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Novel H5N1 HA Cleavage Site in Aswan Egypt
Recombinomics Commentary
March 21, 2007

US NAMRU-3 has generated HA and NA sequences from the two confirmed cases in Aswan (10F and 2M).  The two HA sequences, A/Egypt/2321-NAMRU3/2007 and A/Egypt/2331-NAMRU3/2007  differ by a single nucleotide from each other, and have the novel HA cleavage site, GERRRRKR, previously reported in whooper swans from Mongolia.  The NA sequences from Aswan are identical to each other, and closely related to the NA sequences from Beni Suef, A/Egypt/06
36-NAMRU-3/2007 and Fayyoum, A/Egypt/1394-NAMRU3/2007.  The HA from the two earlier sequences have a 3 BP deletion and are easily distinguished from the most recent HA sequences, indicating the two sequences from Aswan are reassortants.

The two most recent sequences do not have M230I and one patient has already recovered.  Similarly, the two prior cases also recovered and they also lacked M230I.  In contrast, all patients with M230I have died.

These genetic differences suggests some of the clinical presentations and outcomes may be H5N1 encoded and the sequences generated by NAMRU-3 provide a wealth of information on the evolution of H5N1.

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