Genetics and Evolution of Infectious Diseases

3rd Edition - July 9, 2024
Editor: Michel Tibayrenc
Language: English
Hardback ISBN:
9 7 8 - 0 - 4 4 3 - 2 8 8 1 8 - 0
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 2 8 8 1 9 - 7

Genetics and Evolution of Infectious Diseases, Third Edition discusses the evolving field of infectious diseases and their continued impact on the health of populations, especiall… Read more

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Genetics and Evolution of Infectious Diseases, Third Edition discusses the evolving field of infectious diseases and their continued impact on the health of populations, especially in resource-limited areas of the world where they must confront the dual burden of death and disability due to infectious and chronic illnesses. Although substantial gains have been made in public health interventions for the treatment, prevention, and control of infectious diseases, in recent decades the world has witnessed the emergence of the human immunodeficiency virus (HIV) and the COVID-19 pandemic, increasing antimicrobial resistance, and the emergence of many new bacterial, fungal, parasitic, and viral pathogens.

Fully updated and revised, this new edition presents the consequences of such diseases, the evolution of infectious diseases, the genetics of host-pathogen relationship, and the control and prevention strategies that are, or can be, developed. This book offers valuable information to biomedical researchers, clinicians, public health practitioners, decisions-makers, and students and postgraduates studying infectious diseases, microbiology, medicine, and public health that is relevant to the control and prevention of neglected and emerging worldwide diseases.

Cover image
Title page
Table of Contents
Copyright
Contributors
Part 1. Methodological/Generalist Chapters
Chapter 1. A New Official Definition of Virus Species Has Led to a Controversial Linnaean Latinized Binomial Format of Virus Classification
1. The Nature of Virus Classification
2. The Late Acceptance of the Species Concept in Virus Classification
3. Properties Used for Demarcating New Virus Species Are Not the Same as the Diagnostic Properties Used for Identifying the Members of an Established Virus Species
4. Popular Anglicized Non-Latinized Virus Species Names Were Subsequently Abandoned
5. The ICTV Introduced Names of Virus Species that Correspond to the Italicized Version of the Virus Name, Thereby Creating Unnecessary Confusion
6. The New ICTV Definition of Virus Species Is at Odds with the Definition of Species in Other Biological Classifications
7. Adrian Gibbs Questions the Merits of a New ICTV Latinized Binomial Nomenclature for Virus Species Associated with Metagenomic Sequences
8. Ontology and Epistemology of Viruses and Living Organisms
Chapter 2. A Completionist Approach to Discovering and Characterizing Bacterial Diversity
1. Introduction—Toward a Completionist Bacterial Systematics
2. Genomes Enable Completionist Systematics at the Species Level
3. The Ecological Breadth of Recognized Species Taxa
4. Sexual Isolation and Ecological Divergence in the Origins of Species-like Lineages That can Coexist Indefinitely
5. How Modes of Speciation Affect the Correspondence Between Sequence Clusters and Ecotypes
6. Genomes Enable Completionist Systematics at the Ecotype Level
7. Rapprochement Between Theory-based and Tradition-based Systematics of Bacteria
Chapter 3. Population Structure of Pathogenic Bacteria
1. Introduction
2. Recombination and Selection in Bacterial Populations
3. Bacterial Population Structure Within and Between Hosts
4. Geography and Bacterial Population Structure
5. Conclusions
Chapter 4. Diverse Strategies and Evolutionary Histories of Fungal Pathogens
1. Introduction
2. A Brief Overview of Fungal Pathogens
3. Selected Examples of Human Pathogens
4. Facultative Pathogenesis and Adaptation Versus Exaptation
5. Virulence Factors
6. Host and Environment Populations, and Emergence of New Fungal Pathogens
7. Conclusions
Chapter 5. Molecular Epidemiology of Pathogenic Microorganisms and the Predominant Clonal Evolution Model
1. Introduction: What Is Molecular Epidemiology?
2. Brief Recall on the PCE Model
3. Bacterial Species
4. Parasite Species
5. Yeasts
6. Concluding Remarks
Glossary of Specialized Terms
Chapter 6. Parasite–Host Coevolution
1. Introduction
2. Common Parasites and Their Definition/Description
3. Viruses
4. Red Queen Hypothesis and the Evolutionary Arms Race
5. Rapidly Evolving Pathogens—RNA Viruses as a Model
6. Where Did Viruses Come From? Viral Evolution
7. How Do Viruses Evolve and Selection Pressures Not Just on Individual Pathogens With Mutations, but on Groups of Pathogens? Mutant Clouds/Quasispecies
8. Phylogenetics Reveals Coevolutionary Patterns
9. Parasite–Host Relationships in Human Infectious Diseases
10. Parasite–Host Relationships in Animal Infectious Diseases
11. Host Immunogenetics Adaptations
12. Parasite Manipulation of Host Behavior
13. A Parasite-absent World
14. Conclusions
Chapter 7. Human Genetic Variability and Transmissible Diseases
1. Introduction
2. A Population Genetics∗ Framework for the Study of Transmissible Diseases
3. Communicable Diseases: A Phenomenon of Co-Evolution Involving Two or Three Actors
4. Conclusions on Human Genetic Variability and Susceptibility to Communicable Diseases
Glossary of Specialized Terms
Chapter 8. Pathogens as Tracers of Past Human Demography and Migrations
1. Introduction
2. Pathogen Genomics to Infer Host History
3. Bacteria
4. Viruses
5. Conclusion
Chapter 9. Evolutionary Responses to Infectious Disease
1. Introduction
2. Parasites as Our Friends
3. Demography and Parasites
4. Agriculture
5. Some Lessons from Malaria
6. The Columbian Exchange
7. Disease and Standard of Living in Preindustrial Societies: A Simple Model
8. Population Limitation
9. Disease, Mating, and Reproductive Strategy
10. Prosperity and the Postindustrial Era Mortality Decline
Chapter 10. Infectious Disease Genomics
1. Introduction
2. Vaccine Target
3. New Drug Discovery
4. Drug Target
5. Therapeutic Response and Drug Resistance
6. Vector Control
7. Clinical Application
8. Conclusion
Chapter 11. Proteomics and Host–Pathogen Interactions: Still a Bright Future?
1. Introduction
2. Interest of Proteomics to Study Host–(Vector)–Pathogen Interactions
3. Retrospective of Pioneering Proteomics Studies
4. Evolution of Conceptual Approaches to Decipher the Host–Pathogen Interactions for Microorganisms With Simple or Complex Life Cycle
5. Five-Year View
6. Conclusions
Glossary
Short Biographical Lines for Contributors
Chapter 12. Genomic Epidemiology and Surveillance of Antimicrobial Resistance
1. Antimicrobial Resistance: A Current Major Threat
2. Genomic Epidemiology and Surveillance in the Fight Against AMR
3. Genotypic Prediction of Antimicrobial Resistance
4. Case Studies: Genomics and AMR in Clinically Relevant Bacteria
5. Future Perspectives: A Gold Standard Becoming Routine?
6. Conclusions
Chapter 13. Evolution of Resistance to Insecticides in Disease Vectors
1. Introduction
2. Insecticide Classification and Modes of Action
3. Mechanisms of Resistance
4. Methods for Testing and Monitoring Insecticide Resistance in Mosquitoes
5. Features of Insecticide Resistance
6. Factors Governing the Evolution of Insecticide Resistance
7. Insecticide Resistance in Disease Vectors
8. Approaches to Insecticide Resistance Management
9. Conclusion
Chapter 14. Genetics of Tsetse Flies (Diptera: Glossinidae), Vectors of Human and Animal Trypanosomoses
1. Introduction
2. Reminder on the Taxonomy of Tsetse Flies
3. Some Important Life Traits of Tsetse regarding Population Genetics
4. Populations Genetics of Tsetse Flies
5. Future Work
Chapter 15. Genetics of the Triatominae (Hemiptera: Reduviidae), Vectors of Chagas Disease
1. Introduction
2. The Triatominae, Vectors of Chagas Disease
3. Evolution and Taxonomy of the Triatominae
4. Cytogenetics of the Triatominae
5. Genetic Diversity and Population Structure of Triatominae Species
6. Conclusions and Future Directions
Chapter 16. Modern Morphometrics of Arthropods: A Phenotypic Approach to Species Recognition and Population Structure
1. Introduction
2. Landmark-Based Geometric Morphometry
3. Pseudolandmark-Based Geometric Morphometry (Outlines)
4. Allometry
5. Some Considerations About the Genetics of Metric Change
6. Some Considerations About Phenotypic Variation
7. Taxonomic Questions
8. Population Structure Studies
9. Conclusion
Glossary
CHAPTER 17. Microbial Sequence Typing Strategies for Genetic and Genomic Data
1. Introduction
2. DNA-Based Typing Approaches
3. DNA-Based Typing Analyses
4. Microbial Sequence Typing Applications
5. Conclusions and Prospects
Chapter 18. Proteomics, Bioinformatics, and Infectious Diseases
1. Introduction
2. Proteomics of Infectious Diseases
3. Combining Proteomics and Bioinformatics Towards Fighting Infectious Diseases
4. Concluding Remarks and Future Directions
Chapter 19. Genomics of Infectious Diseases and Private Industry
1. Introduction
2. Customers and Applications
3. Commercial Sequencing Instruments, Reagents, and Software
4. Library Preparation
5. Genomics Service Companies and Infectious Diseases
6. Conclusion
Chapter 20. Emerging Zoonoses, Biodiversity, and Ecosystems
1. Introduction
2. A Long History
3. One Health
4. Conclusion
Chapter 21. Epigenetics and Transmissible Diseases
1. Introduction and Definition of Epigenetics
2. Epigenetics and Its Role in Infectious Diseases
3. The Role of Infectious Diseases in Epigenetic Alterations
4. Potential Role of Laboratory Tests in Detecting Infectious Diseases Based on Epigenetic Signatures
5. Strategies to Limit the Impact of Infectious Diseases on Epigenetics
6. Potential Applications of Epigenetic Factors in Preventive Medicine
7. Conclusion and Future Perspectives
Chapter 22. The Evolution of SARS-CoV-2 and Influenza A Virus at the Human–Animal Interface
1. Introduction: New Perspectives on the Bidirectional Human–Animal Interface
2. A Tangled History of Influenza A Virus Evolution in Humans and Swine
3. Viral Adaptations Required for Influenza A Virus Host Switches
4. SARS-CoV-2 Evolution at the Human–Animal Interface
5. Future Perspectives
Chapter 23. Emerging Viruses
1. Introduction: Emergent Viruses and the Virosphere
2. Ecological and Societal Drivers of Viral Emergence
3. The Sources of Viral Emergence
4. Genetic and Molecular Determinants of Viral Emergence
5. Viral Establishment Following Cross-Species Transmission
6. Closing Remarks and Future Perspectives
Part 2. Specialized Chapters
Chapter 24. Genetic Exchange in Trypanosomatids and its Relevance to Epidemiology
1. Introduction
2. Trypanosoma brucei
3. Trypanosoma cruzi
4. Leishmania
Chapter 25. Genomic Insights Into the Past, Current, and Future Evolution of Human Parasites of the Genus Plasmodium
1. Introduction
2. Evolution of Plasmodium: The Last 10 Million Years
3. Evolution of Plasmodium: The 20th Century
4. Future Challenges From Continuing Plasmodium Genome Adaptation
Chapter 26. Host Adaptation in the Mycobacterium Genus: An Evolutionary and Genomic Perspective
1. Overview: Tuberculosis Disease and Historic Events in Mycobacterial Genetics
2. Host–Pathogen Co-evolution of the Tubercle Bacillus in Humans and Other Mammals
3. Evolution of the MTBC From a Genomic Perspective
4. Evolution in the Laboratory Environment and In Vitro Attenuation of Bacteria From the MTBC
5. Short-term Evolution of M. tuberculosis During Infection, Drug Treatment, and Disease
6. Adaptative Cues of the MTBC as the Most Successful Pathogens
7. Pending Questions and Concluding Remarks
List of Authors or Contributors
Chapter 27. Evolution, Phylogenetics, and Phylogeography of Mycobacterium tuberculosis complex
1. Introduction to Mycobacterium tuberculosis Complex Genetic Diversity Studies
2. An Introduction to Genomics and Computational Analysis Methods of Whole-Genome Sequencing Data
3. Lineage 1: The “East-African Indian” (EAI) Lineage According to Sola et al. (2001) or “Indo-Oceanic” According to Gagneux et al. (2006)
4. Lineage 2: The “Beijing” or East-Asian Lineage
5. Lineage 3: The Delhi or Central-Asian (CAS) Lineage According to Filliol et al. (2002) or “East-African Indian” According to Gagneux et al. (2006)
6. Lineage 4: The By-default “T” Lineage (Sola et al. 1999) Renamed as “Euro-American” Lineage (Gagneux et al. 2006)
7. Lineages 5 and 6: Mycobacterium africanum (Maf) West African 1 and 2
8. Focus on Lineage 7
9. The Lineage 8 (Uganda, Rwanda)
10. The Lineage 9 and 10: Newly Discovered M. africanum Sublineages
11. Animal Lineages and Mycobacterium canettii
12. Variability of the Clinical Expression of the Tuberculosis Disease and of Virulence of MTBC as a Function of the Lineage
13. Conclusion
Chapter 28. The Evolution of Staphylococcus aureus
1. Introduction
2. Evolution of Staphylococcus aureus
3. Methicillin Resistance and the Staphylococcal Cassette Chromosome mec
4. Typing Methods for S. aureus Characterization
5. Molecular Dynamics in MRSA Evolution
6. Global MRSA Lineages
7. Concluding Remarks
Chapter 29. Origin and Emergence of HIV/AIDS
1. History of AIDS
2. Human Immunodeficiency Viruses are Closely Related to Simian Immunodeficiency Virus From Nonhuman Primates
3. HIV-1 Is Derived From SIVs Circulating Among African Apes
4. Origin of HIV-2: An Other Emergence, an Other Epidemic
5. Ongoing Exposure of Humans to a Large Diversity of SIVs: Risk for a Novel HIV?
6. Conclusion
Chapter 30. Zoonotic Origin and Evolution of SARS Coronavirus
1. A Brief History of SARS
2. SARS Coronavirus (SARS-CoV)
3. The Animal Link of SARS-CoV
4. Natural Reservoirs of SARS-CoV
5. Molecular Evolution of SARS-CoV in Humans and Animals
6. Preparedness of Future SARS-like Disease Emergence
7. Concluding Remarks
Chapter 31. Ecology and Evolution of Avian Influenza A Viruses in Wild Birds
1. Role of Wild Birds as a Reservoir for a Diversity of Viruses
2. Avian Influenza A Virus
3. AIV Ecology in Waterfowl
4. Beyond the Duck-Centric, Temperate Northern Hemisphere Model of LPAIV Ecology
5. Effect of Infection on Birds
6. Evolution and Genetics
7. The Role of Wild Birds in the HPAIV H5N1 Panzootic
Chapter 32. Evolution of SARS-COV-2
1. Introduction
2. Coronaviruses
3. Origin of SARS-CoV-2
4. Genetic Diversity of SARS-CoV-2
5. Evolution of SARS-CoV-2
6. Conclusion
Chapter 33. Molecular Tools for Systematic and Epidemiological Investigations of Socioeconomically Important Parasitic Nematodes of Animals and Humans
1. Background and Historic Account
2. Critical Evaluation of Internal Transcribed Spacers of Nuclear Ribosomal DNA as Specific Markers for Parasitic Nematodes
3. Taxonomic Investigations
4. Phylogenetic Investigations
5. Diagnostic and Epidemiological Investigations
6. Nemabiome Investigations
7. Considerations and Extensions
8. Mitochondrial Genetic Markers
9. Technological Advances and Prospects
10. Concluding Remarks
Index

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Michel Tibayrenc