Genetics and Evolution of Infectious Diseases

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Genetics and Evolution of Infectious Diseases
Genetics and Evolutionof Infectious Diseases
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Contents
List of Contributors
1 - Recent Developments in the Definition and Official Names of Virus Species∗
	1. Introduction
	2. The Logic of Hierarchical Virus Classification
	3. Bionominalism: Are Species Classes or Individuals?
	4. The Virus Species Problem
	5. Properties Used for Defining Virus Species and Identifying Individual Viruses
	6. A Virus Species Cannot Be Defined Solely by the Properties of Viral Genomes
	7. The New ICTV Definition of Virus Species
	8. Non-Latinized Binomial Names for Virus Species
	9. Discussion
	References
2 - A Theory-Based Pragmatism for Discovering and Classifying Newly Divergent Species of Bacterial Pathogens
	1. Introduction
	2. Ecological Breadth of Recognized Species
	3. The Stable Ecotype Model of Bacterial Speciation
	4. Demarcating Putative Ecotypes From Sequence Data
	5. Ecological Diversity Within Putative Ecotypes
	6. Models of Frequent Speciation
		6.1 Speedy Speciation Model
		6.2 Species-Less Model
		6.3 Nano-Niche Model
	7. Other Models Where Ecotypes Are Not Discernible as Sequence Clusters
		7.1 Recurrent Niche Invasion Model
		7.2 Cohesive Recombination Model
		7.3 Geotype Plus Boeing Model
	8. Are Bacterial Ecotypes Cohesive?
	9. Incorporating Ecology Into Bacterial Systematics
	Acknowledgments
	References
3 - Population Structure of Pathogenic Bacteria
	1. Introduction
	2. Recombination in Bacterial Populations
		2.1 Emergence and Persistence of Sequence Clusters
		2.2 Heterogeneity in Recombination
		2.3 The Structure of the Pan-Genome of Species and Populations
		2.4 Gene Flow Across Species Boundaries
	3. Evolutionary Processes Shape Intra- and Interhost Bacterial Population Structure
		3.1 Intrahost Evolution: A Snapshot of Larger-Scale Population Dynamics
		3.2 Interhost Evolution and Population Structure
	4. Genomic Analysis Tools for Studying Bacterial Population Structure
	5. Conclusions
	References
4 - Epidemiology and Evolution of Fungal Pathogens in Plants and Animals
	1. Introduction
		1.1 Major Human and Animal Pathogenic Fungi
			1.1.1 Ascomycetes: The Candida Species Complex, Aspergillus fumigatus, Pneumocystis, the Dimorphic Fungi, and Others
			1.1.2 Basidiomycetes: The Pathogenic Cryptococcus Species Complex
			1.1.3 Globally Emerging Fungal Infections in Wildlife Species
	2. New and Emerging Mycoses
		2.1 Evolution and Emergence of Pathogenic Cryptococcus gattii Genotypes in the Pacific Northwest
			2.1.1 The Global Emergence of the Amphibian Pathogen Batrachochytrium dendrobatidis
		2.2 Origin of Human Pathogens: Cryptococcus and Candida From Saprobes Associated With Insects
	3. Plant Pathogenic Fungi
	4. New and Emerging Plant Diseases
	5. Modern Molecular Epidemiological Tools for Investigating Fungal Diseases
	6. Population Genetics of Pathogenic Fungi
		6.1 Reproductive System
			6.1.1 Analysis of the Reproductive System
		6.2 Dispersal, Migration, and Gene Flow
			6.2.1 Rate and Direction of Gene Flow
			6.2.2 Dispersal Distance
			6.2.3 Distribution of Gene Flow in Time and Along the Genome
		6.3 Population Subdivision
			6.3.1 Measures of Differentiation
			6.3.2 Evolutionary Trees
			6.3.3 Model-Based Bayesian Clustering Algorithms
			6.3.4 Multivariate Methods
		6.4 Conclusion
	7. Genomics of Fungi: What Makes a Fungus Pathogenic?
		7.1 Comparative Genomics of Plant Pathogens
		7.2 Comparing Animal and Plant Pathogens
	8. Conclusion
	References
5 - Clonal Evolution
	1. Introduction
	2. Definitions
	3. The Origin of Life, the Origin of Propagation, and Recombination
	4. Clonal Modes
	5. Quantifying the Importance of Asexuality in the Biosphere
	6. Genetic Consequences of Asexuality
	7. Evolution and the Paradox of Sex
	8. Clonal Microevolution
		8.1 Neutral Loci Variability in Clonal Populations (Population Genetics Structure)
		8.2 Selection and Adaptation in Clonal Populations
	9. Conclusions
	Abbreviation List
	Acknowledgments
	References
6 - Coevolution of Host and Pathogen
	1. Coevolution of Host and Pathogen
		1.1 Introduction to Coevolution of Host and Pathogen
		1.2 Antagonistic Coevolution
		1.3 The Evolution of Pathogen Virulence
	2. The Process of Antagonistic Coevolution
		2.1 Introduction to the Process of Antagonistic Coevolution
		2.2 Migration, Mutation, and Recombination
		2.3 Generation Time
		2.4 Environmental and Community Context
		2.5 The Influence of the Microbiome on Host–Pathogen Interactions
		2.6 The Effect of the Abiotic Environment on Coevolution
	3. Testing for Host–Pathogen Coevolution
		3.1 Introduction to Testing for Host–Pathogen Coevolution
		3.2 Direct Comparisons Between Coevolving Organisms Across Time
		3.3 Measuring Population Genetic Change
		3.4 Pathogen-Mediated Rare Host Advantage
		3.5 Pathogen Local Adaptation
	4. Implications of Coevolution
		4.1 Diversification and Speciation
		4.2 The Maintenance of Genetic Diversity
	5. Summary/Future Outlook
	References
7 - Microbes as Tracers of Past Human Demography and Migrations
	1. Introduction
	2. Using Pathogens as Genetic Tracers for Host History
	3. Candidates
		3.1 Bacteria
			3.1.1 Helicobacter pylori
			3.1.2 Mycobacterium tuberculosis
		3.2 Viruses
			3.2.1 The Human Polyomavirus
	4. Conclusion
	Abbreviations
	References
8 - Phylogenetic Analysis of Pathogens
	1. Introduction
	2. The Uses of Phylogenies
	3. The Logic of Phylogeny Reconstruction
	4. Characters and Samples
	5. The Practice of Phylogeny Reconstruction
	6. Choosing a Method
	7. Representing Phylogenies: Trees
	8. Phylogenetic Networks
	References
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. Disease and Standard of Living in Preindustrial Societies: A Simple Model
	7. Population Limitation
	8. Disease, Mating, and Reproductive Strategy
	9. Prosperity and the Postindustrial Era Mortality Decline
	References
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
	References
11 - Proteomics and Host–Pathogen Interactions: A Bright Future?
	1. Introduction
	2. Interest of Proteomics to Study Host–Pathogen Interactions
	3. Retrospective Analysis of Previous Proteomics Studies
		3.1 Deciphering of the Molecular Strategies Involved in Parasite Immune Evasion
		3.2 Host Proteome Responses to Parasite Infection
		3.3 Biomarkers Linked to Infection Process by a Pathogen Using SELDI-TOF-MS Technology
	4. Toward New Conceptual Approaches to Decipher the Host–Parasite Interactions for Parasites With Simple or Complex Life Cycle
		4.1 A Holistic Approach to Disentangle the Host and Parasite Genome Responses During Their Interactions
		4.2 Pathogeno-Proteomics: A New Avenue to Decipher Host–Vector–Pathogen Interactions
	5. Population Proteomics: An Emerging Discipline to Study Host–Parasite Interactions
		5.1 Prospects With Population Proteomics for Any Living Organisms
		5.2 Human Population Proteomics
	6. Conclusion
	References
12 - The Evolution of Antibiotic Resistance
	1. Introduction
	2. Mechanisms and Sources of Antibiotic Resistance
	3. Evolution of Antibiotic-Resistance Genes
		3.1 Antibiotic-Resistance Genes as Targets of Evolution
		3.2 Adaptive Evolution of the Proteins Encoding for Antibiotic-Resistance Genes
		3.3 Defining Evolutionary Trajectories and Identifying Evolutionary Constriction Constraints As an Approach to Predict the Anti ...
	4. Limitations to Adaptation and the Cost of Resistance
		4.1 The Genetics of Adaptation
		4.2 From Genotype to Phenotype: The Many Ways Toward Fitness Compensation
		4.3 Beyond Model Organisms: Epidemiological and Experimental Fitness Cost in Mycobacterium tuberculosis
	5. Can the Evolution of Antibiotic Resistance be Predicted?
	6. Conclusions and Perspectives
	Glossary
	List of Abbreviations
	Acknowledgments
	References
13 - Modern Morphometrics of Medically Important Arthropods
	1. Introduction
		1.1 Modern and Traditional Morphometrics
	2. Landmark-Based Geometric Morphometry
		2.1 Landmark-Based Size
			2.1.1 Size Variable: The Centroid Size
		2.2 Landmark-Based Shape
			2.2.1 Procrustes Residuals, Partial Warps, Relative Warps, and Tangent Space Variables
		2.3 Semilandmarks for Curves Shape
	3. Pseudo-Landmark-Based Shape
		3.1 Outline-Based Shape
		3.2 Outline-Based Size
	4. Allometry
	5. Measurement Error
	6. Some Considerations About the Genetics of Metric Change
		6.1 Shape As a Polygenic Character
		6.2 Genetic Drift
		6.3 Heritability
		6.4 Hidden Genetic Variability
		6.5 Hybridism
	7. Phenotypic Plasticity
	8. A Special Case of Shape Change: the Character Displacement
	9. The Regulation of Phenotype
		9.1 Canalization
		9.2 Developmental Stability
	10. Applications in Medical Entomology
		10.1 Species Identification and Detection
		10.2 Characterization Tool at the Individual Level
		10.3 Biodiversity
		10.4 Reinfestation Studies
		10.5 Population Structure
			10.5.1 Gene Flow and the Flow of Migrants
			10.5.2 Environmental Variance of Size Versus of Shape
			10.5.3 Biogeographical Islands
			10.5.4 The Need for a Heuristic
	Glossary
	Acknowledgments
	References
14 - Evolution of Resistance to Insecticide in Disease Vectors
	1. Introduction
	2. Insecticide Resistance: Definition and History
		2.1 Synthetic Insecticides
		2.2 Alternative Insecticides
	3. Mechanisms of Resistance
		3.1 Metabolic Resistance
			3.1.1 Glutathione S-Transferases
			3.1.2 Cytochrome P450 Monooxygenases
			3.1.3 Carboxylesterases
		3.2 Target-Site Modification
			3.2.1 GABA Receptors
			3.2.2 Voltage-Gated Sodium Channels
			3.2.3 Acetylcholinesterase
		3.3 Other Resistance Mechanisms
			3.3.1 Growth Regulators
			3.3.2 Toxin Receptors
		3.4 Resistance Generalities
	4. Conclusion
	References
15 - Genetics of Major Insect Vectors
	1. Introduction
		1.1 Significance and Control of Vector-Borne Disease
		1.2 Contributions of Genetic Studies of Vectors to Understanding Disease Epidemiology and Effective Disease Control Methods
	2. Genetics of Tsetse Flies and African Trypanosomiasis
		2.1 Introduction
		2.2 The Family Glossinidae
		2.3 Genetics and Population Genetics of Tsetse Flies
			2.3.1 Cytogenetics
			2.3.2 Genetic Variability Based on Microsatellite Loci and mtDNA
			2.3.3 Population Structure of Tsetse Flies
		2.4 Tsetse Population Management
		2.5 Further Work Needed
	3. Genetics of the Triatominae (Hemiptera, Reduviidae) and Chagas Disease
		3.1 Introduction
		3.2 Chagas Disease Vectors
		3.3 Evolution of the Triatominae
			3.3.1 The Five Triatominae Tribes
		3.4 Cytogenetics of the Triatominae
		3.5 Genetic Diversity of the Triatominae
		3.6 Population Structure of the Triatominae
		3.7 Conclusions and Future Directions
	4. The Anopheles gambiae Complex
		4.1 Introduction
		4.2 Population Genetic Structure in Anopheles gambiae
			4.2.1 Temporal Structure
			4.2.2 Geographical Structure
			4.2.3 Nondimensional Structure
		4.3 The Unique Relationship Between Anopheles coluzzii and Anopheles gambiae
		4.4 Significance of Anopheles gambiae Population Genetics to Malaria Transmission and Control
		4.5 Conclusions
	5. Genetics of the Order Ixodida
		5.1 Introduction
		5.2 Systematics, Biogeography, and Medical/Veterinary Significance
		5.3 Cytogenetics
		5.4 Phylogenetics and Molecular Diagnostics
		5.5 Genetic Diversity and Population Genetics
		5.6 Genomics and Genetic Mapping
		5.7 Perspectives for Control and Future Directions
	Glossary
	Acknowledgments
	References
16 - Multilocus Sequence Typing of Pathogens: Methods, Analyses, and Applications
	1. Introduction
	2. Molecular Design and Development of Multilocus Sequence Typing
	3. Multilocus Sequence Typing Databases
	4. Advantages and Disadvantages of Multilocus Sequence Typing
	5. Analytical Approaches
		5.1 Allele-Based Methods
		5.2 Nucleotide-Based Methods
			5.2.1 Phylogenetic Relatedness
			5.2.2 Population Dynamics
	6. Applications of Multilocus Sequence Typing
		6.1 Molecular Epidemiology and Public Health
		6.2 Species Diagnosis and Phylogenetics
	7. Conclusions and Prospects
	Acknowledgments
	References
17 - Next-Generation Sequencing, Bioinformatics, and Infectious Diseases
	1. Analyzing Big Data
	2. Comparative Genomics
	3. Transcriptomics
	4. Single-Cell Technologies
	5. High-Throughput Sequencing
	6. De Novo Genome Assembly
	7. Whole-Genome Sequence Analysis
	8. RNA-Seq (Transcriptomics)
	9. Concluding Remarks
	References
18 - Genomics of Infectious Diseases and Private Industry
	1. Introduction
	2. Technologies and Instrument Platforms
		2.1 Sanger Sequencing
		2.2 Next-Generation Sequencing Based on Sequencing-by-Synthesis
			2.2.1 Short-Read Sequencing: Reversible Termination Sequencing-by-Synthesis
			2.2.2 Single-Molecule Sequencing: Real-Time, Long-Read Sequencing-by-Synthesis
		2.3 Nanopore-Based Sequencing
			2.3.1 Microarrays
		2.4 Software
	3. Customers and Their Needs
		3.1 Research
		3.2 Clinical Biology and Public Health
		3.3 Other Applications of Genomics
	4. Industry Landscape
	5. Conclusion
	References
19 - Current Progress in the Pharmacogenetics of Infectious Disease Therapy
	1. Introduction
	2. Pharmacogenetics of HIV Therapy
		2.1 Nucleoside/Nucleotide Reverse Transcriptase Inhibitors
		2.2 Nonnucleoside Reverse Transcriptase Inhibitors
		2.3 Protease Inhibitors
		2.4 Entry and Integrase Inhibitors
	3. Pharmacogenetics of Antimalarial Therapy
		3.1 Artemisinin Compounds
		3.2 Primaquine
		3.3 Amodiaquine
		3.4 Mefloquine
		3.5 Proguanil
		3.6 Quinine
	4. Pharmacogenetics of Antituberculous Therapy
	5. Summary and Perspective
	References
20 - Genetic Exchange in Trypanosomatids and Its Relevance to Epidemiology
	1. Introduction
	2. Trypanosoma brucei
		2.1 Genetic Crosses
		2.2 Location of Genetic Exchange
		2.3 Mendelian Inheritance and Meiosis
		2.4 Inheritance of Kinetoplast DNA
		2.5 Implications for Epidemiology
	3. Trypanosoma cruzi
		3.1 Trypanosoma cruzi Diversity
		3.2 Genome Sequence of a Natural Hybrid
		3.3 Genetic Crosses
		3.4 Location of Genetic Exchange
		3.5 Behavior of Experimental Hybrids
		3.6 Mechanism of Genetic Exchange in Experimental and Natural Hybrids
		3.7 Implications for Epidemiology
	4. Leishmania
		4.1 Evidence of Genetic Exchange in Natural Populations
		4.2 Genetic Crosses
		4.3 Implications for Epidemiology
	Abbreviations
	Acknowledgments
	References
21 - Genomic Insights Into the Past, Current, and Future Evolution of Human Parasites of the Genus Plasmodium
	1. Introduction
		1.1 Overview of Plasmodium Phylogeny and Description of Species Infecting Homo sapiens
		1.2 Population Genetics and Design of Public Health Interventions
		1.3 Genomic Signals of Selection due to Host Immunity
		1.4 Summary of Genomic Studies of the Genus
	2. Evolution of Plasmodium: The Last 10Million Years
		2.1 Role of Host Transitions in Speciation Events Within the Genus
		2.2 Plasmodium falciparum and Plasmodium reichenowi: Divergent Host Specificities?
		2.3 Speciation Between Plasmodium ovale curtisi and Plasmodium ovale wallikeri: Separate Host Transitions?
		2.4 Importance of Host Specificity
	3. Evolution of Plasmodium: The 21st Century in Three Courses
		3.1 Entree: Zoonoses—A Legacy of Habitat Destruction for Wild Primates?
			3.1.1 Emergence of Plasmodium knowlesi Zoonosis
		3.2 Plat du Jour: Chemotherapy and the Evolution of Drug-Resistant Parasites
			3.2.1 Lessons Learned From the Evolution of Parasite Resistance to Chloroquine
			3.2.2 Evolution of Parasite Resistance in the Artemisinin Combination Therapy Era
		3.3 Dessert: Selection for Immunological Escape Variants by Malaria Vaccines: A Real or Imagined Threat?
	4. Evolution of Plasmodium, and the Eradication Agenda
	References
22 - Integrated Genetic Epidemiology of Chagas Disease
	1. What Is Integrated Genetic Epidemiology?
	2. Chagas Disease: A Major Health Problem in Latin America and Other Countries
	3. The Chagas Disease Cycle
	4. Host Genetic Susceptibility to Chagas Disease
		4.1 Candidate Gene Approach
		4.2 Classical HLA Associations
		4.3 Further MHC Associations
		4.4 Cytokine and Cytokine Receptor Genes
		4.5 Chemokine and Chemokine Receptor Genes
		4.6 Associations and Other Genes
		4.7 A Genome-Wide Approach
		4.8 The Future
	5. Vector Genetic Diversity
	6. Parasite Genetic Diversity
	7. Concluding Remarks
	Glossary
	References
23 - Adaptive Evolution of the Mycobacterium tuberculosis Complex to Different Hosts
	1. Overview: Disease and Mycobacterial Genetics
	2. Host–Pathogen Coevolution of the Tubercle Bacillus
		2.1 Mycobacterium tuberculosis
		2.2 Mycobacterium africanum
		2.3 Mycobacterium canettii
		2.4 Mycobacterium bovis
		2.5 Other Animal-Adapted Strains: Mycobacterium caprae and Mycobacterium pinnipedii
	3. Evolution of the Mycobacterium tuberculosis Complex From a Genomic Perspective
	4. Evolution in the Laboratory Environment and In Vitro Attenuation of Bacteria From the Mycobacterium tuberculosis Complex
	5. Short-Term Evolution of Mycobacterium tuberculosis During Infection, Drug Treatment, and Disease
	6. Adaptive Cues of the Mycobacterium tuberculosis Complex As the Most Successful Pathogens
	7. Pending Questions and Concluding Remarks
	References
24 - The Evolution and Dynamics of Methicillin-Resistant Staphylococcus aureus
	1. Introduction
	2. The Staphylococcal Cassette Chromosome mec
	3. Evolution of Staphylococcus aureus and MRSA
		3.1 Mobile Genetic Elements
	4. Molecular Epidemiology of MRSA
	5. Conclusion
	References
25 - Origin and Emergence of HIV/AIDS
	1. History of AIDS
	2. Human Immunodeficiency Viruses Are Closely Related to Simian Immunodeficiency Virus From Nonhuman Primates
		2.1 Discovery of the First Simian Immunodeficiency Virus
		2.2 Simian Immunodeficiency Viruses in African Non-human Primates
		2.3 Pathogenicity of Simian Immunodeficiency Viruses in Their Natural Hosts
		2.4 Evolution and Phylogeny of Simian Immunodeficiency Viruses
	3. HIV-1 Is Derived From Simian Immunodeficiency Viruses Circulating Among African Apes
		3.1 Simian Immunodeficiency Viruses From Chimpanzees and Gorillas Are the Ancestors of HIV-1 in Humans
		3.2 The Cross-Species Transmissions Resulting in HIV-1 Viruses in Humans Occurred in West–Central Africa
		3.3 HIV-1 Started to Diverge in the Human Population at the Beginning of the 20th Century
		3.4 Simian Immunodeficiency Viruses Are Transmitted to Humans by Exposure to Infected Primates
	4. Origin of HIV-2: Another Emergence, Another Epidemic
	5. Ongoing Exposure of Humans to a Large Diversity of Simian Immunodeficiency Viruses: Risk for a Novel HIV?
		5.1 Exposure to Simian Immunodeficiency Virus–Infected Nonhuman Primates is Still Ongoing
		5.2 Simian Immunodeficiency Virus Prevalences and Cross-Species Transmissions
		5.3 Host Restriction Factors
		5.4 Viral Adaptation
		5.5 Human Factors
		5.6 Ongoing Cross-Species Transmissions From Other Retroviruses From Primates to Humans
	6. Conclusion
	References
26 - Evolution of SARS Coronavirus and the Relevance of Modern Molecular Epidemiology
	1. A Brief History of SARS
	2. SARS Coronavirus
	3. The Animal Link
	4. Natural Reservoirs of SARS-CoV
	5. Molecular Evolution of SARS-CoV in Humans and Animals
		5.1 Rapid Adaptation of SARS-CoVs in Humans
		5.2 Generation of Viral Genetic Diversity by Recombination
		5.3 Receptor Usage and Evolutionary Selection
	6. Coronavirus Surveillance in Wildlife Animals
	7. Concluding Remarks
	References
27 - Ecology and Evolution of Avian Influenza Viruses
	1. Introduction to Influenza A Virus
		1.1 Taxonomy and Host Range
		1.2 Influenza A Virus Structure and Genome Organization
		1.3 Influenza A Virus Classification
	2. Influenza Viruses in Birds
		2.1 Low Pathogenic Avian Influenza Virus Subtypes in Wild Birds
		2.2 Low Pathogenic Avian Influenza Virus Transmission and Epidemiology in Wild Birds
		2.3 Low Pathogenic Avian Influenza and Highly Pathogenic Avian Influenza Viruses in Domestic Birds
		2.4 Highly Pathogenic Avian Influenza H5N1 and H5NX Virus in Wild Birds
	3. Evolutionary Genetics of Avian Influenza Viruses
		3.1 Ecological Insights From Evolutionary Analysis: Natural Reservoirs
		3.2 Highly Pathogenic Avian Influenza H5N1 Virus
	4. Future Perspective
	Acknowledgments
	References
Index
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