Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico

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 identif...

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Main Authors:	Lu, Lu, Lycett, Samantha J., Leigh Brown, Andrew J.
Format:	Online
Language:	English
Published:	Public Library of Science 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165766/

id	pubmed-4165766
recordtype	oai_dc
spelling	pubmed-41657662014-09-22 Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico Lu, Lu Lycett, Samantha J. Leigh Brown, Andrew J. Research Article 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. Public Library of Science 2014-09-16 /pmc/articles/PMC4165766/ /pubmed/25226523 http://dx.doi.org/10.1371/journal.pone.0107330 Text en © 2014 Lu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Lu, Lu Lycett, Samantha J. Leigh Brown, Andrew J.
spellingShingle	Lu, Lu Lycett, Samantha J. Leigh Brown, Andrew J. Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico
author_facet	Lu, Lu Lycett, Samantha J. Leigh Brown, Andrew J.
author_sort	Lu, Lu
title	Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico
title_short	Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico
title_full	Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico
title_fullStr	Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico
title_full_unstemmed	Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico
title_sort	determining the phylogenetic and phylogeographic origin of highly pathogenic avian influenza (h7n3) in mexico
description	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.
publisher	Public Library of Science
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165766/
_version_	1613134411955437568

Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico

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