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H5N1 Evolution in Egypt

Recombinomics Commentary
December 12, 2007

The recent OIE report from Egypt detailed H5N1 outbreaks since February 2006.  There were 922 outbreaks and the 178 report provided map coordinates for each outbreak.  A satellite map of these outbreaks can be seen here here here here and the most recent cases are here.  The most recent infection involved ducks on a roof top in Giza city on November 24, 2007. Although most outbreaks involved domestic poultry, some also included wild birds, including pigeons.  The report also detailed an extensive immunization program, listing the number of birds vaccinated in each governorate.

The report and map coordinates provide a dramatic view of the outbreaks, which help explain the recent evolution of H5N1 in Egypt, especially in 2007.  Sequence analysis of the human cases in Egypt indicates that the more recent cases were significantly more diverse genetically, than isolates from the spring of 2006.  This increased diversity was also seen in the poultry isolates.  Although the more recent sequences maintained the Egyptian regional markers seen in early 2006, the isolates had a number of polymorphisms appended onto the Egyptian background.  These changes included NA G743A, which appeared on multiple Egyptian backgrounds in 2007.  The same change was appended onto clade 2.2 backgrounds in isolates from Moscow and Ghana.  More recently this change was also in wild bird isolates from Krasnodar and Germany, which represent yet another genetic background that traces back to the Uva Lake wild bird outbreak in the summer of 2006.  Like the other genetic backgrounds that acquired G743A in 2007, the 2006 isolates from Uva Lake did not have G743A.

Although the G743A represents a dramatic example of the concurrent acquisition of the same polymorphism onto multiple genetic backbones, many additional polymorphisms were appended onto the Egyptian backbone.  These newly acquired changes, including a 3 BP deletion could be found in earlier H5N1 isolates, including clade 2.2 isolates from Germany.

Tracing these isolates provides very specific information linked to H5N1 evolution, and the high concentration of H5N1 in Egypt provides an environment for multiple co-infections, leading to recombination and newly emerging H5N1 genomes.

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