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    Epidemiological studies of highly pathogenic avian influenza in Vietnam : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University
    (Massey University, 2010) Minh, Phan Quang
    This thesis utilises data on highly pathogenic avian influenza (HPAI) subtype H5N1 from the Vietnamese national surveillance system and purpose-designed field studies to enhance the understanding of the epidemiological features of HPAI H5N1 in Vietnam. The findings obtained from the first study show that the presence of a HPAI H5N1 human case was associated with an increase in the likelihood of disease being detected in poultry one and four weeks later, indicating that the occurrence of clinical disease in poultry is not a useful predictor of subsequent human cases in the same locality. The analyses from the second study demonstrate that the epidemiology of HPAI H5N1 in poultry in Vietnam has changed over time and the infection transmission occurs by a combination of local and long-distance spread. The findings from a cross-sectional survey of management practices of itinerant grazing ducks suggest that surveillance strategies for this type of duck management should focus on both layer and larger flocks as they are more likely to be moved outside of their home district, facilitating long-distance disease spread. The results from a matched case-control study in poultry identify factors associated with the presence of HPAI H5N1 and provide evidence that disease control strategies should emphasise the reduction of household-level, rather than village-level, risks for disease. In the last study, spatio-temporal interaction of disease risk in poultry was observed within a distance of 10 kilometres and 12 days following the detected onset of clinical signs. Household-tohousehold infection rate within a commune was approximately 50 times greater than the household-to-household infection rate between communes. These findings show that the predominant mechanism of HPAI H5N1 infection transfer was local spread. The lessons learnt from the series of studies presented here should assist Vietnamese animal health authorities to implement the necessary systems and infrastructure that will allow novel and emerging disease syndromes to be investigated promptly and efficiently.
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    Avian influenza and avian paramyxoviruses in the New Zealand bird population : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Virology at Massey University, Palmerston North, New Zealand
    (Massey University, 2002) Stanislawek, Wlodzimierz Leonard
    A comprehensive study using virological and serological approaches was carried out to determine the occurrence of avian paramyxoviruses (APMVs) and avian influenza viruses (AIVs) in live healthy mallard ducks (Anas platyrhynchos) in addition to caged birds, wild birds (other than waterfowl), and poultry. Thirty-three viruses were isolated from 321 tracheal and cloacal swabs from mallard ducks and were characterised as: 6 AIV (two H5N2 and four H4N6), 10 APMV-1, and 17 APMV-4. Of 335 serum samples tested for AIV antibodies, 109 (32.5%) sera were positive by nucleoprotein-blocking ELISA (NP-B-ELISA). Serum samples (315) were examined for antibody to APMV-1, -2, -3, -4, -6, -7, -8, and -9 by the haemagglutination inhibition (HI) test. The largest number of reactions, with titres up to ≥1/64, was to APMV-1 (93.1%), followed by APMV-6 (85.1%), APMV-8 (56%), APMV-4 (51.7%), APMV-7 (47%), APMV-9 (15.9%), APMV-2 (13.3%), and APMV-3 (6.0%). All of the H5N2 isolates of AIV and the APMV-1 isolates from this and earlier New Zealand studies had low pathogenicity indices when assessed by the Intravenous Pathogenicity Index (IVPI) with the result 0.00 and Intracerebral Pathogenicity Index (ICPI) with results 0.00-0.16. Partial genomic and antigenic analyses were also consistent with the isolates being non-pathogenic. Phylogenetic analysis of the 10 APMV-1 isolates showed nine to be most similar to the reference APMV-1 strain D26/76 originally isolated in Japan and also to the Que/66 strain, which was isolated in Australia. The other isolate was very similar to a virus (MC 110/77) obtained from a shelduck in France. Antibodies to APMV-1, -2, and -3 were detected in 4.8, 1.7, and 2.6%, respectively, of caged bird samples. The majority of these caged birds were "exotic" or "fancy" poultry breeds. Amongst wild birds, 4.2% had titres to APMV-2 and over half of these were passerine birds; 1.7% of the samples had titres to APMV-1 and 0.8% to APMV-3 antigen. No APMVs or AIVs were isolated from any of the cloacal swabs collected from these birds. Of the 1778 poultry serum samples tested only five reacted with APMV-3 antigen and these were later found to be cross-reactions to APMV-1. No reactions were detected with APMV-2 antigen. Although, we can be confident that APMV-1 is present in caged birds, wild birds, and poultry of New Zealand, there is no conclusive evidence of the presence of APMV-2 and APMV-3 in poultry or APMV-3 in wild birds. The results also do not provide conclusive evidence for the presence of APMV-2 in wild birds. Despite New Zealand being free from ND and highly pathogenic avian influenza (HPAI) in commercial poultry and the lack of evidence of pathogenic APMV-1 and AIVs in other birds, a number of possibilities were suggested by which virulent strains of APMV-1 and HPAI viruses could emerge in New Zealand including: (1) introduction by migratory birds; (2) importation of live birds and avian products: and (3) mutation in endemic viruses of low virulence. The findings from this study and elsewhere emphasise the importance of good biosecurity measures on poultry farms, to prevent the introduction of viruses of low virulence, as well as monitoring for the presence and type of APMV-1 and AIV in wild and domestic birds. The situation is likely to be dynamic with new strains emerging and the occurrence of clinically important introductions is a real possibility.
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    Epidemiological studies of Avian influenza viruses in Hong Kong : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Massey University, Palmerston North, New Zealand
    (Massey University, 2006) Kung, Nina Yu-Hsin
    Eight studies of the epidemiological dynamics of avian influenza viruses were conducted on poultry in Hong Kong, with special focus on the movement of birds through the live poultry marketing system, and the implications for avian influenza transmission. The first involved analysis of virus isolation data from faecal samples obtained from cooperating stalls in live poultry markets in Hong Kong in a routine sampling program undertaken between 1999 and 2001. This showed that two subtypes of avian influenza viruses, H9N2 and H6N1, have become well established in the Hong Kong live poultry markets, especially in chickens (mainly H9N2) and quail (mainly H6N1). In addition, a wave of H5N1 virus infection occurred in 2001 after it had been absent through the earlier period of the study. The second study was an evaluation of long term changes in the marketing systems for live poultry in Hong Kong, their likely effects on avian influenza epidemiology, and documented evidence of the prevalence of various H subtypes of avian influenza in sampling undertaken during three periods from 1975 to 2001. The third project involved two cross-sectional studies and one longitudinal study on local quail farms in Hong Kong. Results showed that quail could act as a reservoir host for H9N2 and H6N1 subtype viruses, but each subtype differed in its epidemiology. H9 virus usually infected quail at around 10 days of age, whereas H6 infected quail at 15-20 days of age. At 35 days of age (usual market age in Hong Kong), a proportion of market quail were likely to be susceptible to H6 (50%) and H9 viruses (20%), and were able to transmit the virus in the markets. Due to these findings, the Hong Kong Government closed the quail farming operations and restricted the sale of quail in live poultry markets. A longitudinal study was conducted on three live poultry market stalls to assess the time from stall entry to sale, and evaluate the influence of this delay on avian influenza virus transmission to other poultry in the same stall. Participating stalls varied from high volume/rapid turnover to low volume/slow turnover. Turnover for tagged poultry was rapid, although some chickens became infected with H9 virus before sale. Birds which stayed longer, such as quail, became infected and maintained infection in the stall. As well as spread by direct contact and on typical fomites, keeping of pet roosters and re-use of washing water were identified as factors increasing the ability of avian influenza strains to persist in market stalls. An experimental replica of a market stall was created to study the transmission of low pathogenic avian influenza virus (H9N2) in a controlled environment, with different rates of population turnover and different immune status with respect to both H5 and H9 subtypes. Transmission was influenced by distance between birds, the proportion of birds carrying antibody to H9 and the rate of introduction of susceptible birds, but not by the use of H5N2 vaccine. In order to assess the effectiveness of temporary depopulation of stalls, a study was conducted to compare the prevalence of avian influenza virus and Newcastle disease virus before and shortly after the monthly rest day in live poultry markets in Hong Kong, by virus isolation. Prevalence of H9N2 avian influenza virus was reduced by the rest day, but Newcastle disease virus prevalence was unaffected. During the 2002 avian influenza H5N1 outbreak in local chicken farms, a case-control study was undertaken to identify risk factors that may have contributed to this outbreak. A questionnaire was administered by interview to collect the data for this study. Multivariate logistic regression models showed that movement of people and fomites from live poultry markets to farms were important influences on transmission, and that the live bird markets were the likely source of virus for farms. A spatial stochastic computer model was constructed to predict the spread of avian influenza virus in local chicken farms and live poultry markets in Hong Kong, and the effectiveness of control measures. The data used in model parameter setting was derived from the case-control study. The reference model produced an epidemic curve which was similar to the true epidemic curve in the 2002 outbreak. Control strategies such as rest day and vaccination were evaluated within the model, and found to produce results comparable with field experience. Results from these studies clarify various aspects of the epidemiological features and transmission dynamics of avian influenza viruses, and provide guidance on appropriate control and prevention strategies for highly pathogenic avian influenza viruses within poultry marketing systems in Asia.
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    Modelling avian influenza in bird-human systems : this thesis is presented in the partial fulfillment of the requirement for the degree of Masters of Information Science in Mathematics at Massey University, Albany, New Zealand
    (Massey University, 2009) Zhao, Yue
    In 1997, the first human case of avian influenza infection was reported in Hong Kong. Since then, avian influenza has become more and more hazardous for both animal and human health. Scientists believed that it would not take long until the virus mutates to become contagious from human to human. In this thesis, we construct avian influenza with possible mutation situations in bird-human systems. Also, possible control measures for humans are introduced in the systems. We compare the analytical and numerical results and try to find the most efficient control measures to prevent the disease.
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    Surveillance for diseases of poultry with specific reference to avian influenza : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University
    (Massey University, 2008) Lockhart, Caryl Yolanda
    This thesis addresses issues related to surveillance for disease in commercial and non-commercial poultry populations. The motivation for this work has largely arisen from the unprecedented outbreaks of highly pathogenic avian influenza (HPAI) H5N1 that have occurred in 52 countries in Asia, Africa and Europe since 2003. A series of studies are presented using data derived from two countries, Vietnam and New Zealand. The two Vietnamese studies provide in-depth epidemiological analyses of the outbreak of HPAI H5N1 from December 2003 to March 2004. The three New Zealand studies deal with issues related to the development of effective surveillance strategies for HPAI — informed both directly and indirectly by the findings from the Vietnamese studies. This approach provides an example of how ‘lessons’ learnt from countries that have experienced large scale infectious disease epidemics can be used to assist in the design of surveillance activities in (as yet) unaffected countries. The descriptive analyses of the 2003 – 2004 outbreak of HPAI H5N1 in Vietnam indicate that the epidemic was seeded simultaneously in the north and south of the country in the later part of 2003 with 87% of provinces affected by February 2004. HPAI risk was concentrated around the Mekong and Red River Deltas. The broad scale spatial distribution of disease is likely to have been associated with regional differences in the poultry farming, trade in poultry, and environmental conditions such as the presence of bodies of water which would support reservoir species for the virus. A Bayesian zero-inflated Poisson regression model was used to quantify the influence of environmental and demographic factors on the spatial distribution of HPAI positive communes. In areas where disease was reported, our results show that HPAI risk was positively associated with the presence of irrigation and negatively associated with elevation. After controlling for these fixed effects, a single large area of elevated risk in the Red River Delta area was identified, presumably arising from similarities in the likelihood of reporting disease or the presence of factors increasing disease transmission and spread. Further investigations to elucidate likely transmission mechanisms, targeting this area of the country, would be a profitable area of future research. The second part of this thesis presents three studies that address issues related to the development of effective surveillance strategies for HPAI in New Zealand. The first was a cross-sectional study to enumerate the prevalence of backyard poultry ownership in two areas (one urban and the other rural) close to a large provincial city in the North Island of New Zealand. The prevalence of poultry ownership was 2% (95% CI 1% – 4%) in the urban area and 19% (95% CI 12% – 30%) in the rural area. The relatively low numbers of land parcels where poultry are present indicates that these areas, in the event of an infectious disease incursion, would be unlikely to pose a risk for spread of infectious agent. A cross-sectional survey of all members of the Poultry Industry Association of New Zealand was conducted in the later half of 2007. Respondents were asked to document contacts made with other enterprises related to feed, live birds and hatching eggs, table eggs and poultry product, and waste litter and manure. Patterns of contact were analysed using social network analyses. Each of the four networks had scale-free properties, meaning that for each movement type there were small numbers of enterprises that had contacts with large numbers of enterprises (potential ‘super-spreaders’ of disease). The presence of an undetected infectious disease in enterprises with super-spreader characteristics increases the likelihood that an epidemic will propagate rapidly through the population, assuming there is a directly proportional relationship between the number of contacts an enterprise makes and the probability that disease will be transferred from one location to another. While the finding that feed suppliers had large numbers of poultry farm contacts in the feed network came as no surprise, what was of greater interest was that there were small numbers of poultry farms that reported off-farm movements of feed. This should serve as an important reminder for disease control authorities: movement (and other) restrictions applied during the course of an animal health emergency should be applied across a range of industry sectors, recognising that some industry participants may practice activities that are not entirely typical for their enterprise type (e.g. poultry farms on-selling feed to other farms). In the absence of perfect and up-to-date network data, knowledge of the characteristics of individual enterprises that render them more likely to be atypical (e.g. size, type, and geographic location) would be of value, since this information could be used to inform a risk based approach to disease surveillance and control. A scenario tree model was developed as an approach for evaluating the effectiveness of New Zealand’s passive surveillance system for HPAI. The model was developed in two stages. In the first, factors thought to influence the geographic distribution of NAI risk of introduction and spread (and therefore surveillance strategy) were combined to create a spatial risk surface. In the second stage, a scenario tree model of the passive surveillance system for NAI was developed using the spatial risk surface and the HPAI surveillance strategy prescribed by Biosecurity New Zealand. The model was most sensitive to farmers reporting the presence of suspected cases of disease. This implies that the sensitivity of the system as a whole stands to increase if the importance of reporting suspicious clinical signs is reiterated to poultry producers. The studies presented in this thesis have presented a range of techniques and methodological approaches that are sufficiently generic to be used in any country to inform the design of surveillance strategies for a variety of animal diseases, not just those of poultry. Although epidemiology, as a discipline, is endoured with a vast range of analytical techniques that can be used to enhance the understanding of factors influencing the spread of disease among animal populations, the quality of data used to support these techniques is often lacking. The challenge in the years ahead, for both developed and developing countries, is to set in place the appropriate infrastructures to collect details of animal populations consistent in quality over time and space.