World-wide amphibian declines sparked concern and encouraged investigation into potential causes beginning in the 1980’s. Infectious disease has been identified as one of the major potential contributors to amphibian declines. For example, Ranavirus has caused amphibian die-offs throughout the United States. Investigators isolated Ranavirus from dead or moribund amphibians during large-scale die-offs of amphibians in the Cades Cove area of Great Smoky Mountains National Park in 1999-2001. In 2009, after nearly a decade without follow-up monitoring, I undertook an investigation to determine if the virus persisted in the area, and if so, to assess spatial, temporal, and taxonomic patterns in prevalence. Three amphibian breeding ponds, including Gourley Pond, the site of these earlier mortality events, were monitored for Ranavirus during the 2009 amphibian breeding season. A peak in prevalence occurred at Gourley Pond corresponding to a massive amphibian die-off. Prevalence varied among three different taxonomic groups during this mortality event with the highest prevalence, 84%, detected in larval Ambystomatids, 44.4% prevalence in adult Newts, and no virus detected in adult Plethodontids. I did not detect virus at either of the other two breeding ponds despite equivalent sampling effort, similar community composition, and close proximity to Gourley Pond. These results suggest that the severity and spatial extent of Ranavirus in Cades Cove remains unchanged since its initial detection a decade ago. Also, despite the observed massive die-offs there is no evidence of local amphibian extinction at Gourley Pond.

The objectives of this study were to determine the distribution of Borrelia burgdorferi (Bb), the bacterium that causes Lyme disease, and its tick vector (Ixodes scapularis) in the Thousand Islands in Ontario, and to assess the effects of various factors, including host populations, temperature, and vegetation, on the distribution of Bb and ticks in this new endemic region. Data were collected via drag sampling and small mammal trapping at 12 sites and multimodel inference was used to evaluate variables. There was inter-island variation in the abundance of ticks and prevalence of Bb in ticks. Important predictors of tick numbers and infection prevalence included deer abundance, distance to the United States, temperature, species richness, and relative mouse abundance. These results will contribute to management strategies to reduce Lyme disease risk in the Thousand Islands and to our understanding of the effects of biodiversity on disease risk. / Canadian Cooperative Wildlife Health Centre; Ontario Ministry of Natural Resources; Parks Canada; Public Health Agency of Canada; Ontario Graduate Scholarship

Emerging infectious diseases continue to represent serious threats to global human health. Novel zoonotic pathogens are continually being recognised, and some ultimately cause significant disease burdens and extensive epidemics. Research and public health initiatives often face emerging pathogens with limited knowledge and resources. Inferences from empirical modelling have begun to uncover the factors determining cross-species transmission and emergence in humans, and subsequently guide risk assessments. However, the dynamics of virulence and transmissibility during the process of emergence are not well understood. Here, I focus on RNA viruses, a priority pathogen type because of their potential for rapid evolution. I use comparative trait-based analyses to investigate how aspects of both host and virus ecology contribute to the risk of virulence and transmissibility within human RNA viruses. To explore these questions, data were collected via systematic literature search protocols. In the first half of this thesis, I focus on viral determinants of virulence and transmissibility. I ask whether virulence can be predicted by viral traits of tissue tropism, transmission route, transmissibility and taxonomic classification. Using a machine learning approach, the most prominent predictors of severe virulence were breadth of tissue tropism, and nonvector-borne transmission routes. When applied to newly reported viruses as test set, the final model predicted disease severity with 87% accuracy. Next, I assess support for hypothesised routes of adaptation during emergence using phylogenetic state-switching models. Propensity for adaptation in small ‘stepwise’ movements versus large ‘off-the-shelf’ jumps differed between virus taxa, though no single route dominated, suggesting multiple independent trajectories of adaptation to human hosts. In addition, phylogenetic regressions showed vector and respiratory-transmitted viruses to be more likely to progress through early stages of emergence. In the second half of this thesis, I focus on how dynamics of virulence and transmissibility differ with respect to nonhuman host diversity, identity, and ecology. Using a regression framework, I observe that viruses with a broader mammalian host range exhibited higher risk of severe virulence, but lower risk of transmissibility, which may reflect potential trade-offs of host specificity. Furthermore, viruses with artiodactyl hosts exhibited lower risk of severe virulence and viruses with bat or nonhuman primate hosts exhibited higher risk of transmissibility. Next, I test hypotheses that mammal species with faster-paced life history may be predisposed to host viruses with greater virulence and transmissibility. Mammal body mass was used as an established proxy for pace of life history. In regression analyses, mammals with faster-paced life history hosted more viruses with severe virulence, though evidence for a relationship with transmissibility was limited. The broad-scale associations presented in this thesis suggest the evolution of virulence and human-to-human transmissibility during zoonotic emergence is a multifactorial, highly dynamic process influenced by both virus and host ecology. Despite this, general characteristics of high-risk emerging viruses are evident. For example, severe virulence was associated with broad niche diversity of both tissue tropisms at the within-host scale, and host species at the macroecological scale. However, risk factors for virulence and human-to-human transmissibility often did not coincide, which may imply an overarching trade-off between these traits. These analyses can contribute to preparedness and direction within public health strategies by identifying likely candidates for high-impact emergence events among previously known and newly discovered human viruses. The inherent connectivity between RNA viruses, their nonhuman hosts and the resulting implications for human health emphasise the holistic nature of emerging diseases and supports the One Health perspective for infectious disease research.

Cumulative stressors influence the infection development, health and survival of wild Pacific salmon (Oncorhynchus spp.). Infectious disease is generally assumed to be the ultimate cause of death of wild adult salmon, but empirical evidence demonstrating links between infections and early mortality (i.e., prior to spawning) is lacking, especially as a function of cumulative migratory stressors. The influences of high river temperature and fishery capture and release on infection development and early mortality was explored in three Pacific salmon species. Adults were captured at river entry and held in freshwater tanks for the duration of river migration (days–weeks). Tank temperatures reflected either optimal (cool), warm (climate change scenario), or dynamic (changes in river temperature, behavioral thermoregulation) thermal conditions during migration. A subset of fish in all temperature groups was treated with a fishery bycatch release simulation (gillnet entanglement, air exposure) at the start of the holding period. We tracked shifts in physiology, immune activity and multiple infections using repeated biopsy (gill, blood) and molecular tools. Laboratory experiments were complimented by a telemetry study to assess impacts on behavior in the river. Novel application of high-throughput qPCR on nonlethally-sampled gill measured infections (bacteria, viruses, protozoa) concurrently with host immune gene expression, and was complemented by blood plasma chemistry to assess physiology. Ecologically relevant high temperatures increased mortality, infection development and stress metabolites and impaired host osmoregulatory function. Fishery stress reduced survival, especially after long entanglements and at high temperature, which reduced the capacity of individuals to resolve stress and infections. Females were more drastically affected, and mortality was delayed by more than a week. Fish with heavy infections in the river migrated more rapidly but traveled less distance. Sublethal effects of stressors included reduced migration rates and suppressed maturation indices that could delay maturity and extend river residence. Finally, river-exposed fish carried heavier infections and died sooner than those that bypassed the lower river, suggesting a causal influence of infections on early mortality. These findings support river-derived infections as causal factors contributing to the early mortality of adult Pacific salmon in fresh water and clarify its mechanisms, which comprise influences of multiple infections, sex, species, water temperature and fishery stress. / Graduate / 2019-04-15

AN ABSTRACT OF THE DISSERTATION OF GRETCHEN ELIZABETH PADGETT-FLOHR for the Doctor of Philosophy degree in Zoology, presented on March 5, 2009 at Southern Illinois University of Carbondale. TITLE: BATRACHOCHYTRIUM DENDROBATIDIS IN CENTRAL CALIFORNIA AMPHIBIANS MAJOR PROFESSOR: Eric Schauber Amphibian chytridiomycosis has been identified as a disease responsible for the decline and extinction of many amphibian taxa world wide, but little research has been conducted on the disease in Mediterranean climates. To address this gap in the data I studied the amphibian assemblage present across a ~6,475 ha site in central California and investigated the occurrence of the etiological agent, Batrachochytrium dendrobatidis (BD) from organismal, community, landscape and historical perspectives. I initially tested the accuracy and reliability of a proposed diagnostic screening test for BD in four larval species that occur on the site. The screening test proposed by Fellers et al. (2001) and Vredenburg and Summers (2001) consisted of examining larval amphibian mouthparts for abnormalities and or defects, based on their hypothesis that mouthpart defects are clinical signs of BD infection. Sensitivity and specificity of the diagnostic screening test were 76% and 58%, respectively, indicating that the proposed screening test was not a reliable diagnostic test for BD infection for the four species I examined. I conducted controlled laboratory experiments to examine the consequences of BD infection in the two threatened California species that occur on my study site: Rana draytonii and Ambystoma californiense. Both species were susceptible to infection, but all infected animals survived the 18-month study. Infected A. californiense sloughed skin at three times the rate of uninfected salamanders, a pattern that may have long-term energetic costs potentially leading to population-level consequences of sublethal infection by BD. I conducted a retrospective survey of the California Academy of Sciences' (San Francisco, California, USA) amphibian collection, testing for BD in four amphibian species collected from central California between 1897 and 2005 to assess whether the pathogen is novel versus endemic. The earliest detection of BD was in two Rana catesbeiana collected in 1961, and the data support the hypothesis that BD was a novel pathogen introduced into central California prior to 1961 that spread geographically and taxonomically from at least one point of introduction and is now endemic throughout most of central California. I analyzed how environmental factors, amphibian community composition, land use practices, and landscape structure affect the dynamics of the pathogen's distribution on my study site in central California. The distribution of BD in ponds within the landscape varied markedly between years and increases were associated with precipitation, mean minimum and maximum temperatures, and presence of particular species. Pseudacris regilla infection patterns were highly indicative of overall patterns of pond BD status. Fourteen ponds were identified as BD hotpots (BD-positive three of four years). Occurrences of the pathogen within the landscape were spatially autocorrelated and ponds in close proximity to BD hotspots were more likely to test positive. Local land use, (presence/absence of grazing or recreational activity and developed lands), apparently did not influence BD status of a pond. My studies show that BD was likely a novel pathogen introduced into California ca. 1961 that has since become established as an endemic pathogen throughout most of central California. The listed amphibian species that occur in central California can be infected with BD but appear to be resistant to manifesting amphibian chytridiomycosis, and the data from the studies herein could support one of two hypotheses: that natural selection acting over the past 48 years has selected for those individuals that were resistant to the disease; or that the species on my site have always been resistant to BD. The research I conducted further supports the hypothesis that BD is locally vectored by native amphibians (e.g. P. regilla) moving between ponds and that local ecological constraints likely limit vectoring of BD by non-native species. These findings contribute substantially to elucidating and understanding the responses of amphibian populations to disease/pathogen introduction and lay groundwork for future investigations into the host-pathogen-environment relationship as it relates to declining amphibian populations.

Orientador: Milton Cezar Ribeiro / Resumo: Os hantavírus provocam doenças de alta letalidade e já foram alvo de diversas propostas de investigação. Com o avanço da tecnologia, da Ciência e dos movimentos Open, trabalhar com um volume massivo de dados é muito mais possível hoje do que 20 anos atrás. Há uma demanda por estudos que possam sumarizar, disponibilizar e avaliar o papel da biodiversidade em processos de difusão de doenças zoonóticas. Nesta tese, que se iniciou como um entendimento da extensão e distribuição da biodiversidade da Mata Atlântica, busquei compreender a patogeografia da hantavirose. A dinâmica da infecção por hantavirose pode depender de diversos fatores interagindo, como clima e paisagem, bem como a distribuição de populações de roedores hospedeiros. No primeiro capítulo eu apresento a iniciativa ATLANTIC que permite livre acesso a dados de biodiversidade. No segundo capítulo eu busco compreender a extensão espacial da Mata Atlântica e levantar a discussão sobre áreas para delimitação de estudos ecológicos, um aspecto essencial para se investigar patogeografia. No terceiro capítulo busco entender os fatores que melhor explicam a variação na proporção de roedores de espécies potencialmente reservatório de tipos letais de hantavírus encontrados na Mata Atlântica. Neste capítulo também exploro a ideia de hotspots de vulnerabilidade à doença em humanos. No quarto capítulo, investiguei as consequências da alteração da paisagem na incidência de hantavirose no Brasil, gerando mapas de risco a partir de ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Hantaviruses cause diseases with high lethality and have been the target of several research proposals. With the advancement of technology, science, and Open movements, working with massive data is much more possible today than it was 20 years ago. There is a demand for studies that can summarize, make available and evaluate the role of biodiversity in processes of diffusion of zoonotic diseases. In this thesis, which began as an understanding of the extent and distribution of Atlantic Forest biodiversity, I aimed to understand the dynamics and eco-epidemiology of hantavirus. The dynamics of hantavirus infection may depend on several interacting factors such as climate and landscape, as well as the distribution of host rodent populations. In the first chapter I introduce the ATLANTIC initiative that allows free access to biodiversity data, which I have participated in intensely. In the second chapter I seek to understand the spatial extent of the Atlantic Forest and to raise the discussion about delimiting areas of ecological studies, an essential aspect to investigate pathogeography. In the third chapter I seek to understand the drivers that best explain the variation in the proportion of rodents of potentially reservoir species of lethal types of hantavirus found in the Atlantic Forest. In this chapter I also explore the idea of disease vulnerability hotspots in humans. In the fourth and final chapter, I investigated the consequences of landscape change on the incidence of ... (Complete abstract click electronic access below) / Doutor

Originally endemic to South America, the nine-banded armadillo (Dasypus novemcinctus) has recently expanded its range northward to Illinois. With this range expansion comes concern from both wildlife managers and the general public regarding potential incoming pathogens and unknown impacts on native wildlife. My research, conducted during 2018-2020 in southern Illinois, addressed the following 3 objectives intended to provide information regarding this novel species: (1) test for the presence of Trypanosoma cruzi and Mycobacterium leprae, (2) model the potential distribution of armadillos, and (3) attempt several different armadillo capture methods. For Objective 1, I tested roadkilled specimens for T. cruzi and M. leprae, 2 pathogens known to infect humans, using PCR and ELISA, respectively. All 81 samples tested for T. cruzi and all 25 samples tested for M. leprae were negative. The latter case is consistent with the enemy release hypothesis, suggesting armadillos have evaded parasites present in their native environment due to geographical distance. The absence of T. cruzi in the sampled individuals implies dispersing individuals are more robust than those at the center of their range. For Objective 2, I used MAXENT to model potential armadillo distribution in 51 counties in southern Illinois using 39 presence locations. Modeling identified low-intensity development to be the most important predictor of armadillo presence. For Objective 3, I attempted to capture armadillos using spotlighting on roads, staking out burrows, unbaited single-door cage traps, and unbaited double-door cage traps. Based on trap nights per capture, I found the use of double-door cage traps to be the most efficient method. My study will aid in managing colonizing armadillo populations by presenting information regarding dynamics of disease transmission, predicting areas of armadillo presence, and capture methods.

<p>Infectious  diseases  are  becoming  increasingly  common  and  problematic  for  wildlife populations in many parts of the world. Disease prevalence and severity fluctuate over time, often due to the ubiquitous pressure of seasonality, or  the cyclic changes in ecological systems. However, for  many  host-pathogen  systems,  our  understanding of important  seasonal  drivers of  disease remains fragmented. For example, when seasonality of a disease is studied in medium and high latitudes, winter is often neglected, despite this being a period of physiological and immunological challenges associated with extreme environmental conditions. Therefore, my aim is to examine  drivers  of winter Infection dynamics of the amphibian fungal pathogen <em>Batrachochytrium dendrobatidis</em>. First, <em>B. dendrobatidis </em>infection prevalence was measured from spring through fall to understand local infection levels and anthropogenic influences (Chapter 1). Next, laboratory  experiments examined the effects of <em>B. dendrobatidis </em>on critical thermal minimum of two anuran species to identify how this pathogen influences the ability of hosts to survive winter (Chapter 2). Another laboratory experiment tested how road de-icing salt (commonly used in winter) influences <em>B. dendrobatids </em>and a tadpole host condition and subsequent host-pathogen interactions (Chapter 3). Finally, a field-based exploration of <em>B. dendrobatidis </em>infection dynamics was conducted during winter to understand how infections vary during in this season and between two overwintering strategies (Chapter  4). Winter  infection  dynamics  in  many  host-pathogen  systems are largely understudied, but the knowledge gained by this work can demonstrate how harsh environmental conditions of winter that can exacerbate otherwise benign infections, and affect the ability of hosts to sustain infections during winter. This work can therefore inform predictions and investigations of  infection  dynamics in  subsequent  seasons to  better  understand  the  seasonality  of  wildlife diseases.</p>

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