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H5N1 Cluster in Qena Egypt Raises Concerns
Recombinomics Commentary
June 12, 2007

Donia Ali Tghyan who did not exceed the second year from its age lies now in a non stable condition in Al Bakri's facility hospital, after a doctor that named Shehata Mahmoud suspected its condition inside his special clinic and accelerated its transfer to the hospital of Qina fevers.

And she Leone had entered it a week and left it without the suspicion of its condition or the necessary taking towards her and as a result to the non settlement of its condition and appearance of the injury symptoms on it clearly, have been transferred in a car prepared for Al Bakri's facility hospital.

The above translation suggests the latest confirmed H5N1 case (4F) in Qena, Egypt developed symptoms at the beginning of this month, like the recent fatal case (10F), although the situation update indicates she developed symptoms on June 7.

The translation, like media reports on the earlier case, indicates an H5N1 diagnosis was not made initially.  The failure to diagnose these cases early is not a surprise because H5N1 cases this late in the season are unusual, and earlier cases in southern (upper) Egypt were mild.  The confirmation of mild cases raised concerns, because such cases would be easily missed.

NAMRU-3 generated HA and NA sequences from the earlier cases.  The HA sequences readily divided the cases into two sub-clades.  Although all isolates had Qinghai markers as well as regional markers identified by isolates from Egypt, Israel, Gaza, and Djibouti in early 2006, the recent cases had a large number of sub-regional markers appended onto the genetic background defined by the isolates from early 2006.  The grouping of these cases and geographical locations are listed below, including those with the 3 BP deletion.  However, the two most recent isolates below had reverted to the wild type Qinghai cleavage site, and the patient that died this month had reverted 8 of the 14 sub-regional markers.

This rapid reversion raises concerns that the evolution of the H5N1 linked to mild cases may become more virulent.  The latest fatality is the first child to die of H5N1 in Egypt and the mild nature of the earlier cases, coupled with the clustering in time and space, raises concerns that the number of H5N1 cases may be significantly higher than indicated in the confirmed totals.

Moreover, the two recent HA sequences that had reverted sub-regional markers did have N98D (N103D in H3 numbering), which was present in early H1N1 cases, including those from 1918.

Careful monitoring of this region is indicated.

3 BP deletion
A/Egypt/0636-NAMRU3/2007  Beni Suef
A/Egypt/1394-NAMRU3/2007  Fayoum
A/Egypt/2621-NAMRU3/2007  Qena
A/Egypt/2629-NAMRU3/2007  Qena
A/Egypt/2631-NAMRU3/2007  Qalubiea

Mongolian cleavage site
A/Egypt/2321-NAMRU3/2007  Aswan
A/Egypt/2331-NAMRU3/2007  Aswan
A/Egypt/2616-NAMRU3/2007  Aswan
A/Egypt/2620-NAMRU3/2007  Menia
A/Egypt/2750-NAMRU3/2007  Menia
A/Egypt/4081-NAMRU3/2007  Qena

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