Global genetic variation and transmission dynamics of H9N2 avian influenza virus

The H9N2 influenza viruses are extensively circulating in the poultry population, and variable genotypes can be generated through mutation, recombination and reassortment, which may be better adapted to infect a new host, resist drug treatment or escape immune pressure. The LPAI H9N2 viruses have the potential to evolve towards high levels of virulence in human. Some studies about the regional dispersal were reported, but global dissemination and the drivers of the virus are poorly understood, particularly at the genome scale. Here, we have analysed all eight gene segments of 168 H9N2 genomes sampled randomly aiming to provide a panoramic framework for better understanding the genesis and genetic variation of the viruses, and utilized phylogeography and spatial epidemiology approaches to uncover the effects of the genetic variation, predictors and spread of H9N2 viruses. We found that more frequent reassortment events involve segments PA, NP and NS, and 21 isolates have possible mosaic structure resulting from recombination events. Estimates of gene-specific global dN/dS ratios showed that all genes were subject to purifying selection. However, a total of 13 sites were detected under positive selection by at least two of three methods, which located within segments HA, NA, M2, NS1 and PA. Additionally, we inferred that NA segment has the highest rate of nucleotide substitution, and its tMRCA estimate is the youngest than the remaining segments' inference. About the spatial history, air transportation of human was identified as the predominant driver of global viral migration using GLM analysis, and economic factors and geographical distance were the modest predictors. Higher migration rates were estimated between five pairs of regions (>0.01) indicating the frequent migration of the viruses between discrete geographical locations. Further, our Markov jumps analysis showed that viral migration is more frequent between Southern China and Northern China, and high rate of gene flow was observed between America and East Asia. Moreover, the America together with Southeast Asia acted as the primary hubs of global transmission, forming the trunk of evolutionary tree. These findings suggested a complex interaction between virus evolution, epidemiology and human behaviour.