http://www.digitaljournal.com/tech/science/new-method-to-track-avian-flu/article/371200

New method to track Avian flu

Posted Feb 16, 2014 by Tim Sandle
With various cases of Avian flu appearing in several regions of the world, scientists have honed in a new technique to help track the spread of the diseases across different territories and populations.
This colorized transmission electron micrograph shows H1N1 influenza virus particles like hemaggluti...
This colorized transmission electron micrograph shows H1N1 influenza virus particles like hemagglutinin and neuraminidase. Surface proteins on the virus particles are shown in black. National Institutes of Health (NIH)
U.S. National Institutes of Health
The main focus has been with the highly pathogenic avian influenza strain H5N1.
Influenza A virus subtype H5N1 is also known as "bird flu". The virus is highly pathogenic. Research, reported by the Harvard Gazette, has recently shown that a highly contagious strain of H5N1, one that might allow airborne transmission between mammals, can be reached in only a few mutations. This raises the specter of a pandemic or even bioterrorism.
In the new study, researchers have tracked the spread of an H5N1 variant in Egypt, a country recently identified as a major epicenter for the virus. The technique developed is called ‘phylogeography’. This works by by combining viral sequence data and geographical information over time, as well as evaluating features associated with viral carriers, researchers can better understand how viruses spread across a landscape through animal and human populations.
This allowed the researchers to trace the preponderance and transmission routes of H5N1 in Egypt. The group's findings revealed a geographic spread of the 2.2.1.1 viral form of H5N1 across Egypt's four primary areas: Cairo, Nile Delta, Canal and Upper Egypt. Statistical analysis suggests the northern governorate of Ash Sharqiyah as the point of origin for the spread of H5N1. Most of the identified routes of transmission appeared in the densely populated Delta region of Egypt. The Al Qalybiyah governate in particular appears to be a popular area for viral transition, though dispersion to and from this region remains uncertain, requiring further research.
From this, the scientists hope that the method can be rolled out to look at other areas and other types of viruses.
The research was led by Matthew Scotch, a researcher at Arizona State University's Biodesign Institute. The findings have been published in the journal BMC Genomics, in a paper titled “Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt”.