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Egyptian Human and Bird HA H5N1 Sequences Are Similar

Recombinomics Commentary
April 5, 2006

The HA sequence of a human H5N1 isolate from Egypt, A/Egypt/2782-NAMRU3/2006(H5N1), has been released.  The description of a 30 year-old male from Qalubiya Governorate most closely matches the second patient reported to have H5N1 bird flu symptoms in Egypt.  He has since recovered.  The human H5N1 sequence is most closely related to a bird sequence from Egypt, A/chicken/Egypt/960N3-004/2006(H5N1).  Both sequences are the Qinghai strain with HA cleavage site of GERRRKKR.  Both also have a polymorphism, P239S, downstream from the receptor binding domain.

The number of suspect H5N1 patient in Egypt continue to rise and more human and poultry sequences are expected.  These sequences create a database that allows tracking of the H5N1 via shares polymorphisms.  Moreover, the sequences trace the evolution of the H5N1, which has a Qinghai genetic background and a number of regional polymorphisms acquired by recombination.

The diversity of the Qinghai sequences highlights the need for rapid release of the data.  The first human sequences from the area, including A/Turkey/12/2006(H5N1), remain in a private WHO database and have not been released.

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