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Phylogeny of German H5N1 in 2007

Recombinomics Commentary
November 26, 2007

The paper, “Phylogenetic analyses of highly pathogenic avian influenza virus isolates from Germany in 2006 and 2007 suggest at least three separate introductions of H5N1 virus” includes detail on three isolates collected in Germany during the summer of 2007.  A/Cygnus olor/Germany/R1349/07 is from the south, A/Cygnus olor/Germany/R1359/07 is from central Germany, as is A/Podiceps nigricollis/Germany/R1393/07.  The paper includes a phylogenetic tree which shows all three sequences clustering together, but each sequence is distinct, supporting independent introductions by wild birds.  The sequences are most closely related to A/grebe/Tyva/Tyv06-02/2006, which was isolated from the massive wild bird outbreak in and around Uva Lake in Mongolia in 2006.

The location on the tree is virtually identical to A/chicken/Krasnodar/300/2007. isolated September 5, 2007.  Based on comments by Defra. All of these sequences will be closely related to H5N1 in the Czech Republic, France, and England.  They will likely have NA G743A, which was appended onto at least seven genetic backgrounds in 2007, including the Krasnodar isolate.

The outbreak at Uva Lake was massive and on a par with Qinghai Lake in May, 2005.  Therefore the dominance of this sequence in countries to the west of China is not a surprise.  This subclade appears to have spread throughout Europe and may have been the parental donor for NA G743A which was so widely appended onto earlier clade 2.2 sequences.

The HA and NA sequences (accession numbers AM749442-AM749445b, AM773724 AM773725) should be available at Genbank shortly.

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