Virus As Populations Composition Complexity Quasispecies Dynamics and Biological Implications 2nd Edition by Esteban Domingo ISBN 0128163313 978-0128163313

Cover image

Title page

Table of Contents

Copyright

Foreword

Preface for the second edition

Acknowledgments

Chapter 1. Introduction to virus origins and their role in biological evolution

1.1. Considerations on biological diversity

1.2. Some questions of current virology and the scope of this book

1.3. The staggering ubiquity and diversity of viruses: limited morphotypes

1.4. Origin of life: a brief historical account and current views

1.5. Theories of the origins of viruses

1.6. Teachings from mycoviruses

1.7. Being alive versus being part of life

1.8. Virus and disease

1.9. Viral and cellular dynamics and the tree of life

1.10. Overview and concluding remarks

Chapter 2. Molecular basis of genetic variation of viruses: error-prone replication

2.1. Universal need for genetic variation

2.2. Molecular basis of mutation

2.3. Types and effects of mutations

2.4. Inferences on evolution drawn from mutation types

2.5. Mutation rates and frequencies for DNA and RNA genomes

2.6. Evolutionary origins, evolvability, and consequences of high mutation rates: fidelity mutants

2.7. Hypermutagenesis and its application to generating a variation: APOBEC and ADAR activities

2.8. Error-prone replication and maintenance of genetic information: instability of laboratory viral constructs

2.9. Recombination in DNA and RNA viruses

2.10. Genome segment reassortment

2.11. Transition toward viral genome segmentation: implications for general evolution

2.12. Mutation, recombination, and reassortment as individual and combined evolutionary forces

2.13. Overview and concluding remarks

Chapter 3. Darwinian principles acting on highly mutable viruses

3.1. Theoretical frameworks to approach virus evolution

3.2. Genetic variation, competition, and selection

3.3. Mutant distributions during DNA and RNA virus infections

3.4. Positive versus negative selection: two sides of the same coin

3.5. Selection and random drift

3.6. Viral quasispecies

3.7. Sequence space and state transitions

3.8. Modulating effects of mutant spectra: interference, cooperation and complementation. An ensemble as the unit of selection

3.9. Viral populations in connection with biological complexity

3.10. Overview and concluding remarks

Chapter 4. Interaction of virus populations with their hosts

4.1. Contrasting viral and host population numbers

4.2. Types of constraints and evolutionary trade-offs in virus-host interactions

4.3. Codon usage as a selective constraint: virus attenuation through codon and codon-pair deoptimization

4.4. Modifications of host cell tropism and host range

4.5. Trait coevolution: mutual influences between antigenic variation and tropism change

4.6. Escape from antibody and cytotoxic T cell responses in viral persistence: fitness cost

4.7. Antigenic variation in the absence of immune selection

4.8. Constraints as a demand on mutation rate levels

4.9. Multifunctional viral proteins in interaction with host factors: joker substitutions

4.10. Alternating selective pressures: the case of arboviruses

4.11. Overview and concluding remarks

Chapter 5. Viral fitness as a measure of adaptation

5.1. Origin of the fitness concept and its relevance to viruses

5.2. The challenge of fitness in vivo

5.3. Fitness landscapes

5.4. Population factors on fitness variations: collective fitness and perturbations by environmental heterogeneity

5.5. Quasispecies memory and fitness recovery

5.6. The relationship between fitness and virulence

5.7. Fitness landscapes for survival: the advantage of the flattest

5.8. Fitness and function

5.9. Epidemiological fitness

5.10. Overview and concluding remarks

Chapter 6. Virus population dynamics examined with experimental model systems

6.1. Value of experimental evolution

6.2. Experimental systems in cell culture and in vivo

6.3. Viral dynamics in controlled environments: alterations of viral subpopulations

6.4. Persistent infections in cell culture: virus-cell coevolution

6.5. Teachings from plaque-to-plaque transfers

6.6. Limits to fitness gain and loss

6.7. Competitive exclusion principle and Red Queen hypothesis

6.8. Studies with reconstructed quasispecies

6.9. Quasispecies dynamics in cell culture and in vivo

6.10. Overview and concluding remarks

Chapter 7. Long-term virus evolution in nature

7.1. Introduction to the spread of viruses. Outbreaks, epidemics, and pandemics

7.2. Reproductive ratio as a predictor of epidemic potential. Indeterminacies in transmission events

7.3. Rates of virus evolution in nature

7.4. Long-term antigenic diversification of viruses

7.5. Comparing viral genomes. Sequence alignments and databases

7.6. Phylogenetic relationships among viruses. Evolutionary models

7.7. Extinction, survival, and emergence of viral pathogens. Back to the mutant clouds

7.8. Overview and concluding remarks

Chapter 8. Quasispecies dynamics in disease prevention and control

8.1. Medical interventions as selective constraints

8.2. Different manifestations of virus evolution in the prevention and treatment of viral disease

8.3. Antiviral vaccines and the adaptive potential of viruses

8.4. Resistance to antiviral inhibitors

8.5. Molecular mechanisms of antiviral resistance

8.6. Antiviral resistance without prior exposure to antiviral agents

8.7. Fitness or a fitness-associated trait as a multidrug-resistance mechanism

8.8. Viral load, fitness, and disease progression

8.9. Limitations of simplified reagents and small molecules as antiviral agents

8.10. “Hit early, hit hard”

8.11. Information and global action

8.12. Overview and concluding remarks

Chapter 9. Trends in antiviral strategies

9.1. The challenge

9.2. Practiced and proposed strategies to confront the moving target challenge with antiviral inhibitors

9.3. Lethal mutagenesis and the error threshold

9.4. Virus extinction by mutagenic agents

9.5. Lethal mutagenesis in vivo: complications derived from multiple mechanisms of drug action—the case of ribavirin

9.6. Virus resistance to mutagenic agents: multiple mechanisms and evidence of abortive escape pathways

9.7. Virus extinction as the outcome of replacement of virus subpopulations: tempo and mode of mutation acquisition

9.8. The interplay between inhibitors and mutagenic agents in viral populations: sequential versus combination treatments

9.9. Prospects for a clinical application of lethal mutagenesis

9.10. Some atypical proposals

9.11. Overview and concluding remarks

Chapter 10. Collective population effects in nonviral systems

10.1. Concept generalization

10.2. Viruses and cells: the genome size-mutation-time coordinates revisited

10.3. Darwinian principles and intrapopulation interactions acting on bacterial cell populations

10.4. The dynamics of unicellular parasites in the control of parasitic disease

10.5. Cancer dynamics: heterogeneity and group behavior

10.6. Collective behavior of prions

10.7. Molecular mechanisms of variation and clonality in evolution

10.8. Genomes, clones, consortia, and networks

10.9. An additional level of virus vulnerability?

10.10. Overview and concluding remarks

Subject Index

Author Index