H5N1 Human and Duck Sequence Identities in Indonesia
Recombinomics Commentary
July 28, 2007
H5N1 partial HA bird sequences from Indonesia have been released at GenBank. One of the sequences, A/muscovy duck/Jakarta/Sum201/2006 is an exact match with the human sequences A/Indonesia/CDC823/2006 between positions 99-1077, signaling human H5N1 infections via waterfowl.
The human sequence is from a 9M from south Jakarta who died September 22. 2006, Another recently released duck sequence from Jakarta, A/duck/Jakarta/Smlt306/2006 only has 2 differences with the above sequences, providing additional linkages between the human case and waterfowl.
The two duck isolates also have a rare polymorphism, A586G, which is largely limited to clade 2.2 Egyptian cases. They also have A958C, which is almost exclusively found in Qinghai clade 2.2 isolates.
These linkages point toward migratory waterfowl as a source for human H5N1 cases in Indonesia. Earlier, there were match failures between the sequences from the human cases, and the H5N1 from poultry. However, most of the poultry sequences were from chickens. The first bird sequence with the novel HA cleavage site, RESRRKKR, was from a duck in Indramayu, and many of the recent matches between human and bird H5N1 in Indonesia involved waterfowl.
The linkage between the transportation and transmission of H5N1 in waterfowl was clearest in countries west of China, because all H5N1 isolates are clade 2.2, and most wild bird isolates are from waterfowl. Moreover, the spread of H5N1 was linked to detection of H5N1 in nature reserves, such as Qinghai Lake, Chaney Lake, Erhel Lake, as well as the Volga Delta, Danube Delta, and Nile Delta.
These recent H5N1 sequences from Indonesia provide additional linages between H5N1 infections in humans and waterfowl.
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