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Another H5N1 Confirmed Case in Fayyoum
Recombinomics Commentary
February 14, 2007

Nadia Mohammed Abdel Hafez, 37, from the oasis province of Fayyum south of the capital, went to hospital on Monday complaining of a high temperature and bronchitis, health ministry spokesman Abdel Rahman Shaheen said.

The last person to die from the disease in Egypt, a teenage girl, also came from Fayyum.

Shaheen said Abdel Hafez had been transferred to a government facility in Cairo, where she is being treated with the anti-bird flu drug Tamiflu.

The latest confirmed H5N1 case in Egypt is from Fayyoum, as was the prior case.  These two cases were also near the third case this year, in Beni Suef.  The sequence of the HA and NA from the Beni Suef case was similar to the case from Fayyoum.  Both sequences had distinctive polymorphisms indicating the H5N1 was the Qinghai strain from Egypt, but the two recent sequences were readily distinguished from the prio three cases this season, which included two sequences from the Gharbiya cluster, which had the Tamiflu resistance marker, N294S.  The two recent sequences also did not have HA M230I, which was in the fist three human H5N1 HA sequences of this season.

Although the two recent sequences from patients south of Cairo did not have some of the polymorphisms seen in earlier isolates, the sequences did have additional evidence  of acquisitions via recombination.  Both sequences had the identical 3 nucleotide deletion in HA.  Since both sequences were similar, the common deletion was expected.  However, the same deletion was in 2006 H5N1 from Hunan.  The two Hunan sequences, A/
chicken/Hunan/2246/2006 and A/chicken/Hunan/2292/2006 were not the Qinghai strain and had a novel cleavage site REGGRRKR, which was quite distinct from the common Qinghai cleavage site of GERRRKKR.  The remained of the HA and NA sequences were quite distinct, yet the four sequences had the same 3 nucleotide deletion, strongly suggesting that the deletion was not a coincidental match, but that the deletion was acquired by the Qinghai sequence via recombination.

The most recent H5N1 also had S227N, which has also been seen in additional Qinghai isolates from Egypt and
Turkey, providing additional support for recombination.

It seems likely that several of these features will be in the H5N1 from the latest case.

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