This book unifies general concepts of plant and animal virus evolution and covers a broad range of topics related to theoretical and experimental aspects of virus population dynamics and viral fitness.
Timely topics such as viral mechanisms to cope with antiviral agents, the adaptability of the virus to new hosts, emergence of new viral phenotypes, and the connections between short- and long-term virus evolution are included.
By comparing plant and animal viruses, universal mechanisms responsible for fitness variations, viral emergence and disease mechanisms are explored.
Although emphasis is put on specific plant and human viral pathogens, relevant similarities and differences to other viruses are highlighted. Additionally, readers will learn more about the adaptability of coronaviruses, including the recently emerged SARS-CoV-2, the causative agent of the COVID-19 pandemic.
The book is aimed at students and scientists interested in basic and applied aspects of plant and animal virus population dynamics and evolution.
Author(s): Esteban Domingo, Peter Schuster, Santiago F. Elena, Celia Perales
Series: Current Topics in Microbiology and Immunology, 439
Publisher: Springer
Year: 2023
Language: English
Pages: 349
City: Cham
Foreword
Contents
Virus Evolution on Fitness Landscapes
1 Introduction
2 Landscape Models and Landscape Features
2.1 Classes of Landscapes
2.2 Abstract Rugged Landscapes
2.3 Additivity, Epistasis, and Elementary Landscapes
2.4 Kauffman's NK Model
2.5 Neutrality
2.6 Holey Landscapes
3 The RNA Model
3.1 RNA Secondary Structures
3.2 Counting Structures
3.3 Minimal Free Energy Structures
3.4 Neutral Networks and Compatible Sequences
3.5 Neutral Networks and Random Graphs
3.6 Evolution and Neutral Networks
3.7 Shape Space Covering
3.8 Suboptimal Structures and Compatibility
3.9 Kinetic Effects of RNA Folding
4 Topology of Sequence and Shape Spaces
4.1 Accessibility
4.2 Evolution in silico and Discontinuous Transitions
4.3 Accessibility and the Topology of Phenotype Space
4.4 Coarse Graining and Quotients
5 Quasispecies—Populations in Sequence Space
5.1 Replication and Selection
5.2 Replication, Mutation and Selection
5.3 Quasispecies on Uniform Class Landscapes
5.4 Simple Fitness Landscapes
5.5 Realistic Random Landscapes
5.6 Finite Population Size
6 Empirical Landscapes
6.1 Estimating Landscapes Parameters
6.2 Local Inference of Landscapes
7 Conclusions and Outlook
References
Viral Fitness Landscapes Based on Self-organizing Maps
1 Introduction
2 Fitness Landscapes
3 Self-organizing Maps
4 Real Fitness Landscapes
4.1 HIV-1 Biological Clones
4.2 SOM-Based 3D Fitness Landscape from Complete HIV-1 RNA Sequences, Using Experimentally Determined Fitness Values
4.3 SOM-Based 3D Fitness Landscape from HIV-1 RNA Sequences of the V1-V2 Region in Env Gene, Based on Experimentally Determined Fitness Values. Analysis of Related Variants
5 Fitness Landscapes Based on Haplotype Frequencies
5.1 HCV Populations. Ultra-Deep HCV RNA Sequencing
5.2 SOM-Based 3D Fitness Landscape Derived from Haplotype Frequencies
6 Discussion
References
Virus Evolution Faced to Multiple Host Targets: The Potyvirus—Pepper Case Study
1 Introduction
2 A Plethora of Recessive Resistances Mediated by eIF4E Alleles with Contrasted Spectrum of Action and Durability: A Model of Plant-Virus Co-evolution
3 Quantitative Resistance as a Mixture of Virus-Specific and Generic Effects
4 A Hypothetical Scenario for Evolution of Complex Resistance Systems
5 Conclusion
References
The Role of Extensive Recombination in the Evolution of Geminiviruses
1 Introduction
2 The Family Geminiviridae
2.1 General Features, Classification, Genome Organization and Replication
2.2 DNA Satellites Associated with Geminiviruses
3 Recombination in the Family Geminiviridae: Occurrence and Patterns
4 Experimental Evolution of Recombination
5 Recombination Events with Evolutionary and Pathological Implications
5.1 Tomato Yellow Leaf Curl Viruses in the Western Mediterranean Basin
5.2 Cassava Mosaic Viruses in Sub-Saharan Africa
5.3 Cotton Leaf Curl Viruses in Pakistan
6 Recombination Events Involving DNA Satellites
6.1 Recombination Between Geminiviruses and DNA Satellites
6.2 Recombination Between DNA Satellites
7 Conclusion
References
Plant Virus Adaptation to New Hosts: A Multi-scale Approach
1 The Multi-scale Nature of Virus Evolution
1.1 Challenges for Modeling Multi-scale Evolving Systems
2 The Pervasiveness of Fitness Trade-Offs
3 The Lowest Level: Evolution Within Cells
4 Cell-To-Cell Transmission and the Colonization of Different Tissues
4.1 The Cellular Contagion Rate and the Spread of Infection
4.2 MOI and the Effective Number of Infectious Units Per Cell
5 Beyond the Individual Host
5.1 Plant Virus Spread and the Basic Reproductive Number
5.2 Constraints Associated to Horizontal and Vertical Transmission Modes
5.3 A Trade-Off Between Within-Host Accumulation and Virulence
5.4 Transmission Bottlenecks Between Hosts
6 Evolutionary Consequences of Host Heterogeneity in the Landscape
6.1 The Complexity of Virus-Host Infection Networks
7 An Integrative New Paradigm: The Multilayer Network
8 Concluding Remarks
References
Viral Fitness, Population Complexity, Host Interactions, and Resistance to Antiviral Agents
1 Fitness Concept and Its Application to Viruses
2 Experimental Fitness Measurements in Cell Culture
3 Experimental Fitness Measurements in vivo
4 Limitations of Fitness Determinations
5 Overview of Fitness Landscapes for Viruses
5.1 Fitness and Virus Propagation Regimen
5.2 Intra-mutant Spectrum Fitness Profiles
6 Fitness in the Development of Antiviral Resistance
6.1 Fitness Cost of Escape Mutants
6.2 High Fitness as Promoter of Antiviral Resistance
7 Mechanisms of Antiviral Resistance Alternative to Direct Selection of Escape Mutants
8 Lessons for COVID-19
9 Conclusions and Prospects
References
Mechanisms and Consequences of Genetic Variation in Hepatitis C Virus (HCV)
1 HCV Introduction
1.1 HCV Impact on Human Health
1.2 Molecular Biology of HCV
1.3 HCV Phylogeny
2 Mechanisms of Genetic Diversity
2.1 Mutation
2.2 Recombination
2.3 Impact of Genetic Variability
3 Final Considerations
References
Mammarenavirus Genetic Diversity and Its Biological Implications
1 Arenaviridae: History and Current Taxonomy
2 Mammarenavirus Impact on Virology and Human Health
2.1 Mammarenavirus Impact on Human Health
2.2 Mammarenavirus as Highly Tractable Experimental Systems for the Investigation of Virus-Host Interactions
3 Molecular and Cell Biology of Mammarenaviruses
3.1 Mammarenavirus Genome Organization
3.2 Mammarenavirus Life Cycle
4 Mammarenavirus Phylogenetic Relationships
5 Mechanisms of Mammarenavirus Genetic Diversity
5.1 Mammarenavirus Mutation Frequencies
5.2 RNA Recombination in Mammarenaviruses
5.3 Mammarenavirus Genomic Reassortments
6 Mammarenavirus Origin and Geographic Distribution
7 Co-evolution of Mammarenaviruses and Their Natural Reservoirs: Intra- versus Inter-host Genetic Variation of Mammarenaviruses
8 Contribution of Genetic Variability to Mammarenavirus Pathogenesis
8.1 Contribution of Viral Quasispecies to Arenavirus Pathogenesis
8.2 Selection of Immunosuppressive Variants During LCMV Persistence
8.3 LCMV Variants and Growth Hormone Deficiency Syndrome
9 Lassa Virus: Origin, Evolution, and Contribution of Genetic Variability to Detection and Pathogenesis
10 Implications of Mammarenavirus Genetic Variability for the Development of Vaccines and Antiviral Drugs
10.1 Mammarenavirus Genetic Variation and Vaccine Development
10.2 Lethal Mutagenesis as a Novel Antiviral Strategy to Combat Mammarenavirus Infections
10.3 Novel Combination Drug Therapy to Combat Mammarenavirus Infections
References
Genome Structure, Life Cycle, and Taxonomy of Coronaviruses and the Evolution of SARS-CoV-2
1 An Introduction to Coronaviruses
2 Discontinuous transcription and subgenomic mRNAs
3 Coronaviruses beyond their sequence: RNA structures
4 SARS-CoV-2 Evolution and Epidemiological Dynamics
5 Disease Spread and Epidemiology
References
Epilogue: CTMI. 13.3.22
