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

South Asian dairy smallholders: A scoping review of practices and zoonoses

Objective: To identify and discuss on-farm management practices linked to bacterial zoonosis risk in smallholder dairy farmers in South Asia. Methods: This scoping review was conducted as per the PRISMA-ScR guidelines. Five hundred and two publications were retrieved from five online databases using a comprehensive search strategy. Studies were selected if they discussed a farm management practice which impacted human health within a South Asian country. Results: Twenty-two studies were included. Seven management practices relevant to farmers, livestock and their shared environment were identified including raw milk consumption, farm hygiene management, personal protective equipment uses, animal vaccination, cleaning udders, hand washing and disposal of afterbirth materials. Preventive practices were found to be utilized at lower frequencies compared to risk increasing practices. Awareness of bacterial zoonoses is particularly low within the region. Conclusions: Based on the results of this review, it was determined that improving farmer awareness of bacterial zoonotic diseases may favor several of the presented leverage points within the South Asian smallholder dairy system. Relying on formal school education to improve this awareness may not solve this problem, instead, more focus on accessible and affordable zoonoses education and farming programs is required

Estimation of a Within-Herd Transmission Rate for African Swine Fever in Vietnam

We describe results from a panel study in which pigs from a 17-sow African swine fever (ASF) positive herd in Thái Bình province, Vietnam, were followed over time to record the date of onset of ASF signs and the date of death from ASF. Our objectives were to (1) fit a susceptible-exposed-infectious-removed disease model to the data with transmission coefficients estimated using approximate Bayesian computation; (2) provide commentary on how a model of this type might be used to provide decision support for disease control authorities. For the outbreak in this herd, the median of the average latent period was 10 days (95% HPD (highest posterior density interval): 2 to 19 days), and the median of the average duration of infectiousness was 3 days (95% HPD: 2 to 4 days). The estimated median for the transmission coefficient was 3.3 (95% HPD: 0.4 to 8.9) infectious contacts per ASF-infectious pig per day. The estimated median for the basic reproductive number, R0, was 10 (95% HPD: 1.1 to 30). Our estimates of the basic reproductive number R0 were greater than estimates of R0 for ASF reported previously. The results presented in this study may be used to estimate the number of pigs expected to be showing clinical signs at a given number of days following an estimated incursion date. This will allow sample size calculations, with or without adjustment to account for less than perfect sensitivity of clinical examination, to be used to determine the appropriate number of pigs to examine to detect at least one with the disease. A second use of the results of this study would be to inform the equation-based within-herd spread components of stochastic agent-based and hybrid simulation models of ASF

Estimation of a Within-Herd Transmission Rate for African Swine Fever in Vietnam

We describe results from a panel study in which pigs from a 17-sow African swine fever (ASF) positive herd in Thái Bình province, Vietnam, were followed over time to record the date of onset of ASF signs and the date of death from ASF. Our objectives were to (1) fit a susceptible-exposed-infectious-removed disease model to the data with transmission coefficients estimated using approximate Bayesian computation; (2) provide commentary on how a model of this type might be used to provide decision support for disease control authorities. For the outbreak in this herd, the median of the average latent period was 10 days (95% HPD (highest posterior density interval): 2 to 19 days), and the median of the average duration of infectiousness was 3 days (95% HPD: 2 to 4 days). The estimated median for the transmission coefficient was 3.3 (95% HPD: 0.4 to 8.9) infectious contacts per ASF-infectious pig per day. The estimated median for the basic reproductive number, R0, was 10 (95% HPD: 1.1 to 30). Our estimates of the basic reproductive number R0 were greater than estimates of R0 for ASF reported previously. The results presented in this study may be used to estimate the number of pigs expected to be showing clinical signs at a given number of days following an estimated incursion date. This will allow sample size calculations, with or without adjustment to account for less than perfect sensitivity of clinical examination, to be used to determine the appropriate number of pigs to examine to detect at least one with the disease. A second use of the results of this study would be to inform the equation-based within-herd spread components of stochastic agent-based and hybrid simulation models of ASF

Capturing Household Structure and Mobility within and between Remote Aboriginal Communities in Northern Australia Using Longitudinal Data: A Pilot Study

Cultural practices and development level can influence a population’s household structures and mixing patterns. Within some populations, households can be organized across multiple dwellings. This likely affects the spread of infectious disease through these communities; however, current demographic data collection tools do not record these data. Methods: Between June and October 2018, the Contact And Mobility Patterns in remote Aboriginal Australian communities (CAMP-remote) pilot study recruited Aboriginal mothers with infants in a remote northern Australian community to complete a monthly iPad-based contact survey. Results: Thirteen mother–infant pairs (participants) completed 69 study visits between recruitment and the end of May 2019. Participants reported they and their other children slept in 28 dwellings during the study. The median dwelling occupancy, defined as people sleeping in the same dwelling on the previous night, was ten (range: 3.5–25). Participants who completed at least three responses (n = 8) slept in a median of three dwellings (range: 2–9). Each month, a median of 28% (range: 0–63%) of the participants travelled out of the community. Including these data in disease transmission models amplified estimates of infectious disease spread in the study community, compared to models parameterized using census data. Conclusions: The lack of data on mixing patterns in populations where households can be organized across dwellings may impact the accuracy of infectious disease models for these communities and the efficacy of public health actions they inform