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Migratory Bird H5 Sequences in 2003 Shantou Chicken

Recombinomics Commentary

July 7, 2005

Today's Nature describes H5N1 bird flu isolates from migratory birds at Qinghai Lake.  These isolates are unique and the sequences will soon be publicly available at GenBank.  The most closely related H5N1 currently available is A/Ck/ST/4231/03(H5N1) and the closely related A/Ck/Yamagichi/7/04(H5N1).  These two isolates are closely related to the other four H5N1isolates from Japan (A/chicken/Kyoto/3/2004, A/chicken/Oita/8/2004 , A/crow/Kyoto/53/2004, A/crow/Osaka/102/2004 as well as two H5N1 isolates from South Korea (A/chicken/Korea/ES/03, A/duck/Korea/ESD1/03).

However, the Shantou sequence also has a number of rare polymorphisms that are found in a wide variety of H5 sero-types that stretch from Europe to Russia to Australia, strongly suggesting that the Shantou sequences evolved from migratory birds that fly over Asia and Europe.  Included in the list are A/Anas platyrhynchos/Chany Lake/9/03(H5N3), A/Mallard/64650/03 (H5N7), A/duck/Primorie/2633/01 (H5N3) A/chicken/Italy/8/98 (H5N2), A/duck/Singapore/3/97 (H5N3), A/Guinea Fowl/Italy/330/97 (H5N2), A/Duck/Potsdam/1402-6/86 (H5N2), A/Duck/Potsdam/2216-4/84 (H5N6), A/Duck/Ireland/113/83 (H5N8), A/Turkey/Ireland/1378/83 (H5N8), A/Duck/Hong Kong/698/79 (H5N3), A/Duck/Ho Chi Minh/14/78 (H5N3), A/duck/Hong Kong/342/78 *H5N2), A/Duck/Hong Kong/205/77 (H5N3), A/shearwater/Australia/75 (H5N3).

The sequences at Qinghai have the PB2 mutation at 627 that confers virulence for a large number of sero-types, which may be related to the large number of migratory bird deaths.  The shared sequences above indicate the migratory birds can transmit to domestic ducks sold in live markets such as those in Shantou, Japan, or South Korea and the birds are likely responsible for the new sequences which appear each season throughout Asia.

However, the latest H5N1 isolates from Qinghai Lake are particularly lethal in mammals, killing laboratory mice in just 4 days and readily transmissible among migratory birds at Qingahi Lake.  The widespread distribution of shared polymorphisms suggests the Qinghai sequences will be appearing throughout Asia and Europe. These sequences also support transmission of sequences from India to Qinghai Lake, since the Qinghai polymorphisms are so widely dispersed.

Analysis of the new Qinghai sequences will determine if the above observations on the Shantou sequence extends to Qinghai Lake, but clearly Shantou 4231, which was isolated in 2003, demonstrates that migratory bird sequences are in domestic chickens in Shantou, and suggest H5N1 is widely distributed in China and the rest of Asia.

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