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Accelerated H5N1 Evolution in Egypt

Recombinomics Commentary 21:21
March 1, 2008

The recently released H5N1 poultry sequences from Egypt demonstrate an accelerated rate of genetic change, coupled with a high frequency of non synonymous changes, which include positions which have changed to multiple amino acids.  The dramatic changes signal vaccine escape.

These developments have been recent and appear to be associated with an expanded vaccine program.  The dramatic increase in genetic diversity is cause for concern. 

Egypt has had over 1000 outbreaks described in OIE reports and the two confirmed cases this week raise the number of reported cases to 45, the highest in any country outside of Asia.  Moreover, the two cases this week developed pneumonia, in contrast to the cases reported a year ago.

The recent HA sequences have multiple positions which have changed to more than one amino acid.  Position 144 has had three recent changes, R144K, R144I, and R144S.  Similarly, position 158 has changed to two amino acids, D158N and D158G.  This type of rapid change may signal escape from recent vaccines.

These data raise serious concern about the rate and direction of H5N1 evolution in Egypt.  Release of the human H5N1 from cases at the end of 2007, as well as the two cases reported this week would be useful.

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