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H5N1 Fatality in Qena Egypt
Recombinomics Commentary
June 9, 2007

A 10-year-old Egyptian girl who contracted the H5N1 bird flu virus died on Saturday, bringing the number of fatalities from the disease in the most populous Arab country to 15, the health ministry said.

The girl, identified as Mayyada Tuhami, is reported to have fallen ill on June 1 after coming into contact with infected household birds but did not enter hospital until roughly a week later

The above comments describe the most recent H5N1 fatality in Egypt.  This is the first human Qinghai case reported in June, when influenza activity in the northern hemisphere is greatly reduced.  It is also the first fatal case in southern Egypt, where the cases this season were mild.

Last year there were a few bird infections in June (A/goose/Egypt/13009N3-SM2/2006 and A/duck/Egypt/13010N3-CLEVB/2006).  Those isolates were from the Nile Delta and formed a new branch of Egyptian H5N1 sequences.  Similarly, those from Aswan formed another branch, and the HA sequences had an HA cleavage site that matched Qinghai Mongolian were related to the last H5N1 fatal case in Egypt, A/Egypt/2751-NAMRU3/2007, who was from Cairo.

However, the human cases in southern Egypt were genetically distinct from the sequences from Nile Delta isolates.  Sequences from central Egypt, including those from siblings in Mena, had a 3 BP HA deletion and formed a distinct branch in phylogenetic trees sequences from whooper swans.

Sequences from children in the south fell on both branches, but all cases were mild.  None of the sequences from the mild cases in the south matched the sequences from the Nile Delta.

Therefore, the sequence of the latest case will be of interest.  These sequences fro this season had acquired a number of new polymorphisms, which were appended onto the Egyptian Qinghai genetic background. 

Last season, several patients from the north had acquired HA M230I.  All of these patients died.  Moreover, the patients in the Gharbiya cluster had a change in the receptor binding domain, V223I.  Although the Gharbiya patients died in 2006, an H5N1 isolate, A/chicken/Egypt/1890N3-HK49/2007, from a chicken in Gharbiya in February, 2007, also had V223I and M230I, indicating the two polymorphisms were circulating in Egypt this year.

In addition, the sequences, A/Egypt/2621-NAMRU-3/2007 and A/Egypt/2629-NAMRU-3/2007, from siblings from Mena had an NA acquisition, G743A, which was also in the above chicken, raising concerns regarding additional exchanges of polymorphisms in Egypt.

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