Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis

Figures & data

Fig. 1 Phylogeography models of H5N1 and H7N9.

Bayesian MCC phylogeneies and between-region diffusion networks on HA gene segments of H5N1 (left panel) and H7N9 (right panel) in China. The sequences are classified according to their location grouped by economic division. Bohai Economic Rim (BER): Beijing, Hebei, Shandong; Central (CT): Anhui, Henan, Hubei, Hunan, Jiangxi, Shanxi; North-east (NE): Heilongjiang, Jilin, Liaoning; North-west (NW): Gansu, Ningxia, Qinghai, Shaanxi, Xinjiang; Pan-Pearl River Delta (PRD): Fujian, Guangdong; South-west (SW): Guangxi, Guizhou, Sichuan, Tibet, Yunnan, Chongqing; Yangtze-River Delta (YRD): Jiangsu, Shanghai, Zhejiang. Trees have been scaled according to taxa dates (representing sample collection date)

Fig. 2 Level of Bayes Factor support for each transmission route.

The left and right panels display the level of Bayes Factor (BF) support for each of the transmission routes considered for H5N1 and H7N9 analyses respectively. The x-axis represents the origin location and the y-axis represents the destination. Level of BF support is coloured according to classifications described in Table S1.

Fig. 3 Generalised linear model.

From left to right, the two panels show (i) Bayes Factor (BF), and (ii) Mean Coefficients (meanCeffects) and their 95% highest posterior credible intervals. Plots for H5N1 and H7N9 are displayed side by side. For all predictors excluding Distance, green and orange colours represent origin and destination locations respectively. In the BF plots, the dashed line indicates BF = 3. In the meanCeffects plot, the dashed line indicates 0. Note BF results are displayed on a log10 scale

Potential predictors collated for generalised linear model (GLM) analysis

Category	Predictor name	Description
Anthropogenic	ruralPop	Rural population (%)
	pollution	Sum of smoke and dust, sulphur dioxide, nitrogen oxides (10,000 tonnes)
Agricultural	poultrySales	Sales of poultry per capita rural household (kg)
	Vaccination	Average 2014 monthly H5N1 vaccination rate (%)
Environmental	natureReserves	Percentage of nature reserves in the region (%)
	humidity	Average relative humidity of major cities (%)
Sampling bias	sampleSize	Total number of sequences used in the analysis
Geographical	Distance	Distance between two locations, calculated using latitude and longitude coordinates