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H5N1 Sequences from 2004 Isolates in Japan

Recombinomics Commentary
February 6, 2005

The sequences from all 8 genes of 5 isolates from last season's outbreak of avian influenza (bird flu) in Japan are available at GenBank

The sequences have a number of polymorphisms that are unique to the isolates from Japan and these polymorphisms are found in most or all 8 genes.  Some of the common alterations which have been found in many H5N1 isolates including those from Vietnam and Thailand were also in the isolates from Japan.  They share a poly-basic cleavage site in HA, and 20 aa deletion in NA, and a 5 aa deletion in NS. 

The poly-basic cleavage site has one less aa, and matched isolates from Yunnan as well as the isolate from the duck that was smuggled into Taiwan at the end of 2003, A/duck/China/E319-2/03(H5N1).  The Japan isolates also had several polymorphisms unique to A/Ck/ST/4231/2003(H5N1)
and / or A/chicken/Guangdong/174/04(H5N1). 

Within the Japan clade, the two isolates from Kyoto were closely related to each other and the two remaining chicken isolates (from Oita and Yamaguchi) shared a few polymorphisms.

The polymorphisms unique to Vietnam and Thailand that were in mammalian isolates were not in the isolates from Japan.

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