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Suspect H5N1 Fatality from Southern Jakarta
Recombinomics Commentary
October 16, 2006

The boy, who wasn't named by officials, was admitted to the Sulianti Saroso Hospital for Infectious Diseases on Thursday and died Saturday night, said Director Dr. Santoso Suroso.

He was believed to have become infected by dead chickens near his home in south Jakarta, Suroso said.

Almost all of the fatal human cases have been linked to contact with chickens or their droppings.

The above comments describe a suspect H5N1 bird flu fatality from southern Jakarta.  Although the above report, as well as WHO updates, suggests the human infection is from chickens in the area, the sequences from chickens on Java have failed to match the human H5N1 sequences on Java.

The match failure was discussed at length at a WHO in Jakarta in June, 2006.  Sequences of human cases on Java had a novel cleavage site and mapped to the bottom branch of a phylogenetic tree of H5N1 isolates in Indonesia had no bird isolates that were on that branch.  Since that vast majority of bird flu tests on suspect bird flu patients are limited to those with some sort of linkage to dead or dying birds, the presence of dead or dying birds in H5N1 patients does not provide evidence that the human infection was due to the bird infections.  These sequences from the bird isolates clearly indicate that the human infections are not from the H5N1 positive birds.

Since most of the bird sequences tested by June, 2006 were from isolates collected prior to the end of 2005, 91 samples collected from October, 2005 to March 2006 were sent to a WHO affiliated lab in Australia.  After the June meeting, sequences of human isolates were released.  All of the human isolates on Java had the novel cleavage site and fell onto the lower branch of the HA tree.  Sequences in the other 7 gene segments from these isolates also matched each other, and failed to match the bird sequences.

The tests on the 91 samples yielded over 50 sequences but the only match from a bird on Java was from a duck in Indramayu.  However, this isolate match H5N1 from three patients from 2005.  It did not match the vast majority of human isolates from Java.

The only non-human isolate that did match the human isolates was from a cat on Indramyu, which was also closely related to human H5N1 isolates from Indramayu.

There have been no additional sequences from Australia, indicating that attempts to find matching sequences on Java have failed.  Recent media reports suggest additional cat H5N1 infections have been detected.  A broader screening of mammals and wild birds would be useful.

 It is clear that most of the human H5N1 infections on Java are not from H5N1 in poultry and limiting human H5N1 testing to those with links to dead or dying poultry is generating an underestimate of H5N1 human infections.

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