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Tuva and Mongolia H5N1 Bird Flu Sequences Are Similar

Recombinomics Commentary

July 26, 2006

The full sequence of all eight gene segments from a crested grebe, A/grebe/Tyva/Tyv06-2/06(H5N1),  in Tyva (Tuva) has been released.  The sample was collected June 24, 2006 and provides the most current view of the evolution of the H5N1 bird flu Qinghai strain.  The isolate comes from a recent massive die-off that rivals the Qinghai outbreak at Qinghai Lake in China in 2005.

The current outbreak extends from the Russian province of Tuva, into northern Mongolia.  Recently, and H5N1 isolate from a whooper swan in Mongolia, A/whooper swan/Mongolia/2/06(H5N1),  was also made available at GenBank.  The two sequences are remarkably similar.  They have a number of recently acquire polymorphisms that are not found in other Qinghai strain, yet the polymorphisms are in both the Mongolian and Russian isolates.  These shared polymorphisms are in all eight gene segments as listed below

The shared polymorphisms indicate the Qinghai strain of H5N1 continues to evolve.  Unlike the polymorphisms in western Africa, the similarity between these recent isolates is striking.  There are differences and some additional polymorphisms are shared with other isolates such as mute swan isolate from Italy or Astrakhan, but these two isolates have more similarities than the various isolates from Nigeria, Niger, and the Ivory Coast.

However, these are early collections, and additional birds will bring in new H5N1 sequences to Mongolia.  Similarly, many of the isolates from Africa, Europe, and the Middle East are now at Chany Lake, generating new combinations of sequences.

These newly acquired sequences can be used to classify the isolates and show that the strain is constantly evolving via evolution as shown by discordant newly acquired polymorphisms.

The widespread detection of the Qinghai strain raises surveillance issues.  Wild life conservation groups failed to find H5N1 in Africa and few countries have detected H5N1 in live wild birds, although detection in dead birds has been widespread.

These recent sequences demonstrate an expanded geographical reach and added genetic complexity generated by recombination.  The Qinghai stain of H5N1 will soon be mixing with the H5 found to be widespread in Canada in 2005.  The first published sequence has acquired swine sequences, indicating the swine can serve as reservoirs and create new H5N1 sequences worldwide,

PB2 A1398G T1460C

PB1 T87C C557T G1362T T2196C

PA T147C G228A T571C T1594C G1825G

HA G59A C796T A1300GG1562T

NP C74T G343A

NA C162T C979T G1361A

MP C559A

NS T41A A849G A851G

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