Quantifying the Effects of Measures to Control Highly Pathogenic Avian Influenza H5N1 in Poultry in Southeast Asia

Despite the ongoing efforts to contain its spread, H5N1 is now considered endemic within poultry in various settings worldwide, threatening both the livelihoods of those involved in poultry production in affected countries and posing a continuous public health risk. The reasons for the varying levels of success in controlling H5N1 in Southeast Asia need to be better understood. In this thesis, various different methods of quantifying the effects of individual control measures, using the types of data available in various different contexts, are discussed and applied. In the first half of this thesis a spatio-temporal survival model is fitted to H5N1 outbreak surveillance data from Vietnam and Thailand using a Bayesian framework in order to account for unobserved infection times. Following vaccination in Vietnam it was found that transmissibility had been successfully reduced but, during a wave of outbreaks in 2007, that this coincided with a reduction in the rate of at which outbreaks were reported following the introduction of infection, limiting the overall impact this reduction in transmissibility had on the total epidemic size. In Thailand, active surveillance was found to be successful in contributing to the control of infection. Furthermore, backyard producers, whilst responsible for the majority of outbreaks, were, on average, less likely to transmit infection than those involved in more intensive production. In the second half of the thesis, the use of final size methods to assess the effectiveness of vaccination from trial data is explored. This involved an investigation into the effects of different assumptions regarding the action by which vaccination confers immunity and fitting estimates of transmissibility to data collected from outbreak investigations in the context of a field trial of vaccination in Indonesia, where, making strong assumptions about the underlying infection process, a reduction in both within and between flock transmissibility was detected for outbreaks occurring in areas where vaccination was being carried out