Abstract
BackgroundAvian influenza virus (AIV) causes both severe outbreaks and endemic disease among poultry and has caused sporadic human infections in Asia, furthermore the routes of transmission in avian species between geographic regions can be numerous and complex. Using nucleotide sequences from the internal protein coding segments of AIV, we performed a Bayesian phylogeographic study to uncover regional routes of transmission and factors predictive of the rate of viral diffusion within China.ResultsWe found that the Central area and Pan-Pearl River Delta were the two main sources of AIV diffusion, while the East Coast areas especially the Yangtze River delta, were the major targets of viral invasion. Next we investigated the extent to which economic, agricultural, environmental and climatic regional data was predictive of viral diffusion by fitting phylogeographic discrete trait models using generalised linear models.ConclusionsOur results highlighted that the economic-agricultural predictors, especially the poultry population density and the number of farm product markets, are the key determinants of spatial diffusion of AIV in China; high human density and freight transportation are also important predictors of high rates of viral transmission; Climate features (e.g. temperature) were correlated to the viral invasion in the destination to some degree; while little or no impacts were found from natural environment factors (such as surface water coverage). This study uncovers the risk factors and enhances our understanding of the spatial dynamics of AIV in bird populations.
Highlights
Avian influenza virus (AIV) causes both severe outbreaks and endemic disease among poultry and has caused sporadic human infections in Asia, the routes of transmission in avian species between geographic regions can be numerous and complex
The NS segment has a lower substitution rate (1.66 × 10−03) and earlier to most recent common ancestors (TMRCA) (1554, Highest Posterior Density (HPD): 1175–1836) due to the divergent alleles A and B [46], the detailed evolutionary rate and TMRCA estimations for each AIV segment can be found in Additional file 1: Table S4
Epidemiological studies suggested that highly pathogenic avian influenza (HPAI) H5N1 outbreaks in poultry mostly occurred in areas which overlapped with habitats for wild birds, whereas outbreaks in wild birds were mainly found in areas where food and shelter are
Summary
Avian influenza virus (AIV) causes both severe outbreaks and endemic disease among poultry and has caused sporadic human infections in Asia, the routes of transmission in avian species between geographic regions can be numerous and complex. Two types of locations are considered as potential hotspots of influenza outbreaks and of particular importance; areas with high ecological complexity and those with high densities of domesticated birds and trade activity. Areas with a high ecological complexity include those which are rich in nature reserves, water resources, and on the flyway route of migratory birds. This creates an environment in which domestic ducks and wild aquatic birds live together, sharing water, food, and habitat.
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