http://www.recombinomics.com/News/12310501/H5N1_WBF_TT_Russia.html - http://www.recombinomics.com/News/12310501/H5N1_WBF_TT_Russi a.html
Recombinomics Commentary
December 31, 2005

The recent OIE summary http://www.oie.int/eng/info/hebdo/aIS_38.htm#Sec4 - report from Russia leaves no doubt that the H5N1 detected in Russia, the Volga Delta, and the Crimea Peninsula is transmitted and transported by wild bird H5N1 closely related to the isolates from Qinghai Lake.  The report includes a phylogenetic tree of sequences from http://www.oie.int/cartes/TABA18_52RUS2.PDF - HA and http://www.oie.int/cartes/TABA18_52RUS3.PDF - NA and includes the following isolates:

A/b/Omsk/03/2005
A/chicken/Chelyabinsk/05/2005
A/chicken/Crimea/06/2005
A/chicken/Kurgen/03/2005
A/duckTumen/02/2005
A/duck/Novosibirsk/04e1/2005
A/duck/Novosibirsk/02e1/2005
A/goose/Altai/01/2005
A/goose/Chelyabinsk/01/2005
A/gull/Kurgan/02/2005
A/mallard/Kalmykia/09/2005
A/swan/Astrakhan/04/05
A/wild duck/Kurgan/01/2005
A/wild duck/Omsk/01/2005
A/wild duck/Tumen/01/2005
A/wild duck/Tumen/04/2005

The above sequences are most closely related to
A/ http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=336241&lvl=3&lin=f&keep=1&srchmode=1&unlock - bar-headed goose/Qinghai/12 /05
A/ http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=336237&lvl=3&lin=f&keep=1&srchmode=1&unlock - bar-headed goose/Qinghai/05 /05
that is constant with sequences disclosed and deposited from isolates from a wild grebe (A/ http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=353252&lvl=3&lin=f&keep=1&srchmode=1&unlock - grebe/Novosibirsk/29 /2005), as well as isolates from Tula (A/ http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=358754&lvl=3&lin=f&keep=1&srchmode=1&unlock - chicken/Tula/10 /2005)and the http://www.recombinomics.com/News/09300503/H5N1_Novosibirsk_Recombinants_Europe.html - Novosibirsk area.

These new wild bird sequences are also consistent with the http://www.recombinomics.com/News/10160502/H5N1_Species_Russia.html - mission report on H5N1 in asymptomatic wild birds collected by hunters in Russia.  The above isolates would have an HA cleavage site sequence of GERRRKKR, which has also been reported for recent H5N1 isolates from Romania, Croatia, and Turkey.

Although these isolates are linked to the same wild bird lineage, recent media reports suggest more genetic variation, including a RERRRKKR http://www.recombinomics.com/News/12210502/H5N1_Cleavage_Evolution.html - cleave site for some of the Ukraine isolates.  Moreover, these isolates are closely related to H5N1 isolates from http://www.recombinomics.com/News/11200501/H5N1_Novel_Mongolia_Swan.html - Mongolia and http://www.recombinomics.com/News/12200501/H5N1_Novel_Hunan_Human.html - Hunan province. Although recent reports indicate these isolates indicate novel cleavage sites have been identified in whooper swan isolates in Mongolia and a chicken in Hunan closely linked to a familial cluster in Hunan.

The wealth of information provided by the Russian OIE reports and Genbank deposits stands in marked contrast to the lake of any 2005 isolates from Indonesia and the lack of deposits from China since Qinghai Lake.  Both of these countries have reported numerous H5N1 infection sin humans an poultry and all of the OIE reports from China indicate viruses from these outbreaks has been classified as HPAI based on an biological IVPI test which would allow for easy isolation of virus from experimentally infected chickens.

The latest sequence data clearly shows that H5N1 is being spread by migratory birds and is rapidly evolving.  Deposits of 2005 isolates from the countries reporting H5N1 outbreaks would be useful.

http://www.recombinomics.com/H5N1_Map_2005_QinghaiL.html - Map

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