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H5N1 Wild Bird Sequences in Egypt
Recombinomics Commentary
November 17, 2006

HA sequences from H5 isolated from wild birds in Egypt have been released.  Although Egypt reported H5N1 to the OIE in February of this year, the two new sequence indicate H5N1 was isolated in a teal in December, 2005.  The HA sequence from that isolate, A/teal/Egypt/14051-NAMRU3/2005, is the Qinghai strain, with the common HA cleavage site, GERRRKKR.  It has a polymorphism found in a subset of Qinghai isolates, which is found in the first isolate from Turkey, as well as poultry isolates in Egypt, and human isolates in Egypt and Djibouti (see list here), including the most recent confirmed case, which has M230I, a polymorphism adjacent to the receptor binding domain that is found in all three human influenza strains, serotypes H1N1 and H3N2 for influenza A, as well as influenza B.

A second teal isolate, A/teal/Egypt/9885-NAMRU3/2005, is low path H5, with regions that match H5 low path in Europe and other migratory isolates in Asia.  However, the Egyptian isolate has regions of identity with high path H5N1, including other Qinghai strains.  Moreover, many of the polymorphisms are found in H5N1 isolates in China.  Thus, the low path H5 in Egypt has evidence of recombination with H5N1 in Asia, including the Qinghai strain.

The acquisitions of high path polymorphisms by low path isolates are cause for concern.  H5N1 sequences can also be found in low path H5 in North America also, in addition to swine and human polymorphisms.  These acquisitions continue to offer opportunities for changes in virulence as well as receptor binding specificity, as Qinghai isolates in the Middle East continue to acquire mammalian polymorphisms, of which PB2 E627K has become fixed.
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