yaotli/endemic

From emergence to endemicity: highly pathogenic H5 avian influenza viruses in Taiwan

Yao-Tsun Li, Hui-Ying Ko, Joseph Hughes, Ming-Tsan Liu, Yi-Ling Lin, Katie Hampson, Kirstyn Brunker

medRxiv

A/goose/Guangdong/1/96-like (GsGd) highly pathogenic avian influenza (HPAI) H5 viruses cause severe outbreaks in poultry when introduced. Since emergence in 1996, control measures in most countries have suppressed local GsGd transmission following introductions, making persistent transmission in domestic birds rare. However, geographical expansion of clade 2.3.4.4 sublineages has raised concern about establishment of endemic circulation, while mechanistic drivers leading to endemicity remain unknown. We reconstructed the evolutionary history of GsGd sublineage, clade 2.3.4.4c, in Taiwan using a time-heterogeneous rate phylogeographic model. During Taiwan’s initial epidemic wave (January 2015 - August 2016), we inferred that localised outbreaks had multiple origins from rapid spread between counties/cities nationwide. Subsequently, outbreaks predominantly originated from a single county, Yunlin, where persistent transmission harbours the trunk viruses of the sublineage. Endemic hotspots determined by phylogeographic reconstruction largely predicted the locations of re-emerging outbreaks in Yunlin. The transition to endemicity involved a shift to chicken-dominant circulation, following the initial bidirectional spread between chicken and domestic waterfowl. Our results suggest that following their emergence in Taiwan, source-sink dynamics from a single county have maintained GsGd endemicity, pointing to where control efforts should be targeted to eliminate the disease.

Figure 1

Data/cluster

script/cluster.R

Figure 2.

Data/baphiq_website.tsv, cTW.outbreak.tsv, lm.tsv

Data/cTW.fasta

Figure 3.

Data/contin

xml/cTW.contin-rmjp-gtr-grid-sttre2-prob.xml

xml/cTW.m2um_kml/

Figure 4.

Data/discrete

xml/cTW.geoEpochUncertin-rmjp-gtr-grid-mj.xml, cTW.geoSimUncertainEpoch-rmjp-gtr-grid.x2.xml

xml/cTW.geoUncertin-subYL_1.xml, cTW.geoUncertin-subYL_2.xml

script/persistence.R

Figure 5.

Data/glm

xml/cTW.geoEpochUncertainGLM-empirical.xml, cTW.geoEpochUncertainGLM-randEff-empirical.xml

xml/cTW.geoEpochUncertainGLM-size_cropland_rand-empirical.xml, cTW.geoEpochUncertainGLM-size_dist_rand-empirical.xml, cTW.geoEpochUncertainGLM-size_farm_rand-empirical.xml

xml/cTW.geoUncertainGLM-rmjp-gtr-grid-mj-randEff.xml

xml/rmjp_empirical.trees.xz

Figure 6.

Data/predict

script/polygons-general.R

Figure 7.

Data/host

xml/cTW.hostEpoch-rmjp-gtr-grid-mj.xml, cTW.hostEpoch-mN2-gtr-grid-mj.xml

Table

Data/selection

yaotli / endemic