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  • Indonesia, FAO, OIE pledge to publish H5N1 data

    Indonesia, FAO, OIE pledge to publish H5N1 data

    Aug 3, 2006 (CIDRAP News) ? In an apparent policy shift, Indonesia promised today to freely share genetic data on H5N1 avian influenza viruses, according to a Bloomberg news report.

    That announcement comes 2 days after the United Nations Food and Agriculture Organization (FAO) and the World Organization for Animal Health (OIE) pledged to "systematically" publish avian flu virus sequences and urged others to follow suit.

    The two announcements raise the prospect of better tracking of mutations in the virus, which should help in the development of vaccines to use in case the H5N1 virus evolves into a strain capable of causing a human pandemic.

    Indonesia's health minister, Siti Fadilah Supari, said the country will deposit avian flu virus data in GenBank, a public database of genetic sequences, according to today's Bloomberg report. She said data from the recent family case cluster in Sumatra involving person-to-person transmission would be included.

    The journal Nature reported Jul 28 that until very recently, Indonesia had shared few, if any, H5N1 virus samples from birds over the past year. Peter Roeder, an FAO official in Indonesia, was quoted as saying the FAO had received no sequence data from poultry viruses from August 2005 until very recently, when 91 samples arrived at an OIE facility in Geelong, Australia.

    The Indonesian announcement was welcomed by the World Health Organization (WHO), according to Bloomberg. "We are very pleased with the Indonesian government decision. This will be important for the international response to avian influenza," George Petersen, WHO representative in the country, told Bloomberg.

    The OIE and FAO announced Aug 1 that their joint network of expertise on avian influenza, called OFFLU, would "systematically make avian influenza virus sequences accessible to the entire scientific community," according to an FAO news release. The groups promised to send virus samples to the US National Institutes of Health for sequencing and would deposit the sequence data in GenBank.

    "With this gesture OFFLU reiterates its call to the world's scientists, international organizations and countries for a global sharing of virus strains and sequences," the FAO said.

    Virus strains are often considered intellectual property, and some experts believe that sharing them can possibly hamper research progress and scientific publication, the FAO statement said.

    OFFLU was launched in April 2005 with the aim of sharing avian flu data and virus samples internally and with the wider scientific community, the FAO said. In February of this year, OFFLU launched a campaign for openness when Dr. Ilaria Capua of Italy, chair of the network's Scientific Committee, published sequence data on H5N1 strains from Nigeria and Italy and urged 50 colleagues around the world to share their data.

    In March, the OFFLU Scientific Committee decided "to put new emphasis on the need for further collection, characterization, and exchange" of avian flu viruses and for expansion of sequence data, the FAO reported. At about the same time, Capua and four OFFLU colleagues wrote a letter to the journal Science promising to make H5N1 samples available for sequencing.

    http://www.cidrap.umn.edu/cidrap/con...06sharing.html[/B]
    ...when you have eliminated the impossible, whatever remains, however improbable, must be the truth. - Sherlock Holmes

  • #2
    Re: Indonesia, FAO, OIE pledge to publish H5N1 data

    Commentary at

    Comment


    • #3
      Re: Indonesia, FAO, OIE pledge to publish H5N1 data

      Bird flu data now open to all Tb. Arie Rukmantara, The Jakarta Post, Jakarta
      Bowing to international pressure, Indonesia has said foreign scientists can have full access to the country's data on bird flu, the infectious disease that has claimed 43 lives here.
      The move is expected to help international scientists understand how the H5N1 bird flu virus works. Researchers are especially interested in the limited human-to-human transmission of the virus that happened in May in North Sumatra in the world's largest cluster of infections.
      Scientists fear bird flu could become more easily transmissible among humans, sparking a deadly global pandemic.
      "I've learned that scientists across the world have complained that they could not access the data and made statements as if we had hidden it," Health Minister Siti Fadilah Supari told a press conference here Thursday.
      "For the sake of basic human interests, the Indonesian government declares that genomic data on bird flu viruses can be accessed by anyone."
      In its July 13 edition, the respected journal Nature reported scientists were complaining that they were hindered from studying the virus because the Indonesian government had declined to release the data from bird flu samples.
      In a recent interview with The Jakarta Post, the minister admitted the government had kept the data to itself and its partners while conducting its own research.
      Siti said the decision to open up access to the information came after a suggestion from the medical committee of the Indonesian Academy of Sciences, a government-sanctioned forum of experts.
      Professor Sangkot Marzuki of the academy said the committee made the suggestion because emerging diseases like bird flu should be addressed promptly, involving as many stakeholders as possible.
      He said the academy had considered the potential benefits that the government could reap by developing vaccines and drugs based on its data, and from royalties from intellectual rights.
      Health experts have been debating for decades whether genomic data from new viruses and other microscopic materials should be owned by the organizations that sponsor the research, or placed in the public domain so that the world can have access to it.
      Siti said opening up global access could be the key to unlocking such important information as the origin of the virus, how it causes disease, how it is mutating, the sources of infection, and how to prevent or cure the virus.
      "But in future cooperation on bird flu with other countries, the delivery of specimens should be regulated under 'Material Transfer Agreement' documents as is commonly practiced in scientific cooperation," she added.


      Comment


      • #4
        Re: Indonesia, FAO, OIE pledge to publish H5N1 data

        http://www.recombinomics.com/News/08...ia_Pledge.html

        Indonesia Pledges to Release H5N1 Bird Flu Sequences

        Recombinomics Commentary
        August 3, 2006

        Indonesia's health minister, Siti Fadilah Supari, said the country will deposit avian flu virus data in GenBank, a public database of genetic sequences, according to today's Bloomberg report. She said data from the recent family case cluster in Sumatra involving person-to-person transmission would be included.

        The journal Nature reported Jul 28 that until very recently, Indonesia had shared few, if any, H5N1 virus samples from birds over the past year.

        The above comments indicate Indonesia has pledge to release the H5N1 sequences in the private WHO database at Los Alamos. These sequences can be released by simply removing the password protection. This was recently done for the human H5N1 sequences from Turkey, which were sumitted by the WHO H5 group and have the characteristic ISDN numbers assigned at Los Alamos.. Earlier, this was also done for H5N1 from the first human case in Indonesia. Although that sequence was deposited in the WHO data base on August 1, 2005, it was not released until March 25, 2006.

        The phylogenetic tree from the H5N1 meeting in Jakarta has 37 human HA sequences. Only one is public, which is A/Indonesia/5/05(H5N1), the index case for the country. The only other gene segment from that patient is the NA sequences. The other six sequences from this patient as well as all eight sequences from the 37 patients described above have been sequestered at the WHO database. These human sequences do not match public avian sequences from Indonesia (or any other location). 91 recent avian samples have been sent to Australia for sequencing. The human and recent avian sequences will be useful in the interpretation of the evolution of H5N1 in Indonesia as well as predictions of future vaccine target sequences..

        Similarly, there are about 100 sets of sequences from Europe that also remain sequestered although Weybridge has promised to release these sequences, which represent many of the isolates from Europe and the Middle East. Examples of reassortment in Israel and India have already been identified in the limited number of public Qinghai sequences.

        Release of all eight gene segments from these isolates would be useful.

        .
        "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

        Comment


        • #5
          Thanks to Declan Butler

          A HUGE thanks is owed to (amongst others) Declan Butler @ Nature.

          Thanks, Declan!
          ...when you have eliminated the impossible, whatever remains, however improbable, must be the truth. - Sherlock Holmes

          Comment


          • #6
            Thanks to Dr. Niman

            A HUGE thanks is also owed to (amongst others) Dr. Niman for badgering these folks about this issue for ... how long now?

            Thanks, Dr. Niman!
            ...when you have eliminated the impossible, whatever remains, however improbable, must be the truth. - Sherlock Holmes

            Comment


            • #7
              Re: Thanks to Dr. Niman

              Originally posted by Theresa42
              A HUGE thanks is also owed to (amongst others) Dr. Niman for badgering these folks about this issue for ... how long now?

              Thanks, Dr. Niman!
              I will believe when I see it. I have an e-mail into Los Alamos to find out if and when. Since the media reports keep talking about GenBank, I would not be surprised if this is just more buck passing. The sequences could be released immediately, because they are already on the private side of Los Alamos.

              I still think the sequences are controled by the sequencers, which for human Indonesia H5n1 sequences would be HKU and CDC (each have done independent sequencing and have full sequences for each isolate they obtained from the clinical samples).

              Comment


              • #8
                Re: Thanks to Dr. Niman

                Originally posted by niman
                I will believe when I see it. I have an e-mail into Los Alamos to find out if and when. Since the media reports keep talking about GenBank, I would not be surprised if this is just more buck passing. The sequences could be released immediately, because they are already on the private side of Los Alamos.

                I still think the sequences are controled by the sequencers, which for human Indonesia H5n1 sequences would be HKU and CDC (each have done independent sequencing and have full sequences for each isolate they obtained from the clinical samples).
                Oh, and here I was sitting holding my breath. Are you saying that's not advisable?
                ...when you have eliminated the impossible, whatever remains, however improbable, must be the truth. - Sherlock Holmes

                Comment


                • #9
                  Re: Thanks to Dr. Niman

                  Originally posted by Theresa42
                  Oh, and here I was sitting holding my breath. Are you saying that's not advisable?
                  Yes, I would definitely advise against breath holding. The sequences are deposited at Los Alamos within days of isolation. The sequence from the first confirmed case in Indonesia was deposited August 1, 2005 into Los Alamos by the WHO H5 group. All they really have to do is say take off the password for the other sequences. The phylogenetic trees can't be drawn without the sequence data, so as of June, 2006 there were at least 37 human sequences in the data base. Both Hong Kong University and the CDC are members of the WHO H5 group, so they would deposit the sequences as soon as they were complete.

                  The media reports keep talking about GenBank, which would required a separate deposit (Los Alamos uploads GenBank flu sequences, but GenBank sequences would require a separate deposit and would take weeks to months to appear).

                  The human Indonesian sequences as well as the human Turkey sequences are only at Los Alamos, even though they were released weeks or months ago. Many additional H5N1 sequences from earlier isolates in southeast Asia are also only at Los Alamos (Los Alamos accession numbers all begin with ISDN).

                  The repeated media references to GenBank instead Los Alamos is cause for concern.
                  </IMG>

                  Comment


                  • #10
                    Re: Indonesia, FAO, OIE pledge to publish H5N1 data

                    *Sigh* ( << letting breath out )

                    People are so annoying....
                    ...when you have eliminated the impossible, whatever remains, however improbable, must be the truth. - Sherlock Holmes

                    Comment


                    • #11
                      Re: Indonesia, FAO, OIE pledge to publish H5N1 data

                      You let it out an hour too early. Commentary at

                      Comment


                      • #12
                        Re: Indonesia, FAO, OIE pledge to publish H5N1 data

                        Originally posted by niman
                        You let it out an hour too early. Commentary at

                        http://www.recombinomics.com/News/08...a_Release.html


                        Yeah -- exciting! I can hardly believe it. Yay!!

                        ...when you have eliminated the impossible, whatever remains, however improbable, must be the truth. - Sherlock Holmes

                        Comment

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