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Indonesian H5N1 Bird and Human Sequences Do Not Match

Recombinomics Commentary

July 3, 2006

The recent meeting in Jakarta on human H5N1 in Indonesia raised additional question on the origin of the human H5N1.  The meeting included a phylogenetic tree of HA sequences from human, cat, and bird isolates.  The human and cat sequences formed a separate branch which did not include avian sequences.  The names of those isolates are listed below and are on lower branch of the phylogenetic tree.

The report in Jakarta also listed those bird flu isolates with their novel cleavage site RESRRRKKA.  All such isolates are on the lower branch of the tree which has all human isolates in Indonesia other than the Karo cluster and the second reported case.  Included in the lower branch is a cat sequence, feline/IDN/CDC1/06.

The slide that listed the amantadine resistant isolates included the age, gender, date, and location of the human case.  These cases extend from the first reported case in July of 2005, IND/05/05, through cases in May 2006, IDN/554H/06 and IDN/557H/06.  The cases include isolates in and around Jakarta as well as a case in East Java.  Thus; although the human cases have been isolated for almost a year and throughout the island of Java, none of the human isolates match a bird isolate.

A recent phylogenetic tree has 19 bird and two swine H5N1 isolates from isolates across Indonesia.  Thus, the number of non-human isolates in Indonesia now exceeds fifty and only the cat isolate falls on the human branch which has 20 H5N1's isolated in Hong Kong (in addition to corresponding isolates by the CDC).

The failure of the twenty human isolates to match the 50 avian isolates suggests birds are not the source of H5N1 in most of the human cases in Indonesia.  In spite of this failure to match,  WHO updates continue to cite bird deaths in some sort of association with the human cases.  However, H5N1 is widespread in birds in Indonesia, and the sequences indicate that the correlation between human and avian H5N1 does not exist, based on the sequences described in the Jakarta meeting and released in the form of phylogenetic trees.

The failure to match human and avian sequences raise serious credibility issues regarding WHO updates.  The two cased listed above were described in the Who update of May 29

One newly confirmed case is an 18-year-old man from East Java Province. He developed symptoms on 6 May and was hospitalized on 17 May. He is now recovering. The investigation found a history of exposure to dead chickens in his home within the week prior to symptom onset. No further cases of influenza-like illness have been identified during the investigation and monitoring of his close contacts.

An additional case occurred in a 39-year-old man from West Jakarta. He developed symptoms on 9 May, was hospitalized on 16 May, and died on 19 May. The investigation determined that the man cleaned pigeon faeces from blocked roof gutters at his home shortly before symptom onset. No further potential source of exposure was identified.

The isolate from the 18M, IDN/554H/06, and 39M, IDN/557H/06.were both similar to the first human Indonesian isolate IDN/05/05 and have the same RESRRKKR cleavage site.  No reported avian isolates from 2003 to 2005 have this cleavage site or sufficient similarity to be placed on the same branch of the phylogenetic tree, yet the updates continue to use dead or wild birds as a likely cause of the human infections.  WHO is well aware of the failure to find match bird isolates, yet bird contacts are used in updates and Indonesia uses history of contact with dead or dying birds as a criteria for H5N1 testing.

These approaches fail to address the true origins of H5N1 infections in Indonesia and create a climate of deception.  The WHO and Indonesian approaches for surveillance and containment of H5N1 in humans in Indonesia are increasing causes for concern.

Indonesian human isolates on lower branch of HA phylogenetic tree


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