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Krasnodar Wild Bird and Domestic Poultry H5N1 Match

Recombinomics Commentary
December 3, 2007

The full gene sequences of H5N1 from a mute swan in Krasnodar, A/Cygnus cygnus/Krasnodar/329/07(H5N1), are being released at Genbank.  The isolate was collected on September 6, 2007, one day after A/chicken/Krasnodar/300/07(H5N1) was collected from a poultry outbreak.  The chicken sequence has been described.  It traces back to the massive wild bird outbreak at Uva Lake in Mongolia in the summer of 2006, and is closely related to recent sequences from England, Germany, France, Czech Republic, and Kuwait.

The swan sequence is virtually identical to the chicken sequence.  Four gene segments (HA, NP, MP, and NS) are exact matches.  PB1 and PA differ by one BP, while PB2 and NA each differ by two BP.  Thus, the sequences are over 99.95% identical (6 differences in over 12,000 positions).

Like the chicken sequence, the swan sequence has NA G743A, the polymorphism that was appended onto multiple genetic clade 2.2 backgrounds in 2007, including the recently released sequences from Germany.

The sequence data again supports independent introductions of Qinghai (clade 2.2) sequences into Europe this year.  The most recent sequences have all traced back to the wild bird outbreak at Uva Lake and suggest H5N1 has become endemic in Europe, with the Uva Lake strain becoming dominant.

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