Gharbiya Receptor Binding Domain Changes in Egyptian Poultry
Recombinomics Commentary 01:05
January 31, 2008
HA sequences from Egypt were released at Genbank. Although the characterization sheets do not include the collection dates, the sequences themselves are more evolved versions of last seasons H5N1 sequences from Egypt. They have the common broad regional markers, and many are evolved versions of clinically relevant sequences.
Two markers of interest are receptor binding domain changes, V223I and M230I. Both markers were present in sequences from the Gharbiya cluster. All three cluster members died, as did all patients infected with M230I.
This season four of the five H5N1confirmed patients died. Both V223I and M230I are present in the released poultry sequences. Seven had V223I. All seven also had M230I (see list below). In addition, four sequence had M230I. One, A/duck/Egypt/9399NAMRU3-CLEVB202/2007, had M230I coded as it was in the Gharbiya cluster. The other three, A/chicken/Egypt/3049NAMRU3-CLEVB175/2007,
A/turkey/Egypt/9398NAMRU3-CLEVB195/2007, and
A/duck/Egypt/3043NAMRU3-CLEVB56/2007 had coding found in H7 isolates. This coding convergence for M230I was also seen last season.
The above data helps explain the high cases fatality rate in the initial cases this season. It seems likely than most will have M230I, which is generally found in northern Egypt. Most of the confirmed cases in Egypt this season were from the north.
No NA sequences were released. The Gharbiya cluster sequences also had the oseltamivir (Tamiflu) resistance marker N294S. Like the other H5N1 marker H274Y, the marker was evolutionarily fit. It was present in the H5N1 prior to Tamiflu treatment.
The released sequences do not include Uva Lake sequences, which have been widely reported in Europe since the summer of 2007.
Release of the human sequences, as well as NA sequences from the recent poultry isolates, would be useful.
Sequences with V223I and M230I
A/chicken/Egypt/9385NAMRU3-CLEBV125/2007
A/chicken/Egypt/9386NAMRU3-CLEVB136/2007
A/chicken/Egypt/9390NAMRU3-CLEVB157/2007
A/chicken/Egypt/9392NAMRU3-CLEVB167/2007
A/chicken/Egypt/9391NAMRU3-CLEVB158/2007
A/chicken/Egypt/9387NAMRU3-CLEVB148/2007
A/chicken/Egypt/3051NAMRU3-CLEVB78/2007
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