Two-stage algorithms for visually exploring spatio-temporal clustering of avian influenza virus outbreaks in poultry farms

Abstract

The development of visual tools for the timely identification of spatio-temporal clusters will assist in implementing control measures to prevent further damage. From January 2015 to June 2020, a total number of 1463 avian influenza outbreak farms were detected in Taiwan and further confirmed to be affected by highly pathogenic avian influenza subtype H5Nx. In this study, we adopted two common concepts of spatio-temporal clustering methods, the Knox test and scan statistics, with visual tools to explore the dynamic changes of clustering patterns. Since most (68.6%) of the outbreak farms were detected in 2015, only the data from 2015 was used in this study. The first two-stage algorithm performs the Knox test, which established a threshold of 7 days and identified 11 major clusters in the six counties of southwestern Taiwan, followed by the standard deviational ellipse (SDE) method implemented on each cluster to reveal the transmission direction. The second algorithm applies scan likelihood ratio statistics followed by AGC index to visualize the dynamic changes of the local aggregation pattern of disease clusters at the regional level. Compared to the one-stage aggregation approach, Knox-based and AGC mapping were more sensitive in small-scale spatio-temporal clustering.

Integrating Citizen Scientist Data into the Surveillance System for Avian Influenza Virus, Taiwan

“…gov/EID/article/29/1/22-0659-App2.pdf), although other bridging species could also play major roles. Furthermore, increased occurrence of HPAI in wild birds resulted in disease and death of fairly large numbers of birds (>10,000 individuals) and affected diverse species (47) HPAIV transmission and could be incorporated into spatiotemporal data analysis together with other genetic or bird behavior data in the future (25).…”

“…Furthermore, increased occurrence of HPAI in wild birds resulted in disease and death of fairly large numbers of birds (>10,000 individuals) and affected diverse species ( 47 ). Mortality data for birds, especially nonmigratory species, could be indicators for HPAIV transmission and could be incorporated into spatiotemporal data analysis together with other genetic or bird behavior data in the future ( 25 ).…”

“…From the Council of Agriculture, Taiwan, we obtained the complete poultry farm census dataset, established in 2017 and based on an islandwide survey that used remote satellite imaging technology conducted by the Taiwan Agriculture Research Institute. The poultry farm outbreaks dataset was obtained from the surveillance system established by the Bureau of Animal and Plant Health Inspection and Quarantine, Taiwan, as described previously ( 20 , 25 ). During 2015–2017, a total of 1,223 poultry farm outbreaks were reported and laboratory confirmed in Taiwan (1,003 outbreak poultry farms in 2015, 38 in 2016, and 182 in 2017).…”