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North American Sequences in Japanese Swan H5N1
Recombinomics Commentary 20:36
May 19, 2008

The sequence data released on isolates from two whooper swans in Japan has indicated that they are reassortants, with a clade 2.3.2-like HA, but clade 2.3.4-like for the remaining genes.  Initial media reports out of South Korea also emphasized that the sequences were clade 2.3.2, which has not produced a reported human case prior to the H5 positive soldier.  However, more recent media reports out of South Korea note similarities between isolates in South Korea and human sequences in Vietnam.

The reassorted genes in the isolates form Japan signal dual infections, as so the polymorphisms that are most easily explained by recombination.  The whooper swan isolates have HA M230I, which would likely increase the likelihood of a bird infection, since M230I is present in all three strains of seasonal flu (H1N1, H3N2, and influenza B)

Polymorphism acquisitions can also be used to trace the movement of the various isolates.  The PB2 sequence has three consecutive polymorphisms that have previously been seen in North American isolates (see list here).  These sequence support movement of H5N1 along the East Asian flyway which feeds into Alaska in North America.  The sequences, as well as the location of these isolates in northern Japan, raise concerns that H5N1 is migrating toward North America.  This migration is also supported by the timing of the outbreaks in Japan and South Korea (see satellite map).

Clade 2.3 has not been reported previously in South Korea or Japan. The record size of the outbreak in South Korea provides new opportunities for further evolution of H5N1 as birds migrate out of those countries and into Siberia and Alaska. 

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