Swiss and German H5N1 Sequences are Similar
Recombinomics Commentary
August 1, 2007
H5N1 HA sequences from Switzerland were released at Genbank (see list below). The sequences were from isolates in 2006 and were similar to three Swiss sequences released earlier. All 13 sequences are closely related to a subset from Germany.
In 2006, three distinct sub-clades were found in Germany. In northern Germany, the isolates (Clade 2.2.2.1) were closely related to isolates from Denmark. Another series (Clade 2.2.2.2), was related to isolates more broad geographical distribution (Italy, Czech Republic, and Ukraine). The third series (Clade 2.2.2.3) contained NA G743A, which was appended onto isolates in Moscow, Egypt, and Ghana in 2007. This series also had HA polymorphisms subsequently found in 2006/2007 isolates, including M230I in Egypt, and G295A and C1480T in the human isolate from Nigeria (see figure 2). All 10 of the new sequences had G295A and C1480T.
The sequences from Switzerland were from the northern border shared with Bavaria in Germany (see satellite map). These new sequence increase the number of Clade 2.2.2.3 isolates, which acted as donor sequences for isolates in Egypt and western Africa.
Recently, new isolates were found in Germany. These isolates are distinct from the three sub-clades identified in 2006. They are most closely related to sequences from Siberia (Tyva) and Mongolia. The sequences from these isolates would be useful.
Additional donor sequences may be present which can be appended onto downstream sequences.
A/mallard/Switzerland/V537/2006
A/duck/Switzerland/V426/2006
A/little
grebe/Switzerland/V330/2006
A/common
pochard/Switzerland/V592/2006
A/mute
swan/Switzerland/V68/2006
A/common
pochard/Switzerland/V505/2006
A/common
pochard/Switzerland/V762/2006
A/mallard/Switzerland/V558/2006
A/duck/Switzerland/V389/2006
A/duck/Switzerland/V487/2006
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