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Suspect H5N1 Cluster in Jakarta
Recombinomics Commentary
January 8, 2007

Six patients are currently treated in the Friendship Hospital, Jakarta East, till Monday (8/1).

They experienced the sign of the deadly illness.

The six patients generally still have relatives's relations.

Ramli was treated three days set after being stated positive contracted bird flu.

Followed by the mother, the brother, as well as his three neighbours, this morning.They lived in the Rawabebek region, Angke, Jakarta North.

But the hospital side was not yet prepared to give the explanation.

The team of the justified doctor was discussing this condition in a special meeting.

The above translation describes a suspected H5N1 bird flu cluster in Jakarta.  The index case (14M) has already been confirmed, and now three family members and three neighbors in northern Jakarta have been admitted with symptoms.

If confirmed, this would be the largest cluster to date on Java.  Last year, a large cluster in Karo in North Sumatra was reported, but the H5N1 in the Karo cluster was distinct from the H5N1 in human cases on Java, including cases in and around Jakarta. 

All but one H5N1 from humans on Java have had the novel cleavage site, RESRRKKR, which has been found in one duck from Indramayu in January, 2006.  That sequence match a small subset of human isolates, but an isolate from a cat in Indramayu matched the majority of the human H5N1 sequences from Java.

Thus, there is concern that migratory birds would bring new sequences into the area and recombine with the local version of H5N1, which is Clade 2 sub-clade 1 in Indonesia.  Hong Kong has also just confirmed H5N1 in a wild bird, which was also reported at this time last year.  The H5N1 sequences from last season in Hong Kong were related to the Fujian strain (Clade 2 sub-clade 3). Similarly, the Qinghai strain was just confirmed in South Korea.

Recently there was also a cluster reported in Gharbiya in the Nile Delta, the site of additional wild bird migration.  H5N1 in Egypt is the Qinghai strain (Clade 2 sub-clade 2).  Like Indonesia and Hong Kong, the new versions of H5N1 are created by recombination, which uses the resident strain as a genetic background, and appends new polymorphisms, which match across various strains.

In Indonesia, Qinghai sequences, including the novel Qinghai cleavage site of GERRRKKR has been reported in Bali, Indonesia.  Similarly, Qinghai sequences have been found in Fujian isolates in China.

When migratory birds deliver these new sequences, new problems follow.

More information on the family members and neighbors of the confirmed case would be useful.  The cluster in Egypt has already produced the largest cluster reported to date in Egypt, and similar results in Indonesia would not be a surprise.

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