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Unclear Source of H5N1 in Fatal East Java Indonesia Case

Recombinomics Commentary

July 4, 2006

The case, which was fatal, occurred in a 5-year-old boy from Tulungagung district, East Java Province. The boy became ill on 8 June, was hospitalized on 14 June and died two days later on 16 June.

An investigation found a history of chicken deaths in the boy's household two weeks before symptom onset. Laboratory testing of poultry in the sub-district confirmed the presence of H5N1 in chickens. Monitoring of close contacts has detected no further cases.

The above comments from the WHO update on Indonesia again fail to provide the critical information needed to link the human fatality to H5N1 infected chickens.  The comments above are similar to prior updates that cite H5N1 in the neighborhood, but fail to find a matching sequence.  As the list of human cases grow, this failure to match sequences is creating increasing concern.

H5N1 in poultry in Indonesia is widespread, and most testing of H5N1 in humans requires some linkage to dead or dying poultry.  This selection diminishes the relevance of the H5N1 in the neighborhood or on the premises of a fatal H5N1 case.  To date, there are two outbreaks that match H5N1 in poultry and both outbreaks involve non-farmers with links to fertilizer.  There have been no links showing dead birds on a farm have a sequence that is closely related to the corresponding human case or any human case other than the two clusters mentioned above.

Most of the human H5N1 isoaltes come from fatal cases, so it is likely that H5N1 will be isolated from the East Java patient.  Outbreaks of H5N1 bird flu in the case's household or neighborhood should identify matching H5N1 if the infection is linked to poultry.  The vast majority of the human isolates in Indonesia have a novel cleavage site, RESRRKKR.  This sequence correlates with H5 that is readily distinguished from H5 in Indonesian poultry and the novel cleavage site has been identified in a fatal East Java case.  The only reported exposure of for the earlier East Java case was gutter cleaning. The only matching non-human sequence, feline/IDN/CDC1/06, has been in a cat.

One of the first confirmatory test of H5N1 involves the sequence of the HA cleavage site.  This sequence does not require isolation of the virus and can be generated with a simple PCR test.  This type of data should be included in the WHO update, which suggest that the human case is from the H5N1 in poultry in the neighborhood, but after almost one year of human testing, there have been no reports of the novel cleavage site in H5N1 from poultry in Indonesia or elsewhere.

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