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H5N1 Bird Flu in Russia and Kazakhstan from China

Recombinomics Commentary

August 1, 2005

In 2003, an H5 avian influenza virus was isolated and sequenced by the Laboratory to Investigate and Monitor Emerging Zoonotic Diseases (Novosibirsk, Russia) from a wild mallard duck on Lake Chany in the south of Western Siberia. The A/mallard/Chany/9/03 avian influenza virus was related, but not identical, to H5N1 avian influenza viruses currently circulating in domestic poultry in Asia.

We are grateful to Dr. Lanard for her attentive observation. It might be assumed that CIDRAP actually meant the 1st known H5N1 "outbreak" rather than "appearance" (of the virus) in Russia.

There are no assumptions required.  The "H5N1" in question above is not H5N1, but is H5N3.  The only H5's at GenBank from Russia are the isolate in question, A/Anas platyrhynchos/Chany Lake/9/03(H5N3), and two isolates from Primorie, A/duck/Primorie/2621/01(H5N2) and A/duck/Primorie/2633/01(H5N3).  Although the N from the Cheny Lake isolate is not at GenBank, there is little reason to suspect it is H5N1 and strong evidence that it is not closely related to H5N1 from China.

The H5's from Russia are much more closely related to H5's from Europe.  The Russian isolates do not have a multi-basic cleavage site and are LPAI.  A simple BLAST search of the Chany Lake sequences returns the following isolates as the ten most closely relate - A/mallard/Netherlands/3/99(H5N2), A/Mallard/64650/03(H5N7), A/Chicken/Italy/312/97(H5N2), A/Guinea Fowl/Italy/330/97(H5N2), A/Chicken/Italy/367/97(H5N2), A/chicken/Italy/8/98(H5N2), A/duck/Malaysia/F119-3/97(H5N3), A/turkey/England/50-92/91(H5N1), A/duck/Primorie/2633/01(H5N3), (A/Chicken/Italy/9097/97(H5N9).

Thus, there is only one H5N1 in the top 10, at that H5N1 is from England. The only isolate from Asia is H5N3 from Malaysia. In these migratory birds, it is common to see many reassortants.  Thus, although all 10 isolates most closely related are H5, it is associated with N1, N2, N3, N7, and N9, further demonstrating that reassortment has little to do with H5 pathogenicity.  The H5's in Asia do usually have N1, but the N1 in most of the recent isolates has a 20 amino acid deletion and the sequence is easily distinguished from the N's associated with H5's from Europe.

Because of the associations, the announcement that the isolate from Novosibirsk was H5N2 was met with skepticism.  The H5's in Russia that are associated with N2 are not highly pathogenic.  The H5 in Novosibisrk however was killing ducks and geese, which are usually resistant to all H5's.  Also dying were chickens and turkeys, strongly suggesting that the H5 was similar to the H5N1 from China, where geese were dying at Qingahi Lake, Qinghai,  and Tacheng and Changji in Xinjiang,.

Thus, the announcement on Friday that H5N1 was in Russia was not surprising nor was today's announcement that its sequence was similar to the sequence from China.  Thus, for the first time HPAI was reported in Russia, and that was followed by a similar outbreak in Kazakhstan.  In all cases migratory birds were affect and domestic or migratory geese had died.

The migration is now spreading from Chany Lake.  To the west outbreaks have been reported in the Omsk region, and to the southeast there is an outbreak in Altai.  These are in addition to several outbreaks on the east, south, and west of Chany Lake.

More outbreaks in Russia, China, Europe and southern migratory destinations are expected in the upcoming weeks.

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