Commentary
Clade 2.2.3 Recombination With Endemic H5N1 In Ukraine
Recombinomics Commentary 18:31
June 17, 2008
Partial HA sequences have been released from the Ukraine. One sequence, A/chicken/Syvash/02/2005, was an early clade 2.2 sequence that differed from the consensus sequence at three positions. Two of those polymorphisms, A1114C and T1123C, are in the other recently released sequence, A/chicken/Krasnogvardeysk/58/2008, indicating H5N1 has become endemic in the Ukraine and polymorphisms from 2005 are still present. However, the upstream region of the 2008 isolate matches other clade 2.2.3 isolates, including another 2008 isolate from Ukraine, A/chicken/Lobzenko/01/2008. Thus, the Krasnogvardeysk sequence is a recombinant between Ukraine sequences that were present in 2005, and clade 2.2.3 sequences present in the Ukraine in 2008.
Clade 2.2.3 sequences linking back to the Uvs Lake outbreak began to appear in the region in early 2007. In the summer of 2007, these sequences were reported in Germany, the Czech Republic, and France. In the fall of 2007 and early 2008, Uvs Lake clade 2.2.3 sequences were reported throughout Europe and also in Saudi Arabia.
Thus, even though clade 2.2.3 has become dominant in the area, in regions such as the Ukraine, some of the earlier polymorphisms are being acquired by the clade 2.2.3 isolates.
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