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

Avian influenza H5N1 subtype has caused a global public health concern due to its high pathogenicity in poultry and high case fatality rates in humans. The recently emerged H7N9 is a growing pandemic risk due to its sustained high rates of human infections, and recently acquired high pathogenicity in poultry. Here, we used Bayesian phylogeography on 265 H5N1 and 371 H7N9 haemagglutinin sequences isolated from humans, animals and the environment, to identify and compare migration patterns and factors predictive of H5N1 and H7N9 diffusion rates in China. H7N9 diffusion dynamics and predictor contributions differ from H5N1. Key determinants of spatial diffusion included: proximity between locations (for H5N1 and H7N9), and lower rural population densities (H5N1 only). For H7N9, additional predictors included low avian influenza vaccination rates, low percentage of nature reserves and high humidity levels. For both H5N1 and H7N9, we found viral migration rates from Guangdong to Guangxi and Guangdong to Hunan were highly supported transmission routes (Bayes Factor > 30). We show fundamental differences in wide-scale transmission dynamics between H5N1 and H7N9. Importantly, this indicates that avian influenza initiatives designed to control H5N1 may not be sufficient for controlling the H7N9 epidemic. We suggest control and prevention activities to specifically target poultry transportation networks between Central, Pan-Pearl River Delta and South-West regions.

H5N1亚型禽流感因其对家禽的高致病性以及人类感染后的高病死率，已引发全球公共卫生层面的广泛关注。新近出现的H7N9亚型禽流感则因持续高发的人类感染病例，以及新近在家禽中获得的高致病性，正成为日益严峻的大流行风险。本研究针对265株H5N1和371株H7N9血凝素序列展开贝叶斯系统地理学分析，这些序列分离自人类、动物及环境样本，旨在识别并对比中国境内H5N1与H7N9的传播迁移模式及其扩散速率的预测因子。H7N9的传播动态及其预测因子的贡献度与H5N1存在显著差异。空间扩散的关键决定因素包括：地域间的邻近性（对H5N1与H7N9均适用），以及较低的农村人口密度（仅针对H5N1）。针对H7N9，额外的预测因子还包括低禽流感疫苗接种率、较低的自然保护区占比以及较高的湿度水平。针对H5N1与H7N9两种亚型，本研究均发现，从广东到广西、广东到湖南的病毒迁移路径为高可信度的传播路径（贝叶斯因子>30）。本研究揭示了H5N1与H7N9在大范围传播动态上的根本性差异。尤为重要的是，这表明针对H5N1制定的禽流感防控举措，或不足以遏制H7N9的疫情传播。本研究建议，防控工作应针对性聚焦华中、泛珠三角及西南地区之间的家禽运输网络。