Today, on the third anniversary of WHO’s Global Alert about the mysterious respiratory disease soon to be named “SARS”, more researchers are calling for liberation of the H5N1 sequence data sequestered in various national laboratories.
The link below leads to a Helen Branswell article, which quotes experts who are joining Italian flu researcher Ilaria Capua’s call for all labs to release their H5N1 sequences to public data-bases. The article also quotes WHO officials and others describing the obstacles in the path of this desired goal.
Perhaps the weight of Flu Wiki-dom can be brought to bear on our respective countries’ officials, through letters? A petition?
Wow, this is great news. Thanks for posting this Path Forward.
From the article
“”There are some members of the lab network that balk at sharing data. We can’t speak for them and speculate why,” adds Cheng, who would not identify the holdouts.
Maria Cheng won’t name them, but I will:
There are many people who visit this site from the US and the UK. Please write your representatives and demand that the sequence information from flu viruses be put in a public database (GenBank) so that the world’s scientists can try to fight the H5N1 monster. Our children are depending on us.
Important Topic.
Who to write?
Anyone want to start a petition??
Re: naming names:
Don’t forget Alan Douglas at the UK Mill Hill lab.
The UK Independent wrote on January 15 that he isolated the H5N1 virus strain that killed three Turkish children. The Independent quoted him as gleefully saying:
“We are the only ones in the world who have grown this virus. A lot of people are asking for it now, obviously. The Americans are going to be last on the list, I can tell you.”
“Hiding data — it isn’t just China anymore” (and never was)
bumped
Pathforward, thanks for adding Alan Douglas (UK) to the list of hoarders.
DemFromCT: What’s the most effective way to influence representatives in the US to get the CDC to release their sequences? The first one I want to see is: A/Indonesia/5/2005, the strain being used to develop the new vaccine. So, the US got it from Indonesia and is making a vaccine from it, but no-one but Julie Gerberding and some vaccine developers in the US get to know why a new vaccine was needed. Nice, real nice.
The sequences from China are still vital to get, but it will be hard to apply pressure to them until Western countries come clean.
Calls are better than letters are better than faxes are better than emails. All the numbers and addresses are in the above links.
Speaking of naming names. Most of the sequences in Asia are held by Hong Kong (Yi Guan and Malik Peris) / St Jude (Robert Webster) combo. They have all of the human Indonesian sequences, including the one being used in a US vaccine.
http://www.recombinomics.com/News/03110601/H5N1_Pandemic_Vaccine_Indonesia.html
It is worth noting that in the original Science (Eserink) article, Yi Guan said he would consider releasing the sequences if WHO chnaged its polcy. In the CP (Branswell) article, WHO would consider a change if the researchers changed their policy.
This is really a game of press releases. H5N1 doesn’t read press releases and readers of this board shouldn’t either.
The story is in the sequnece. WHO and consultants have the book of sequences locked up in their private reading room - and they really don’t know how to read (if it’s not reassortment or random mutation it is not in their vocabulary).
So, if Yi Guan and Peris have the Indonesian sequences, then so does the Chinese government. Interesting. But the Canadians don’t. Who else doesn’t have access to these vital sequences? I’d be pretty mad if I lived in a country that was being denied access to these sequences. Why, I might even bring it up at the next WHO meeting or at the UN.
For more names at WHO related to H5N1
Media Contact: Dick Thompson
Human H5N1: Klaus Stohr
Animal H5N1: Mike Perdue
WHO International Flu Centers (names, phone, FAX. email)
Here are the 8 WHO reference labs (password not included)
WHO reference laboratories for diagnosis of influenza A/H5 infection
23 March 2004
Department of Microbiology Faculty of Medicine University of Hong Kong University Pathology Building Queen Mary Hospital Hong Kong Special Admistrative Region of China Fax: + 852 2855 1241
National Influenza Centre Government Virus Unit 382 Nam Cheong Street Shek Kip Mei Kowloon Hong Kong Special Administrative Region of China Fax: +852 2319 5989
Unité de Génétique Moléculaire des Virus Respiratoires Institut Pasteur 25 rue du Docteur Roux 75724 Paris Cedex 15 France Fax: +33 1 4061 3241
WHO Collaborating Centre for Reference and Research on Influenza National Institute of Infectious Diseases Gakuen 4–7−1, Musashi-Murayama Tokyo 208–0011 Japan Fax: +81 42 561 0812 or +81 42 565 2498
WHO Collaborating Centre for Reference and Research on Influenza National Institute for Medical Research The Ridgeway Mill Hill London NW7 1AA United Kingdom Fax: +44 208 906 4477
WHO Collaborating Center for Studies on the Ecology of Influenza in Animals Virology Division Department of Infectious Disease St. Jude Children’s Research Hospital 332 North Lauderdale Street Memphis TN 38105–2794 United States of America Fax: +1 901 523 2622
WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza Centers for Disease Control and Prevention 1600 Clifton Road, Mail Stop G16 Atlanta GA 30333 United States of America Fax: +1 404 639 2334
WHO Collaborating Centre for Reference and Research on Influenza
45 Poplar Road
Parkville, Victoria 3052
Australia
Tel: +61 3 9389 1340
Fax
61 3 9389 1881
http://www.influenzacentre.org
More names:
Dr M. Tashiro
Department of Viral Diseases and Vaccine Control
National Institute of Infectious Diseases
Gakuen 4–7−2
Musashi-Murayama
Tokyo 208–0011
Japan
Telephone: +81 42 565 2498
Fax: +81 42 565 2498
http://idsc.nih.go.jp/index.html
Dr A. Hay
National Institute for Medical Research
The Ridgeway, Mill Hill
London NW7 1AA
United Kingdom
Telephone: +44 208 959 3666
Fax: +44 208 906 44 77
Dr N. Cox
Influenza Branch
Division of Viral and Rickettsial Diseases
National Centers for Infectious Diseases Centers for Disease Control and Prevention
1600 Clifton Road, Mailstop G16
Atlanta, Georgia 30333
United States of America
Telephone: +1 404 639 3591
Fax: +1 404 639 2334
Influenza news on:http://www.cdc.gov/flu/weekly/fluactivity.htm
Reference Laboratories ( these appear to be new additions)
Dr G. Grohmann
Immunology and Vaccines
Therapeutic Goods Administration Laboratories
P.O. Box 100, Woden ACT, 2606 Australia Telephone: +61 2 6232 8490 Fax: +61 2 6232 8564 http://www.tga.gov.au
Dr J. Wood
Division of Virology
National Institute for Biological Standards and Control
Blanche Lane, South Mimms, Potters Bar,
Hertfordshire EN6 3QG
United Kingdom
Telephone: +44 1 707 641 000
Fax: +44 1 707 646 730
e-mail: enquiries@nibsc.ac.uk
Dr R. Levandowski
Division of Viral Products
Centre for Biologics Evaluation and Research
Food and Drug Administration
1401 Rockville Pike, Rockville, MD 20852
United States of America
Telephone: +1 301 827 1908
Fax: +1 301 402 5128
Can we as a group draft a standardized communication that can be emailed, fax’d, mailed, or recited over the phone? One that includes key points of emphasis / appeals like:
Someone else add please!
I suspect we have enough info to make a like noise this morning.
Let’s do it.
I think, Rudi Cilibrasi already sent such a petition some months ago. It should be here at fluwiki or at curevents. I’ll search for a link…
Here are the names in today’s WSJ who were e-mailed to let the sequences go
mike perdue (E-mail); ian brown (E-mail); Alberto. Laddomada (E-mail); ‘Alan Hay’; Cristianne Bruschke (E-mail); Juan Lubroth (E-mail); Alejandro SCHUDEL (E-mail); alex thiermann (E-mail); Aaamarangon (E-mail); Dennis Alexander (E-mail); Steve Edwards (E-mail); B.Vallat ; isabella donatelli (E-mail); Aaaofflu (E-mail); aadundon (E-mail); ron a. m. fouchier (E-mail); aacattoli (E-mail); David Swayne (E-mail); isabel minguez (E-mail); Olga Zorman-Rojs (E-mail); vladimir savic (E-mail); veronique jestin (E-mail); thierry van den berg (E-mail); ruth manvell (E-mail); Poul Jørgensen (E-mail); philippe vannier (E-mail); Paola De Benedictis (E-mail); ortrud werner (E-mail); maria pittman (E-mail); jill banks (E-mail); jeanet van der goot (E-mail); guus koch (E-mail); elke starick (E-mail); ab osterhaus (E-mail); ‘Chris Olsen’; ‘David Suarez’; ‘Dennis Senne’; ‘Dr. Webster, Robert’; ‘Hiroshi Kida’; ‘Jackie Katz’; ‘Joseph Domenech’; ‘Paul Selleck’; ‘Richard Webby’; ‘Sasha Klimov’; ‘Stacy Schultz-Cherry’; ‘Wenqing Zhang’; ‘Yi Guan’; ‘Yoshi Kawaoka’
Text of WSJ story at
http://www.curevents.com/vb/showthread.php?p=343671#post343671
Most of the e-mail addresses for the “dirty thirty” are fairly public (listed in publications).
Dr. Capua’s letter, reported in the journal Science on March 3, has touched a nerve in the scientific community. Scientists and agriculture officials from Switzerland, Croatia, Slovenia, the United Kingdom, Iran and Niger have written Dr. Capua giving her permission to make public viral sequences made from samples they submitted to her lab, or have done so themselves in a show of solidarity, she says. Nancy Cox, chief of the influenza branch at the Centers for Disease Control and Prevention in Atlanta, replied to the letter with a personal note saying, “I applaud your decision,” according to Dr. Capua.
Dr. Perdue, of the WHO, goes still further, saying the exclusive-access system should change and adding that his sentiment is shared by others within the organization who have privately congratulated Dr. Capua on her effort.
and what’s the official reaction of WHO ? They should demonstrate now, how quickly they can react ;-)
gs: I agree completely. The Director-General needs to indicate that from now on, it will be WHO policy to require all WHO affiliated labs to deposit their sequences within 24 hours of sequencing (Bermuda Rules or maybe Geneva Rules). Anyone who fails to comply will lose their affiliation with WHO. Any country that doesn’t agree to these terms will thus no longer be able to hide under the shadowy system that now obtains.
Re: Nancy Cox. So, who is blocking her from releasing the CDC influenza sequences?
[“The EU reference laboratory for Avian Influenza in Weybridge (UK) is concealing results from tests taken in 15 countries, reports Svenska Dagbladet
Ongoing tests of bird flu found in Sweden show that the virus carries the Z-type gene - the most agressive of the five genotypes of the H5N1 strain.
However, the already complicated mapping of the virus is being made more difficult because other countries’ laboratories are not publishing results on the genetic form of the viruses they analyse.
“We will make our results public as soon as they are ready and it would be great if everybody did the same,” said Swedish researcher Bernt Klingeborn, also referring to the the EU- and UN-funded bird flu laboratory in Weybridge.
“The virus is developing fast and we don’t have time to wait for the results to be printed in a science publication,” he added.”]
bumped
bumped again. And will be bumpoed again.
Monotreme,I think WHO should at least say _something_ now. They are actually building a quick-action-force but their strategy is waiting…
Going away for a few days, will use a few hours to write letters. (Longhand). Am going to a meeting with a bunch of very active, intelligent, educators, and retired engineers. They are letter writer par excellance, and this may be the most important issue among the important issues they all dwell on. Concerned citizens of the world so to speak.Don’t know if I’ll pique their interest (each has their own hobbyhorse, enviorement, politics local, state and international.) I’ll see if it flys.
bumped
Each on their usual hobbyhorses. Had three copies which some didn’t even look at. Never beat a dead horse so I left it at that.Interesting thing. The levees in NO should be redone by hurricane season, but only for Cat 3. Things never change.Left one copy with someone who will be doing a report on Pandemic and National Security. Perhaps he will read it at home.Good people, but as with most of us, they have their spheres of interest.
Will send off some longhand letters on my poshest stationary. Sometimes people will pay attention to details like that. Secretaries and interns less likely to trash something that looks good.
Iranian swan sequence released
http://www.recombinomics.com/News/03140601/H5N1_Iran_Sequence.html
Three have a common link to the Italian swan sequence, but the other polymorphisms are found in Asia. These are NOT random mutations. They are found in other H5N1 isolates that are likely candidates for dual infections when the Qinghai strain was circulating in Asia.
why are they not random mutations ? Couldn’t it be that these occurred independently in East-Asia and Iran ? Couldn’t it be, that some mutations are just more likely than others, depending on the 3d-structure ?
Why would they just “happen” to be southeast Asia and why would the ALL happen to be southeast Asia?
Editorial
Nature 440, 255–256 (16 March 2006) | doi:10.1038/440255b Dreams of flu data Top of page Abstract
The lack of an accessible store of information is undermining the fight against avian flu.
____
Three cheers, then, to Ilaria Capua of the Tri-Veneto Region Experimental Animal Health Care Institute in Italy, who last month threw down the gauntlet to her colleagues by refusing to put her latest data on Nigeria and Italy in these private networks. Instead she uploaded them to GenBank and called on her colleagues worldwide to do likewise. Only in this way can researchers establish and track the global pattern of the evolution of the bird-flu virus.
Imagine scientists anywhere being able to log on to a publicly available, searchable Internet database, updated in real time, with full clinical and sequence data on each human case, and accurate and complete poultry data. Dream on. The WHO’s clunky online Global Health Atlas, which gives rough aggregate data for many diseases, doesn’t have a category for H5N1 under influenza. The Global Infectious Diseases Epidemiology Online Network (GIDEON) database contains only the data on avian flu that it extracts from the WHO’s updates and reports from the ProMED reporting system for infectious diseases. ProMED itself has pioneered outbreak alerting, notably during the SARS crisis, but its content consists largely of media cuttings. Such aggregation is often done faster and better by bloggers, and by the Global Public Health Intelligence Network (GPHIN), a Canadian intelligence operation that provides an early warning system that screens media and blogs in seven languages in real time.
The world badly needs a database for outbreaks of avian flu. But international agencies are failing to rise to the challenge.
NY Times editorial: Secret Avian Flu Archive
Published: March 15, 2006
At a time when health authorities are racing to head off a possible avian flu pandemic, it is distressing to learn that the World Health Organization is operating a secret database that holds the virus’s genetic information. A lone Italian scientist has challenged the system by refusing to send her own data to the password-protected archive. Instead, she released the information publicly and urged her colleagues to do the same. She is surely right. The limited-access archive should be opened or bypassed immediately to encourage research on this looming health menace.
The campaign by Ilaria Capua, an Italian veterinarian who works on avian influenza, was spotlighted in recent articles in the journal Science and The Wall Street Journal. The hidden data could be of immense value in determining how the virus is evolving and in developing effective vaccines or drugs. The possibility of breakthroughs can increase only if many more scientists can analyze the data.
The rationale for the closed system is that the restrictions encourage scientists who are worried about being scooped by rivals to share their data on a limited basis even before they have published their findings in a journal. Confidentiality is also needed, some say, to encourage skittish countries, worried about bad publicity or the loss of intellectual property, to release the genetic sequences of viruses found on their territory.
Those arguments seem insubstantial now that some top W.H.O. officials and other health authorities have called for opening the exclusive-access system. Academic and national pride must not be allowed to slow potentially crucial health research.
someone knows more about GIDEON,GPHIN ?
Do they have a webpages, a forum ?
The offlu webpage is a bit disappointing..
http://www.offlu.net/
gs-
Gideon is likely less complete than GenBank or LANL.
NS1, look here:
http://www.setbb.com/fluwiki2/viewtopic.php?t=89&mforum=fluwiki2
do you think I am missing a considerable amount of sequences ?
WHO: Bird Flu Database Should Be Public
By BRADLEY S. KLAPPER The Associated Press Friday, March 17, 2006; 6:37 PM
GENEVA — The U.N. health agency, under criticism for keeping its database on bird flu research out of public view, said some countries and scientists that have contributed their samples and research have yet to agree to share the information.
The password-protected database, details of which were first reported on earlier this month in the journal Science and The Wall Street Journal, was created in 2003 at the request of southeast Asian countries first hit by the deadly H5N1 strain of bird flu, said Dick Thompson, spokesman for infectious diseases at the World Health Organization.
WHO has been urging countries and researchers to allow genetic sequences of the virus stored in the database to be made available publicly, but countries and scientists have so far resisted, Thompson said. He did not name the countries opposed to releasing the information or elaborate on their concerns.
“These are not our viruses and this isn’t our information,” Thompson told The Associated Press.
bumped
do we have an estimate at least, which and how many sequences there are in the secret WHO-database ? Or is this information also secret ?
Just to put things in perspective. I did not speak to the reporter from the Independent in person. He asked me a few questions over the telephone. I was angry that our unconfirmed sequence results were suddenly reported in the Washington Post without an initial statement of our results from the W.H.O. (very unprofessional). The reporter had assumed that the viruses from Turkey had been studied elsewhere. I merely stated that we were the only group that had them at that time. This was not said ‘gleefully’, but was stated as a fact. The team at Mill Hill make all results obtained, both antigenic and genetic freely available and we are as frustrated about the lack of co-operation as you appear to be. As far as the comment about availability to the US; this was said toungue in cheek, and the viruses were despatched to Japan, US, Hong Kong etc within 7 days. Don’t take newspaper articles too seriously
Alan Douglas – at 18:11
We’re a ‘don’t believe everything you hear or read’ lot, Dr. Douglas ;-)
We very much appreciate you writing in. I fully accept your characterization about the news article. I hope you appreciate our concern in return.
The team at Mill Hill make all results obtained, both antigenic and genetic freely available and we are as frustrated about the lack of co-operation as you appear to be.
This is a very important statement, and I’m hopeful this issue can be put to rest at some point in the very near future. Collaboration and transparency, working together, is the only possible way to properly approach this world-wide threat. Experts like you will have to keep us posted as to whether the goals are being met.
We, in return, will need to be patient and not believe everything we read. But we will continue to push for an Open Access approach. If there are ways you think we can help with the “lack of co-operation”, please let us know.
Alan Douglas: “The team at Mill Hill make all results obtained, both antigenic and genetic freely available and we are as frustrated about the lack of co-operation as you appear to be.”
I just did a search of the GenBank nucleotide database, but did not find any sequences from isolates from patients in Turkey. Have you deposited these sequences? If not, why not?
Thanks for addressing this issue.
Dr. Douglas,
Thank you for communicating directly with the Wiki community. This is much appreciated. Whatever we can do to bat down rumours, we are willing to help. Please keep in touch.
See also the thread on The Chikungunya Epidemics and What We Can Learn from Them?
I have made enquiries regarding the recent viruses that we have isolated and sequenced here at Mill Hill. I had no idea that all results were only submitted to W.H.O. and thus a ‘secret database’.Apparently, all novel viruses now are covered by a ‘copyright’ which is held by the originating national laboratiry. Most of this information, especially the regarding sequences from bird isolates, is therefore not even available to us. This is incredinly frustrating as the sequential changes cannot be properly followed. None of this secrecy occurred when I worked in the Influenza centre here and there were only 2 World influenza centres (UK & US). The current situation is a fiasco and highlights the hypocrisy of the title, National Collaborative Centres (collaborative???).
Alan Douglas: Thanks for responding. From your post, I take it that you and the other scientists at Mill Hill would have no objection to depositing H5N1 sequences in GenBank as soon as they are completed? Would you agree to apply the Bermuda Rules to H5N1 sequences?
As I stated previously, I am no longer involved directly with the flu centre. I am lending my expertise by carrying out the isolations etc in the high level containment facility. I am not involved with the global glory hunting that seems prevalent nowadays. I also have nothing to do with the results once obtained. Availability of sequences is down to the originating laboratories in each country, and it seems that it is they who are very ‘protective’. We cannot do anything about this directly, but we can still try to apply moral pressure as often as we can. It’s all a question of diplomacy.
I think I’m confused as to who is blocking the sequences from being deposited at GenBank: Is it Sir John Skehel, Institute Director at Mill Hill or the Director of a lab in Turkey? Pardon my ignorance, but the news stories give conflicting information. For example, this came out today:
WHO expects agreement on system to open up controversial bird flu databas.
Some countries that provide viruses to the database do so with the stipulation that the information not be openly shared, based on concerns outside scientists will swoop in and publish the most exciting results, claiming scientific glory denied their own researchers.
And some of the laboratories in the network which do huge amounts of work for WHO without financial compensation initially balked as well.
Fukuda said the public health needs associated with the H5N1 threat are forcing a change in the longstanding model of research, where scientists kept their data private until publication in a journal.
I realize you may not be able to answer this, but what I’m trying to figure out is who, exactly, is blocking deposit of sequences in GenBank. At Weybridge, Ian Brown has admitted that he has blocked release of most of the H5N1 sequences he has until a paper is published.
As I said before, it seems to be the individual directors of the originating laboratories who are blocking the release of the sequences. It is these people who want to publish papers. It seems that nowadays what was once a routine isolation report is now somehow a serious scientific publication. Sir John Skehel has no influence regarding this matter, and the Influenza centre at Mill Hill is only responsible for receipt and reporting to W.H.O. They, and the originating labs, hold all the diagnostic data. The buck stops there.
They, and the originating labs
Thank you. Very helpful.
Alan Douglas: Thanks for the clarification. From your response, I conclude that Sir John Skehel would have no objection to depositing H5N1 sequences in GenBank immediately after completion.
Now, how do we find out who is the director of the “originating lab” for the Turkish isolates from patients? Anyone know who this is? Is it Dr Neziha Yilmaz? He is listed as the contact person for the National Influenza Center in Turkey. Here is his contact information:
If this is the right person, it would be great if Oric or someone else in Turkey could contact him and find out if he is the one blocking the release of sequences from patients.
Old thread closed to speed Forum access
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