Thesis (M.S. in zoology)--Washington State University, August 2008. / Includes bibliographical references.

New and emerging diseases in human and animal populations appear to be predominately associated with generalist pathogens that are able to infect multiple hosts. Carnivores are susceptible to a wide range of these pathogens and can act as effective samplers of their vertebrate prey, which are important reservoirs of many emerging diseases. This thesis evaluates the utility of carnivores as sentinels for pathogens present in their prey by exploration of four selected pathogen-prey-sentinel combinations in three rural study sites of varying habitat in northern England and Scotland over a twenty-two month period (2007-2009). Selected pathogens were Coxiella burnetii, Leptospira spp., Encephalitozoon cuniculi, and rabbit haemorrhagic disease virus (RHDV), selected prey species were wild rodents and rabbits, and selected carnivores were foxes, domestic cats and corvids. Seroprevalence to C.burnetii, Leptospira spp and E.cuniculi was assessed using adapted or novel test methodologies to enable their use for multiple mammalian species, however these were not applicable to corvids. RHDV seroprevalence was not assessed due to low acquisition of rabbit samples. Overall, seroprevalence to all three pathogens was significantly higher in predators than prey, at 24.2% and 12.4 % for C.burnetii, 22.73% and 1.95% for Leptospira spp and 39.06% and 5.31% for E.cuniculi in predator and prey species respectively. A similar pattern was found in all study areas and was consistent irrespective of individual prey or predator species, although serological evidence of exposure to E.cuniculi was not detected in domestic cats in any area. A semi-quantitative assessment of the time and financial costs of the study approach and application to hypothetical examples indicates that sampling carnivores is a much more costeffective approach to pathogen detection than sampling prey. The results indicate that carnivores can act as useful sentinels for broad-scale detection of pathogen presence and relative levels of prevalence in prey and predator populations. Careful selection of predator species and methods of sample acquisition are necessary to maximise their utility, and issues associated with diagnostic test performance and validation must also be acknowledged. Suggestions are made as to how this principle might be applied to future surveillance programmes. In addition, the study is the first report on the seroprevalence of C.burnetii, Leptospira spp and E.cuniculi in multiple wildlife species (field voles, bank voles, wood mice, foxes), the first detection of antibodies to C. burnetii in wildlife and cats, the first detection of antibodies to L mini, L hardjo prajitno and L hardjo bovis in wild rodents, and to L mini in cats, and the first detection of antibodies to E.cuniculi in wild rodents and foxes in the UK.

Emerging infectious diseases (EID) pose a serious threat to global public health. Computational epidemiology is a nascent subfield of public health that can provide insight into an outbreak in advance of traditional methodologies. Research in this dissertation will use fuse nontraditional, publicly available data sources with more traditional epidemiological data to build and parameterize models of emerging infectious diseases. These methods will be applied to avian influenza A (H7N9), Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV), and Ebola virus disease (EVD) outbreaks. This effort will provide quantitative, evidenced-based guidance for policymakers and public health responders to augment public health operations. / Ph. D.

Avaliou-se o impacto da fragmentação florestal na diversidade de carrapatos de vida-livre e a presença de patógenos nestes carrapatos em remanescentes florestais do Pontal do Paranapanema, estado de São Paulo, Brasil. Estes fragmentos florestais abrigam uma rica e importante biodiversidade, com espécies endêmicas e ameaçadas como o mico-leão-preto (Leontopithecus chrysopygus), a anta (Tapirus terrestris), a onça pintada (Panthera onca), o macuco (Tinamus solitarius) e várias outras espécies de aves, mamíferos, répteis, anfíbios e peixes. Aproximadamente 90% das espécies de carrapatos parasitam exclusivamente hospedeiros selvagens. O restante pode ter animais domésticos e humanos como hospedeiros. Embora a maioria das pesquisas tenha sido dirigida a espécies de importância econômica, os carrapatos que parasitam animais selvagens possuem relevante papel na manutenção dos níveis de patógenos em populações de vida livre. Algumas destas espécies, por exemplo, demonstraram que podem parasitar hospedeiros não selvagens e promover o surgimento de zoonoses. Em habitats fragmentados, a diversidade de espécies vertebradas é menor se comparado a habitats com pouca alteração antrópica. Portanto, a fragmentação do habitat diminui a diversidade de espécies de carrapatos também. Para estudar a relação entre a fragmentação florestal e a ecologia das populações de carrapatos foram coletados carrapatos em 8 fragmentos florestais pelo método de arrasto de flanela e inspeção visual da vegetação. Os índices de comparação utilizados foram de similaridade de Jaccard, de diversidade de Shannon e complexidade do fragmento florestal de Patton. Utilizou-se o modelo de regressão linear para compara os índices de Shannon e Patton. Um total de 2149 ninfas de Amblyomma spp foi coletado e foram identificadas as espécies de 629 carrapatos. As espécies coletadas foram Amblyomma cajennense (94,28%), A. coelebs (1,59%), A. naponense (2,86%), A. ovale (0,64%), A. nodosum (0,32%), A. brasiliense (0,16%) e Haemaphysalis juxtakochi (0,16%). Nenhum indivíduo testado foi positivo pelo teste da hemolinfa. Os resultados mostraram uma tendência de correlação entre a fragmentação floresta, e a diversidade de espécies de carrapatos. / This study evaluated the impact of forest fragmentation on diversity of freeliving ticks and prevalence of tick pathogens in remaining forest fragments in the Pontal do Paranapanema, São Paulo state, Brazil. These forest fragments shelter rich and important biodiversity, with endemic and threatened species such as the black lion tamarin (Leontopithecus chrysopygus), the tapir (Tapirus terrestris), jaguar (Panthera onca), the solitary tinamou (Tinamus solitarius) and various other species of birds, mammals, reptiles, amphibians and fish. Approximately 90% of tick species parasitize exclusively wild hosts. The remainder can also have domestic animals and humans as hosts. Although most research has been directed to species of economic importance, ticks that parasitize wild animals are also relevant due to their role in maintaining enzootic pathogen levels in wild populations. Some of these species, for example, have been shown to cross-over onto non-wild hosts and promote emergent zoonoses. In fragmented habitats, the diversity of vertebrate species is normally lower than comparable habitats with minimal anthropic alteration. Thus, habitat fragmentation decreases the diversity of tick species too. To study the relationship between forest fragmentation and population ecology of ticks, ticks were collected in 8 forest fragments using dragging and visual inspection of vegetation. The index used were Jaccard´s similarity, diversity f Shannon and Patton. The linear regression model was used to compare Shannon and Patton indexes. A total of 2149 nymphs of Amblyomma spp. And 629 identified ticks was collected. The species of ticks collected was Amblyomma cajennense (94,28%), A. coelebs (1,59%), A. naponense (2,86%), A. ovale (0,64%), A. nodosum (0,32%), A. brasiliense (0,16%) e Haemaphysalis juxtakochi (0,16%). All ticks were negative by hemolimph test. The results showed a tendency of correlation between forest fragmentation and diversity of tick species.

published_or_final_version / Public Health / Master / Master of Public Health

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.

The thesis is focused on the epidemic of Ebola between years 2014 and 2015 and response of the Czech Republic. The main objective of the thesis is to assess the strategy of the Czech Republic in order to eliminate import of Ebola. The thesis is using study of documents and its effort is a complex overview of the given matters. Used documents are especially information and reports of international and Czech organizations, regulations, expert articles, electronic inquiries and media reports. There was defined 5 research questions. First question is focused on the demographic and epidemiological characteristics of the epidemic in West Africa. Second question was analysing steps, which were performed within the system of preparedness for highly contagious infections in the Czech Republic. I have divided the whole strategy of the Czech Republic into 10 points. They consist of the enforcing of International Health Regulation (2005), Decision no. 1082/2013/EU of the EP and of the Council, National action plan for the case of event, which is subject to International Health Regulation and two directives, implementation of special measures on international airports, conclusion of cooperation agreements, transmission of information within the Czech Republic, simulation actions and humanitarian aid. Third question was analysing the respondence of arrival cards at the Václav Havel Airport in Prague. Respondence was approx. 40 %. (Jágrová, 2016a) Fourth question is assessing the efficiency of implemented measures using the recorded cases of suspicion. Although there was not any case of infection in the Czech Republic, it may be concluded, that implemented measures are efficient. Fifth question is focused on the assessment of implemented measures and suggestions, how the response of the Czech Republic may be improved. Preparedness of the Czech Republic was assessed as very good by experts. Also it may be concluded from results, that preparedness is sufficient. Suggested measures, how the response of the Czech Republic may be improved, are related to the system of rapid alert of the public, creation of team for humanitarian aid, maintaining of sufficient capacities and realization of simulation actions.

Avaliou-se o impacto da fragmentação florestal na diversidade de carrapatos de vida-livre e a presença de patógenos nestes carrapatos em remanescentes florestais do Pontal do Paranapanema, estado de São Paulo, Brasil. Estes fragmentos florestais abrigam uma rica e importante biodiversidade, com espécies endêmicas e ameaçadas como o mico-leão-preto (Leontopithecus chrysopygus), a anta (Tapirus terrestris), a onça pintada (Panthera onca), o macuco (Tinamus solitarius) e várias outras espécies de aves, mamíferos, répteis, anfíbios e peixes. Aproximadamente 90% das espécies de carrapatos parasitam exclusivamente hospedeiros selvagens. O restante pode ter animais domésticos e humanos como hospedeiros. Embora a maioria das pesquisas tenha sido dirigida a espécies de importância econômica, os carrapatos que parasitam animais selvagens possuem relevante papel na manutenção dos níveis de patógenos em populações de vida livre. Algumas destas espécies, por exemplo, demonstraram que podem parasitar hospedeiros não selvagens e promover o surgimento de zoonoses. Em habitats fragmentados, a diversidade de espécies vertebradas é menor se comparado a habitats com pouca alteração antrópica. Portanto, a fragmentação do habitat diminui a diversidade de espécies de carrapatos também. Para estudar a relação entre a fragmentação florestal e a ecologia das populações de carrapatos foram coletados carrapatos em 8 fragmentos florestais pelo método de arrasto de flanela e inspeção visual da vegetação. Os índices de comparação utilizados foram de similaridade de Jaccard, de diversidade de Shannon e complexidade do fragmento florestal de Patton. Utilizou-se o modelo de regressão linear para compara os índices de Shannon e Patton. Um total de 2149 ninfas de Amblyomma spp foi coletado e foram identificadas as espécies de 629 carrapatos. As espécies coletadas foram Amblyomma cajennense (94,28%), A. coelebs (1,59%), A. naponense (2,86%), A. ovale (0,64%), A. nodosum (0,32%), A. brasiliense (0,16%) e Haemaphysalis juxtakochi (0,16%). Nenhum indivíduo testado foi positivo pelo teste da hemolinfa. Os resultados mostraram uma tendência de correlação entre a fragmentação floresta, e a diversidade de espécies de carrapatos. / This study evaluated the impact of forest fragmentation on diversity of freeliving ticks and prevalence of tick pathogens in remaining forest fragments in the Pontal do Paranapanema, São Paulo state, Brazil. These forest fragments shelter rich and important biodiversity, with endemic and threatened species such as the black lion tamarin (Leontopithecus chrysopygus), the tapir (Tapirus terrestris), jaguar (Panthera onca), the solitary tinamou (Tinamus solitarius) and various other species of birds, mammals, reptiles, amphibians and fish. Approximately 90% of tick species parasitize exclusively wild hosts. The remainder can also have domestic animals and humans as hosts. Although most research has been directed to species of economic importance, ticks that parasitize wild animals are also relevant due to their role in maintaining enzootic pathogen levels in wild populations. Some of these species, for example, have been shown to cross-over onto non-wild hosts and promote emergent zoonoses. In fragmented habitats, the diversity of vertebrate species is normally lower than comparable habitats with minimal anthropic alteration. Thus, habitat fragmentation decreases the diversity of tick species too. To study the relationship between forest fragmentation and population ecology of ticks, ticks were collected in 8 forest fragments using dragging and visual inspection of vegetation. The index used were Jaccard´s similarity, diversity f Shannon and Patton. The linear regression model was used to compare Shannon and Patton indexes. A total of 2149 nymphs of Amblyomma spp. And 629 identified ticks was collected. The species of ticks collected was Amblyomma cajennense (94,28%), A. coelebs (1,59%), A. naponense (2,86%), A. ovale (0,64%), A. nodosum (0,32%), A. brasiliense (0,16%) e Haemaphysalis juxtakochi (0,16%). All ticks were negative by hemolimph test. The results showed a tendency of correlation between forest fragmentation and diversity of tick species.

Philosophiae Doctor - PhD / Bionomics of vector-borne pathogens (VBPs) is a complex phenomenon that involves understanding the ecology of arthropod borne pathogens and vertebrate hosts potentially involved in their transmission cycles. Investigations into the bionomics of viral and bacterial VBPs circulating in Baringo and Homa Bay Counties of Kenya were carried out. Specifically, vertebrate hosts represented in mosquito bloodmeals, presence of arboviruses in blood fed mosquitoes and patients presenting with acute undiagnosed febrile illnesses in rural health facilities, and tick borne pathogens (TBPs) diversity in ticks of animals were identified. Mosquitoes were trapped by BG sentinel and CDC light traps, while ticks were sampled directly from domestic animals and tortoises close to human habitation along the shores and adjacent islands of Lakes Victoria and Baringo in Kenya. Blood and sera were also sampled from patients presenting with acute febrile illnesses visiting four rural health facilities in Homa Bay County. Mosquitoes and ticks were sorted and identified to species using standard morphological taxonomic keys. All the biological samples (blood-fed mosquitoes, ticks and blood/sera) were processed using molecular and culture procedures for detection of VBPs (arboviruses, Ehrlichia, Anaplasma, Rickettsia and protozoa). Among 445 blood-fed Aedeomyia, Aedes, Anopheles, Culex, Mansonia, and Mimomyia mosquitoes, 33 bloodmeal hosts were identified including humans, eight domestic animal species, six peridomestic animal species and 18 wildlife species. Further detection of Sindbis and Bunyamwera viruses was done on blood-fed mosquito homogenates by Vero cell culture and RTPCR in Culex, Aedeomyia, Anopheles and Mansonia mosquitoes from Baringo that had fed on humans and livestock. In TBPs assay, 585 tick pools were analysed consisting of 4,126 ticks collected in both study areas. More ticks were sampled in Baringo (80.5%), compared to Homa Bay (19.5%). In Baringo, agents of ehrlichiosis were detected from Amblyomma and Rhipicephalus ticks including Ehrlichia ruminantium (12.3%), Ehrichia canis (10.5%) and Paracoccus sp. (4.4%). Agents of anaplasmosis included Anaplasma ovis (7.2%), Anaplasma platys (4.4%) and Anaplasma bovis (4.0%), all from Hyalomma, Amblyomma and Rhipicephalus ticks, as well as agents of rickettsiosis, including Rickettsia africae, Rickettsia aeschlimannii, Rickettsia rhipicephali, Rickettsia montanensis and a Rickettsia sp. that was not conclusively characterized. Babesia caballi, Theileria sp. and Hepatozoon fitzsimonsi were also detected from both Rhipicephalus ticks and Amblyomma ticks. In Homa Bay, Ehrichia ruminantium (17.5%) and Ehrichia canis (9.3%) were isolated from Amblyomma latum and Rhipicephalus pulchellus, as well as Anaplasma platys (14.4%) and Anaplasma ovis (14.4%) from Amblyomma and Rhipicephalus species. In determination of the occurrence of arboviruses among patients presenting with acute febrile illnesses, acute Bunyamwera 3 (0.9%) and Sindbis 2 (0.6%) infections were detected by RT-PCR and cell culture and Sindbis seroprevalence was determined by plaque assay. Though a significant proportion of these patients tested positive for low Plasmodium parasitemia, none were co-infected with Plasmodium parasites and arboviruses. This study highlights the presence and relative importance of zoonotic VBPs in both study areas.

Three main research products are reported in this dissertation. This research focused on estimation of the seroprevalence rates in agricultural workers with exposure to pigs and poultry, and determination of risk factors for infection. Chapter 2, "Are swine workers in the United States at increased risk of infection with zoonotic influenza virus?", reports controlled, cross-sectional seroprevalence studies among farmers, meat processing workers, veterinarians, and control subjects. Using a hemagglutination inhibition assay against six influenza A virus isolates, all 3 exposed study groups demonstrated markedly elevated titers against the H1N1 and H1N2 swine influenza virus isolates, compared with control subjects. Chapter 3, "Infection due to 3 avian influenza subtypes in United States veterinarians", describes a controlled, cross-sectional seroprevalence study that examined veterinarians in the United States for evidence of previous avian influenza virus infection. Using a microneutralization assay against 9 influenza A virus strains, veterinarians exposed to birds demonstrated statistically significant elevated titers against the H5, H6, and H7 avian influenza virus isolates compared with control subjects. In chapter 4, "Cases of swine influenza in humans: a review of the literature", all known human cases of swine influenza are compiled and analyzed. Fifty cases of apparent zoonotic swine influenza virus infection, including 37 civilians and 13 military personnel, were identified, with a case-fatality rate of 14% (7 of 50 persons). Most civilian subjects (61%) reported exposure to swine. These studies provide strong evidence that transmission of zoonotic influenza likely occurs much more frequently than previously thought, and that individuals with occupational exposure to pigs and birds are at elevated risk for acquiring zoonotic influenza infections. Agricultural workers should be included in pandemic influenza planning, should receive information and training on how to use personal protective equipment, and should be offered human influenza vaccine to reduce the risk of creating viral reassortants. In the event of a pandemic, workers should be considered for antiviral medications and pandemic strain vaccines.