H5N1 Linkage Between Northern Germany and Egypt
Recombinomics Commentary
April 10, 2007
Recently released HA sequences (see list here) from northern Germany contained M230I in an eagle owl isolate. M230I had been detected in human and avian Qinghai isolates from the Nile Delta in Egypt this season, which were reported for the first time. The recently released sequences demonstrated that M230I, as well as additional sub-regional polymorphisms in Egypt were in northern Germany in February, 2006. The HA sequences from Germany fell into two groups. One was similar to cat and swan isolates previously released, while a second group was similar to Bavarian sequences from northern Germany.
Partial NA sequences from these isolates were also released, and the NA sequences divided the sequences into the same pattern. Eight of the isolates (see list below), had two polymorphisms, G743A and A1043G. The two polymorphisms were in 15 of the northern Germany isolates released earlier (see list below). G743A is also in three 2007 avian isolates from the Gharbiya governorate in the Nile Delta, A/chicken/Egypt/1890N3-HK45/2007, A/chicken/Egypt/1891N3-CLEVB/2007, A/chicken/Egypt/1892N3-HK49/2007.
A/chicken/Egypt/1892N3-HK49/2007 also had M230I, which was in the eagle owl sequence, providing additional evidence for acquisition of polymorphisms via recombination.
The 2007 sequences in Egypt have more diversity than the 2006 isolates. As shown above, many of the recently acquired changes can be traced back to Qinghai sequences in Germany and Mongolia, including HA M230I in Germany in 2006, V223I in Mongolia in 2005, the novel cleavage site in Mongolia in 2005, and the NA sequence described above in Germany in 2006. Although all of the above polymorphisms were on a Qinghai genetic background, the earlier sequences did not have the Egyptian regional markers which were on isolates from the 2005/2006 season as well as the 2006/2007 season in Germany.
The polymorphism acquisitions help define migratory pathways of these polymorphisms, which can be used to predict vaccine targets for future isolates.
Recent subset from northern Germany
A/duck/Germany/R592/06
A/duck/Germany/R603/06
A/great crested grebe/Germany/R1226/06
A/tufted duck/Germany/R1240/06
A/falcon/Germany/R899/06
A/pochard/Germany/R348/06
A/gull/Germany/R882/06
A/eagle owl/Germany/R1166/06
Earlier subset from northern Germany
A/mallard/Bavaria/1/2006
A/buzzard/Bavaria/13/2006
A/buzzard/Bavaria/5/2006
A/common buzzard/Bavaria/11/2006
A/common pochard/Bavaria/7/2006
A/eagle owl/Bavaria/10/2006
A/falcon/Bavaria/15/2006
A/goldeneye duck/Bavaria/19/2006
A/goosander/Bavaria/18/2006
A/goosander/Bavaria/20/2006
A/swan/Bavaria/16/2006
A/swan/Bavaria/17/2006
A/swan/Bavaria/21/2006
A/swan/Bavaria/6/2006
A/tufted duck/Bavaria/4/2006
Media sources
Recombinomics Presentations