sharon sanders
Editor-in-Chief & President
We find it unacceptable that US health agencies may submit biological samples into the GISAID data base without also submitting the same into the Genbank data base.
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Virus Samples Deposited Into GenBank vs. GISAID - FluTrackers Opinion on USA gov participation - Updated
- Thread starter sharon sanders
- Start date
Ronan Kelly
Retired 2020
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Agreed 100%.
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Agreed 100%.
Roehl_JC
Moderator
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
ditto
change we can believe in
cooperation and transparency and realtime information sharing
please provide all data sequences to GenBank too. :applause:
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
ditto
change we can believe in
cooperation and transparency and realtime information sharing
please provide all data sequences to GenBank too. :applause:
Sally Furniss
Well-known member
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Submit to Genbank, please.
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Submit to Genbank, please.
Niko
Editor, Senior Moderator
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
double ditto
This is an outrage. If public funds are used for viral samples, tests and/or studies, results should be released immediately.
Thank you!
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
double ditto
This is an outrage. If public funds are used for viral samples, tests and/or studies, results should be released immediately.
Thank you!
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Thank you FluTrackers for taking a stand on this issue.
I totally agree.
AND release those that are deposited at GISAID.
After all, this is everyone's pandemic.
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Thank you FluTrackers for taking a stand on this issue.
I totally agree.
AND release those that are deposited at GISAID.
After all, this is everyone's pandemic.
Gert van der Hoek
In Memoriam - Editor, Senior Moderator
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Forgive my ignorance
em
- What is the difference between GISAID and Genbank?
- Why would it be important to publish the sequences at Genbank too?
- Why would one choose to publish at GISAID and not at Genbank?
- Do we know an official statement explaining the current policy?
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Forgive my ignorance
em- What is the difference between GISAID and Genbank?
- Why would it be important to publish the sequences at Genbank too?
- Why would one choose to publish at GISAID and not at Genbank?
- Do we know an official statement explaining the current policy?
sharon sanders
Editor-in-Chief & President
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
GISAID does not allow public posting of sequences that are on deposit with them.
Genbank does.
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
GISAID does not allow public posting of sequences that are on deposit with them.
Genbank does.
Gert van der Hoek
In Memoriam - Editor, Senior Moderator
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Thank you.
So it is something like the difference between Microsoft Windows and an open-source system such as Linux.
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Thank you.
So it is something like the difference between Microsoft Windows and an open-source system such as Linux.
sharon sanders
Editor-in-Chief & President
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Yes.
Only very few "flubies" have access to the GISAID data base and since they can not publicly post the actual sequence data this creates an information vacuum. Anyone can join and then share the information with anyone else who has subscribed. GISAID has this protocol in place to encourage researchers and countries etc. to place their sequences for viewing. Evidently these entities are concerned about patent protection and the policy forbidding the public posting of the sequences gives them some level of comfort in this regard.
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Yes.
Only very few "flubies" have access to the GISAID data base and since they can not publicly post the actual sequence data this creates an information vacuum. Anyone can join and then share the information with anyone else who has subscribed. GISAID has this protocol in place to encourage researchers and countries etc. to place their sequences for viewing. Evidently these entities are concerned about patent protection and the policy forbidding the public posting of the sequences gives them some level of comfort in this regard.
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Microsoft bugs dont kills ... :flask:
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Hardly,
Microsoft bugs dont kills ... :flask:
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
When attempts were made to get open sequences before we had an unseemly blame game. The WHO said they would like to but could not without permission from the Nation States, many of the States said it was not us but the sequencing labs' needed to be able to publish (the bread and butter of academic promotion) before general release and the labs said they need permission of the States. There was an internet petition for sequence release and Ilaria Capua started a petition of notables among the sequencing labs (link) - but all to no avail as it was never possible to pin-point the exact source(s) of the blockage.
However here we have one country sequencing data collected from their own citizens on there own territory paid for by their own tax payers. This time it should be a lot easier to pin down who is trying to block release. The real reason we may actually succeed this time is not the above but the fact your public is half awake to the dangers of flu. The only way this will work is if your Congressional representatives think there is political mileage in it. There is a limited window of opportunity, over this flu season, when it is enough of an issue for them to think they can make hay. The attempts to grab the spotlight over the ‘Wall Street grabs vaccine’ non-story shows that there are plenty of politicians and media outlets that might run with it if some sort of critical mass can be achieved.
If you could achieve this it would be a lot easier to shame other nations to follow suite. In the UK our political structures are different and it is very difficult to move MPs to action on anything but very local issues.
I have GSAID and genebank access and it has been very frustrating over the last few days, while I have been trying to make a rational argument on the meaning the Ukrainian sequences, not to be able to post the relevant data to show just how similar many of these sequences are. The risk is if I – or anyone else – goes too far GSAID may tighten up even further or labs will just post to an even more restrictive database.
P.S. Ditto
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
When attempts were made to get open sequences before we had an unseemly blame game. The WHO said they would like to but could not without permission from the Nation States, many of the States said it was not us but the sequencing labs' needed to be able to publish (the bread and butter of academic promotion) before general release and the labs said they need permission of the States. There was an internet petition for sequence release and Ilaria Capua started a petition of notables among the sequencing labs (link) - but all to no avail as it was never possible to pin-point the exact source(s) of the blockage.
However here we have one country sequencing data collected from their own citizens on there own territory paid for by their own tax payers. This time it should be a lot easier to pin down who is trying to block release. The real reason we may actually succeed this time is not the above but the fact your public is half awake to the dangers of flu. The only way this will work is if your Congressional representatives think there is political mileage in it. There is a limited window of opportunity, over this flu season, when it is enough of an issue for them to think they can make hay. The attempts to grab the spotlight over the ‘Wall Street grabs vaccine’ non-story shows that there are plenty of politicians and media outlets that might run with it if some sort of critical mass can be achieved.
If you could achieve this it would be a lot easier to shame other nations to follow suite. In the UK our political structures are different and it is very difficult to move MPs to action on anything but very local issues.
I have GSAID and genebank access and it has been very frustrating over the last few days, while I have been trying to make a rational argument on the meaning the Ukrainian sequences, not to be able to post the relevant data to show just how similar many of these sequences are. The risk is if I – or anyone else – goes too far GSAID may tighten up even further or labs will just post to an even more restrictive database.
P.S. Ditto
Last edited by a moderator:
gsgs
Registered User
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
change the laws, so the submitting lab or country
can publish while keeping the "originality"
I don't understand what the exact legal problem is here.
Maybe someone can expain.
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
change the laws, so the submitting lab or country
can publish while keeping the "originality"
I don't understand what the exact legal problem is here.
Maybe someone can expain.
gsgs
Registered User
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
http://www.nature.com/nature/journal/v461/n7261/full/461168a.html
Rapid release of prepublication data has served the field of genomics well.
Attendees at a workshop in Toronto recommend extending the practice to
other biological data sets.
Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1
http://www.nature.com/nature/journal/v461/n7261/full/461168a.html
Rapid release of prepublication data has served the field of genomics well.
Attendees at a workshop in Toronto recommend extending the practice to
other biological data sets.
sharon sanders
Editor-in-Chief & President
As people can see by the title of this thread, we have had our own "interesting" situation with GISAID. I received odd phone calls and emails.
Now Science has done an intensive investigation into the organization.
https://www.science.org/content/arti...demic-database
CONTROL ISSUES
GISAID offers a safe space to post viral genomes. Peter Bogner, its perplexing creator and overseer, may be jeopardizing its future
Bogner appears to have inflated or outright invented aspects of his higher education and work experience on different versions of his CV, and news stories about him on GISAID’s website have been altered. Bogner also has clashed bitterly with a Swiss research institute over money GISAID owed it.
snip
More troubling, many scientists complain about GISAID’s confusing and arbitrary access procedures, which some say hamper important research. Several virologists say their data stream has been interrupted without an explanation, in apparent retaliation for even mild criticism of GISAID. Marion Koopmans of Erasmus University Medical Center, says she has received multiple calls from Bogner “with a rather intimidating tone.” So have colleagues, she adds. “I have heard similar experiences from quite a few.”
snip
A group led by Kristian Andersen at Scripps Research says it also felt Bogner’s wrath, for a February paper that included a reference suggesting the first SARS-CoV-2 genome revealed to the public was not posted on GISAID—as it has insisted—but on a virology discussion forum. The day the Scripps team published its paper, it lost access to GISAID’s data stream. Gangavarapu, who closely collaborates with the Andersen group, received a text message from Meyers that same day, with a screenshot of the offending reference and the message: “good luck with getting further support. I warned you … .”
snip
In 2020, Duncan MacCannell, chief science officer for CDC’s Office of Advanced Molecular Detection, set up SPHERES, an effort to coordinate SARS-CoV-2 sequencing in labs across the United States. He encouraged SPHERES member labs to post their sequences not just in GISAID, but also in GenBank. In August 2022, MacCannell received a blistering email from the “GISAID Secretariat,” which said it had contacted CDC leadership about him “on the advice of the U.S. Department of State.” A “quick glance at your social media is all one needs to observe your relentless efforts to perpetuate baseless claims that seek to undermine the credibility of GISAID and its staff, and attempts to whittle away at GISAID’s existence,” said the email, which Science obtained from CDC via a FOIA request.
more....
https://www.science.org/content/arti...demic-database
Now Science has done an intensive investigation into the organization.
https://www.science.org/content/arti...demic-database
CONTROL ISSUES
GISAID offers a safe space to post viral genomes. Peter Bogner, its perplexing creator and overseer, may be jeopardizing its future
- 19 APR 2023
- BYMARTIN ENSERINK, JON COHEN
Bogner appears to have inflated or outright invented aspects of his higher education and work experience on different versions of his CV, and news stories about him on GISAID’s website have been altered. Bogner also has clashed bitterly with a Swiss research institute over money GISAID owed it.
snip
More troubling, many scientists complain about GISAID’s confusing and arbitrary access procedures, which some say hamper important research. Several virologists say their data stream has been interrupted without an explanation, in apparent retaliation for even mild criticism of GISAID. Marion Koopmans of Erasmus University Medical Center, says she has received multiple calls from Bogner “with a rather intimidating tone.” So have colleagues, she adds. “I have heard similar experiences from quite a few.”
snip
A group led by Kristian Andersen at Scripps Research says it also felt Bogner’s wrath, for a February paper that included a reference suggesting the first SARS-CoV-2 genome revealed to the public was not posted on GISAID—as it has insisted—but on a virology discussion forum. The day the Scripps team published its paper, it lost access to GISAID’s data stream. Gangavarapu, who closely collaborates with the Andersen group, received a text message from Meyers that same day, with a screenshot of the offending reference and the message: “good luck with getting further support. I warned you … .”
snip
In 2020, Duncan MacCannell, chief science officer for CDC’s Office of Advanced Molecular Detection, set up SPHERES, an effort to coordinate SARS-CoV-2 sequencing in labs across the United States. He encouraged SPHERES member labs to post their sequences not just in GISAID, but also in GenBank. In August 2022, MacCannell received a blistering email from the “GISAID Secretariat,” which said it had contacted CDC leadership about him “on the advice of the U.S. Department of State.” A “quick glance at your social media is all one needs to observe your relentless efforts to perpetuate baseless claims that seek to undermine the credibility of GISAID and its staff, and attempts to whittle away at GISAID’s existence,” said the email, which Science obtained from CDC via a FOIA request.
more....
https://www.science.org/content/arti...demic-database
sharon sanders
Editor-in-Chief & President
Michael Worobey
@MichaelWorobey
·
5h
The overseer of the world's largest repository of SARS-CoV-2 sequences may have used a fake identity to help promote the Chinese government's dubious "it-came-from-imported-frozen-food" explanation for why COVID emerged in China. (Impressive of
@macroliter
to go public.)
4
6
20
2,180
Michael Worobey
@MichaelWorobey
·
5h
This raises all kinds of questions about the integrity of decisions made by Bogner on behalf of Authorized Users of GISAID, as well as its funders, the WHO, and other stakeholders. If Peter Bogner really was using a fictitious "Steve Meyers" to try to steer scientific...
2
10
985
Michael Worobey
@MichaelWorobey
·
5h
consensus on COVID origins towards China's favoured scenario, I hope GISAID's funders, its Scientific Advisory Council, and the WHO will ask him as soon as possible his justification for doing this. Or try to talk to Steve Meyers about it.
sharon sanders
Editor-in-Chief & President
Michael Worobey
@MichaelWorobey
·
5h
The overseer of the world's largest repository of SARS-CoV-2 sequences may have used a fake identity to help promote the Chinese government's dubious "it-came-from-imported-frozen-food" explanation for why COVID emerged in China. (Impressive of
@macroliter
to go public.)
4
6
20
2,180
Michael Worobey
@MichaelWorobey
·
5h
This raises all kinds of questions about the integrity of decisions made by Bogner on behalf of Authorized Users of GISAID, as well as its funders, the WHO, and other stakeholders. If Peter Bogner really was using a fictitious "Steve Meyers" to try to steer scientific...
2
10
985
Michael Worobey
@MichaelWorobey
·
5h
consensus on COVID origins towards China's favoured scenario, I hope GISAID's funders, its Scientific Advisory Council, and the WHO will ask him as soon as possible his justification for doing this. Or try to talk to Steve Meyers about it.
So interesting....
This is the email I sent that broke our relationship with GISAID. I do not post emails without permission so I can not post the response from GISAID but I can characterize it as not good.
From: "FluTrackers" <flutrackers@earthlink.net>
To: "Peter Bogner" <peter@gisaid.org>
Subject: H7N9 Sequences at GISAID
Date: Apr 2, 2013 1:43 PM
Hi Peter,
I was wondering if you could release the H7N9 sequences from China from your GISAID database for wide public distribution. I do not know what permissions you need from the Chinese government but I think it is in their best interest to consider this request.
I also think it is a good public relations move for GISAID that will help to counteract the critics who say that your database is "private".
These sequences are important ones with public health consequences. Not all sequences are alike. Some are generated solely for research purposes. This is not the case here. A wide public airing of all data related to these sequences may actually result in faster and safer treatment options if H7N9 starts to spread among the populations.
I think for humanitarian purposes the data from and about these particular sequences should be "Open Access".
sincerely,
Sharon
------------------------------------------------------------------
Also....
From: "FluTrackers" <flutrackers@earthlink.net>
To: "rebecca garten cdc" <rebecca.garten@cdc.hhs.gov>
Subject: CDC Isolate Submittals to GenBank & GISAID
Date: Feb 26, 2013 8:54 AM
Hi Ms. Garten,
I am writing you to understand what your policy is regarding isolate submittals to GISAID and GenBank.
For instance, it appears that no H3N2 type influenza isolates in the possession of the CDC have been submitted to GenBank so far this year, but there are 18 such submittals at GISAID.
Do you favor GISAID? And why? Is there a CDC/HHS policy about this issue that I can have a link to?
I believe submitting primarily to GISAID, and not GenBank, is not in the spirit of "open access" recently endorsed by the Obama administration: http://www.whitehouse.gov/blog/2013/...unded-research
I am not debating the fine GISAID project. It is worthwhile. However, I believe that the public interest is best served by isolates being submitted to GenBank - in addition to any other data bank in the world.
As a point of courtesy, I disclose that I may publish and/or forward any response to this email.
sincerely,
Sharon Sanders
Editor-in-Chief
FluTrackers.com Inc.
http://www.flutrackers.com/forum/index.php
sharon sanders
Editor-in-Chief & President
I can disclose that I never received any email from the "GISAID Secretariat" or the US state department for suggesting that the CDC deposit sequences in GenBank in addition to GISAID in 2013 - LOL
(see post #15 for the reference)
(see post #15 for the reference)
sharon sanders
Editor-in-Chief & President
Apparently there is quite a shock about the revelations in the article. I believe the writers and contributors 100%.
Circa 2007- 2010:
I was contacted a few times and strongly encouraged to ban off this site someone (let's say Ms. X) who was critical of the policies of GISAID. A personal friend of Ms. X who was also a member of this site, and lived in the middle of the US, was contacted too. Also, a threat was made about how Ms. X lived in the country where the server had been relocated and they better be careful because GISAID had government connections in that country and they knew about this member. Are you kidding me? I did not ban that member.
I received other phone calls. One was to invite me to an infectious disease conference, expenses paid, in Hong Kong. What? I declined. Another offer was to introduce me to the head of the CDC at that time. I also declined this. Also, as I remember there was an invitation to Washington D.C. - I don't quite remember the circumstance of this. I think I was invited there because Santa Monica was a long way to travel to meet Bogner and it was represented to me that GISAID had a small office in the capital. I declined.
Apparently the problem for GISAID was that at the time we had a very high google ranking and when you googled for GISAID, our threads about them appeared on the 1st page.
In addition, I was told of the research into another person who had been formerly posting on this site and that this person had a lot of "problems" as did Ms. X. It was clear to me that GISAID was collecting information about people.
I was also told that the WHO had tried to steal the GISAID server and it was spirited out of Switzerland just in time.
I was really beginning to think....wow....ummm....this is some crazy stuff.
Then I wrote the email in 2013 above and was threatened with legal action. That was the end.
I never said much about this before because FluTrackers was not impacted. I didn't realize the extent of the behavior. I thought these were desperate attempts to get the GISAID project off the ground. I had no idea this behavior was a continuous and long term thing.
Circa 2007- 2010:
I was contacted a few times and strongly encouraged to ban off this site someone (let's say Ms. X) who was critical of the policies of GISAID. A personal friend of Ms. X who was also a member of this site, and lived in the middle of the US, was contacted too. Also, a threat was made about how Ms. X lived in the country where the server had been relocated and they better be careful because GISAID had government connections in that country and they knew about this member. Are you kidding me? I did not ban that member.
I received other phone calls. One was to invite me to an infectious disease conference, expenses paid, in Hong Kong. What? I declined. Another offer was to introduce me to the head of the CDC at that time. I also declined this. Also, as I remember there was an invitation to Washington D.C. - I don't quite remember the circumstance of this. I think I was invited there because Santa Monica was a long way to travel to meet Bogner and it was represented to me that GISAID had a small office in the capital. I declined.
Apparently the problem for GISAID was that at the time we had a very high google ranking and when you googled for GISAID, our threads about them appeared on the 1st page.
In addition, I was told of the research into another person who had been formerly posting on this site and that this person had a lot of "problems" as did Ms. X. It was clear to me that GISAID was collecting information about people.
I was also told that the WHO had tried to steal the GISAID server and it was spirited out of Switzerland just in time.
I was really beginning to think....wow....ummm....this is some crazy stuff.
Then I wrote the email in 2013 above and was threatened with legal action. That was the end.
I never said much about this before because FluTrackers was not impacted. I didn't realize the extent of the behavior. I thought these were desperate attempts to get the GISAID project off the ground. I had no idea this behavior was a continuous and long term thing.
sharon sanders
Editor-in-Chief & President
I want to make a public notice that if I am contacted in the future about any of the information on this thread I may publicly post that correspondence.