Virus as populations: composition, complexity, dynamics, and biological implications
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Format: | Buch |
Sprache: | English |
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Amsterdam [u.a.]
Elsevier / Academic Press
2016 [2015 erschienen]
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Online-Zugang: | Inhaltsverzeichnis |
Beschreibung: | XVI, 412 S. graph. Darst. 19,1 x 2,9 x 23,5 cm |
Internformat
MARC
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264 | 1 | |a Amsterdam [u.a.] |b Elsevier / Academic Press |c 2016 [2015 erschienen] | |
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Datensatz im Suchindex
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adam_text | Titel: Virus as populations
Autor: Domingo, Esteban
Jahr: 2016
Contents
Foreword................................................................................................................................................xi
Acknowledgements.............................................................................................................................xiii
CHAPTER 1 Introduction to Virus Origins and Their Role in Biological
Evolution......................................................................................1
1.1 Considerations on Biological Diversity.......................................................................2
1.2 Some Questions of Current Virology and the Scope of This Book.............................3
1.3 The Staggering Ubiquity and Diversity of Viruses: Limited Morphotypes.................4
1.4 Origin of Life: A Brief Historical Account and Current Views..................................8
1.4.1 Early Synthesis of Oligonucleotides: A Possible Ancestral Positive
Selection...........................................................................................................10
1.4.2 A Primitive RNA World....................................................................................11
1.4.3 Life from Mistakes, Information from Noninformation: Origin of
Replicons..........................................................................................................13
1.4.4 Uptake of Energy and a Second Primitive Positive Selection..........................15
1.5 Theories of the Origins of Viruses.............................................................................17
1.5.1 Viruses Are Remnants of Primeval Genetic Elements.....................................18
1.5.2 Viruses Are the Result of Regressive Microbial Evolution..............................19
1.5.3 Viruses Are Liberated Autonomous Entities....................................................20
1.5.4 Viruses Are Elements for Long-Term Coevolution..........................................20
1.5.5 Viruses from Vesicles.......................................................................................21
1.6 Being Alive Versus Being Part of Life......................................................................22
1.7 Role of Viruses in the Evolution of the Biosphere....................................................23
1.7.1 Current Exchanges of Genetic Material...........................................................24
1.7.2 Symbiotic Relationships...................................................................................25
1.8 Virus and Disease......................................................................................................25
1.9 Overview and Concluding Remarks..........................................................................26
References..................................................................................................................27
CHAPTER 2 Molecular Basis of Genetic Variation of Viruses: Error-Prone
Replication................................................................................35
2.1 Universal Need of Genetic Variation.........................................................................36
2.2 Molecular Basis of Mutation.....................................................................................37
2.3 Types and Effects of Mutations.................................................................................40
2.4 Inferences on Evolution Drawn from Mutation Types..............................................43
2.5 Mutation Rates and Frequencies for DNA and RNA Genomes................................44
2.6 Evolutionary Origins, Evolvability, and Consequences of High Mutation Rates:
Fidelity Mutants.........................................................................................................48
V
vi Contents
2.7 Hypermutagenesis and its Application to Generate Variation: APOBEC
and ADAR Activities.................................................................................................52
2.8 Error-Prone Replication and Maintenance of Genetic Information: Instability of
Laboratory Viral Constructs......................................................................................53
2.9 Recombination in DNA and RNA Viruses................................................................54
2.9.1 Molecular Occurrence Versus Observed Recombination.................................56
2.10 Genome Segment Reassortment................................................................................58
2.11 Transition Toward Viral Genome Segmentation: Implications for
General Evolution......................................................................................................58
2.12 Mutation, Recombination, and Reassortment as Individual and Combined
Evolutionary Forces...................................................................................................59
2.13 Overview and Concluding Remarks..........................................................................62
References..................................................................................................................63
CHAPTER 3 Darwinian Principles Acting on Highly Mutable Viruses................73
3.1 Theoretical Frameworks to Approach Virus Evolution.............................................74
3.1.1 Theory and Experiment....................................................................................77
3.2 Genetic Variation, Competition, and Selection..........................................................78
3.3 Mutant Distributions During DNA and RNA Virus Infections.................................79
3.4 Positive Versus Negative Selection: Two Sides of the Same Coin............................81
3.5 Selection and Random Drift......................................................................................83
3.6 Viral Quasispecies.....................................................................................................84
3.6.1 The Origins of Quasispecies Theory................................................................84
3.6.2 Deterministic Versus Stochastic Quasispecies..................................................86
3.6.3 Mutant Spectra, Master Genomes, and Consensus Sequences.........................89
3.6.4 Measurement of Quasispecies Complexity: Insights from
New Generation Sequencing...........................................................................91
3.6.5 Some Key Points on the Impact of Quasispecies in Virology..........................97
3.7 Sequence Space and State Transitions.......................................................................99
3.7.1 Virus Evolution as a Movement in Sequence Space.........................................99
3.7.2 Exploration of Sequence Space and the Sampling Problem: Viral
Population Size as a Key Parameter...............................................................101
3.8 Modulating Effects of Mutant Spectra: Complementation and Interference:
An Ensemble as the Unit of Selection.....................................................................104
3.8.1 Molecular Mechanisms of Complementation and Interference......................108
3.8.2 Individual Versus Group Selection.................................................................110
3.8.3 Stochastic Effects in Selected Collectivities...................................................110
3.9 Viral Populations in Connection with Biological Complexity................................111
3.10 Overview and Concluding Remarks........................................................................113
References................................................................................................................114
Contents vii
CHAPTER 4 Interaction of Virus Populations with Their Hosts.......................123
4.1 Contrasting Viral and Host Population Numbers....................................................124
4.1.1 Productive Power of Some Viral Infections....................................................126
4.1.2 Population Size Limitations and the Effect of Bottlenecks: The Effective
Population Size...............................................................................................127
4.2 Types of Constraints and Evolutionary Trade-Offs in Virus-Host Interactions.......131
4.2.1 Long-term History Dictates Basal Constraints...............................................132
4.2.2 Cell-dependent Constraints: No Free Lunch..................................................132
4.2.3 Constraints in Host Organisms: Contrast with Man-made Antiviral
Interventions...................................................................................................134
4.3 Codon Usage as a Selective Constraint: Virus Attenuation Through Codon
and Codon-pair Deoptimization..............................................................................135
4.3.1 The Synonymous Codon Space Can Affect an Evolutionary Outcome.........137
4.4 Modifications of Host Cell Tropism and Host Range.............................................138
4.4.1 Nonstructural Viral Proteins and RNA in Cell Tropism and Host Range
of Viruses........................................................................................................142
4.5 Trait Coevolution: Mutual Influences Between Antigenic Variation and
Tropism Change.......................................................................................................144
4.6 Escape from Antibody and Cytotoxic T Cell Responses in Viral Persistence:
Fitness Cost..............................................................................................................147
4.7 Antigenic Variation in the Absence of Immune Selection.......................................148
4.8 Constraints as a Demand on Mutation Rate Levels.................................................149
4.9 Multifunctional Viral Proteins in Interaction with Host Factors:
Joker Substitutions...................................................................................................151
4.10 Alternating Selective Pressures: The Case of Arboviruses......................................153
4.11 Overview and Concluding Remarks........................................................................154
References................................................................................................................156
CHAPTER 5 Viral Fitness as a Measure of Adaptation...................................169
5.1 Origin of the Fitness Concept and Its Relevance to Viruses....................................170
5.1.1 Measurement of Viral Fitness.........................................................................170
5.1.2 Power and Limitations of Fitness Measurements...........................................172
5.1.3 Dissection of Fitness Determinants................................................................173
5.2 The Challenge of Fitness In Vivo.............................................................................174
5.3 Fitness Landscapes..................................................................................................175
5.3.1 Justification of Ruggedness in Fitness Landscapes for Viruses.....................177
5.4 Population Factors on Fitness Variations: Collective Fitness and
Perturbations by Environmental Heterogeneity.......................................................178
5.5 Quasispecies Memory and Fitness Recovery..........................................................180
5.5.1 Implications of Quasispecies Memory: Harbinger Mutations........................183
viii Contents
5.6 The Relationship Between Fitness and Virulence...................................................184
5.7 Fitness Landscapes for Survival: The Advantage of the Flattest.............................187
5.8 Fitness and Function................................................................................................189
5.9 Epidemiological Fitness...........................................................................................189
5.10 Overview and Concluding Remarks........................................................................190
References................................................................................................................191
CHAPTER 6 Virus Population Dynamics Examined with Experimental Model
Systems...................................................................................197
6.1 Value of Experimental Evolution.............................................................................198
6.2 Experimental Systems in Cell Culture and In Vivo..................................................199
6.2.1 To Culture is to Disturb ...............................................................................200
6.2.2 Experimental Evolution In Vivo......................................................................202
6.3 Viral Dynamics in Controlled Environments: Alterations of Viral
Subpopulations........................................................................................................203
6.4 Persistent Infections in Cell Culture: Virus-cell Coevolution..................................205
6.4.1 Back Again 4000 Million Years: Contingency in Evolution..........................208
6.5 Teachings from Plaque-to-Plaque Transfers............................................................209
6.5.1 Muller s Ratchet and the Advantage of Sex....................................................212
6.5.2 Molecular Basis of Fitness Decrease: Deep Fluctuations, Massive
Extinctions, and Rare Survivors.....................................................................213
6.6 Limits to Fitness Gain and Loss..............................................................................215
6.7 Competitive Exclusion Principle and Red Queen Hypothesis.................................216
6.7.1 Contingent Neutrality in Virus........................................................................218
6.8 Studies with Reconstructed Quasispecies................................................................218
6.9 Quasispecies Dynamics in Cell Culture and In Vivo...............................................219
6.10 Overview and Concluding Remarks........................................................................219
References................................................................................................................220
CHAPTER 7 Long-term Virus Evolution in Nature...........................................227
7.1 Introduction to the Spread of Viruses. Outbreaks, Epidemics, and Pandemics.......228
7.2 Reproductive Ratio as a Predictor of Epidemic Potential. Indeterminacies in
Transmission Events................................................................................................229
7.3 Rates of Virus Evolution in Nature..........................................................................232
7.3.1 Influence of the Time of Sampling.................................................................233
7.3.2 Interhost Versus Intrahost Rate of Evolution..................................................235
7.3.3 Rate Discrepancies and the Clock Hypothesis...............................................237
7.4 Long-term Antigenic Diversification of Viruses.....................................................238
7.4.1 Widely Different Number of Serotypes Among Genetically Variable
Viruses............................................................................................................239
7.4.2 Similar Frequencies of Monoclonal Antibody-escape Mutants in Viruses
Differing in Antigenic Diversity.....................................................................242
Contents ix
7.5 Comparing Viral Genomes. Sequence Alignments and Databases.........................243
7.6 Phylogenetic Relationships Among Viruses. Evolutionary Models........................246
7.7 Extinction, Survival, and Emergence of Viral Pathogens. Back to the
Mutant Clouds.........................................................................................................248
7.7.1 Factors in Viral Emergence.............................................................................251
7.7.2 Complexity Revisited.....................................................................................255
7.8 Overview and Concluding Remarks........................................................................255
References................................................................................................................256
CHAPTER 8 Quasispecies Dynamics in Disease Prevention and Control.........263
8.1 Medical Interventions as Selective Constraints.......................................................264
8.2 Different Manifestations of Virus Evolution in the Prevention and Treatment
of Viral Disease........................................................................................................265
8.3 Antiviral Vaccines and the Adaptive Potential of Viruses.......................................266
8.3.1 Some Requirements for the Design of Vaccines to Control Highly
Variable Viruses..............................................................................................266
8.3.2 Vaccination-Induced Evolution.......................................................................268
8.4 Resistance to Antiviral Inhibitors............................................................................269
8.4.1 Replicative Load and Antiviral Resistance.....................................................271
8.4.2 Barriers to Drug Resistance............................................................................275
8.4.3 Drug Efficacy, Mutant Frequencies, and Selection of Escape Mutants..........277
8.4.4 Phenotypic Barrier and Selective Strength.....................................................280
8.4.5 Multiple Pathways and Evolutionary History in the Acquisition of Drug
Resistance.......................................................................................................281
8.5 Molecular Mechanisms of Antiviral Resistance......................................................282
8.5.1 Some Examples with HIV-1...........................................................................282
8.5.2 Mutation Site and Functional Barrier.............................................................283
8.5.3 Additional Considerations on Escape Mutant Frequencies............................283
8.6 Antiviral Resistance Without Prior Exposure to Antiviral Agents..........................285
8.7 Fitness or a Fitness-Associated Trait as a Multidrug-Resistance Mechanism.........285
8.8 Viral Load, Fitness, and Disease Progression..........................................................288
8.9 Limitations of Simplified Reagents and Small Molecules as Antiviral Agents......289
8.10 Hit Early, Hit Hard ...............................................................................................290
8.11 Information and Global Action................................................................................291
8.12 Overview and Concluding Remarks........................................................................292
References................................................................................................................293
CHAPTER 9 Trends in Antiviral Strategies....................................................299
9.1 The Challenge..........................................................................................................300
9.1.1 Virus as Moving Targets.................................................................................302
9.2 Practiced and Proposed Strategies to Confront the Moving Target
Challenge with Antiviral Inhibitors.........................................................................302
x Contents
9.2.1 Combination Treatments.................................................................................302
9.2.2 Split Treatments..............................................................................................303
9.2.3 Targeting Cellular Functions...........................................................................304
9.2.4 Use of Drugs That Stimulate the Host Innate Immune System......................305
9.2.5 Combined Use of Immunotherapy and Chemotherapy..................................305
9.3 Lethal Mutagenesis and the Error Threshold...........................................................305
9.3.1 Reconciliation of Theory and Experiment: A Proposal..................................306
9.4 Virus Extinction by Mutagenic Agents....................................................................311
9.4.1 The Search for New Mutagenic Nucleotide Analogs.....................................316
9.5 Lethal Mutagenesis In Vivo: Complications Derived From Multiple
Mechanisms of Drug Action —The Case of Ribavirin...........................................317
9.6 Virus Resistance to Mutagenic Agents: Multiple Mechanisms and Evidence of
Abortive Escape Pathways.......................................................................................319
9.6.1 Unpredictable Effects of Some Polymerase Substitutions.............................321
9.6.2 Polymerase Fidelity and Modulation of Nucleotide Incorporation................321
9.7 Virus Extinction as the Outcome of Replacement of Virus Subpopulations:
Tempo and Mode of Mutation Acquisition..............................................................323
9.8 The Interplay Between Inhibitors and Mutagenic Agents in Viral Populations:
Sequential Versus Combination Treatments............................................................324
9.9 Prospects for a Clinical Application of Lethal Mutagenesis...................................327
9.10 Some Atypical Proposals.........................................................................................328
9.11 Overview and Concluding Remarks........................................................................329
References................................................................................................................330
CHAPTER 10 Collective Population Effects in Nonviral Systems......................339
10.1 Concept Generalization...........................................................................................339
10.2 Viruses and Cells: The Genome Size-Mutation-Time Coordinates Revisited.........340
10.2.1 A Comparison of Antiviral and Antibiotic Resistance...............................342
10.3 Darwinian Principles and Intrapopulation Interactions Acting on
Cell Populations.......................................................................................................343
10.4 The Dynamics of Unicellular Parasites in the Control of Parasitic Disease............344
10.5 Cancer Dynamics: Heterogeneity and Group Behavior..........................................345
10.5.1 The Two-Component Theory of Cancer: Similarities with Other
Biological Systems.....................................................................................346
10.6 Collective Behavior of Prions..................................................................................347
10.7 Molecular Mechanisms of Variation and Clonality in Evolution............................349
10.8 Genomes, Clones, Consortia, Networks, and Power Laws......................................351
10.9 An Additional Level of Virus Vulnerability?...........................................................354
10.10 Overview and Concluding Remarks........................................................................356
References................................................................................................................357
Further Reading..................................................................................................................................363
Author Index.......................................................................................................................................367
Subject Index......................................................................................................................................399
|
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author | Domingo, Esteban 1943- |
author_GND | (DE-588)13067687X |
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dewey-raw | 579.2 |
dewey-search | 579.2 |
dewey-sort | 3579.2 |
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physical | XVI, 412 S. graph. Darst. 19,1 x 2,9 x 23,5 cm |
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publisher | Elsevier / Academic Press |
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spelling | Domingo, Esteban 1943- Verfasser (DE-588)13067687X aut Virus as populations composition, complexity, dynamics, and biological implications Esteban Domingo Amsterdam [u.a.] Elsevier / Academic Press 2016 [2015 erschienen] XVI, 412 S. graph. Darst. 19,1 x 2,9 x 23,5 cm txt rdacontent n rdamedia nc rdacarrier virology cabt epidemiology cabt population dynamics cabt viruses cabt interactions cabt HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028338164&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
spellingShingle | Domingo, Esteban 1943- Virus as populations composition, complexity, dynamics, and biological implications virology cabt epidemiology cabt population dynamics cabt viruses cabt interactions cabt |
title | Virus as populations composition, complexity, dynamics, and biological implications |
title_auth | Virus as populations composition, complexity, dynamics, and biological implications |
title_exact_search | Virus as populations composition, complexity, dynamics, and biological implications |
title_full | Virus as populations composition, complexity, dynamics, and biological implications Esteban Domingo |
title_fullStr | Virus as populations composition, complexity, dynamics, and biological implications Esteban Domingo |
title_full_unstemmed | Virus as populations composition, complexity, dynamics, and biological implications Esteban Domingo |
title_short | Virus as populations |
title_sort | virus as populations composition complexity dynamics and biological implications |
title_sub | composition, complexity, dynamics, and biological implications |
topic | virology cabt epidemiology cabt population dynamics cabt viruses cabt interactions cabt |
topic_facet | virology epidemiology population dynamics viruses interactions |
url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028338164&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
work_keys_str_mv | AT domingoesteban virusaspopulationscompositioncomplexitydynamicsandbiologicalimplications |