Avian influenza is an infectious disease of birds caused by the Type A strain of the influenza virus. The disease, which was first identified in Italy more than 100 years ago, occurs worldwide (World Health Organization, 2006a). The current outbreak of the highly pathogenic avian influenza A (H5N1), which began in Southeast Asia in mid-2003, is the largest and most severe on record. Never before in the recorded history of this disease have so many countries been simultaneously affected. Since the last pandemic in 1968-1969, the risk of an influenza pandemic has not been considered greater than at the present time. The importance of intervention strategies had become increasingly evident throughout the world. The World Health Organization provides a generic outline for preparedness plans to assist countries in their preparations to respond to a possible avian influenza pandemic. These guidelines may be modified as the epidemiology of avian influenza evolves. The South African National Department of Health has developed national guidelines in the form of an avian influenza preparedness plan. These draft guidelines do not provide detailed Environmental Health work methods and - procedures for the effective surveillance and control of the disease. The general purpose of this study is to develop a standardised set of Environmental Health work methods and - procedures, which will contribute to the effective surveillance and control of avian influenza in the Eastern Cape province – South Africa. Within the context of the purpose of this study, a qualitative, explorative, descriptive, inductive and deductive research design will be used. The methods of data collection will be documentary research, telephonic as well as in-depth personal interviews. In this study, documentary research will be the primary method of data collection. With a qualitative approach, the researcher will be the human instrument for data analysis. The process of qualitative data analysis will be based on data reduction and interpretation; and will be conducted as an activity simultaneously with data collection, data interpretation and narrative reporting writing.

The aim of this study was to develop a standardised set of Environmental-Health work methods and procedures, with the purpose of contributing to the effective surveillance and control of Cholera in the KwaZulu-Natal province, South Africa. The researcher followed a qualitative research design, which was explorative, descriptive, inductive and deductive by nature. The methods of data collection were documentary research and focus-group interviews. A documentary research approach was employed as the primary method of data collection for the study. The researcher has used semi-structured questions to obtain relevant information from the participants in the focus groups. The purpose of using semi-structured questions in the focus groups was to draw on their knowledge and experience of communicable disease surveillance and control in relation to Cholera, as well as to ascertain their views on the role of the Environmental-Health Practitioners in the Communicable - Disease Outbreak- Response Teams at the three different spheres of government. The process of qualitative data analysis was followed. This was based on data reduction and interpretation; and it was conducted as an activity simultaneously with data collection, data interpretation (coding) and narrative writing. The information obtained from the analysed data assisted in the development of the environmentalhealth work methods and procedures for the surveillance and control of Cholera in the KwaZulu-Natal province, South Africa. In this study, firstly, the epidemiology of Cholera was described and analysed against the background of its manifestation in South Africa. Secondly, the national health care system, with specific reference to the place and role of environmental health practitioners at national, provincial and municipal spheres – in relation to Cholera surveillance and control – was analysed. Thirdly, the relevant research that has been done globally has been analysed against the background of the findings of the above, together with work methods and procedures to be used by environmental-health practitioners during the surveillance and control of Cholera in the KwaZulu-Natal Province, South Africa. These include, inter alia: Work methods and procedures for Cholera case investigation; Work methods and procedures for sanitary investigations; and Work methods and procedures for identifying the sources of contamination in environmental waters. Finally, the conclusion and limitations was presented, and appropriate recommendations were made. These include: he need to educate all role - players, on the recent developments in the identification of Vibrio cholerae from environmental surface waters; Communication systems should be developed that allow the Director: Environmental Health to communicate urgent environmental health information directly to the Minister of Health; he training of environmental-health practitioners on detailed work methods and procedures for the surveillance and control of Cholera; and the existing national Cholera control guidelines need to be updated to include relevant environmental health situations when emergencies arise.

Avian influenza is a contagious viral disease caused by influenza virus type A. Avian influenza can be disastrous (if it occurs), due to the short incubation period (about 1--4 days). Thus it is important to study this disease so that we are more prepared to manage it in the future. A classical system of differential equations (the half-saturated incidence model) and three Filippov models --- an avian-only model with culling of infected birds, an SIIR (Susceptible-Infected-Infected-Recovered) model with quarantine of infected humans and an avian-only model with culling both susceptible and infected birds --- that are governed by ordinary differential equations with discontinuous right-hand sides (i.e., differential inclusion) are proposed to study the transmission of avian influenza. The effect of half-saturated incidence is investigated, and the outcome of this model is compared with the bilinear incidence model. Both models remain endemic whenever their respective basic reproduction numbers are greater than one. The half-saturated incidence model generates more infected individuals than the bilinear incidence model. This may be because the bilinear incidence model is underestimating the number of infected individuals at the outbreak. For the Filippov models, the number of infected individuals is used as a reference in applying control strategies. If this number is greater than a threshold value, a control measure has to be employed immediately to avoid a more severe outbreak. Otherwise, no action is necessary. We perform dynamical system analysis for all models. The existence of sliding modes and the flow on the discontinuity surfaces are determined. In addition, numerical simulations are conducted to illustrate the dynamics of the models. Our results suggest that if appropriate tolerance thresholds are chosen such that all trajectories of the Filippov models are converging to an equilibrium point that lies in the region below the infected tolerance threshold or on the discontinuity surface, then no control strategy is necessary as we consider the outbreak is tolerable. Otherwise, we have to apply control strategies to contain the outbreak. Hence a well-defined threshold policy is crucial for us to combat avian influenza effectively.

The thesis traces the successive urban responses made by the Hong Kong government from 1997 to 2014, in an attempt to achieve “imagined immunity” for the city. The urban responses being analysed are efforts to regulate the ways in which “live poultry” (especially live chickens) is metabolized and circulating in the city. The efforts are made to re-order the human-birds-microbes relationships in Hong Kong - a process conceptualized as “re-urbanization of nature.” The consequence of these re-urbanization of nature processes, led to changes in the specific practice of consuming “live poultry” in the city. Four periods of re-urbanization of nature are identified in the analysis, and it is argued that in each wave of restructuring there were markedly different frames constructed to generate distinctive meanings of the “contagion condition,” imagined urban immunity, and practices of re-urbanization of nature. Their meanings and resultant practices were products of negotiations, within an entangled web of human and nonhuman features in particular periods. The context of these interventions and the biopolitical contestations are analyzed in the thesis. It is then argued that such contingencies and context-sensitive processes, call for further studies of post-epidemic urban changes. The thesis also explores the possibility of developing a theoretical framework of “urban biopolitical immunology” to accomplish the inquiry. By so doing, it seeks to contribute to studies of the politics of contemporary epidemics, and to research on the production of urban nature.

Os vírus da influenza aviária têm provocado epidemias e pandemias através dos tempos, a pandemia mais devastadora que se tem notícia, a gripe espanhola em 1918, teve sua origem no vírus aviário do tipo A subtipo H1N1. Desde 2003 o vírus aviário do subtipo H5N1 infectou 442 pessoas e levou a morte 262. Além do aspecto de saúde os vírus da gripe aviária causam grande impacto econômico. O Brasil como maior exportador de frango do mundo tem muito a perder caso a gripe aviária chegue ao país. Devido às aves selvagens serem o reservatório natural influenza A, é que se faz necessário a execução do monitoramento. Apesar de existir programas de monitoramento contínuo de aves selvagens na Europa, EUA, Canadá, Japão entre outros, pouco foi feito no Brasil. Amostras coletadas de 671 aves foram testadas por meio das técnicas de GeneScan, PCR em tempo real e RT-PCR e Duplex Nested-PCR. / The avian influenza virus has caused epidemics and pandemics through the ages, the most devastating pandemic that we know, the Spanish flu in 1918, had its origin in the avian virus type A subtype H1N1. Since 2003 the avian virus subtype H5N1 has infected 442 people and led to death 262. Besides the health aspect of the avian influenza viruses cause major economic impact. Brazil as the largest exporter of chicken in the world has much to lose if bird flu reaches the country. Because wild birds are the natural reservoir of influenza A, is that it is necessary to implement the monitoring. Although programs exist for continuous monitoring of wild birds in Europe, USA, Canada, Japan and others, little has been done in Brazil. Samples collected from 671 birds were tested by GeneScan techniques, real-time PCR and RT-PCR and nested-PCR Duplex.

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.

In this thesis, I investigated the relationship between host and pathogen in multi-host and multi-pathogen systems at the interface between wildlife and domestic species. The term “epidemiological interaction” was central to my thesis, and was defined as “any ecological interaction between two host populations resulting in the transmission of one or more pathogen”. Epidemiological interactions are related to the processes of transmission between hosts and I investigated how these epidemiological interactions between different host populations could be investigated in a given ecosystem. I developed two research frameworks to estimate these epidemiological interactions: 1) an a priori approach based on the host data and assuming that the mobility of hosts and the resulting contacts between host populations would be crucial factors influencing the epidemiological interactions; 2) an a posteriori approach based on the pathogen data, assuming that epidemiological pathways previously used by some pathogen species can be used in the future by other pathogens. The animalpathogen model used to test the first approach was the bird-avian influenza viruses’ model. Longitudinal counting and sampling protocols of domestic and wild birds over two years were used to analyse community composition and abundance of hosts to compare with the prevalence of avian influenza viruses. I could, for the first time, show a persistence of low pathogenic avian influenza strains in an African ecosystem, and investigate the relationships with both the potential maintenance hosts (Afro-tropical ducks and resident species) and hosts that introduced the virus into the system from Europe or Asia (paleartic migrants). With the estimation of epidemiological interaction using host community data, I estimated the contact rate between wild and domestic avian compartments (intensive poultry, backyard and farmed ostrich compartments) and assigned a risk to this interaction based on dynamic and non dynamic factors for each bird species. This approach highlights the species or seasons at risk for the domestic compartments (or for the wild bird compartments depending on the perspective) in order to orientate surveillance or control options. This type of data and framework can also be used in mechanistic modelling to predict the spread of a pathogen after its introduction in one compartment. I tested the host approach in a broader dataset at the Southern African region level with similar counting and sampling database in multiple study sites, showing that the variability of host communities across the region could explain the variability of pathogen detection (however, finding a causal relationship was impossible). Finally, I theoretically developed the pathogen approach by combining tools used in parasite community ecology, molecular epidemiology and social network analysis and gave a theoretical example using a rodent and human macro and microparasite dataset. This thesis has explored the field of transmission ecology and offered ways to quantify the processes of transmission between host populations. Theoretically, I have developed a fundamental reflexion around epidemiological interactions and formulated hypotheses on their potential for being independent of the parasite species. Practically, I have developed tools to provide information for decision-making in order to improve efficiency of surveillance and control programmes at the wildlife/domestic interface particularly adapted to detect emerging infectious disease spill-over process. / Thesis (PhD)--University of Pretoria, 2011. / Zoology and Entomology / unrestricted

The H9N2 subtype of avian influenza A virus (aIAV) is circulating among birds worldwide, leading to severe economic losses. H9N2 cocirculation with other highly pathogenic aIAVs has the potential to contribute to the rise of new strains with pandemic potential. Therefore, rapid detection of H9 aIAVs infection is crucial to control virus spread. A qualitative reverse transcription recombinase polymerase amplification (RT-RPA) assay for the detection of aIAV subtype H9N2 was developed. All results were compared to the gold standard (real-time reverse transcription polymerase chain reaction (RT-PCR)). The RT-RPA assay was designed to detect the hemagglutinin (HA) gene of H9N2 by testing three pairs of primers and a probe. A serial concentration between 106 and 100 EID50 (50% embryo infective dose)/mL was applied to calculate the analytical sensitivity. The H9 RT-RPA assay was highly sensitive as the lowest concentration point of a standard range at one EID50/mL was detected after 5 to 8 min. The H9N2 RT-RPA assay was highly specific as nucleic acid extracted from H9 negative samples and from other avian pathogens were not cross detected. The diagnostic sensitivity when testing clinical samples was 100% for RT-RPA and RT-PCR. In conclusion, H9N2 RT-RPA is a rapid sensitive and specific assay that easily operable in a portable device for field diagnosis of aIAV H9N2.

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