct DNA replication are encoded by early The polyprotein is processed by both viral and cellular
mRNAs 163 proteinases 186
Poxviruses produce large concatemeric DNA molecules that Nonstructural proteins organize protein processing, viral
are resolved into monomers 164 RNA replication, and capping 187
Postreplicative mRNAs have 5 end poly(A) extensions and 3 Flavivirus RNA synthesis is carried out on membranes in
end heterogeneity 164 the cytoplasm 188
Mature virions are formed within virus "factories" 165 Virus assembly also takes place at intracellular
Extracellular virions are extruded through the plasma membranes 189
membrane by actin tails 166
Poxviruses make several proteins that target host immune
defenses 167 18. Togaviruses 191
Most togaviruses are arthropod borne, transmitted between
vertebrate hosts by mosquitoes 192
16. Picornaviruses 169
Togavirus virions contain a nucleocapsid with icosahedral
Picornaviruses cause a variety of human and animal diseases symmetry wrapped in an envelope of the same
including poliomyelitis and the common cold 170 symmetry 192
Poliovirus: a model picornavirus for vaccine development Togaviruses enter cells by low pH-induced fusion inside
and studies of replication 170 endosome vesicles 193
ftoc.qxd 9/19/06 8:13 AM Page xviii
xviii Contents
Nonstructural proteins are made as a polyprotein that is Rabies is a fatal human encephalitis caused by a
cleaved by a viral protease 193 rhabdovirus 215
Partly-cleaved nonstructural proteins catalyze synthesis of Measles is a serious childhood disease caused by a
full-length antigenome RNA 194 paramyxovirus 215
Replication and transcription: synthesis of genome and Paramyxovirus and rhabdovirus virions have distinct
subgenomic RNAs 196 morphologies 216
Structural proteins are cleaved during translation and Viral envelope proteins are responsible for receptor binding
directed to different cellular locations 196 and fusion with cellular membranes 217
Assembly of virions and egress at the plasma membrane 197 Genome RNA is contained within helical nucleocapsids 218
Effects of mutations in viral proteins on cytopathic Paramyxoviruses enter the cell by fusion with the plasma
effects and on pathogenesis 198 membrane at neutral pH 218
Alphaviruses have been modified to serve as vectors for Gene order is conserved among different paramyxoviruses
the expression of heterologous proteins 199 and rhabdoviruses 219
Alphavirus vectors have multiple potential uses 199 Viral messenger RNAs are synthesized by an RNA
polymerase packaged in the virion 220
Viral RNA polymerase initiates transcription exclusively at
19. Coronaviruses 201
the 3' end of the viral genome 220
Coronaviruses cause common colds in humans and important The promoter for plus-strand RNA synthesis consists of two
veterinary diseases 202 sequence elements separated by one turn of the
A newly emerged coronavirus caused a worldwide epidemic ribonucleoprotein helix 220
of severe acute respiratory syndrome (SARS) 202 mRNAs are synthesized sequentially from the 3' to the 5' end
The SARS coronavirus may have passed from animals to of the genome RNA 222
humans via direct contact 202 The P/C/V gene codes for several proteins by using
Coronaviruses have large, single-stranded, positive sense alternative translational starts and by mRNA
RNA genomes 203 "editing" 223
Coronaviruses fall into three groups based on genome Functions of P, C and V proteins 224
sequences 203 N protein levels control the switch from transcription to
Coronaviruses have enveloped virions containing helical genome replication 224
nucleocapsids 204 Virions are assembled at the plasma membrane 224
Coronavirus virions contain multiple envelope proteins 204
Coronavirus spike proteins bind to a variety cellular
21. Filoviruses 226
receptors 205
The virus envelope fuses with the plasma membrane or an Marburg and Ebola viruses: sporadically emerging viruses
endosomal membrane 206 that cause severe, often fatal disease 227
The replicase gene is translated from genome RNA into a Filoviruses are related to paramyxoviruses and
polyprotein that is processed by viral proteinases 206 rhabdoviruses 228
RNA polymerase, RNA helicase, and RNA modifying Filoviruses cause hemorrhagic fever 228
enzymes are coded by the replicase gene 207 Filovirus genomes contain seven genes in a conserved
Replication complexes are associated with cytoplasmic order 228
membranes 207 Filovirus transcription, replication and assembly 230
Genome replication proceeds via a full-length negative- Cloned cDNA copies of viral mRNAs and viral genome
strand intermediate 208 RNA are used for study of filoviruses 230
Transcription produces a nested set of subgenomic Multi-plasmid transfection systems allow recovery of
mRNAs 208 infectious filoviruses 230
Subgenomic mRNAs are most likely transcribed from Filovirus glycoprotein mediates both receptor-binding and
subgenomic negative-sense RNA templates 208 entry by fusion 231
The alternative model of discontinuous transcription of Ebola virus uses RNA editing to make two glycoproteins
antigenome RNA is unlikely to be correct 209 from the same gene 232
Assembly of virions takes place at intracellular membrane Does the secreted glycoprotein play a role in virus
structures 211 pathogenesis? 232
Adaptability of Coronaviruses 212 Minor nucleocapsid proteinVP30 activates viral mRNA
synthesis in Ebola virus 233
Matrix protein VP40 directs budding and formation of
20. Paramyxoviruses and Rhabdoviruses 214
filamentous particles 234
The mononegaviruses: a group of related negative-strand Most filovirus outbreaks have occurred in equatorial
RNA viruses 215 Africa 234
ftoc.qxd 9/19/06 8:13 AM Page xix
Contents xix
Filovirus infections are transmitted to humans from an Genome replication begins when newly synthesized NP
unknown animal origin 235 protein enters the nucleus 255
Spread of filovirus infections among humans is limited to Nucleocapsids are exported from the nucleus in a complex
close contacts 235 with matrix protein and NS2 256
Pathogenesis of filovirus infections 236 The NS1 protein interferes with polyadenylation of cellular
Clinical features of infection 236 mRNAs 256
NS1 also inhibits activation of PKR, an important antiviral
pathway induced by interferon 257
22. Bunyaviruses 238
Viral envelope proteins assemble in the plasma membrane
Most bunyaviruses are transmitted by arthropod vectors, and direct budding of virions 257
including mosquitoes and ticks 239 Neuraminidase cleaves sialic acid, the cellular receptor that
Some bunyaviruses cause severe hemorrhagic fever, binds to HA 257
respiratory disease, or encephalitis 240 Influenza virus strains vary in both transmissibility and
Bunyaviruses encapsidate a segmented RNA genome in a pathogenicity 257
simple enveloped particle 240 Genetic variability generates new virus strains that can cause
Bunyavirus protein coding strategies: negative-strand and pandemics 258
ambisense RNAs 240 The 1918 pandemic influenza A virus was probably not a
L RNA codes for viral RNA polymerase 241 reassortant virus 258
M RNA codes for virion envelope glycoproteins 242 Genome sequences from some previous influenza A virus
S RNA codes for nucleocapsid protein and a nonstructural strains confirm the antigenic shift hypothesis 258
protein 243 Highly pathogenic influenza A strains in poultry farms could
After attachment via the virion glycoproteins, bunyaviruses lead to a new pandemic 259
enter the cell by endocytosis 243
Bunyavirus mRNA synthesis is primed by the capped 5? ends
24. Reoviruses 261
of cellular mRNAs 243
Coupled translation and transcription may prevent Reoviruses were the first double-stranded RNA viruses
premature termination of mRNAs 244 discovered 262
Genome replication begins once sufficient N protein is Some members of the Reoviridae are important
made 244 pathogens 262
Virus assembly takes place at Golgi membranes 245 Reoviridae have segmented genomes made of double-
Evolutionary potential of bunyaviruses via genome stranded RNA 262
reassortment 246 Reovirus virions contain concentric layers of capsid
proteins 263
The attachment protein binds to one or two cellular
23. Orthomyxoviruses 248
receptors 265
Influenza viruses cause serious acute disease in humans, and During entry, the outer capsid is stripped from virions and
occasional pandemics 249 the core is released into the cytoplasm 265
Influenza virus infections of the respiratory tract can lead to Enzymes in the viral core synthesize and cap messenger
secondary bacterial infections 249 RNAs 266
Orthomyxoviruses are negative-strand RNA viruses with Translation of reovirus mRNAs is regulated 267
segmented genomes 249 Interferon and PKR: effects on viral and cellular protein
Eight influenza virus genome segments code for a total of ten synthesis 267
different viral proteins 251 Synthesis of progeny double-stranded genomes occurs within
Hemagglutinin protein binds to cell receptors and subviral particles 268
mediates fusion of the envelope with the endosomal Reoviruses induce apoptosis via activation of transcription
membrane 252 factor NF- B 269
M2 is an ion channel that facilitates release of nucleocapsids Studies of reovirus pathogenesis in mice 270
from the virion 252
Nucleocapsids enter the nucleus, where mRNA synthesis and
25. Retroviruses 272
RNA replication occur 253
Capped 5 ends of cellular pre-messenger RNAs are used as Retroviruses have a unique replication cycle based
primers for synthesis of viral mRNAs 254 on reverse transcription and integration of their
Viral mRNAs terminate in poly(A) tails generated by genomes 273
"stuttering" transcription 255 Viral proteins derived from the gag, pol and env genes are
Two influenza A mRNAs undergo alternative splicing in the incorporated in virions 273
nucleus 255 Retroviruses enter cells by the fusion pathway 274
ftoc.qxd 9/19/06 8:13 AM Page xx
xx Contents
Viral RNA is converted into a double-stranded DNA copy by HTLV-1 Rex regulates polyadenylation, splicing, and
reverse transcription 275 nuclear export of viral RNAs 296
A copy of proviral DNA is integrated into the cellular HTLV-1 Tax regulates transcription of viral and cellular
genome at a random site 277 genes 297
Sequence elements in the long terminal repeats direct Cell transformation by HTLV-I is mediated by Tax 299
transcription and polyadenylation by host cell The interleukin-2autocrine loop stimulates T-cell
enzymes 277 proliferation 299
Differential splicing generates multiple mRNAs 279 Activation of the Jak-Stat pathway by p12I mimics
The Gag/Pol polyprotein is made by suppression of interleukin-2 stimulation 299
termination and use of alternative reading frames 279 Cell Cycle Progression: p16INK4A and cyclin-dependent
Virions mature into infectious particles after budding from kinases 300
the plasma membrane 280 The mitotic spindle checkpoint and MAD1 300
Acute transforming retroviruses express mutated forms of Downregulation of p53 activity by Tax allows T cell
cellular growth signalling proteins 281 proliferation 301
Retroviruses lacking oncogenes can transform cells by Diseases caused by HTLV-1 develop slowly and can be
insertion of proviral DNA near a proto-oncogene 282 severe 301
Coinfection by HIV-1 and HTLV-1 is an emerging
problem 302
26. Human Immunodeficiency Virus
Antiviral therapy of disease caused by HTLV-1 has not met
Type 1 284
with great success 302
Human immunodeficiency virus type 1 (HIV-1) and acquired
immunodeficiency syndrome 285
28. Hepadnaviruses 303
HIV-1 infection leads to a progressive loss of cellular
immunity and increased susceptibility to opportunistic At least seven distinct viruses cause human hepatitis 304
infections 285 The discovery of hepatitis B virus 304
HIV-1 is a complex retrovirus 287 Dane particles are infectious virions; abundant noninfectious
HIV-1 targets cells of the immune system by recognizing particles lack nucleocapsids 305
CD4 antigen and chemokine receptors 287 The viral genome is a circular, partly single-stranded DNA
Virus mutants arise rapidly because of errors generated with overlapping reading frames 305
during reverse transcription 288 Nucleocapsids enter the cytoplasm via fusion and are
Unlike other retroviruses, HIV-1 directs transport of proviral transported to the nucleus 305
DNA into the cell nucleus 288 Transcription of viral DNA gives rise to several mRNAs and
Latent infection complicates the elimination of a pregenome RNA 307
HIV-1 289 The roles of hepatitis B virus proteins 308
The Tat protein increases HIV-1 transcription by The pregenome RNA is packaged by interaction with
stimulating elongation by RNA polymerase II 289 polymerase and core proteins 309
The Rev protein mediates cytoplasmic transport of viral Genome replication occurs via reverse transcription of
mRNAs that code for HIV-1 structural proteins 290 pregenome RNA 309
Together, the Tat and Rev proteins strongly upregulate viral Virions are formed by budding in the endoplasmic
protein expression 291 reticulum 311
The Vif protein increases virion infectivity by counteracting Hepatitis B virus can cause chronic or acute hepatitis,
a cellular deoxcytidine deaminase 291 cirrhosis, and liver cancer 312
The Vpr protein enables the preintegration complex to be Hepatits B virus is transmitted by blood transfusions,
transported to the nucleus 291 contaminated needles, and unprotected sex 313
The Vpu protein enhances release of progeny virions from A recombinant vaccine is available 313
infected cells 291 Antiviral drug treatment has real but limited success 313
The Nef protein is an important mediator of
pathogenesis 292
29. Viroids and Hepatitis Delta Virus 315
Viroids are small, circular RNAs that do not encode
27. Human T-Cell Leukemia Virus
proteins 316
Type 1 294
Group A and group B viroids have distinct properties 316
Discovery of the first human retrovirus 294 Viroids replicate via linear multimeric RNA intermediates 317
Like lentiviruses, HTLV-1 codes for regulatory proteins by Three enzymatic activities are needed for viroid
producing doubly-spliced mRNAs 295 replication 317
ftoc.qxd 9/19/06 8:13 AM Page xxi
Contents xxi
How do viroids cause disease? 318 Interferon and the development of CD4-positive helper
Interaction of viroid RNA with cellular RNAs or proteins T-cells 342
may disrupt cell metabolism 318 The role of interferon in macrophage activation and cellular
Plant satellite RNAs resemble viroids but are immunity 343
encapsidated 320 Effects of interferons on antibody production 343
Hepatitis delta virus is a human viroid-like satellite Interferons regulate cell growth and apoptosis 343
virus 320 Viruses have developed numerous strategies to evade the
Hepatitis delta virus may use two different cellular RNA interferon response 343
polymerases to replicate 320 Conclusion: interferons are a first line of defense against
RNA editing generates two forms of hepatitis delta virus infection 344
antigen 322
Conclusion: viroids may be a link to the ancient RNA
32. Antiviral Chemotherapy 346
world 322
The discovery and widespread use of antiviral compounds
began only recently 346
30. Prions 323 Importance of antiviral drugs for basic science 347
How are antiviral drugs obtained? 347
Prions are proteins that cause fatal brain diseases 323
Targeting drugs to specific steps of virus infection 347
Prion diseases were first detected in domestic
Capsid-binding drugs prevent attachment and entry of
ruminants 324
virions 348
Human prion diseases can be either inherited or
Amantadine blocks ion channels and inhibits uncoating of
transmitted 324
influenza virions 349
The infectious agent of prion diseases contains protein but
Nucleoside analogues target viral DNA polymerases 349
no detectable nucleic acid 325
Acyclovir is selectively phosphorylated by herpesvirus
PrPSc is encoded by a host cell gene 325
thymidine kinases 350
Differences between PrPC and PrPSc 326
Acyclovir is preferentially incorporated by herpesvirus DNA
The prion hypothesis: formation of infectious and
polymerases 351
pathogenic prions from normal PrPC 326
Cytomegalovirus encodes a protein kinase that
Is the prion hypothesis correct? 327
phosphorylates ganciclovir 351
Pathology and diagnosis of prion diseases 330
HIV-1 reverse transcriptase preferentially incorporates
Genetics of prion diseases 330
azidothymidine into DNA, leading to chain
Prion diseases are not usually transmitted among different
termination 354
species 330
Nonnucleoside inhibitors selectively target viral replication
Strain variation and crossing of the species barrier 331
enzymes 354
The nature of the prion infectious agent 331
Protease inhibitors can interfere with virus assembly and
maturation 354
Ritonavir: a successful protease inhibitor of HIV-1 that was
31. Interferons 333
developed by rational methods 354
Virus-infected cells secrete interferons, which protect nearby Neuraminidase inhibitors suppress release and spread of
cells against virus infection 334 influenza virus 355
Interferons are a first line of host defense against viruses but Antiviral chemotherapy shows promise for the
therapeutic use has been limited 334 future 357
Interferons , , and are made by different cells and have
distinct functions 335
33. Eukaryotic Virus Vectors 358
Transcription of interferon genes is activated by virus
infection or double-stranded RNA 335 Many viruses can be engineered to deliver and express
Transcriptional activation occurs by binding of transcription specific genes 358
factors to interferon gene enhancers 335 Virus vectors are used to produce high levels of specific
Interferon signal transduction is carried out via the Jak-Stat proteins in cultured cells 359
pathway 337 Gene therapy is an expanding application of virus
Antiviral activities induced by interferon 338 vectors 360
Interferons have diverse effects on the immune system 340 Virus vectors are produced by transfection of cells with
The adaptive immune system 340 plasmids containing deleted genomes 360
Interferons stimulate antigen processing and Virus vectors are engineered to produce optimal levels of
presentation 342 gene products 361
ftoc.qxd 9/19/06 8:13 AM Page xxii
xxii Contents
ADENOVIRUS VECTORS 362 Production of AAV vectors usually requires a helper
Adenovirus vectors are widely used in studies of gene transfer virus 367
and antitumor therapy 362 Applications of adeno-associated virus vectors: treatment of
Replication-defective adenovirus vectors are propagated in hemophilia 368
complementing cell lines 362 Advantages and limitations of AAV vectors 368
Replication-competent adenovirus vectors are useful tools in
antitumor therapy 363
34. Viral Vaccines 370
Advantages and limitations of adenovirus vectors 363
A brief history of viral vaccines 371
RETROVIRUS VECTORS 364
Early vaccine technology was crude but effective 372
Retrovirus vectors incorporate transgenes into the cell
Embryonated chicken eggs and cell culture played major
chromosome 364
roles in recent vaccine development 373
Packaging cell lines express retrovirus enzymatic and
Major categories of viral vaccines 373
structural proteins 364
Advantages and drawbacks of vaccine types 374
Strategies for controlling transgene transcription 364
How do viral vaccines work? 375
Lentivirus vectors are used for gene delivery to nondividing
The role of the immune system in fighting viral
cells 365
infections 375
Production of lentivirus vectors requires additional cis-acting
Some vaccines target mainl