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Vaccine Resistant H5N1 Fixed in Egypt
Recombinomics Commentary 14:55
February 11, 2009

The National Veterinary Labs (NLQP) in Egypt have released 20 HA sequences collected between January 8 and June 15, 2008 (see list here).  17 of these sequences mapped with the vaccine resistant sequences isolated from vaccinated flocks at the end of 2007 / beginning of 2008.  The isolates were found throughout Egypt and were also in Israel (see updated map).  The high frequency in the above sequences, including all sequences from isolates collected since April, indicate this sub-clade has become fixed in Egypt and will likely be found in new cases in Egypt.

Although the sequences have the Egyptian markers from clade 2.2 isolates dating back to 2006, each season a new series of polymorphisms is appended onto this background.  Some polymorphisms, such as G743A, are appended onto multiple distinct backgrounds.  Moreover, the newly acquired polymorphisms link back to various H5N1 in circulation in Asia.

These predictable acquisitions, including a 3 BP deletion from clade 7 sequences in Hunan, support evolution by homologous recombination with significant applications for vaccine target selection.

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