John Drake

University of Georgia | UGA · Odum School of Ecology

Accurate forecasting of contagious illnesses has become increasingly important to public health policymaking, and better prediction could prevent the loss of millions of lives. To better prepare for future pandemics, it is essential to improve forecasting methods and capabilities. In this work, we propose a new infectious disease forecasting model...

Anthropogenic modifications to the landscape have altered several ecological processes worldwide, creating new ecological boundaries at the human/wildlife interface. Outbreaks of zoonotic pathogens often occur at these ecological boundaries, but the mechanisms behind new emergences remain drastically understudied. Here, we test for the influence of...

Ecological systems are complex. Representing heterogeneous knowledge about ecological systems is a pervasive challenge because data are generated from many subdisciplines, exist in disparate sources, and only capture a subset of important interactions underpinning system structure, resilience, and dynamics. Knowledge graphs have been successfully a...

The detection of evolutionary transitions in influenza A (H3N2) viruses’ antigenicity is a major obstacle to effective vaccine design and development. In this study, we describe Novel Influenza Virus A Detector (NIAViD), an unsupervised machine learning tool, adept at identifying these transitions, using the HA1 sequence and associated physico-chem...

Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. For the 2021–22 and 2022–23 influenza seasons, 26 forecasting teams provided national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza hospital admissions for one-to-four weeks ahead. Forecast skill is evaluated...

During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19...

Ebolaviruses have the ability to infect a wide variety of species, with many African mammals potentially serving either as primary reservoirs or secondary amplifying hosts. Previous work has shown that frugivorous bats and primates are often associated with spillover and outbreaks. Yet the role that patterns of biodiversity, either of mammalian hos...

Global climate change is predicted to cause range shifts in the mosquito species that transmit pathogens to humans and wildlife. Recent modeling studies have sought to improve our understanding of the relationship between temperature and the transmission potential of mosquito‐borne pathogens. However, the role of the vertebrate host population, inc...

Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. Forecasting teams were asked to provide national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza hospital admissions for one through four weeks ahead for the 2021-22 and 2022-23 influenza seasons. Across both s...

To support decision-making and policy for managing epidemics of emerging pathogens, we present a model for inference and scenario analysis of SARS-CoV-2 transmission in the USA. The stochastic SEIR-type model includes compartments for latent, asymptomatic, detected and undetected symptomatic individuals, and hospitalized cases, and features realist...

Prediction and control of emerging pathogens is a fundamental challenge for public health. To meet this challenge, new analytic tools are needed to characterize the underlying dynamics of the geographical spread of pathogens, identify predictable changes in their dynamics, and support strategic planning for disease elimination and control. Nonparam...

During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19...

We explore how animal host traits, phylogenetic identity and cell receptor sequences relate to infection status and mortality from ebolaviruses. We gathered exhaustive databases of mortality from Ebolavirus after exposure and infection status based on PCR and antibody tests. We performed ridge regressions predicting mortality and infection as a fun...

The healthy herds hypothesis (HHH) suggests that predators decrease parasitism in their prey. Repeated tests of this hypothesis across a range of taxa and ecosystems have revealed significant variation in the effect of predators on parasites in prey. Differences in the response to predators (1) between prey taxa, (2) between seasons, and (3) before...

Outbreaks of African filoviruses often have high mortality, including more than 11,000 deaths among 28,562 cases during the West Africa Ebola outbreak of 2014-2016. Numerous studies have investigated the factors that contributed to individual filovirus outbreaks, but there has been little quantitative synthesis of this work. In addition, the ways i...

Timely forecasts of the emergence, re-emergence and elimination of human infectious diseases allow for proactive, rather than reactive, decisions that save lives. Recent theory suggests that a generic feature of dynamical systems approaching a tipping point—early warning signals (EWS) due to critical slowing down (CSD)—can anticipate disease emerge...

El orden Carnivora incluye más de 300 especies que varían en tamaño en muchos órdenes de magnitud y habitan en todos los biomas principales, desde las selvas tropicales hasta los mares polares. La gran diversidad de parásitos carnívoros representa una fuente de posibles enfermedades emergentes en humanos. El riesgo zoonótico de este grupo puede deb...

Deforestation alters wildlife communities and modifies human–wildlife interactions, often increasing zoonotic spillover potential. When deforested land reverts to forest, species composition differences between primary and regenerating (secondary) forest could alter spillover risk trajectory. We develop a mathematical model of land-use change, wher...

Many livestock diseases rely on wildlife for the transmission or maintenance of the pathogen, and the wildlife-livestock interface represents a potential site of disease emergence for novel pathogens in livestock. Predicting which pathogen species are most likely to emerge in the future is an important challenge for infectious disease surveillance...

Urban environments are heterogeneous landscapes of social and environmental features, with important consequences for human–nature entanglements, such as that of mosquito‐borne disease. Investigations into this intra‐urban heterogeneity in mosquito dynamics find conflicting results, likely due to the complex socio‐ecological interactions and the im...

Short-term forecasts of the dynamics of coronavirus disease 2019 (COVID-19) in the period up to its decline following mass vaccination was a task that received much attention but proved difficult to do with high accuracy. However, the availability of standardized forecasts and versioned datasets from this period allows for continued work in this ar...

Early warning indicators based on critical slowing down have been suggested as a model-independent and low-cost tool to anticipate the (re)emergence of infectious diseases. We studied whether such indicators could reliably have anticipated the second COVID-19 wave in European countries. Contrary to theoretical predictions, we found that characteris...

Resilience of ecosystems to the sudden decline of large‐bodied species is dependent on characteristics of surviving guild members. However, that response may also be mediated by local habitat conditions. Here, we examine the mechanisms behind the observed lack of functional compensation in the algal‐grazing guild by insect grazers following the dec...

The push and pull of dengue virus serotype evolution influences epidemic potential

Ecological theory suggests that predators can either keep prey populations healthy by reducing parasite burdens or alternatively, increase parasitism in prey. To quantify the overall magnitude and direction of the effect of predation on parasitism in prey observed in practice, we conducted a meta-analysis of 47 empirical studies. We also examined h...

Background Globally, tuberculosis disease (TB) is more common among males than females. Recent research proposes that differences in social mixing by sex could alter infection patterns in TB. We examine evidence for two mechanisms by which social-mixing could increase men’s contact rates with TB cases. First, men could be positioned in social netwo...

Zoonotic disease outbreaks are an important threat to human health and numerous drivers have been recognized as contributing to their increasing frequency. Identifying and quantifying relationships between drivers of zoonotic disease outbreaks and outbreak severity is critical to developing targeted zoonotic disease surveillance and outbreak preven...

Helminths are parasites that cause disease at considerable cost to public health and present a risk for emergence as novel human infections. Although recent research has elucidated characteristics conferring a propensity to emergence in other parasite groups (e.g. viruses), the understanding of factors associated with zoonotic potential in helminth...

Urban environments are heterogeneous landscapes of social and environmental features, with important consequences for human-nature entanglements, such as that of mosquito-borne disease. Investigations into this intra-urban heterogeneity in mosquito dynamics find conflicting results, likely due to the complex socio-ecological interactions and the im...

Short-term forecasts of the dynamics of COVID-19 in the period up to its decline following mass vaccination was a task that received much attention but proved difficult to do with high accuracy. A major obstacle has been capturing variations in the underlying kinetics of transmission resulting from changes in public policy, individual behaviors, an...

The order Carnivora includes over 300 species that vary many orders of magnitude in size and inhabit all major biomes, from tropical rainforests to polar seas. The high diversity of carnivore parasites represents a source of potential emerging diseases of humans. Zoonotic risk from this group may be driven in part by exceptionally high functional d...

Measurement of traffic flow stability and resilience is a critical step toward evaluating the performance of transportation systems and implementing appropriate management strategies. Quantifying changes in the stability and resilience of transportation systems, however, is hampered by the complexity of real traffic dynamics and the diversity of in...

The pandemic of COVID-19 has become one of the greatest threats to human health, causing severe disruptions in the global supply chain, and compromising health care delivery worldwide. Although government authorities sought to contain the spread of SARS-CoV-2, by restricting travel and in-person activities, failure to deploy time-sensitive strategi...

There are many outstanding questions about how to control the global COVID-19 pandemic. The information void has been especially stark in the World Health Organization Africa Region, which has low per capita reported cases, low testing rates, low access to therapeutic drugs, and has the longest wait for vaccines. As with all disease, the central ch...

Background During outbreaks of emerging and re-emerging infections, the lack of effective drugs and vaccines increases reliance on non-pharmacologic public health interventions and behavior change to limit human-to-human transmission. Interventions that increase the speed with which infected individuals remove themselves from the susceptible popula...

Initial efforts to mitigate transmission of SARS-CoV-2 relied on intensive social distancing measures such as school and workplace closures, shelter-in-place orders and prohibitions on the gathering of people. Other non-pharmaceutical interventions for suppressing transmission include active case finding, contact tracing, quarantine, immunity or he...

Invasive mosquitoes are expanding their ranges into new geographic areas and interacting with resident mosquito species. Understanding how novel interactions can affect mosquito population dynamics is necessary to predict transmission risk at invasion fronts. Mosquito life‐history traits are extremely sensitive to temperature, and this can lead to...

Helminths are parasites that cause disease at considerable cost to public health and present a risk for emergence as novel human infections. Although recent research has elucidated characteristics conferring a propensity to emergence in other parasite groups (e.g. viruses), the understanding of factors associated with zoonotic potential in helminth...

Precision health mapping is a technique that uses spatial relationships between socio-ecological variables and disease to map the spatial distribution of disease, particularly for diseases with strong environmental signatures, such as diarrhoeal disease (DD). While some studies use GPS-tagged location data, other precision health mapping efforts re...

The pandemic of COVID-19 has become one of the greatest threats to human health, causing severe disruptions in the global supply chain, and compromising health care delivery worldwide. Although government authorities sought to contain the spread of SARS-CoV-2, the virus that causes COVID-19, by restricting travel and in-person activities, failure t...

White-nose syndrome has caused massive mortality in multiple bat species and spread across much of North America, making it one of the most destructive wildlife diseases on record. This has also resulted in it being one of the most well-documented wildlife disease outbreaks, making it possible to look for changes in the pattern of spatial spread ov...

Historically, emerging and re-emerging infectious diseases have caused large, deadly, and expensive multi-national outbreaks. Often outbreak investigations aim to identify who infected whom by reconstructing the outbreak transmission tree, which visualizes transmission between individuals as a network with nodes representing individuals and branche...

The size of annual outbreaks in seasonally forced host-pathogen systems is poorly understood. We studied contributing factors to the six-fold observed variation in the number of human cases of West Nile virus in New York City in the years 2000–2008. Sampling error and intrinsic noise (demographic stochasticity) explain roughly half of the observed...

Population Biology of Vector-Borne Diseases is the first comprehensive survey of this rapidly developing field. The chapter topics provide an up-to-date presentation of classical concepts, reviews of emerging trends, synthesis of existing knowledge, and a prospective agenda for future research. The contributions offer authoritative and internationa...

COVID-19 has wreaked havoc globally with particular concerns for sub-Saharan Africa (SSA), where models suggest that the majority of the population will become infected. Conventional wisdom suggests that the continent will bear a higher burden of COVID-19 for the same reasons it suffers from other infectious diseases: ecology, socioeconomic conditi...

The majority of known early warning indicators of critical transitions rely on asymptotic resilience and critical slowing down. In continuous systems, critical slowing down is mathematically described by a decrease in magnitude of the dominant eigenvalue of the Jacobian matrix on the approach to a critical transition. Here, we show that measures of...

The COVID-19 pandemic has wreaked havoc globally, and there has been a particular concern for sub-Saharan Africa (SSA), where models suggest that the majority of the population will become infected. Conventional wisdom suggests that the continent will bear a higher burden of COVID-19 for the same reasons it suffers high burdens of other infectious...

Invasive mosquitoes are expanding their ranges into new geographic areas and interacting with resident mosquito species. Understanding how novel interactions can affect mosquito population dynamics is necessary to predict transmission risk at invasion fronts. Mosquito life-history traits are extremely sensitive to temperature and this can lead to t...

Understanding the drivers of biodiversity is important for forecasting changes in the distribution of life on earth. However, most studies of biodiversity are limited by uneven sampling effort, with some regions or taxa better sampled than others. Numerous methods have been developed to account for differences in sampling effort, but most methods w...

Our understanding of ecological processes is built on patterns inferred from data. Applying modern analytical tools such as machine learning to increasingly high dimensional data offers the potential to expand our perspectives on these processes, shedding new light on complex ecological phenomena such as pathogen transmission in wild populations. H...

Ecological systems are prone to dramatic shifts between alternative stable states. In reality, these shifts are often caused by slow forces external to the system that eventually push it over a tipping point. Theory predicts that when ecological systems are brought close to a tipping point, the dynamical feedback intrinsic to the system interact wi...

Diarrheal disease (DD) is responsible for over 700,000 child deaths annually, the majority in the tropics. Due to its strong environmental signature, DD is amenable to precision health mapping, a technique that leverages spatial relationships between socio-ecological variables and disease to predict hotspots of disease risk. However, precision heal...

Campaigns to eliminate infectious diseases could be greatly aided by methods for providing early warning signals of resurgence. Theory predicts that as a disease transmission system undergoes a transition from stability at the disease-free equilibrium to sustained transmission, it will exhibit characteristic behaviours known as critical slowing dow...

Despite medical advances, the emergence and re-emergence of infectious diseases continue to pose a public health threat. Low-dimensional epidemiological models predict that epidemic transitions are preceded by the phenomenon of critical slowing down (CSD). This has raised the possibility of anticipating disease (re-)emergence using CSD-based early-...

During outbreaks of emerging infections, the lack of effective drugs and vaccines increases reliance on non-pharmacologic public health interventions and behavior change to limit human-to-human transmission. Interventions that increase the speed with which infected individuals remove themselves from the susceptible population are paramount, particu...

Schistosomiasis control programs rely heavily on mass drug administration (MDA) campaigns with praziquantel for preventative chemotherapy. Areas where the prevalence and/or intensity of schistosomiasis infection remains high even after several rounds of treatment, termed “persistent hotspots” (PHSs), have been identified in trials of MDA effectiven...

Much of the basic ecology of Ebolavirus remains unresolved despite accumulating disease outbreaks, viral strains and evidence of animal hosts. Because human Ebolavirus epidemics have been linked to contact with wild mammals other than bats, traits shared by species that have been infected by Ebolavirus and their phylogenetic distribution could sugg...

The introduced fungal pathogen Pseudogymnoascus destructans is causing decline of several species of bats in North America, with some even at risk of extinction or extirpation. The severity of the epidemic of white‐nose syndrome caused by P. destructans has prompted investigation of the transmission and virulence of infection at multiple scales, bu...

The Asian tiger mosquito, Aedes albopictus, transmits several arboviruses of public health importance, including chikungunya and dengue. Since its introduction to the United States in 1985, the species has invaded more than 40 states, including temperate areas not previously at risk of Aedes-transmitted arboviruses. Mathematical models incorporate...

Emerging and re-emerging pathogens exhibit very complex dynamics, are hard to model and difficult to predict. Their dynamics might appear intractable. However, new statistical approaches—rooted in dynamical systems and the theory of stochastic processes—have yielded insight into the dynamics of emerging and re-emerging pathogens. We argue that thes...