| Preface | p. xiii |
| Viruses and Host Cells | p. 1 |
| What Is a Virus? | p. 2 |
| Where Are Viruses Found in Nature? | p. 4 |
| What Are the Physical Properties of Viruses? | p. 5 |
| Size | p. 5 |
| The Genome | p. 5 |
| Virion Architecture | p. 6 |
| What Structural Features of Cells Are Important in Their Role as Viral Hosts? | p. 13 |
| Animal Cells | p. 13 |
| Plant Cells | p. 14 |
| Prokaryotic Cells | p. 14 |
| Appendages | p. 18 |
| What Genetic Features of Cells Are Important in the Virus-Host Cell Interaction? | p. 19 |
| The Organization of the Host Cell Genome | p. 19 |
| Posttranscriptional Modification of mRNA | p. 20 |
| Internal Compartmentalization | p. 21 |
| The Cell Cycle | p. 21 |
| How Does a Virus Reproduce? | p. 22 |
| What Are the Basic Techniques Used to Study the Virus-Host Cell Interaction? | p. 23 |
| Animal Virus Techniques | p. 24 |
| Plant Virus Techniques | p. 27 |
| How Are Viruses Named? | p. 28 |
| The Baltimore Classification | p. 29 |
| Summary: What Is a Virus? | p. 31 |
| Getting In: Attachment, Penetration, and Uncoating | p. 35 |
| Why Does a Virus Infect Only Certain Cells and Not Others? | p. 36 |
| What Types of Interactions Occur Between the Virion and the Cell Surface During Attachment? | p. 38 |
| How Do Bacteriophages Recognize Their Host Cells? | p. 41 |
| T4 Attachment to E. coli | p. 42 |
| Other Bacteriophages | p. 44 |
| How Do Bacteriophages Introduce Their Nucleic Acids into Host Cells? | p. 46 |
| Penetration by the Coliphages T2 and T4 | p. 46 |
| Other Bacteriophages | p. 49 |
| How Do Animal Viruses Recognize Their Host Cells? | p. 50 |
| Attachment by Naked Viruses | p. 51 |
| Attachment by Enveloped Viruses | p. 53 |
| How Do Animal Viruses Enter Their Host Cells and Uncoat Their Nucleic Acids? | p. 58 |
| General Mechanisms of Penetration and Uncoating | p. 58 |
| Fusion Proteins | p. 60 |
| Penetration by Enveloped Viruses: Fusion with the Plasma Membrane | p. 61 |
| Penetration by Enveloped Viruses: Endocytosis | p. 66 |
| Penetration by Naked Viruses | p. 69 |
| Transport of the Viral Genome into the Nucleus | p. 69 |
| How Do Plant Viruses Infect Their Host Cells? | p. 69 |
| Summary | p. 71 |
| Expression and Replication of the Viral Genome in Prokaryotic Hosts | p. 75 |
| What Are the Essential Features of Genome Replication and Expression in Prokaryotes? | p. 76 |
| DNA Replication in Prokaryotes | p. 76 |
| Transcription in Prokaryotes | p. 78 |
| Translation in Prokaryotes | p. 79 |
| What Strategies Do Prokaryotic Viruses Use to Facilitate Replication and Expression of Their Genomes? | p. 80 |
| What Structural Features Characterize the Genomes of the Double-Stranded DNA Bacteriophages? | p. 83 |
| The T-Series Coliphages | p. 83 |
| How Do the T-Odd Coliphages Express and Replicate Their Genomes? | p. 85 |
| The Bacteriophage T7 | p. 85 |
| The Bacteriophage T5 | p. 89 |
| How Do the T-Even Coliphages Express and Replicate Their Genomes? | p. 89 |
| How Does Lambda Virus Express and Replicate Its Genome? | p. 94 |
| How Do Single-Stranded DNA Bacteriophages Express and Replicate Their Genomes? | p. 100 |
| How Do RNA Bacteriophages Replicate and Express Their Genomes? | p. 104 |
| General Features of RNA Bacteriophage Replication | p. 104 |
| The Genomes of the RNA Bacteriophages Q[beta] and MS2 | p. 107 |
| How Do the RNA Bacteriophages Regulate the Amount of Each Protein Synthesized During Their Replication? | p. 108 |
| Summary | p. 113 |
| Expression and Replication of the Viral Genome in Eukaryotic Hosts: The RNA Viruses | p. 115 |
| What Features of a Eukaryotic Cell's Genetic System Influence Viral Replication and Gene Expression? | p. 116 |
| What Structural Features Distinguish the Positive-Strand RNA Viruses of Animals? | p. 118 |
| What Strategies Do the Animal Positive-Strand Viruses Use to Express and Replicate Their Polycistronic Genomes? | p. 120 |
| Picornaviruses | p. 121 |
| How Are Host and Poliovirus mRNAs Distinguished? | p. 124 |
| How Is Translation of Poliovirus mRNA Begun? | p. 125 |
| How Does Poliovirus Replicate Its Genome? | p. 126 |
| Togaviruses | p. 129 |
| Coronaviruses | p. 133 |
| How Is a Nested Set of mRNAs Synthesized? | p. 135 |
| What Strategies Do Plant Positive-Strand Viruses Use to Express and Replicate Their Genomes? | p. 137 |
| What Structural Features Distinguish the Negative-Strand RNA Viruses? | p. 140 |
| What Strategies Do Negative-Strand Viruses Use to Express and Replicate Their Genomes? | p. 143 |
| Rhabdoviruses | p. 143 |
| Paramyxoviruses | p. 145 |
| Filoviruses | p. 145 |
| Orthomyxoviruses | p. 147 |
| Can a Viral Genome Have Both Positive- and Negative-Strand RNA? | p. 150 |
| How Do Double-Stranded RNA Viruses Express and Replicate Their Genomes? | p. 151 |
| What Structural Features Distinguish the Retroviruses from Other Positive-Strand RNA Viruses? | p. 154 |
| How Does "Reverse Transcription" Work? | p. 157 |
| How Does Retrovirus Proviral DNA Become Incorporated into the Host Cell's Genome? | p. 160 |
| How Are Retrovirus Genes Expressed? | p. 162 |
| How Do Retroviruses Replicate Their Genomes? | p. 163 |
| How Do the Lentiviruses Differ from the Oncoviruses? | p. 164 |
| Functions of the HIV-1 Regulatory and Accessory Gene Products | p. 165 |
| Summary | p. 167 |
| Expression and Replication of the Viral Genome in Eukaryotic Hosts: The DNA Viruses | p. 171 |
| What Structural Features Distinguish Eukaryotic DNA Viruses? | p. 172 |
| What Outcomes Are Possible When a DNA Virus Infects an Animal Cell? | p. 175 |
| How Do Animal Viruses with Double-Stranded DNA Genomes Express and Replicate Those Genomes? | p. 177 |
| The Papovaviruses | p. 177 |
| The Adenoviruses | p. 181 |
| The Herpesviruses | p. 184 |
| The Poxviruses | p. 186 |
| How Do Animal Single-Stranded DNA Viruses Express and Replicate Their Genomes? | p. 188 |
| How Do Plant Single-Stranded DNA Viruses Express and Replicate Their Genomes? | p. 191 |
| What Features Set Hepadnaviruses and Caulimoviruses Apart from Other Eukaryotic DNA Viruses? | p. 193 |
| The Hepadnaviruses | p. 193 |
| The Caulimoviruses | p. 197 |
| Summary | p. 199 |
| Assembly, Maturation, and Release of Virions | p. 201 |
| What Is the Evidence That Viruses Self-Assemble? | p. 202 |
| What Basic Strategies Are Used to Assemble Capsids? | p. 203 |
| How Are Rigid Helical Virions Assembled? | p. 203 |
| How Does the Assembly of Flexible and Rigid Helical Capsids Differ? | p. 209 |
| How Are the Capsids of Icosahedral RNA Viruses Assembled? | p. 210 |
| The Assembly of Poliovirus | p. 213 |
| How Is the RNA Arranged in an Icosahedral Capsid? | p. 215 |
| How Are Simple Icosahedral DNA Bacteriophages Assembled? | p. 215 |
| How Are the Capsids of Complex Bacteriophages Assembled? | p. 219 |
| What Strategies Do DNA Bacteriophages Use to Fill Their Capsids? | p. 220 |
| How Are the Icosahedral DNA Viruses of Eukaryotes Assembled? | p. 223 |
| How Do Viruses with Segmented Genomes Ensure That Virions Contain a Copy of Each Segment? | p. 223 |
| How Do Viruses Exit Their Host Cells? | p. 224 |
| How Do Naked Viruses Exit Their Host Cells? | p. 224 |
| How Do Enveloped Viruses Acquire Their Envelopes? | p. 225 |
| How Do Nucleocapsids Identify Modified Membrane Locations for Budding? | p. 227 |
| How Does a Virus Target a Particular Membrane Region as the Site of Budding? | p. 227 |
| Do All Viruses Bud Through the Cytoplasmic Membrane? | p. 229 |
| Summary | p. 232 |
| Effects of Viral Infection on Host Cells: Cytological and Inductive Effects | p. 235 |
| What Morphological Changes in Host Cells Are Associated with Viral Infections? | p. 236 |
| What Causes Cytopathic Effects in Animal Cells? | p. 240 |
| What Strategies Do Viruses Use to Inhibit Eukaryotic Host Cell Protein Synthesis? | p. 241 |
| Competition | p. 243 |
| Inhibition of Host mRNA Transport from the Nucleus | p. 244 |
| Degradation of Host mRNA | p. 244 |
| Blockage of Initiation Complex Formation | p. 245 |
| Covalent Modification of Translation-Related Components | p. 245 |
| Increases in Intracellular Cation Concentrations | p. 248 |
| Viral Inhibitory Factors | p. 249 |
| How Do Viruses Inhibit the Transcription of Their Hosts' Genomes? | p. 250 |
| How Do Viruses Inhibit the Replication of Their Hosts' Genomes? | p. 251 |
| How Do Bacteriophages Inhibit the Metabolism of Their Host Cells? | p. 251 |
| How Do Host Cells Fight Back Against the Viruses That Infect Them? | p. 253 |
| What Types of Antiviral Defenses Do Prokaryotic Cells Have? | p. 253 |
| What Types of Antiviral Defenses Do Eukaryotic Cells Have? | p. 256 |
| Interferon Proteins and Interferon Genes | p. 257 |
| Synthesis of Interferon | p. 257 |
| The Action of Interferon | p. 258 |
| The Antiviral State | p. 260 |
| The 2,5-OligoA System | p. 260 |
| The Protein Kinase System | p. 262 |
| Other Interferon-Related Activities | p. 262 |
| What Countermeasures Do Viruses Have to Combat the Host Interferon System Defenses? | p. 262 |
| What Clinical Use Is Made of Interferon and Other Antiviral Agents? | p. 264 |
| Antiviral Drugs | p. 265 |
| Summary | p. 271 |
| Effects of Viral Infection on Host Cells: Integrated Viruses and Persistent Infections | p. 275 |
| Why Is Every Viral Infection Not Productive? | p. 276 |
| What Interaction Between a Bacteriophage and Host Cell Gives Rise to the Lysogenic State? | p. 279 |
| What Genetic Events Permit a Lambda Virus to Become Lysogenic? | p. 283 |
| How Are the Events Leading to the Lytic Cycle Prevented? | p. 285 |
| How Is [lambda] DNA Integration Accomplished? | p. 285 |
| What Determines if a Particular Lambda Virus Infection Results in Lysogeny or the Complete Lytic Cycle? | p. 286 |
| How Is Lysogeny Reversed? | p. 286 |
| What Effects May Lysogeny Have on the Host Bacterium? | p. 287 |
| What Is the Evolutionary Significance of Lysogeny? | p. 290 |
| Under What Circumstances Do Animal Viruses Become Inserted into Their Host Cells' Genomes? | p. 290 |
| What Effect Does Integration of an Animal Virus Have on a Host Cell? | p. 292 |
| How Do Animal Cells Regulate Their Cell Cycles? | p. 294 |
| How Do Retroviruses Transform Animal Cells? | p. 297 |
| Why Do Viral Oncogenes Cause Transformation When Their Equivalent Cellular Proto-Oncogenes Do Not? | p. 299 |
| What Mechanisms Besides Viral Oncogenes Do Retroviruses Use to Transform Cells? | p. 302 |
| How Is Transformation of Animal Cells by DNA Viruses Different from That Caused by RNA Viruses? | p. 304 |
| What Is the Mechanism of Transformation by DNA Viruses? | p. 304 |
| The Papovaviruses | p. 305 |
| The SV40 T Antigens | p. 306 |
| The Adenoviruses | p. 308 |
| What Human Tumors May Be Caused by DNA Viruses? | p. 308 |
| The Papillomaviruses | p. 308 |
| The Herpesviruses | p. 310 |
| Besides Integration into the Host Cell Genome, How May a Virus Infection Persist? | p. 311 |
| What Effect Does a Persistent Infection Have on the Host Organism? | p. 314 |
| How Do the Herpesviruses Establish Their Latent Infections? | p. 315 |
| Summary | p. 315 |
| Subviral Entities, Viral Evolution, and Viral Emergence | p. 321 |
| What Structural Features Distinguish Viroids from Viruses? | p. 322 |
| What Proteins Do Viroids Encode? | p. 324 |
| What Host Enzymes Do Viroids Use to Replicate Themselves? | p. 325 |
| What Is the Mechanism of Viroid Replication? | p. 325 |
| How Do Viroids Cause Plant Diseases? | p. 327 |
| What Other Subviral Entities Have Been Found? | p. 327 |
| How Do Satellite RNAs and Satellite Viruses Replicate? | p. 328 |
| How Is Hepatitis Delta Virus Replicated? | p. 329 |
| What Other Subviral Entities Infect Animal Cells? | p. 330 |
| How Do Prions Replicate? | p. 333 |
| Yeast Prion Model Systems | p. 334 |
| What Is the Origin of the Various Types of Subcellular Entities? | p. 334 |
| The Origins of Subviral Entities | p. 336 |
| What Factors Affect Viral Evolution? | p. 337 |
| What Constrains or Counters the Effects of Mutation and Recombination in the Evolution of Viruses? | p. 338 |
| How Do Nonhuman Viruses Gain the Ability to Infect Humans? | p. 340 |
| Zoonotic Viruses | p. 341 |
| The Origin of HIV | p. 342 |
| Summary | p. 343 |
| The Virologist's Toolkit | p. 347 |
| Characteristics of Selected Viruses | p. 373 |
| Glossary | p. 383 |
| Credits | p. 389 |
| Index | p. 391 |
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