Determining the phylogenetic and phylogeographic origin of highly pathogenic avian influenza (H7N3) in Mexico.

Lu Lu,Andrew J Leigh Brown,Samantha J Lycett

doi:10.1371/journal.pone.0107330

Lu Lu, Andrew J Leigh Brown + Show 1 more

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https://doi.org/10.1371/journal.pone.0107330

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Journal: PloS one	Publication Date: Sep 16, 2014
Citations: 64	License type: CC BY 4.0

Affiliation: University of Edinburgh, University of Glasgow

Abstract

Highly pathogenic (HP) avian influenza virus (AIV) H7N3 outbreaks occurred 3 times in the Americas in the past 10 years and caused severe economic loss in the affected regions. In June/July 2012, new HP H7N3 outbreaks occurred at commercial farms in Jalisco, Mexico. Outbreaks continued to be identified in neighbouring states in Mexico till August 2013. To explore the origin of this outbreak, time resolved phylogenetic trees were generated from the eight segments of full-length AIV sequences in North America using BEAST. Location, subtype, avian host species and pathogenicity were modelled as discrete traits upon the trees using continuous time Markov chains. A further joint analysis among segments was performed using a hierarchical phylogenetic model (HPM) which allowed trait rates (location, subtype, host species) to be jointly inferred across different segments. The complete spatial diffusion process was visualised through virtual globe software. Our result indicated the Mexico HP H7N3 originated from the large North America low pathogenicity AIV pool through complicated reassortment events. Different segments were contributed by wild waterfowl from different N. American flyways. Five of the eight segments (HA, NA, NP, M, NS) were introduced from wild birds migrating along the central North American flyway, and PB2, PB1 and PA were introduced via the western North American flyway. These results highlight a potential role for Mexico as a hotspot of virus reassortment as it is where wild birds from different migration routes mix during the winter.

Highlights

Migratory birds are major candidates for long-distance dispersal of zoonotic pathogens and low pathogenicity (LP), avian-origin influenza A viruses (AIVs) are widely distributed in free-ranging water birds [1]
To investigate the origin of the avian influenza virus (AIV) causing the high pathogenic viruses (HPAI) H7N3 outbreak in Mexico in 2012, an initial phylogenetic analysis using Maximum likelihood was performed for each segment of both the outbreak sequences and a background dataset which comprised all available AIV of North American AIV lineages (Figure 1)
In the HA segment a sublineage mainly composed of H7N2 AIV from domestic birds in New York state is clearly separate from the recent lineage composed of AIV from wild birds, which indicates extensive diversity of LP AIV in wild and domestic birds

Summary

Introduction

Migratory birds are major candidates for long-distance dispersal of zoonotic pathogens and low pathogenicity (LP), avian-origin influenza A viruses (AIVs) are widely distributed in free-ranging water birds [1]. Wild birds spread their viruses to other wild as well as domestic birds as they migrate through an area, allowing extensive reassortment [2]. Migrating wild birds have been implicated in the spread and emergence of HPAI such as HP H5N1 and H7N3. Viral transmission between wild birds and domestic poultry, and consequent genetic exchange, has contributed to genomic reassortment which confounded disease control efforts [6,7]

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