Similarities in H5N1 Sequences from Germany and Denmark
Recombinomics Commentary
October 2, 2006
Full sequences of a cat, A/cat/Germany/606/06(H5N1), and a swan, A/swan/Germany/65R/06(H5N1) were released at Los Alamos. The bird flu isolates were collected in February from northern Germany. The isolates have the characteristic HA cleavage site of the Qinghai strain, GERRRKK, and the mammalian PB2 polymorphism, E627K.
The two sets of sequences are virtually identical to each other and a buzzard isolated from Denmark, A/Buzzard/Denmark/6370/05(H5N1), which was available at the sequencer’s website in March, 2006.
Polymorphisms are present in all eight gene segments which have only been reported for the three Qinghai isolates above. Although there are minor differences which are unique for each sequence, the three isolates clearly are closely related to each other, even though they were isolated from three different species, which were found in early 2006 in geographically close regions in Germany and Denmark.
These three sequences were most closely related to a recent chicken sequence from Nigeria, A/chicken/Nigeria/641/2006(H5N1). This location is linked to the above region via the East Atlantic Flyway.
H5N1 in Nigeria is linked to several independent introductions. Full sequences from another Nigerian isolate, A/chicken/Nigeria/641/2006(H5N1) are most closely related to the eight gene segments from two recent isolates from Sudan, A/chicken/Sudan/1784-7/2006(H5N1) and A/chicken/Sudan/1784-10/2006(H5N1).
These data demonstrate the utility of full sequences to link isolates and identify transport paths, as well as the track the evolution of H5N1, which is driven by the acquisition of these sequences via recombination. The vast majority of the polymorphisms in the Qinghai isolates can be readily found in Clade 1 or Clade 2 isolates from southeast Asia or China.
The above matches also highlight the match failures in Indonesia. Although human and poultry isolates in Indonesia share a number of Indonesian polymorphisms, the human isolates on Java are easily distinguished from the poultry isolates in Indonesia. The novel cleavage site, RESRRKKR, is only one many polymorphisms that distinguishes the isolates. This cleavage site has been reported for one duck isolate on Java in Indramyu and two chicken isolates on Sumatra.
In contrast, all but one human isolate from Java have the novel cleavage site, signaling an independent reservoir for the human infections.
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