H5N1 G743A Migration in Europe Africa and The Middle East
Recombinomics Commentary
November 29, 2007
Sequences from German wild birds infected with H5N1 over the summer have been released. One of the sequences, A/black-necked grebe/Germany/R1393/07, was from central Germany and was one of the more than 300 grebes from the artificial lake at the border of Thuringia and Saxony-Anhalt. The other two sequences were from mute swans in central, A/Cygnus olor/Germany/R1359/07, and southern, A/Cygnus olor/Germany/R1349/07, Germany. All three sequences are closely related to the recent sequence from Krasnodar, A/chicken/krasnodar/300/07 (99.7%, 99.5%, and 99.4% identical). As expected all four sequences map to the same branch on a phylogenetic tree.
Today’s DEFRA report gives similar numbers for the relationship between H5N1 in Suffolk, and the Czech Republic (99.8%) and Germany and France (99.3%). For multiple isolates in Kuwait and Germany, the identities with the Suffolk sequence were 99.4%-99.6% and 99.2%-99.4%, respectively. These numbers suggest all of these isolates trace back to the 2006 massive outbreak at Uva Lake in Mongolia in 2006, but each outbreak represents independent introductions by wild birds.
None of the relationships approach the 99.96% identity between earlier isolates from England and Hungary, which likely were due to poor bio-security leading to transfer of the H5N1 between the two locations linked to birds owned by the same company.
NA sequences from the German isolates were also released, and they were closely related to each other and the Krasnodar NA sequence. Like the Krasnodar sequence, both of the German sequences had G743A, the polymorphism that was appended onto six different genetic backgrounds in Moscow, Egypt, and Ghana. All of these backgrounds were distinct from the German and Krasnodar sequences (and presumably the English, Czech, French, and Kuwaiti sequences, which likely also have G743A).
The earlier detection of G743A on multiple genetic backgrounds suggested that donor sequences were flying around Europe, the Middle East, and Africa undetected, and those donor sequences may have been the sequences identified in Europe and the Middle East in the summer/fall of this year.
Clearly the Uva Lake sequences have become widely detected in the past few months.
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