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H5N1 Tree Sparrows in Henan Contain H3N2 Polymorphisms

Recombinomics Commentary
December 4, 2005

The four recent whole genome sequences of Henan tree sparrows are cause for concern.  The two surface proteins are HPAI H5N1 and the multibaisc HA cleavage site generates a string selective advantage that allows for wide distribution of the additional 6 genes.  These genes have many polymorphisms found in H9N2 and H3N2 isolates.

Many of these polymorphism are in 2003/2004 isolates from South Korea, indicating the sequences are not limited to the terrestrial birds in Henan.  The genes also have considerable amounts of recombination, which is why they were not well defined in the Journal of Virology paper.

These mammalian sequences are of considerable concern, because they are also appearing as novel sequences in human H3N2 isolates as well as canine H3N8 isolates.

As H5N1 wild bird flu sequences come into the area, new recombinants will be formed and distributed.  This may account for the limited success using animal vaccines to control the outbreaks in eastern China.  Since the Henan isolates do not produce symptoms in ducks, they may be much more widespread than the tree sparrow population in Henan.

Avian influenza sequences are clearly recombining and reassorting at a high rate.  The amount of sequence data in Asia has been limited, especially this year, as the recombination rate appears to be accelerating in association with increased genetic diversity and an expanded host range of H5N1.

Release of more sequence data from isolates linked to the recent outbreaks in China as well as earlier collections from indigenous populations of birds worldwide, would be useful


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