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Krasnodor H5N1 Bird Flu Is an Italy Kurgan Recombinant

Recombinomics Commentary

July 11, 2006

H5N1 bird flu sequences from the Qinghai strain are beginning to be published in public databases.  The strain moved into long range migratory birds and increased its global reach markedly in the past 12 months.  First reported in May, 2005, the strain migrated to the west in the summer of 2005 and was reported for the first time in Russia, Kazakhstan, and Mongolia in July  August, 2005.  Prior to this migration, reported H5N1 infections were limited to China and countries to the east and south.  The number of countries reporting H5N1 infection grew from 10 to over 50 ,as H5N1 migrated into Europe, the Middle East, and Africa.

As the strain spread, it provided a real time demonstration of H5N1 evolution via recombination.  These emerging strains could be easily classified by the newly acquired polymorphisms on the Qinghai genetic background.  As countries increase surveillance, the number of isolates continued to grow.  Most of the sequences have not been released, but recent presentations have phylogenetic trees if the Qinghai strain in Europe, China, Russia, and Nigeria.

As the sequence become public, it becomes increasingly easy to identified the sources of the newly acquired sequences. Although the polymorphism appear to be random point mutations, the newly acquired sequences are nit recent mutations and the distribution is not random.

Most of the newly acquired polymorphisms can be found in H5N1 isolates from Asia which were acquired by a variety of Qinghai strains prior to the migration to the west.  However, tracking these polymorphisms shows how they are acquired during dual infections by various Qinghai strains.

One such examples is the recent isolate from a chicken in Krasnodar, A/chicken/Krasnodar/01/2006(H5N1). It has six polymorphisms layered onto the Qinghai genetic background. The first 3 polymorphisms, C181T, G194A, and C223T can be found in A/Cygnus olor/Italy/742/2006, and the remaining three polymorphisms, G445A, G548A, and G1714A are in A/chicken/Kurgan/05/05.  As more sequences are made public, more examples of recombination will become obvious.

The major jump in geographical reach allows for expansion of region versions of H5N1, which can then recombine with newly arriving H5N1.  The expansion creates the opportunity for a large number of dual infections among genetically diverse H5N1's.  The dual infections lead to more recombination and accelerated evolution of H5N1.

This rapid expansion of geographical genetic complexity in long range migratory birds is cause for concern.

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