H5N1 Match Failure in Indonesia Raises Pandemic Concerns
Recombinomics Commentary
October 5, 2006
Tests on 49 samples taken from birds on the islands of Sumatra, Java and Bali showed the H5N1 avian influenza virus has undergone no major changes, the ministry said in a statement today. The analysis was undertaken by a World Organization for Animal Health reference laboratory in Geelong, Australia.
Samples of the H5N1 virus taken from birds were collected between September in 2005 and March.
The above comments provide additional detail on the H5N1 bird samples sent to Australia for sequencing in an attempt to match the human H5N1 sequences from Indonesia. Prior to the sequencing of the above isolates, the bird H5N1 sequences failed to match the human sequences.
However, most of the initial bird sequences were from 2003 through the first half of 2005, while the first human sequence was from July 2005. Therefore, the match failure may have been due to recent H5N1 that were not reflected in the earlier sequences.
91 samples were sent to Australia for sequencing. Since the human isolates had already been sequenced, the question of major changes was not at issue. The human sequences had no evidence of reassortment, but virtually all samples from Java had a novel cleavage site that was associated with a number of additional changes in all 8 gene segments that were in the human isolates, but absent in the poultry isolates.
The HA sequences from over 50 samples from Australia were deposited at Los Alamos over the past few months, and those sequences failed to match the human sequences. Only three of the bird isolates had the novel cleavage site. Two were from chickens in central Sumatra, but all of the human sequences with the novel cleavage site were from a duck in Indramayo on Java. The third bird isolate with the novel cleavage site was from Java, but it only matched a few of the human sequences. The vast majority of the human sequences matched each other, but did not match any bird sequence from Java.
The above comments confirm that the recent bird sequences overlap the human sequences in time and location, but still fail to match, indicating the vast majority of human H5N1 sequences are from a source other than most of the H5N1 infected poultry in Indonesia.
The failure of the above comments to address the match failure is cause for concern.
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