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Kurgan H5N1 Wild Bird Flu Is A Recombinant
Recombinomics Commentary
January 5, 2006
Complete sequences of the eight genes of an H5N1 wild bird flu sequences from Kurgan (A/chicken/Kurgan/3/2005) has been placed on deposit at GenBank and Los Alamos. The sequences is closely related to the wild bird sequences from Qinghai Lake and includes the characteristic HA cleavage site of GERRRKKR, the PB2 polymorphism, E627K, and a wild type M2 ion Channel (sensitive to amantadine). The cleavage site matches the other H5N1 from Russia and Europe and all eight genes are clearly in the H5N1 wild bird clade.
However, like other isolates, the sequence has acquired polymorphisms via recombination with other H5N1 isolates. The Kurgan isolate has polymorphism previously found only in isolates from Mongolia and/or Japan and South Korea. These “northern” polymorphisms have been acquired in several of the genes. However, in addition to these polymorphisms, others have been acquired that have previously been found in recent isolates from Vietnam and Thailand.
These newly acquired polymorphisms indicate the wild bird sequences evolve via a series of recombinations. Although the new polymorphisms appear as point mutation, the polymorphisms are not unpredictable random mutations. They are acquired via recombination with a limited number of parental strains that are recent ands localized.
As H5N1 expands its geographical reach, the genetic complexity of H5N1 sequences has increased and. led to additional acquisition of novel polymorphisms. This increased complexity has been evident in recent OIE reports on H5N1 on the Crimea peninsula and the Volga Delta.
The increase in efficient transmission of H5N1 to humans in Turkey and Indonesia suggests that these acquisitions via recombination are presenting increasing challenges and the H5N1 gene reservoir becomes more diverse and unstable.
Analysis of these changes are limited by delays in making new sequences public. Indonesia has not publicly released any sequences from 2005 and China’s 2005 sequences have been limited to the Qinghai Lake isolates.
Russia has led the way in release of full sequences from recent isolates, as indicated in their recent OIE report as well as the full set of sequences from Kurgan.
Similar prompt release of H5N1 sequence data by other countries would be useful.
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