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Recombination Between H5N1 in Vietnam and Japan / China

Recombinomics Commentary

May 18, 2005

>>  Recent viruses circulating in Northern Viet Nam have lost an
arginine residue in the mutibasic amino cluster at the proteolytic cleavage site of the HA protein. It does not seem to be responsible for reduced pathogenicity since the structure of the cleavage site still remains typical of highly pathogenic viruses. However at this time these are possibilities that have yet to be further investigated by analysing more viruses. <<

The above description confirms that the missing amino acid is in HA and is in the poly-basic (multibasic) cleavage site.  2003 isolates from eastern China were missing a basic amino acid (lysine) in this region.  However, the isolates from northern Vietnam are missing an arginine (the other basic amino acid).  This change however, is not novel.  H5N1 isolates missing an arginine in the polybasic cleavage site were isolated in 2003 from Yunan province in China (A/Dk/YN/
6255/2003,  A/Dk/YN/6445/2003) or Hong Kong (A/Ck/HK/2133.1/2003), as well as in 2004 in various locations in Japan (A/chicken/Kyoto/3/2004, .A/chicken/Yamaguchi/7/2004, A/crow/Osaka/102/2004), and Guangdong Province (A/duck/Guangdong/173/04) and also Yunan (A/Ck/YN/115/2004, A/Ck/YN/374/2004).

Thus, the 2005 isolates in northern Vietnam appear to be recombinants between the 2004 isolates in Vietnam and the 2003 / 2004 isolates in China / Japan.  Earlier reports described antibody to the 2004 H5N1 isolates from Japan, although those poultry workers with antibodies had very low titers and had mild or no symptoms.

More detailed analysis requires public access to these sequences and thus far none of the sequences of 2005 H5N1 isolates are publicly available at GenBank, although sequence data has clearly been generated and analyzed.

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