Bookstore

Principles of Virology, the leading virology textbook in use, is an extremely valuable and highly informative presentation of virology at the interface of modern cell biology and immunology. This text utilizes a uniquely rational approach by highlighting common principles and processes across all viruses. Using a set of representative viruses to illustrate the breadth of viral complexity, students are able to under-stand viral reproduction and pathogenesis and are equipped with the necessary tools for future encounters with new or understudied viruses.

This fifth edition was updated to keep pace with the ever-changing field of virology. In addition to the beloved full-color illustrations, video interviews with leading scientists, movies, and links to exciting blogposts on relevant topics, this edition includes study questions and active learning puzzles in each chapter, as well as short descriptions regarding the key messages of references of special interest.

Volume I: Molecular Biology focuses on the molecular processes of viral reproduction, from entry through release. Volume II: Pathogenesis and Control addresses the interplay between viruses and their host organisms, on both the micro- and macroscale, including chapters on public health, the immune response, vaccines and other antiviral strategies, viral evolution, and a brand new chapter on the therapeutic uses of viruses. These two volumes can be used for separate courses or together in a single course. Each includes a unique appendix, glossary, and links to internet resources.

Principles of Virology, Fifth Edition, is ideal for teaching the strategies by which all viruses reproduce, spread within a host, and are maintained within populations. This edition carefully reflects the results of extensive vetting and feedback received from course instructors and students, making this renowned textbook even more appropriate for undergraduate and graduate courses in virology, microbiology, and infectious diseases.

Principles of Virology - Molecular Biology, Fifth Edition Volume 1

Preface xvii





Acknowledgments xxi





About the Authors xxiii





Key of Repetitive Elements xxv





Part I The Science of Virology 1





1 Foundations 2





Luria's Credo 3





Viruses Defined 3





Why We Study Viruses 3





Viruses Are Everywhere 3





Viruses Infect All Living Things 4





Viruses Can Cause Human Disease 5





Viruses Can Be Beneficial 5





Viruses "R" Us 6





Viruses Can Cross Species Boundaries 6





Viruses Are Unique Tools To Study Biology 6





Virus Prehistory 7





Viral Infections in Antiquity 7





The First Vaccines 8





Microorganisms as Pathogenic Agents 9





Discovery of Viruses 11





The Defining Properties of Viruses 13





The Structural Simplicity of Virus Particles 13





The Intracellular Parasitism of Viruses 13





Cataloging Animal Viruses 18





The Classical System 18





Classification by Genome Type: the Baltimore System 19





A Common Strategy for Viral Propagation 21





Perspectives 21





References 24





Study Questions 24





2 The Infectious Cycle 26





Introduction 27





The Infectious Cycle 27





The Cell 27





Entering Cells 28





Viral RNA Synthesis 29





Viral Protein Synthesis 29





Viral Genome Replication 29





Assembly of Progeny Virus Particles 29





Viral Pathogenesis 29





Overcoming Host Defenses 30





Cultivation of Viruses 30





Cell Culture 30





Embryonated Eggs 35





Laboratory Animals 35





Assay of Viruses 35





Measurement of Infectious Units 35





Efficiency of Plating 38





Measurement of Virus Particles 40





Viral Reproduction: The Burst Concept 49





The One-Step Growth Cycle 49





One-Step Growth Analysis: a Valuable Tool for Studying Animal Viruses 52





Global Analysis 53





DNA Microarrays 54





Mass Spectrometry 56





Protein-Protein Interactions 56





Single-Cell





Virology 56





Perspectives 58





References 59





Study Questions 60





Part II Molecular Biology 61





3 Genomes and Genetics 62





Introduction 63





Genome Principles and the Baltimore System 63





Structure and Complexity of Viral Genomes 63





DNA Genomes 64





RNA Genomes 65





What Do Viral Genomes Look Like? 68





Coding Strategies 69





What Can Viral Sequences Tell Us? 69





The "Big and Small" of Viral Genomes: Does Size Matter? 71





The Origin of Viral Genomes 73





Genetic Analysis of Viruses 74





Classical Genetic Methods 75





Engineering Mutations into Viral Genomes 77





Engineering Viral Genomes: Viral Vectors 83





Perspectives 87





References 87





Study Questions 88





4 Structure 90





Introduction 91





Functions of the Virion 91





Nomenclature 92





Methods for Studying Virus Structure 92





Building a Protective Coat 95





Helical Structures 96





Capsids with Icosahedral Symmetry 99





Other Capsid Architectures 111





Packaging the Nucleic Acid Genome 112





Direct Contact of the Genome with a Protein Shell 112





Packaging by Specialized Viral Proteins 113





Packaging by Cellular Proteins 113





Viruses with Envelopes 115





Viral Envelope Components 115





Simple Enveloped Viruses: Direct Contact of External Proteins with the Capsid or Nucleocapsid 117





Enveloped Viruses with an Additional Protein Layer 118





Large Viruses with Multiple Structure Elements 119





Particles with Helical or Icosahedral Parts 120





Alternative Architectures 123





Other Components of Virions 125





Enzymes 125





Other Viral Proteins 125





Cellular Macromolecules 126





Mechanical Properties of Virus Particles 126





Investigation of Mechanical Properties of Virus Particles 126





Stabilization and Destabilization of Virus Particles 128





Perspectives 128





References 129





Study Questions 130





5 Attachment and Entry 132





Introduction 133





Attachment of Virus Particles to Cells 133





General Principles 133





Identification of Receptors for Virus Particles 135





Virus-Receptor Interactions 137





Entry into Cells 142





Virus-induced Signaling via Cell Receptors 142





Routes of Entry 143





Membrane Fusion 145





Intracellular Trafficking and Uncoating 154





Movement of Viral and Subviral Particles within Cells 154





Uncoating of Enveloped Virus Particles 155





Uncoating of Nonenveloped Viruses 155





Import of Viral Genomes into the Nucleus 159





The Nuclear Pore Complex 159





Nuclear Localization Signals 159





Nuclear Import of RNA Genomes 161





Nuclear Import of DNA Genomes 162





Import of Retroviral Genomes 162





Perspectives 164





References 165





Study Questions 166





6 Synthesis of RNA from RNA Templates 168





Introduction 169





The Nature of the RNA Template 169





Secondary Structures in Viral RNA 169





Naked or Nucleocapsid RNA 170





The RNA Synthesis Machinery 171





Identification of RNA-Dependent RNA Polymerases 171





Three-Dimensional Structures of RNA-Dependent RNA Polymerases 173





Mechanisms of RNA Synthesis 176





Initiation 176





Capping 179





Elongation 179





Functions of Additional Polymerase Domains 181





RNA Polymerase Oligomerization 181





Template Specificity 182





Unwinding the RNA Template 182





Role of Cellular Proteins 183





Paradigms for Viral RNA Synthesis 183





(+) Strand RNA 184





Synthesis of Nested Subgenomic mRNAs 184





( ) Strand RNA 185





Ambisense RNA 189





Double-Stranded RNA 189





Unique Mechanisms of mRNA and Genome Synthesis of Hepatitis Delta Virus 190





Do Ribosomes and RNA Polymerases Collide? 192





Origins of Diversity in RNA Virus Genomes 193





Misincorporation of Nucleotides 193





Segment Reassortment and RNA Recombination 193





RNA Editing 194





Perspectives 195





References 196





Study Questions 197





7 Synthesis of RNA from DNA Templates 198





Introduction 199





Properties of Cellular RNA Polymerases That Transcribe Viral DNA 199





Some Viral Genomes Must Be Converted to Templates Suitable for Transcription 200





Transcription by RNA Polymerase II 201





Regulation of RNA Polymerase II Transcription 203





Common Properties of Proteins That Regulate Transcription 206





Transcription of Viral DNA Templates by the Cellular Machinery Alone 208





Viral Proteins That Govern Transcription of DNA Templates 209





Patterns of Regulation 209





The Human Immunodeficiency Virus Type 1 Tat Protein Autoregulates Transcription 211





The Transcriptional Cascades of DNA Viruses 217





Entry into One of Two Alternative Transcriptional Programs 226





Transcription of Viral Genes by RNA Polymerase III 230





The VA-RNA I Promoter 231





Inhibition of the Cellular Transcriptional Machinery 232





Unusual Functions of Cellular Transcription Components in Virus-Infected Cells 233





Viral DNA-Dependent RNA Polymerases 233





Perspectives 234





References 235





Study Questions 236





8 Processing 238





Introduction 239





Covalent Modification during Viral Pre-mRNA Processing 240





Capping the 5' Ends of Viral mRNA 240





Synthesis of 3' Poly(A) Segments of Viral mRNA 243





Internal Methylation of Adenosine Residues 245





Splicing of Viral Pre-mRNA 246





Regulated Processing of Viral Pre-mRNA 249





Editing of Viral mRNAs 255





Export of RNAs from the Nucleus 257





The Cellular Export Machinery 257





Export of Viral mRNA 258





Posttranscriptional Regulation of Viral or Cellular Gene Expression by Viral Proteins 262





Temporal Control of Viral Gene Expression 262





Viral Proteins Can Inhibit Cellular mRNA Production 264





Regulation of Turnover of Viral and Cellular mRNAs in the Cytoplasm 266





Intrinsic Turnover 266





Regulation of mRNA Stability by Viral Proteins 267





mRNA Stabilization Can Facilitate Transformation 267





Nonsense-Mediated mRNA Decay 267





Noncoding RNAs 271





Small Interfering RNAs and Micro-RNAs 271





Long Noncoding RNAs 276





Circular RNAs 278





Perspectives 278





References 279





Study Questions 281





9 Replication of DNA Genomes 282





Introduction 283





DNA Synthesis by the Cellular Replication Machinery 284





Eukaryotic Replicons 284





Cellular Replication Proteins 287





Mechanisms of Viral DNA Synthesis 287





Lessons from Simian Virus 40 288





Replication of Other Viral DNA Genomes 290





Properties of Viral Replication Origins 294





Recognition of Viral Replication Origins 296





Viral DNA Synthesis Machines 301





Resolution and Processing of Viral Replication Products 301





Exponential Accumulation of Viral Genomes 302





Viral Proteins Can Induce Synthesis of Cellular Replication Proteins 303





Synthesis of Viral Replication Machines and Accessory Enzymes 304





Viral DNA Replication Independent of Cellular Proteins 304





Delayed Synthesis of Structural Proteins Prevents Premature Packaging of DNA Templates 305





Inhibition of Cellular DNA Synthesis 305





Synthesis of Viral DNA in Specialized Intracellular Compartments 305





Limited Replication of Viral DNA Genomes 308





Integrated Parvoviral DNA Can Be Replicated as Part of the Cellular Genome 308





Different Viral Origins Regulate Replication of Epstein-Barr Virus 310





Limited and Amplifying Replication from a Single Origin: the Papillomaviruses 313





Origins of Genetic Diversity in DNA Viruses 315





Fidelity of Replication by Viral DNA Polymerases 315





Modulation of the DNA Damage Response 316





Recombination of Viral Genomes 318





Perspectives 321





References 321





Study Questions 323





10 Reverse Transcription and Integration 324





Retroviral Reverse Transcription 325





Discovery 325





Impact 325





The Process of Reverse Transcription 326





General Properties and Structure of Retroviral Reverse Transcriptases 334





Other Examples of Reverse Transcription 337





Retroviral DNA Integration 340





The Pathway of Integration: Integrase-Catalyzed Steps 341





Integrase Structure and Mechanism 347





Hepadnaviral Reverse Transcription 350





A DNA Virus with Reverse Transcriptase 350





The Process of Hepadnaviral Reverse Transcription 352





Perspectives 358





References 359





Study Questions 360





11 Protein Synthesis 362





Introduction 363





Mechanisms of Eukaryotic Protein Synthesis 363





General Structure of Eukaryotic mRNA 363





The Translation Machinery 364





Initiation 365





Elongation and Termination 375





The Diversity of Viral Translation Strategies 378





Polyprotein Synthesis 378





Leaky Scanning 378





Reinitiation 381





StopGo Translation 382





Suppression of Termination 382





Ribosomal Frameshifting 383





Bicistronic mRNAs 384





Regulation of Translation during Viral Infection 385





Inhibition of Translation Initiation after Viral Infection 385





Regulation of eIF4F 389





Regulation of Poly(A)-Binding Protein Activity 392





Regulation of eIF3 392





Interfering with RNA 392





Stress-Associated RNA Granules 393





Perspectives 395





References 396





Study Questions 397





12 Intracellular Trafficking 398





Introduction 399





Assembly within the Nucleus 400





Import of Viral Proteins for Assembly 401





Assembly at the Plasma Membrane 403





Transport of Viral Membrane Proteins to the Plasma Membrane 404





Sorting of Viral Proteins in Polarized Cells 419





Disruption of the Secretory Pathway in Virus-Infected Cells 421





Signal Sequence-Independent Transport of Viral Proteins to the Plasma Membrane 422





Interactions with Internal Cellular Membranes 426





Localization of Viral Proteins to Compartments of the Secretory Pathway 426





Localization of Viral Proteins to the Nuclear Membrane 426





Transport of Viral Genomes to Assembly Sites 427





Transport of Genomic and Pregenomic RNA from the Nucleus to the Cytoplasm 427





Transport of Genomes from the Cytoplasm to the Plasma Membrane 429





Perspectives 430





References 431





Study Questions 432





13 Assembly, Release, and Maturation 434





Introduction 435





Methods of Studying Virus Assembly and Egress 435





Structural Studies of Virus Particles 436





Visualization of Assembly and Exit by Microscopy 436





Biochemical and Genetic Analyses of Assembly Intermediates 436





Methods Based on Recombinant DNA Technology 439





Assembly of Protein Shells 439





Formation of Structural Units 439





Capsid and Nucleocapsid Assembly 441





Self-Assembly and Assisted Assembly Reactions 445





Selective Packaging of the Viral Genome and Other Components of Virus Particles 447





Concerted or Sequential Assembly 447





Recognition and Packaging of the Nucleic Acid Genome 448





Incorporation of Enzymes and Other Nonstructural Proteins 458





Acquisition of an Envelope 459





Sequential Assembly of Internal Components and Budding from a Cellular Membrane 459





Coordination of the Assembly of Internal Structures with Acquisition of the Envelope 460





Release of Virus Particles 460





Assembly and Budding at the Plasma Membrane 461





Assembly at Internal Membranes: the Problem of Exocytosis 464





Release of Nonenveloped Virus Particles 470





Maturation of Progeny Virus Particles 470





Proteolytic Processing of Structural Proteins 470





Other Maturation Reactions 474





Cell-to-Cell Spread 475





Perspectives 479





References 479





Study Questions 481





14 The Infected Cell 482





Introduction 483





Signal Transduction 483





Signaling Pathways 483





Signaling in Virus-Infected Cells 485





Gene Expression 489





Inhibition of Cellular Gene Expression 489





Differential Regulation of Cellular Gene Expression 492





Metabolism 496





Methods To Study Metabolism 496





Glucose Metabolism 497





The Citric Acid Cycle 501





Electron Transport and Oxidative Phosphorylation 502





Lipid Metabolism 504





Remodeling of Cellular Organelles 507





The Nucleus 509





The Cytoplasm 511





Perspectives 516





References 518





Study Questions 519





Appendix Structure, Genome Organization, and Infectious Cycles of Viruses Featured in This Book 521





Glossary 557





Index 563