Rapid H5N1 Evolution in Egypt Raises Pandemic Concerns
Recombinomics Commentary 05:21
March 2, 2008
New H5N1 poultry sequences have been released by the National Lab of Veterinary Quality Control on Poultry Production in Egypt (see list here). The eighteen HA sequences are largely from isolates collected in December, 2007 or January 2008. Included in this collection are H5N1 sequences from vaccinated flocks. These sequences have an alarming number of new polymorphisms, most of which are non synonymous. As noted earlier, the sequences released from NAMRU-3 had a number of non synonymous changes at targeted positions. The sequences from the National Lab extend these observations.
There are now multiple positions which have changed to two or more amino acids. Position 144 which had changed to three different amino acids (R144K, R144I, and R144S), now includes a fourth amino acid change, R144G. Similarly other positions with two or more changes include K123R and K123N, D158N and D158G, M230I and M230V.
The above changes are seen in a limited analysis. The number may go higher. However, many of these changes are not just in vaccinated flocks. They are present in subsequent collections at a variety of locations in the Nile Delta, raising concerns that these changes are being driven by poorly matched vaccines and these changes are becoming widespread.
This dramatic increase in genetic diversity raises serious pandemic concerns. H5N1 evolves via recombination, and the large number of diverse sequences concentrated in regions fed my the Nile in Egypt increases co-infections and the rate of evolution, which presents significant problems for vaccination programs.
The National Labs in Egypt are to be commended for releasing these sequences in a timely matter. These sequences define a serious problem in Egypt.
Release of the H5N1 sequences from the human cases from the same time period would be useful.
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