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Hokkaido Whooper Swan H5N1 Has M230I and Clade 2.3.4 Genes

Recombinomics Commentary 07:36
May 19, 2008

Sequences from two of the whooper swan isolates from Hokkaido have been made public.  Satoko Onishi and colleagues at Hokkaido University are to be commended on the prompt release of the sequences.  Full sequences from all eight gene segments have been released for one isolate, A/whooper swan/Hokkaido/1/2008, and partial sequences released for the other, A/whooper swan/Hokkaido/2/2008.  Both sets of sequences are closely related to each other.

The HA sequences are most closely to clade 2.3.2 sequences from Vietnam, but they have a large number of non synonymous changes, including M230I.  M230I is a receptor binding domain change found in the Gharbiya cluster and many more recent poultry isolates in Egypt.  It is also found in seasonal flu (H1N1, H3N2, influenza B), and is linked to fatal cases in Egypt.  It is likely that M230I is also in isolates in South Korea, including the H5N1 that infected the soldier.  Although he did recover, he developed pneumonia and lost consciousness.  The sequences from Japan also had polymorphisms that are almost exclusively in clade 2.2 isolates (see list here and here).

Although the HA sequences are most closely related to clade 2.3.2, the other gene segments are closely related to clade 2.3.4, including human isolates such as A/human/China/GD02/2006.  These relationships suggest there have been considerable exchanges of genetic information via recombination and reassortment.  The PB2 sequence also has a region that matches sequences from North America, raising additional concerns that the migratory birds in northern Japan migrate into North America.  The acquisitions signal additional global expansion by clade 2.3 and remain cause for concern.

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