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  • GISAID.org

    http://www.mysinchew.com/node/16913

    Indonesia: Influenza Scientists, WHO Face Off In Virus Row
    2008-10-03


    JAKARTA, INDONESIA: It's a David and Goliath battle that could affect the world's ability to monitor diseases and develop lifesaving vaccines. The key issue: Should Indonesia and other developing nations have a say over crucial genetic data about their own deadly viruses?

    An international network of top influenza scientists says yes, arguing that is the best way to speed development and research, but they are running into resistance from within the World Health Organization, which opposes letting countries keep intellectual property rights to virus samples they provide for research.

    The intensifying standoff was triggered in part by revelations that the WHO, for years looked upon as the protector of the poor, had been keeping coveted information about bird flu and other viruses in a private database in Los Alamos, New Mexico, and making it available to just 15 laboratories.

    Some foreign governments called for a boycott of the global body's 55-year-old virus-sharing system, which had obliged them to freely hand over samples and data.
    The problem with that system, they say, is that developing countries give up intellectual property rights to their virus samples when they provide them to the WHO. The virus samples are then used by private pharmaceutical companies to make vaccines that are awarded patents _ and sold at a profit at prices many poor nations can't afford.

    Acknowledging a need for change, the WHO agreed to work with developing nations to make sure they had better access to lifesaving medicine, an intensely bureaucratic process that is about to enter its second year with no clear end in site.

    In the meantime, leading influenza scientists and health experts came up with their own solution to alleviate the basic concerns of transparency for developing nations, one that appears to be making some at the WHO nervous.

    The scientists' nonprofit organization, which goes by the name of GISAID, launched a publicly accessible online database that _ for the first time ever _ offers basic intellectual property rights to those who submit genetic information.

    That has encouraged many countries including Indonesia, China, Russia
    and others to again start sharing information about their viruses, turning GISAID into the world's largest and most comprehensive influenza database in just four months


    "I'm in favor of what works. If nothing is working, we have to come up with something new," said Bruce Lehman, who served as Commissioner of Patents and Trademarks under U.S. President Bill Clinton. "And if you have a mechanism that is going to encourage the
    dissemination of scientific data, of research, well, then that is going to be positive in terms of coming up with new treatments for disease."

    However, the WHO appears to be going to extreme lengths to stand in GISAID's way, including withholding funding that has been pledged for the database.

    The World Health Organization, meanwhile, is seeking US$10 million for its own database and virus tracking system, even though its own scientists are already using GISAID's free-of-charge site almost exclusively,
    including for last month's virus strain selection for the annual flu shot, said Masato Tashiro, director of WHO's collaborating center at Japan's National Institute of Infectious Diseases.

    Because many scientists played a key role in helping design the system to meet their needs, they are befuddled at the WHO Secretariat's refusal to embrace them. David Heymann, the global body's top flu official, said the reason was simple. For the first time in decades, developing countries are looking at the global body with mistrust, and officials cannot afford to be partial to any group, he said, adding this was a direct order from WHO
    Director-General Margaret Chan.

    Heymann supports keeping viruses in the public domain _ something that effectively strips countries of ownership rights _ and, until recently, other top officials in Geneva maintained it was important some genetic data remained behind closed doors.

    In the most recent dispute over GISAID's free database, the WHO has refused to hand over US$450,000 provided by the U.S. Centers of Disease Control for the database's development well over a year ago. That is a lot of money for the feisty group of influenza scientists, given that their director, Peter Bogner, a former television broadcaster who rallied to their cause two years ago, has largely financed the initiative on his own.

    "We are working with WHO to get these funds mobilized for their intended purposes," said Bill Hall, spokesman for the U.S. Department of Health and Human Services, also frustrated after receiving conflicting reasons for the delay.

    The WHO's Heymann said CDC money had been earmarked for a specific project _ a database _ but not a particular organization. "We have to go through a competitive bidding process," he told AP _ a process in which GISAID would be ineligible to compete because it is a nonprofit organization.

    Developing nations, which have a key stake in the project, meanwhile alleged that a WHO-commissioned report comparing five databanks, from GenBank to Los Alamos, carried out by the global body's four collaborating centers was deliberately kept secret.

    Scientists ranked GISAID superior on almost all levels, from the amount and type of information included to functionality, but several member states said, when requesting an update, they were told no assessment had been carried out.

    Indonesian Health Minister Siti Fadilah Supari said Friday (3 Oct) if the goal was to force members states to use an expensive and substandard database and tracking system created by WHO, it wouldn't work. "It would certainly add the lingering mistrust many feel toward WHO," she said.
    (By ROBIN McDOWELL/ AP

    http://gisaid.org/
    --



    http://www.cidrap.umn.edu/cidrap/con...g2506data.html

    Scientists launch effort to share avian flu data
    Robert Roos News Editor

    Aug 25, 2006 (CIDRAP News) ? Leading medical researchers yesterday announced the formation of a consortium to unlock genetic and other data on avian influenza in the hope of improving the understanding of how viruses such as H5N1 spread and evolve. A letter published online yesterday by Nature,signed by 70 scientists and health officials, announced the launch of the Global Initiative on Sharing Avian Influenza Data (GISAID). Authors of the letter include Dr. Nancy Cox, head of the Influenza Division at the US Centers for Disease Control and Prevention (CDC), and Ilaria Capua, an Italian veterinary virologist who is a leading advocate of greater sharing of H5N1 genetic data.

    "The Initiative is coming together to work around restrictions which have previously prevented influenza information sharing, with the hope that more shared information will help researchers understand how viruses spread, evolve, and potentially become pandemic," states a news release on the GISAID Web site.

    The consortium "is open to all scientists, provided they agree to share their own data, credit the use of others' data, analyze findings jointly, and publish results collaboratively," the release says. The Nature letter says that data will be published in three public databases "as soon as possible after analysis and validation, with a maximum delay of six months."

    Details are still being worked out, but the participants have agreed to deposit genetic data into secure sections?not yet set up?of existing public databases, according to a Nature news article published yesterday. The data will initially be accessible only to the consortium researchers, but will be opened to public access within 6 months.

    The consortium said it will use the three databases participating in the International Nucleotide Sequence Database Collaboration: EBML in the United Kingdom, DDBJ in Japan, and GenBank in the United States.

    Yesterday's announcement is the second major development this week affecting the availability of genetic data on flu viruses. Two days ago the CDC said it was depositing the blueprints for 650 human flu virus genes in GenBank, a public database, and would release data on several hundred more flu viruses each year henceforth. The data are from viruses collected in the United States.

    Scientists have complained in recent months about the withholding of genetic sequences of flu viruses, especially H5N1. The World Health Organization (WHO) obtains such data as its affiliated laboratories analyze viruses, but the WHO releases the data only with permission from the country of origin. Some countries battling H5N1 have refused to allow release of the information. Indonesia, an H5N1 hot spot, had long refused to authorize release of data on its viruses, but earlier this month the government changed its stance.
    In a telephone interview, Cox said the goal of GISAID is to share clinical and epidemiologic information as well as genetic data on avian flu cases.

    "The aim is that eventually the data will be linked together so there will be not only the sequence data but also the clinical and epidemiologic data," she told CIDRAP News. "The sequences become much more meaningful with other data linked to them."
    Clinical information would include such things as the patient's age, whether he or she survived the illness, how long the illness lasted, and what part of the body a specimen was taken from, she said.

    "All of this information is very useful when you're trying to understand the evolution of the virus," Cox said, adding that data would be stripped of personal identifiers.
    Public genetic databases aren't necessarily set up to accommodate additional information beyond the bare sequence data, and some work will be required to remedy that, Cox said. For example, a database should have fields for such information as whether the virus came directly from a clinical specimen or from an isolate obtained by amplifying the original specimen, she explained.

    "All of these details are potentially very important because they can have an impact on the sequence itself," she said. GISAID will include experts in animal and human virology, epidemiology, bioinformatics, and intellectual property issues, according to the Nature letter.

    A concern of developing countries battling the H5N1 virus is that they won't benefit from releasing data derived from samples they collect, because any resulting drugs or vaccines will be too expensive. Because of this, Cox said, "There really is going to be a lot of effort put into the intellectual property rights issue to assure proper acknowledgment of the origin of the sequences and recognize the scientists and the public health workers in the country of origin of the virus."

    A group within the consortium will focus on intellectual property issues, Cox said. They will work to credit the scientists who are on the front lines in affected countries and also "to determine if there are ways the consortium could help facilitate benefits for those countries that are hardest hit by avian flu."

    The equity issue has been discussed a lot, she added. "We don't have the solutions yet, but it's an area that needs to be tackled." Cox said scientists working for pharmaceutical companies could participate in the consortium. "Pharmaceutical manufacturers would be able to look at the data, and, for example, if they 're trying to design new antiviral drugs for H5N1 or other flu viruses, they'd be able to use the data to do that," she said.

    The director of GISAID is Peter Bogner, chief executive of the Bogner Organization, Santa Monica, Calif. He is an author of the Natureletter, along with Cox; Capua, who chairs the scientific committee of the joint avian flu expert panel of the World Organization for Animal Health (OIE) and the United Nations Food and Agriculture Organization; and David J. Lipman, director of the US National Center for Biotechnology Information.

    According to the Naturenews article, Capua started something of a rebellion against the hoarding of avian flu virus data last March, when she put her own H5N1 sequence data into GenBank instead of in the protected database used by WHO-linked labs, and challenged others to do the same.

    Capua then collaborated with Bogner, who talked with many scientists and policymakers about the issue, according to the article. Subsequently, the OIE-FAO avian flu expert panel (OFFLU) endorsed the consortium idea.

    The 70 signers of the Nature letter include researchers and health officials from countries around the world, including those hard-hit by H5N1 avian flu, such as Thailand, Indonesia, Vietnam, China, Cambodia, Egypt, and Turkey, as well as countries not yet affected.


    Cox said the consortium is "really at a very formative stage right now. There's a lot of groundswell of support for it. There's a lot of enthusiasm, but it's just the beginning."

    See also:
    GISAID letter to Nature
    http://www.nature.com/nature/journal...l/442981a.html

    GISAID news release
    http://gisaid.org/press_releases.html

    Nature news story
    http://www.nature.com/news/2006/0608...060821-10.html

  • #2
    Re: Gisaid

    Here is the other side of the coin...

    http://immunocompetent.com/index.php...Id=19&blogId=1

    Swiss-American Venture Claims Blood of Vietnamese H5N1 Survivors (and Much More!)

    Posted by perezoso on 06 October, 2008 13:06

    Think antibodies might be useful to prevent or treat bird flu? Better get out your checkbook, because a company based in San Francisco says it owns all H5N1 antibodies, including all human (and some animal) antibodies against the critical HA gene of the H5N1 "bird flu" virus. The claims are made in an international patent application published on September 18th.

    But wait, it gets even more disgusting: The company also specifically claims DNA (and amino acids) taken from at least 3 Vietnamese survivors of H5N1. The DNA, which encodes antibodies, is contained in human cell lines established from the victims' blood.

    If granted, the patent application could have profound effects in limiting research on antibody treatments against the potentially pandemic H5N1 type of influenza. It could also earn its owners huge profits from the blood of 3 (or 4) Vietnamese persons who were nearly killed by the virus. Who exactly? Well, one of the would-be owners of H5N1 antibodies and pieces of Vietnamese people is none other than a co-founder of Chiron and former Director of Novartis. Sadly, there is no remedial ethics class to which to send these perverted patent applicants.

    The patent application (WO2008110937) was published on 18 September 2008. It was submitted by HuMabs LLC, a relatively unknown company in California. HuMabs is owned, however, by Synergenics, a private venture capital-type firm financed and led by William Rutter. A prominent figure in biotechnology, Rutter is known for co-founding the company Chiron and as a former Director of Switzerland-based life science giant Novartis.

    The scientific lead of HuMabs, and the sole inventor indicated on the patent application, is immunologist Antonio Lanzavecchia, an Italian researcher who leads the Institute for Research in Biomedicine (IRB) located in Bellinzona, Switzerland.

    The blood samples were collected in late 2004 and early 2005 at the Hospital for Tropical Diseases (HTD) in Ho Chi Minh City, Vietnam. Some details have been published about the H5N1 victims whose blood was used.

    Two were men, 22 and 23 years old when infected. They were hospitalized 7 and 3.5 weeks, respectively. A third victim was a 26-year-old woman whose hospitalization was relatively short, at ten days. It is from her blood that the most promising antibody, called FLD21.140, was isolated. There is no published information about the 4th blood donor.

    The collections were part of a research program sponsored by the UK's Wellcome Trust and conducted by Oxford University scientists, who maintain a Wellcome-sponsored research centre at the Hospital. The Oxford scientists say they obtained informed consent from the Vietnamese H5N1 victims, who were treated at the Hospital.

    The blood samples were sent to US and Swiss researchers collaborating with the Oxford team at the US National Institutes of Health (NIH) and the IRB in Switzerland.

    In research with mice, antibodies extracted from the blood samples proved highly effective against Vietnamese-type (Clade 1) H5N1 viruses and partially effective against other (Clade 2) H5N1 types. The antibodies target the HA (hemagglutinin) gene of the influenza virus, preventing or inhibiting infection.

    In parallel, the Wellcome Trust public relations department facilitated media access to the Oxford team in Vietnam, and a feature article about the research appeared in the Times (London) in October 2006.

    The Times author highlighted a charming 11-year-old girl who beat the odds and survived H5N1 and noted, with no apparent irony, that "H5N1 patients are often the rural poor, with no phone and little contact with doctors", and that several of the H5N1 victims interviewed were suffering ongoing financial crises as a result of their hospitalization. Nothing was stated in the article about patents and profits.

    In May 2007, the HTD/Oxford/NIH/IRB team jointly published the mouse experiments, which were portrayed as a significant step forward in H5N1 research. The Wellcome Trust simultaneously put out a press release on 29 May 2007. A footnote to the press release stated "Worldwide rights to the antibody technology have been licensed to HuMabs, LLC, a US-based business with offices in Bellinzona."

    Sixteen months later, in September 2008, the HuMabs/Lanzavecchia patent application was published by the World Intellectual Property Organization (WIPO). The application claims not only DNA from the 4 Vietnamese victims that encodes 11 specific antibodies, it goes much further.

    It specifically claims that HuMabs has invented the DNA and amino acids of ANY human monoclonal antibody against ANY H5N1 strain including all monoclonal antibodies that target the HA gene. The patent application claims many variants of these antibodies, including any that has the same "complementarity determining regions" ("CDRs"). CDRs are short amino acids that help target the virus and fight infection.

    With respect to Clade 2 H5N1 viruses, the patent application claims any antibody that can neutralize them -- animal or human, mono or polyclonal.


    The patent application raises ethical questions for several reasons. It claims the DNA of H5N1 victims as property, potentially enabling profit from the sale of parts and products of the human body.

    This concern is amplified by particulars of this case, specifically, the disparities between the reportedly poor Vietnamese H5N1 victims, and the privileged European scientist and wealthy US venture capitalist who are making the property claims. Details of the consent forms signed by the Vietnamese victims and what, if any, additional agreements exist have not been made public.

    In addition, antibody treatments are generally expensive and difficult to reliably produce, formulate, and distribute, raising questions about who will have access to the treatment (if it works), particularly in the event of a pandemic.

    Many developing countries, and particularly poor citizens thereof, already are unable to access H5N1 treatments due to high costs. Even if HuMabs attempts to make its high-tech treatment available, it may not be possible to produce this in the quantity and at the price necessary for it to be useful to most of the world's population.

    Finally, there is the startling breadth of the patent claims -- to any H5N1 human monoclonal antibody. It amounts to a general patent claim on part of the human body -- any person's body.

    Any person infected with H5N1 or who receives H5N1 vaccines will produce H5N1 antibodies. Thus, HuMab's patent claims DNA and natural products of all humans who have the misfortune of being exposed to H5N1 or the benefit of being vaccinated.

    This patent application is the latest in a string of aggressive H5N1 claims by companies and government laboratories in the United States and Europe. These applications heighten concerns raised by developing countries that the present international system for sharing of influenza viruses (the Global Influenza Surveillance Network, under the World Health Organisation) is unfair, and that the benefits of influenza research should be shared fairly and equitably.

    A WHO Intergovernmental Meeting on Pandemic Influenza Preparedness (PIP IGM) will reconvene in Geneva in November to continue negotiations on the reform of the WHO's Global Influenza Surveillance Network (GISN) which has been criticized for allowing the viruses and other samples it collects for public health to be used for purposes of private profit.

    Comment


    • #3
      Re: Gisaid

      open letter to GISAID asking for publishing of limited pandemic-relevant parameters
      calculated from their sequences, that does not reduce the submitter's rights


      hello Gisaid,

      I'm a computer programmer and have written programs that
      automatically calculate chosen parameters for sequences,
      If it would be allowable for registered members to publish
      the findings, I would offer it free of charge to GISAID.

      parameters could be:
      number of nucleotides that are "A","C","G","T" or just the ratio (A+T)/(A+T+C+G)
      useful to track the host, where a virus evolves as recently demonstrated here:

      http://knol.google.com/k/host-depend...-h1n1-pandemic

      it's i.e. important to determine the host in Indonesia H5N1 which could lead to a devastating pandemic.
      So here we have a method to improve this without growing Indonesia's fears that someone could
      produce a vaccine which they can't afford.You can't use nucleotide-counts for vaccine production.

      Another useful parameter is the number of amino-acid differences from the bird-index.
      That performs the same task and shows how a flu-A virus accumulated amino-acid
      mutations distant from the original waterfowl virus and lets us conclude in what
      host it did evolve.

      Another useful parameter would be the substrain, e.g. as determined by the classification
      at flugenome.org, so we learn about new introductions of other substrains
      into a region or farm.

      Just a few numbers e.g. 0.5565,74,KGD5JF1JF1E, for A/IDN/CDC625/2006(H5N1)
      0.5565 = ratio of A,T nucleotides
      74 = amino-acid differences from the bird-index
      K,G,D,5J,F,1J,F,1E = substrain classification of the 8 segments
      according to flugenome.org (or use other calssification systems
      to specify the substrain-relationship)

      presumably not enough to challenge the submitter's originality or patent-rights
      or produce vaccines from it.
      But enough to significantly inprove our surveillance and risk-assessment and thus
      adapt pandemic preparation plans accordingly or just help to improve poultry protection.


      Guenter Stertenbrink, programmer from Germany, gsgs in the flu-forums
      I'm interested in expert panflu damage estimates
      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

      Comment


      • #4
        book about H5N1, Los Alamos database, Capua, GISAID, "biohackers", rebels, DIYbio, ...

        http://issuu.com/plutopress/docs/delfanti_biohackers

        [I could only "hack" into it by using google's cache]

        http://webcache.googleusercontent.co...d=ivns&strip=1

        5300 lines ==> 66 pages when printed

        243 google-hits for that link
        http://issuu.com/plutopress/docs/delfanti_biohackers
        [most in Italian, Capua-->politics]

        only the original page for that link and gisaid ,
        so presumably there is no internet discussion about this yet.
        I'm interested in expert panflu damage estimates
        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

        Comment


        • #5
          H5N1, Los Alamos database, Capua, GISAID, "biohackers", rebels, DIYbio, ...

          http://issuu.com/plutopress/docs/delfanti_biohackers

          [I could only "hack" into it by using google's cache]


          at that time (2006) I remember, that I didn't consider the Los Alamos database so bad.
          niman still often posted there sequences and most still went to genbank.
          OFFLU had some additional sequences, but not much, nothing important.
          Then China announced to share sequences at genbank and Indonesia started
          to withhold sequences. But at that time we already had many Indonesian
          sequences and it got no new strains, just evolution of the existing strains.
          The main question was whether there was another unknown reservoir in some
          other species, why the avian and human sequences formed two groups.
          Later we found no reservoir and that the groups did mix at last.

          Capua never replied to emails, afair.
          I don't remember having ever heard about the DIYbio mailing list before
          ----------------------------------------------- https://groups.google.com/forum/#!forum/diybio
          zero hits for H5N8, zero hits for H7N9, nine hits for H5N1
          http://diybio.org/
          latest news from Sept.2014
          ----------------------------------------------

          They do not mention in the article the later controversy, that GISAID later removed
          the "rule" that their sequences also got to genbank after some time [6 months ?]
          The critics and turning away by founding members like Salzberg and Capua herself,
          although I'm not yet sure about the reasons for the latter.

          My main problem with GISAID is, that, if I were member, I couldn;t integrate their sequences
          in my files and then analyse them together with genbank sequences and then post about it
          and upload and share it, as I'm doing here at FT.
          E.g. my mutation tables or pictures. From these you could rebuild the sequences.
          I'm not sure whether they would allow lists of recombinations, unusual preservations
          and such. Or just any results, without giving credit to the originating lab or cooperation
          attempts - which would be tedious and just inpracticable for long lists.
          Creation,exchange,combining and redistributing of GISAID sequences together with sequences
          from other databases is not easy or even forbidden.
          Meanwhile many labs use GISAID that used to publish at genbank. Without GISAID
          these sequences might have gone to genbank.
          I'm interested in expert panflu damage estimates
          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

          Comment


          • #6
            checking
            I'm interested in expert panflu damage estimates
            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

            Comment

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