Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt

[tetano]

(Medical Xpress)?Since its first identification in Asia, highly pathogenic avian influenza ? H5N1 ? has caused significant alarm in the scientific community. While the virus' primary target is birds ? tens of millions have already died from it ? it is capable of infecting mammals, including humans, causing serious illness and a frightening rate of mortality.

In a new study, Matthew Scotch, a researcher at Arizona State University's Biodesign Institute, tracks the spread of an H5N1 variant in Egypt ? a country recently identified as a major epicenter for the virus. In results recently appearing in the journal BMC Genomics, Scotch tracks the spread of H5N1 cases using a technique known as phylogeography.

The authors hope that studies of this kind will significantly enhance efforts by public health officials to identify viral outbreaks, limit their spread, coordinate vaccination efforts, reduce mortality and better inform the public of risks.

"Egypt represents an epicenter for H5N1, and there are new variants that have emerged since it was first discovered there in 2006," Scotch says. "We used phylogeography and influenza genome sequences to model diffusion and evolution of the virus."

..

http://medicalxpress.com/news/2014-02-avian-flu-variant-stalks-egypt.html

[sharon sanders]

Re: Avian flu variant stalks Egypt

Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt

Matthew Scotch12*, Changjiang Mei1, Yilma J Makonnen3, Julio Pinto3, AbdelHakim Ali3, Sally Vegso4, Michael Kane5, Indra Neil Sarkar67 and Peter Rabinowitz4

* Corresponding author: Matthew Scotch matthew.scotch@asu.edu

Author Affiliations
1 Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Samuel C Johnson Bldg, Scottsdale, AZ 85259, USA

2 Center for Environmental Security, Biodesign Institute and Security & Defense Systems Initiative, Arizona State University, Tempe, AZ, USA

3 Food and Agriculture Organization of the United Nations (FAO), Cairo, Egypt

4 Yale Occupational and Environmental Medicine Program, Yale University, New Haven, CT, USA

5 Department of Biostatistics, Yale School of Public health, Yale University, New Haven, CT, USA

6 Center for Clinical and Translational Science, Department of Microbiology & Molecular Genetics, University of Vermont, Burlington, VT, USA

7 Department of Computer Science, University of Vermont, Burlington, VT, USA

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BMC Genomics 2013, 14:871 doi:10.1186/1471-2164-14-871


The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2164/14/871


Received: 3 December 2012
Accepted: 4 December 2013
Published: 10 December 2013
? 2013 Scotch et al.; licensee BioMed Central Ltd.
This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract
Background
Influenza A H5N1 has killed millions of birds and raises serious public health concern because of its potential to spread to humans and cause a global pandemic. While the early focus was in Asia, recent evidence suggests that Egypt is a new epicenter for the disease. This includes characterization of a variant clade 2.2.1.1, which has been found almost exclusively in Egypt.

We analyzed 226 HA and 92 NA sequences with an emphasis on the H5N1 2.2.1.1 strains in Egypt using a Bayesian discrete phylogeography approach. This allowed modeling of virus dispersion between Egyptian governorates including the most likely origin.

Results
Phylogeography models of hemagglutinin (HA) and neuraminidase (NA) suggest Ash Sharqiyah as the origin of virus spread, however the support is weak based on Kullback?Leibler values of 0.09 for HA and 0.01 for NA. Association Index (AI) values and Parsimony Scores (PS) were significant (p-value < 0.05), indicating that dispersion of H5N1 in Egypt was geographically structured. In addition, the Ash Sharqiyah to Al Gharbiyah and Al Fayyum to Al Qalyubiyah routes had the strongest statistical support.

Conclusion
We found that the majority of routes with strong statistical support were in the heavily populated Delta region. In particular, the Al Qalyubiyah governorate appears to represent a popular location for virus transition as it represented a large portion of branches in both trees. However, there remains uncertainty about virus dispersion to and from this location and thus more research needs to be conducted in order to examine this.

Phylogeography can highlight the drivers of H5N1 emergence and spread. This knowledge can be used to target public health efforts to reduce morbidity and mortality. For Egypt, future work should focus on using data about vaccination and live bird markets in phylogeography models to study their impact on H5N1 diffusion within the country.

http://www.biomedcentral.com/1471-2164/14/871