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Virology. 2019 Sep 27;538:86-96. doi: 10.1016/j.virol.2019.09.011. [Epub ahead of print]

Inferring host roles in bayesian phylodynamics of global avian influenza A virus H9N2.

Author information

1
State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China; School of Computer Science, University of Auckland, Auckland, New Zealand; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand. Electronic address: jingauckland2017@gmail.com.
2
School of Computer Science, University of Auckland, Auckland, New Zealand; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.
3
State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China.
4
State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China; Department of Earth System Science, Tsinghua University, Beijing, China. Electronic address: bing.xu2013@gmail.com.

Abstract

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.

KEYWORDS:

Avian host transitions; Avian influenza virus; Bayesian; Generalized linear model; H9N2; Phylodynamic; Phylogeographic; Poultry trade

PMID:
31586866
DOI:
10.1016/j.virol.2019.09.011
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