H5N1 Transparency and Openness Pledge in Indonesia
Recombinomics Commentary
June 23, 2006
``Detection of human clusters is a priority,'' they said in a joint statement today. A report of the investigation of the Sumatran cases will be made as soon as possible to boost ``transparency and openness.''
A 37-year-old Sumatran woman suspected of being the first family member to die was buried before samples were taken, so her cause of death can't be determined.
The woman, who sold fruit and vegetables in a local market, owned eight chickens, including three egg-laying hens that were reported to have died about two to seven days before she became ill on April 24, the summary said. She mixed fowl manure with soil with her bare hands to fertilize her garden, it said.
The woman's 10-year-old nephew, 18-month-old niece, 19-year- old son, 18-year-old son and 29-year-old sister became sick between May 2 and 4, and subsequently died, after having close and prolonged contact with the woman during her illness, the summary said. A brother, 25, was also infected and survived.
Chain of Infection
A seventh patient, the father of the 10-year-old boy, contracted his fatal infection from close and unprotected contact with his son during the boy's hospitalization. The 37-year-old woman is the only one for whom exposure to sick or dead chickens or other animals was ascertained, the summary said.
The above comments on transparency and openness should lead to the release of the human H5N1 sequences from the Karo cluster, as well as the other human sequences from Indonesia.
Although the number of confirmed H5N1 human cases in Indonesia has now exceeded 50, only one set of sequences (HA and NA) from the first confirmed case in Indonesia has been released. The other six gene segments from that patient has been withheld, as have sequences all subsequent isolates including the Sumatra cluster.
The latest media reports indicate there is a change that was specific for the father and his 10 year old son, providing genetic evidence for human-to-human transmission. However, these isolates are also Amantadine resistant and have a wild type cleavage site, which differs from the vast majority of earlier isolates from Indonesia.
When Malik Pieris was asked about these changes in the above cluster, he indicated he could not comment because the sequencing was done under contract with the WHO. WHO said hat release of the data was up to the Indonesian government, and the Indonesian government indicated the sequences could be released.
However, the sequences remain password protected at the Los Alamos site, and simple removal of the protection would allow public access. These sequences can be accessed by 15 WHO affiliated consulting labs, but they are not available to other scientists.
The analysis of the sequences is extremely limited. WHO updates focus on reassortment, although there are no examples of H5N1 reassortment with human or swine genes and little indication that such reassortment will be significant. Prior mixing experiments using human and H5N1 genes did not identify significant human / avian combinations.
Changes in polymorphisms are largely focused in positions 226 and 228 in the receptor binding domain. However, H5N1 bird flu is constantly drifty and forming new branches and tries. In depth analysis of this evolution requires a robust and current database, which is made available to a small group that does a limited amount of analysis.
Media Sources
Phylogentic Trees