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Fujian / Qinghai H5N1 Recombinants In Egypt
Recombinomics Commentary 19:41
May 7, 2010

China's national labs in Harbin released 10 HA sequences from Egyptian poultry, including 2 from 2010, 2 from 2009, and 6 from 2008. None of the sequences had 125del. However, one, A/chicken/Egypt/36-4/2008, had a deletion in the HA cleavage site that matched the Fujian sub-clade (2.3.2) found in wild birds at Uvs lake as well as the 2008 outbreak in Japan, South Korea, and Russia. The cleavage site and flanking region covering 200 BP matched clade 2.3.2 isolates indicating these polymorphisms were acquired by homologous recombination.

The movement of Fujian clade 2.3.2 sequences into Egypt was not a surprise.  In early 2008, clade 2.3.2 was in wild birds in Japan and eastern Russia, followed by wild birds at Uvs Lake in 2009.  Birds from Uvs Lake migrate through Egypt, leading to dual infections and acquisitions via recombination. 

Other sequences from Harbin also had regions of identity (see list).  These were Egyptian clade 2.2.1 Qinghai sequences which had Fujian sequences appended onto the clade 2.2.1 background.  These isolates confirm that homologous recombination is common, although under-represented in the H5N1 sequence database, where most recombinant sequences are deposited from labs in northern China, including Harbin.

It is unclear why there are not more examples in the Middle East.  However, the recent report of wild bird  H5N1 sequences in Emus at an Israeli petting zoo suggests Fujian H5N1 clase 2.3,2 may have been recently detected. 

Release of those sequences, as well as additional examples in Egypt would be useful.

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