John M. Drake

The global distribution and burden of dengue

Dengue is a systemic viral infection transmitted between humans by Aedes mosquitoes. For some patients, dengue is a life-threatening illness. There are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread. The contemporary worldwide distribution of the risk of dengue virus infection and its public health burden are poorly known. Here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. We then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. We predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanization. Using cartographic approaches, we estimate there to be 390 million (95% credible interval 284–528) dengue infections per year, of which 96 million (67–136) manifest apparently (any level of disease severity). This infection total is more than three times the dengue burden estimate of the World Health Organization. Stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. The most notable differences are discussed. These new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. We anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help to guide improvements in disease control strategies using vaccine, drug and vector control methods, and in their economic evaluation.

Early warning signals of extinction in deteriorating environments

During the decline to extinction, animal populations may present dynamical phenomena not exhibited by robust populations. Some of these phenomena, such as the scaling of demographic variance, are related to small size whereas others result from density-dependent nonlinearities. Although understanding the causes of population extinction has been a central problem in theoretical biology for decades, the ability to anticipate extinction has remained elusive. Here we argue that the causes of a population’s decline are central to the predictability of its extinction. Specifically, environmental degradation may cause a tipping point in population dynamics, corresponding to a bifurcation in the underlying population growth equations, beyond which decline to extinction is almost certain. In such cases, imminent extinction will be signalled by critical slowing down (CSD). We conducted an experiment with replicate laboratory populations of Daphnia magna to test this hypothesis. We show that populations crossing a transcritical bifurcation, experimentally induced by the controlled decline in environmental conditions, show statistical signatures of CSD after the onset of environmental deterioration and before the critical transition. Populations in constant environments did not have these patterns. Four statistical indicators all showed evidence of the approaching bifurcation as early as 110 days (∼8 generations) before the transition occurred. Two composite indices improved predictability, and comparative analysis showed that early warning signals based solely on observations in deteriorating environments without reference populations for standardization were hampered by the presence of transient dynamics before the onset of deterioration, pointing to the importance of reliable baseline data before environmental deterioration begins. The universality of bifurcations in models of population dynamics suggests that this phenomenon should be general.

Global hot spots of biological invasions: evaluating options for ballast–water management

Biological invasions from ballast water are a severe environmental threat and exceedingly costly to society. We identify global hot spots of invasion based on worldwide patterns of ship traffic. We then estimate the rate of port–to–port invasion using gravity models for spatial interactions, and we identify bottlenecks to the regional exchange of species using the Ford–Fulkerson algorithm for network flows. Finally, using stochastic simulations of different strategies for controlling ballast–water introductions, we find that reducing the per–ship–visit chance of causing invasion is more effective in reducing the rate of biotic homogenization than eliminating key ports that are the epicentres for global spread.

The evidence for Allee effects

Allee effects are an important dynamic phenomenon believed to be manifested in several population processes, notably extinction and invasion. Though widely cited in these contexts, the evidence for their strength and prevalence has not been critically evaluated. We review results from 91 studies on Allee effects in natural animal populations. We focus on empirical signatures that are used or might be used to detect Allee effects, the types of data in which Allee effects are evident, the empirical support for the occurrence of critical densities in natural populations, and differences among taxa both in the presence of Allee effects and primary causal mechanisms. We find that conclusive examples are known from Mollusca, Arthropoda, and Chordata, including three classes of vertebrates, and are most commonly documented to result from mate limitation in invertebrates and from predator–prey interactions in vertebrates. More than half of studies failed to distinguish component and demographic Allee effects in data, although the distinction is crucial to most of the population-level dynamic implications associated with Allee effects (e.g., the existence of an unstable critical density associated with strong Allee effects). Thus, although we find conclusive evidence for Allee effects due to a variety of mechanisms in natural populations of 59 animal species, we also find that existing data addressing the strength and commonness of Allee effects across species and populations is limited; evidence for a critical density for most populations is lacking. We suggest that current studies, mainly observational in nature, should be supplemented by population-scale experiments and approaches connecting component and demographic effects.

Allee effects, propagule pressure and the probability of establishment: risk analysis for biological invasions.

Colonization is of longstanding interest in theoretical ecology and biogeography, and in the management of weeds and other invasive species, including insect pests and emerging infectious diseases. Due to accelerating invasion rates and widespread economic costs and environmental damages caused by invasive species, colonization theory has lately become a matter of considerable interest. Here we review the concept of propagule pressure to inquire if colonization theory might provide quantitative tools for risk assessment of biological invasions. By formalizing the concept of propagule pressure in terms of stochastic differential equation models of population growth, we seek a synthesis of invasion biology and theoretical population biology. We focus on two components of propagule pressure that affect the chance of invasion: (1) the number of individuals initially introduced, and (2) the rate of subsequent immigration. We also examine how Allee effects, which are expected to be common in newly introduced populations, may inhibit establishment of introduced propagules. We find that the establishment curve (i.e., the chance of invasion as a function of initial population size), can take a variety of shapes depending on immigration rate, carrying capacity, and the severity of Allee effects. Additionally, Allee effects can cause the stationary distribution of population sizes to be bimodal, which we suggest is a possible explanation for time lags commonly observed between the detection of an introduced population and widespread invasion of the landscape.

Environmental transmission of low pathogenicity avian influenza viruses and its implications for pathogen invasion

Understanding the transmission dynamics and persistence of avian influenza viruses (AIVs) in the wild is an important scientific and public health challenge because this system represents both a reservoir for recombination and a source of novel, potentially human-pathogenic strains. The current paradigm locates all important transmission events on the nearly direct fecal/oral bird-to-bird pathway. In this article, on the basis of overlooked evidence, we propose that an environmental virus reservoir gives rise to indirect transmission. This transmission mode could play an important epidemiological role. Using a stochastic model, we demonstrate how neglecting environmentally generated transmission chains could underestimate the explosiveness and duration of AIV epidemics. We show the important pathogen invasion implications of this phenomenon: the nonnegligible probability of outbreak even when direct transmission is absent, the long-term infectivity of locations of prior outbreaks, and the role of environmental heterogeneity in risk.

The Role of Environmental Transmission in Recurrent Avian Influenza Epidemics

Avian influenza virus (AIV) persists in North American wild waterfowl, exhibiting major outbreaks every 2–4 years. Attempts to explain the patterns of periodicity and persistence using simple direct transmission models are unsuccessful. Motivated by empirical evidence, we examine the contribution of an overlooked AIV transmission mode: environmental transmission. It is known that infectious birds shed large concentrations of virions in the environment, where virions may persist for a long time. We thus propose that, in addition to direct fecal/oral transmission, birds may become infected by ingesting virions that have long persisted in the environment. We design a new host–pathogen model that combines within-season transmission dynamics, between-season migration and reproduction, and environmental variation. Analysis of the model yields three major results. First, environmental transmission provides a persistence mechanism within small communities where epidemics cannot be sustained by direct transmission only (i.e., communities smaller than the critical community size). Second, environmental transmission offers a parsimonious explanation of the 2–4 year periodicity of avian influenza epidemics. Third, very low levels of environmental transmission (i.e., few cases per year) are sufficient for avian influenza to persist in populations where it would otherwise vanish.

The Potential Distribution of Zebra Mussels in the United States

Abstract The range expansion of zebra mussels (Dreissena polymorpha) in North America has been rapid and costly in both economic and ecological terms. Joint social, political, and scientific ventures such as the 100th Meridian Initiative aim to reduce the spread of zebra mussels by eliminating the unintended transport of the species and preventing its westward expansion. Here we forecast the potential distribution of zebra mussels in the United States by applying a machine-learning algorithm for nonparametric prediction of species distributions (genetic algorithm for rule-set production, or GARP) to data about the current distribution of zebra mussels in the United States and 11 environmental and geological covariates. Our results suggest that much of the American West will be uninhabitable for zebra mussels. Nonetheless, some catchments along the West Coast and in the southeastern United States exhibit considerable risk of invasion and should be monitored carefully. Possible propagule dispersal to these places should be managed proactively.

What Factors Might Have Led to the Emergence of Ebola in West Africa

An Ebola outbreak of unprecedented scope emerged in West Africa in December 2013 and presently continues unabated in the countries of Guinea, Sierra Leone, and Liberia. Ebola is not new to Africa, and outbreaks have been confirmed as far back as 1976. The current West African Ebola outbreak is the largest ever recorded and differs dramatically from prior outbreaks in its duration, number of people affected, and geographic extent. The emergence of this deadly disease in West Africa invites many questions, foremost among these: why now, and why in West Africa? Here, we review the sociological, ecological, and environmental drivers that might have influenced the emergence of Ebola in this region of Africa and its spread throughout the region. Containment of the West African Ebola outbreak is the most pressing, immediate need. A comprehensive assessment of the drivers of Ebola emergence and sustained human-to-human transmission is also needed in order to prepare other countries for importation or emergence of this disease. Such assessment includes identification of country-level protocols and interagency policies for outbreak detection and rapid response, increased understanding of cultural and traditional risk factors within and between nations, delivery of culturally embedded public health education, and regional coordination and collaboration, particularly with governments and health ministries throughout Africa. Public health education is also urgently needed in countries outside of Africa in order to ensure that risk is properly understood and public concerns do not escalate unnecessarily. To prevent future outbreaks, coordinated, multiscale, early warning systems should be developed that make full use of these integrated assessments, partner with local communities in high-risk areas, and provide clearly defined response recommendations specific to the needs of each community.

Rodent reservoirs of future zoonotic diseases

Significance Forecasting reservoirs of zoonotic disease is a pressing public health priority. We apply machine learning to datasets describing the biological, ecological, and life history traits of rodents, which collectively carry a disproportionate number of zoonotic pathogens. We identify particular rodent species predicted to be novel zoonotic reservoirs and geographic regions from which new emerging pathogens are most likely to arise. We also describe trait profiles—complexes of biological features—that distinguish reservoirs from nonreservoirs. Generally, the most permissive rodent reservoirs display a fast-paced life history strategy, maximizing near-term fitness by having many altricial young that begin reproduction early and reproduce frequently. These findings may constitute an important lead in guiding the search for novel disease reservoirs in the wild. The increasing frequency of zoonotic disease events underscores a need to develop forecasting tools toward a more preemptive approach to outbreak investigation. We apply machine learning to data describing the traits and zoonotic pathogen diversity of the most speciose group of mammals, the rodents, which also comprise a disproportionate number of zoonotic disease reservoirs. Our models predict reservoir status in this group with over 90% accuracy, identifying species with high probabilities of harboring undiscovered zoonotic pathogens based on trait profiles that may serve as rules of thumb to distinguish reservoirs from nonreservoir species. Key predictors of zoonotic reservoirs include biogeographical properties, such as range size, as well as intrinsic host traits associated with lifetime reproductive output. Predicted hotspots of novel rodent reservoir diversity occur in the Middle East and Central Asia and the Midwestern United States.