Inferring host roles in bayesian phylodynamics of global avian influenza A virus H9N2
Role of avian hosts in shaping persistence, evolution, and dispersal of global low pathogenic avian influenza virus (LPAIV) H9N2 remains uncertain. Under Bayesian Markov Chain Monte Carlo framework, we used the discrete trait analysis (DTA) to reconstruct host and location switches in the evolutionary history of global H9N2 given hemagglutinin gene sequences from 18 countries/regions between 1976 and 2018. We employed generalized linear models (GLMs) to inform virus migration rates by empirical predictors. Global H9N2 isolates were mostly sampled from domestic Phasianidae in low- and middle-income countries with poor bio-security. Anatidae was inferred as the ancestral source from which the virus spread to domestic waterfowl, and later to domestic Phasianidae who have become the dominant host to sustain the virus, especially in Asia. Poultry trade was a well-supported driver to H9N2 spread across countries/regions. Strict bio-security and separation between wild and domestic poultry can be used to mitigate virus spread.