title: Metapopulation dynamics and determinants of H5N1 highly pathogenic avian influenza outbreaks in Indonesian poultry.
abstract: In 2008, the Indonesian Government implemented a revised village-level Participatory Disease Surveillance and Response (PDSR) program to gain a better understanding of both the magnitude and spatial distribution of H5N1 highly pathogenic avian influenza (HPAI) outbreaks in backyard poultry. To date, there has been considerable collection of data, but limited publically available analysis. This study utilizes data collected by the PDSR program between April 2008 and September 2010 for Java, Bali and the Lampung Province of Sumatra. The analysis employs hierarchical Bayesian occurrence models to quantify spatial and temporal dynamics in backyard HPAI infection reports at the District level in 90 day time periods, and relates the probability of HPAI occurrence to PDSR-reported village HPAI infection status and human and poultry density. The probability of infection in a District was assumed to be dependent on the status of the District in the previous 90 day time period, and described by either a colonization probability (the probability of HPAI infection in a District given there had not been infection in the previous 90 day time period) or a persistence probability (the probability of HPAI infection being maintained in the District from the previous to current 90 day period). Results suggest that the number of surveillance activities in a district had little relationship to outbreak occurrence probabilities, but human and poultry densities were found to have non-linear relationships to outbreak occurrence probabilities. We found significant spatial dependency among neighboring districts, indicating that there are latent spatial processes that are not captured by the covariates available for this study, but which nonetheless impact outbreak dynamics. The results of this work may help improve understanding of the seasonal nature of H5N1 in poultry and the potential role of poultry density in enabling endemicity to occur, as well as to assist the Government of Indonesia target scarce resources to regions and time periods when outbreaks of HPAI in poultry are most likely to occur.
authors: USDA-APHIS-VS-Centers for Epidemiology and Animal Health, 2150 Centre Avenue, Bldg. B, Mail Stop 2W4 Fort Collins, CO 80526 USA. Matt.Farnsworth@aphis.usda.gov
authors: Matthew L
authors: ML
authors: Farnsworth
authors: Stephanie
authors: S
authors: Fitchett
authors: Muhammad Muharram
authors: MM
authors: Hidayat
authors: Caryl
authors: C
authors: Lockhart
authors: Christopher
authors: C
authors: Hamilton-West
authors: Eric
authors: E
authors: Brum
authors: Stephen
authors: S
authors: Angus
authors: Bagoes
authors: B
authors: Poermadjaja
authors: Julio
authors: J
authors: Pinto
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D016000:Cluster Analysis; D004196:Disease Outbreaks / Q000662:veterinary*; D006801:Humans; D007214:Indonesia / Q000453:epidemiology; D053124:Influenza A Virus, H5N1 Subtype / Q000502:physiology*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000635:transmission; D008954:Models, Biological; D011157:Population Dynamics; D011159:Population Surveillance / Q000379:methods; D011200:Poultry; D011201:Poultry Diseases / Q000453:epidemiology* / Q000635:transmission; D015995:Prevalence; D012372:ROC Curve; D012307:Risk Factors