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Novel HA Cleavage Site in H5N1 Hunan Isolate

Recombinomics Commentary

December 20, 2005

The HA gene of the virus is closely related to that of H5N1 viruses isolated from poultry in Fujian Province in 2005, belonging to clade 2. The amino acid residues involved in the receptor-binding site of haemagglutinin are similar to those of other H5 viruses, with a2-3 sialic acid receptor binding specificity, and the haemagglutinin has a polybasic amino acid cleavage site (RERRRRR).

The HA cleavage site of H5N1 isolated in Hunan (A/chicken/Hunan-Xiangtan-he/12/2005) is novel.  It is similar to cleavage sites from H5N1 in northern China (RERRRKR), which is also missing a lysine from the sequence of the cleavage site most commonly reported from H5N1 in Asia, and the conversion of K to R is similar to the novel HA cleavage site of the whooper swan isolates from Mongolia (GERRRRKR).

However, the absence of an exact match with any of the H5N1 sequences at GenBank indicates H5N1 is still rapidly evolving and the lack of 2005 sequences from both humans and animals limits the usefulness of this powerful resource.

H5N1 sequences with the Z genotype have previously been grouped into two large clades and reported human cases in 2004 were limited to clade 1 sequences, which included two amantadine resistance markers.  Most of the sequences from clade 2 were amantadine sensitive, as were all of the H5N1 wild bird flu sequences published thus far.

The novel HA cleavage site suggests the H5N1 in Hunan may have recombined with H5N1 wild bird sequences to generate a novel HA cleavage site.

The publication of more 2005 H5N1 sequences would be useful.


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