Village chicken production and the risk of avian influenza events in Indonesian villages

© 2019 Juan Pablo Villanueva CabezasAs of 2019, Highly Pathogenic Avian Influenza (HPAI) H5N1 is under control in Indonesia as a result of improved biosecurity and vaccination in large poultry enterprises. Nevertheless, the virus still circulates in less specialized village chicken production systems posing economic burden and public health risk. Past field research established that the trading activity associated with village chicken production is the primary pathway for HPAI-H5N1 release and spread in Indonesian villages; lamentably, the scarcity of data on village trading limits the exploration of risk frameworks to identify high-risk HPAI-H5N1 villages. This thesis investigates the village chicken productive landscape (that is, the collective of village chicken systems in a given village) as a determinant of the risk of HPAI-H5N1 events in Indonesian villages. Three core dimensions of these systems: type of village chicken system, village chicken productive dynamics, and risk mitigation strategies, are explored in relation to HPAI-H5N1 in four studies. First, a systematic review and meta-analysis that evaluates the efficacy of commercial vaccines against HPAI-H5N1 in Indonesia. Second, a Leslie matrix model to determine the underlying village chicken population dynamics and their effect on the maintenance of vaccine coverage. Third, an exploration and characterization of the Indonesian village chicken systems, along with the introduction of a deterministic age-structured model that simulates population dynamics and allows estimation of the presumed frequency of trading events to approximate the risk of HPAI-H5N1 release into villages. Fourth, a stochastic susceptible-exposed-infected age-structured model that allows exploration of transmission dynamics in different village chicken productive landscapes and evaluation of plausible risk mitigation strategies. The first study showed that viral drift reduces vaccine efficacy and that seed-homologous vaccine immunogenicity is not a good proxy for efficacy against wild isolates. The meta-analysis demonstrated that extra-label vaccination and the use of alternative seed homologous formulations are emerging sources of heterogeneous vaccine efficacy. The second study demonstrated that a mix of village chicken systems and not a "traditional scavenging" landscape, as suggested in the literature, drives the underlying village chicken population dynamics in Indonesia and these may quickly undermine perfect vaccine coverage. The third study demonstrated the limitations of the current classification of village chicken systems based on farming practice. The hierarchical clustering analysis in this study suggests that village chicken systems transitioned from traditional to semi-commercial modes of operation expressed as produce specialty (non-specialist, bird-specialist, or egg-specialists) and alternative trading strategies. The presumed frequency of trading events based on simulated productive dynamics suggests that the egg-specialists are heavily engaged in trading activities that increase the risk of HPAI-H5N1 release into villages. The fourth study shows that the type of village chicken landscape might not determine the probability of an epidemic event of HPAI-H5N1; however, outbreaks in landscapes that are abundant in bird-specialist and egg-specialist premises may persist longer. The simulations performed suggest that the extinction of the infected population seems invariably required to control these outbreaks. This thesis provides evidence that the Indonesian village chicken productive landscapes may determine the risk of HPAI-H5N1 events in Indonesian villages. This research suggests that a transition from traditional modes towards semi-commercial modes of operation that leads to a more significant presence of egg-specialists in the village results in a higher risk of viral release and likely more persistent epidemic events. The exploration of mitigation strategies which are plausible at the local level revealed challenges of controlling outbreaks in villages. These results emphasize the importance of identifying high-risk villages to enable adequate surveillance that reduces the need for mitigation strategies based on culling. In conclusion, this thesis suggests that an adequate characterization of the village chicken productive landscape may help, or even suffice, to identify villages at high risk of HPAI-H5N1 events, guiding surveillance, education, and future control efforts