Emerging Zoonotic and Wildlife Pathogens: Disease Ecology, Epidemiology, and Conservation

Cover
Emerging Zoonotic and Wildlife Pathogens
Copyright Page
Authors\' Notes
Contents
1 Spillover and emerging infectious diseases
	1.1 Introduction
	1.2 From spillover to pandemic
	1.3 Zoonoses
	1.4 Zoonotic origins of the `Big Three\'
	1.5 Barriers to emergence
	1.6 Ebola virus as a case study of spillover
	1.7 Improved diagnostics and increasing rate of pathogen discovery
	1.8 Epidemiology meets disease ecology
	1.9 Why study the ecology and epidemiology of infectious disease?
	1.10 Notes on sources
	1.11 References
SECTION 1 Describing Outbreaks
	2 The anatomy of disease
		2.1 Modes of pathogen transmission—direct contact
		2.2 Airborne transmission
		2.3 Environmental transmission
		2.4 Vehicle-borne transmission
		2.5 Vector-borne transmission
		2.6 Vertical or congenital transmission
		2.7 Portals of host entry
		2.8 Host exits
		2.9 Infectious, latent, incubation, and symptomatic periods
		2.10 Disease
		2.11 Disease agent groups
		2.12 Summary
		2.13 Notes on sources
		2.14 References
	3 Descriptive epidemiology of disease outbreaks
		3.1 Primary and index cases
		3.2 Epidemic curves
		3.3 Interpreting epidemic curve patterns
		3.4 Common source outbreaks
		3.5 Incubation periods and outbreak exposures
		3.6 Propagated transmission
		3.7 Test validity
		3.8 Test validity, within-host pathogen dynamics, and test type
		3.9 Test validity and local pathogen prevalence
		3.10 Test validity and repeat tests
		3.11 Pooled samples
		3.12 Summary
		3.13 Notes on sources
		3.14 References
	4 Surveillance
		4.1 Surveillance approaches
		4.2 Aggregating data
		4.3 Aggregating data: ecologic fallacy and Simpson\'s paradox
		4.4 Surveillance and zoonotic outbreaks
		4.5 Outbreak surveillance
		4.6 An outbreak case study
		4.7 Summary
		4.8 References
	5 Making simple predictions using models
		5.1 Introduction
		5.2 Mathematical models are simplifications of disease systems
		5.3 Basic compartmental models
		5.4 How does host density affect pathogen transmission?
		5.5 Using simple models to make predictions
		5.6 The basic reproductive number, R0
		5.7 Deterministic vaccination thresholds
		5.8 Deterministic invasion thresholds
		5.9 When do pathogens drive host species to extinction?
		5.10 Predicting long-term dynamics while ignoring random chance
		5.11 Incorporating random chance when predicting long-term dynamics
		5.12 When models are wrong
		5.13 Summary
		5.14 References
SECTION 2 Pathogen Sources
	6 The environment as a pathogen reservoir
		6.1 Introduction
		6.2 Five questions to define `environmental reservoirs\'
		6.3 Soil and plants as environmental reservoirs
		6.4 Faeces as an environmental reservoir
		6.5 Water as an environmental reservoir
		6.6 Summary
		6.7 References
	7 Reservoir hosts
		7.1 Introduction
		7.2 Spillover from a single host reservoir: armadillos and leprosy
		7.3 Multiple reservoir hosts: rabies, dogs, and wildlife
		7.4 Interactions between domestic and wildlife reservoirs
		7.5 Spillover from multiple reservoirs: Lyme disease
		7.6 Reservoir hosts and the dilution effect
		7.7 Multiple reservoir hosts and multiple pathogens: tick-borne diseases
		7.8 Idiosyncrasies of human behaviour and exposure to tick-borne pathogens
		7.9 Contributions of non-reservoir hosts to local disease ecology
		7.10 Summary
		7.11 References
	8 Identifying animal reservoirs during an epidemic
		8.1 Evidence of infection
		8.2 Evidence of exposure is not evidence of reservoir competence
		8.3 Genomic analyses to identify reservoir sources
		8.4 Causal association
		8.5 Finding the reservoir for Hantavirus Pulmonary Syndrome
		8.6 Outbreaks are not always caused by spillover from reservoirs
		8.7 Notes on sources
		8.8 References
SECTION 3 Drivers of Infectious Disease Emergence
	9 Emerging infectious diseases and globalization—travel, trade, and invasive species
		9.1 Travel brings zoonotic infections to non-endemic areas
		9.2 Travel drives stuttering outbreaks in non-endemic areas
		9.3 Travel drives pandemics
		9.4 Wildlife trade drives the spread of infectious diseases
		9.5 Invasive species drive disease emergence
		9.6 Summary
		9.7 Notes on sources
		9.8 References
	10 Climate change and emerging infectious diseases
		10.1 Climate affects host–parasite interactions
		10.2 Thermal performance curves
		10.3 Climate change and shifting distributions
		10.4 Extreme weather events
		10.5 Summary: interpreting complex climate–disease patterns
		10.6 Notes on sources
		10.7 References
	11 Land use change and emerging infectious diseases
		11.1 Introduction
		11.2 What is land use change?
		11.3 Deforestation and forest fragmentation
		11.4 Wild meat
		11.5 Wildlife farming
		11.6 Livestock farming
		11.7 Agriculture and water use
		11.8 Urbanization
		11.9 Poverty traps
		11.10 Summary
		11.11 Notes on sources
		11.12 References
SECTION 4 Conservation, Ecology, and Control
	12 Impacts of emerging infectious disease on wildlife populations
		12.1 Introduction—Arctic foxes and otodectic mange
		12.2 Small carnivore populations threatened by pathogens from domestic dog reservoirs
		12.3 Small carnivore populations threatened by pathogens from wildlife reservoirs
		12.4 Environmental reservoirs and resistant reservoir hosts drive amphibian species to extinction
		12.5 Infectious diseases can make common species rare
		12.6 Summary
		12.7 References
	13 Infectious diseases in ecosystems
		13.1 Communities and ecosystems
		13.2 Bottom-up effects
		13.3 Top-down effects: mesopredator release
		13.4 Top-down effects: trophic cascades
		13.5 Parasites in food webs
		13.6 Ecosystem functions performed by parasites
		13.7 Co-infection
		13.8 Summary
		13.9 References
	14 Infectious disease control
		14.1 Treating infected wildlife: a tale of scabid wombats
		14.2 Vector control and vaccination: conserving the plagued black-footed ferret
		14.3 Control interventions
		14.4 Culling wildlife to prevent wildlife–livestock disease transmission: the case of badgers and bovine tuberculosis
		14.5 Culling and wildlife disease reservoirs, more generally
		14.6 Unintended consequences—bison, elk, cattle, and brucellosis
		14.7 Pathogen invasion and disease control
		14.8 A final case study: Guinea worm disease
		14.9 Summary
		14.10 References
	15 COVID-19, One Health, and pandemic prevention
		15.1 Rapid emergence of a novel pathogen
		15.2 From outbreak to pandemic
		15.3 The source of SARS-CoV-2 spillover
		15.4 Controlling the spread of a pandemic virus … or not
		15.5 Drivers of the COVID-19 pandemic
		15.6 Complexity and wicked problems
		15.7 The One Health approach and interdisciplinary collaboration
		15.8 Preventing pandemics
		15.9 Conclusion
		15.10 Notes on sources
		15.11 References
Index