Virus Samples Deposited Into GenBank - FluTrackers Opinion on USA Participation for A/H1N1 - Updated

[sharon sanders]

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.)

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6
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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...
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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]

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]

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)

[sharon sanders]

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.

[sharon sanders]

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.

[sharon sanders]

• NEWS EXPLAINER
• 04 May 2023

GISAID in crisis: can the controversial COVID genome database survive?

The most popular repository for sharing SARS-CoV-2 sequence data has come under increasing scrutiny. Scientists and funders around the world must now consider what lies ahead for the open sharing of genome data.

snip


GISAID originally intended to enforce data sharing limits only temporarily. Bogner, an entrepreneur based in Santa Monica, California, and the scientists who first presented the idea stated that the sequences submitted to GISAID would be deposited in fully open data repositories such as GenBank, “with a maximum delay of six months”.

That promise was never fulfilled, however.


snip

The GISAID compliance policy seems to have grey areas, which ultimately raise more questions and doubts,” wrote Scaria and Jolly in a joint statement to Nature.

The Science story describes episodes of scientists losing access to GISAID in apparent retaliation for public criticism of the platform, claims which GISAID refutes. It also discusses Bogner’s unconventional background and financial disputes with a vendor providing services to GISAID. “The revelations in the article are pretty shocking. And I do think that they highlight some real concerns about GISAID, and in particular GISAID’s governance,” says Emma Hodcroft, a molecular epidemiologist at the University of Bern.

GISAID says the organization has “never taken any retaliatory action or imposed suspensions” for any reason other than violations of its terms and conditions. It adds that its processes could be improved: “As part of our steps to address governance and operating structure, we consider it a top priority to ensure a fair process for appeals and address the concerns of our users around suspensions.”

GISAID’s governance page lists a scientific advisory council of 12 people, but it is unclear how the council operates. In practice, according to sources close to the platform, Bogner seems to make most decisions. “If you have massively important data sets that have untransparent governance structures that allow for unpredictable retaliation and erratic behaviour, that’s just not the way that a level playing field should work,” says biologist Amber Hartman Scholz, head of the science policy department at Leibniz Institute DSMZ, a collection of microorganisms and cell cultures, in Brunswick, Germany.

snip


What are the possible ways forward?


Despite the problems, the scientists agree that GISAID is likely to remain an important resource for viral genomes. “It’s in the best interest of public health that GISAID and the innovations it has promoted over the past years survive,” says Brito. Jeremy Kamil, a virologist at LSU Health Shreveport in Louisiana, agrees. “To lose GISAID would be unequivocally a tragedy.”

But if GISAID is to have a future, it requires drastic reform and new leadership, its critics say. “A new and transparent governance structure is required, and one that should not be at the whim of a single individual,” says Holmes. That would translate into having clear criteria on who gets access to the platform and which actions would result in sanctions.

The platform also needs to provide mechanisms for scientists submitting sequences to release their data to public-domain archives if they want to do so, says Sanderson. Furthermore, the scientists urge GISAID to acknowledge when the platform collects data from public data sets and to clearly identify those sequences. Currently, scientists who download data from multiple platforms can’t verify whether they are working with duplicate sequences.

To implement those changes, GISAID would need to ideally bring in outside experts in ethics and governance, says Kamil. That would require Bogner to “hand over the keys and back off”, Kamil says.


more....https://www.nature.com/articles/d41586-023-01517-9

[gsgs]

I remember a long telefone call (>3h) in German
with "Meyer" or such. In 2013 or such.
Basically, he insisted that the sequences were "public"
but mustn't be published ;-)
I could join but had to sign the agreement , which
basically includes to keep sequences secret.
And somehow to talk good about GISAID,
I don't remember exactly.

He was curious about Monotreme and Salzberg, who were
critical about GISAID. They posted an article on GISAID
about Salzberg who later calle it "diatribe"
when he heard about it on twitter in 2021.
Salzberg was a founder of GISAID and not happy
that sequences were not copied to genbank as promised.
I had a small wikipedia comment about
GISAID controversy, which was edited
and removed soon later. I had the impression
GISAID wanted to know my connections, my organisation ...
luckily there was none - amateur-sequencer ;-)

However, I think that GISAID apparently became quite useful
the last years , better than genbank, with new features
to organise the data.

They could still copy the sequences to genbank
and keep some "copyright" on those features and
data presentation , why not ?!

[sharon sanders]

Again - public notice: I may publicly publish any correspondence and/or contact that I receive in regard to this thread.

[sharon sanders]

FAFO Department:

Looks like there is a new database to share human virus pathogen genomic data.


"Welcome to Pathoplexus!

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

snip

Pathoplexus is a public pathogen sequence and metadata database built

to provide a transparent platform for sharing pathogen genome data,

to foster collaboration, empower scientific discoveries, and assist in swift public health responses,

to serve as a steward of community data, owing its utility to its users,

to operate in a transparent manner, seeking feedback from the community and welcoming both commendations and critiques,

to maximize the sharing and utility of pathogen genomic data in order to benefit research and public health."

https://pathoplexus.org/

[sharon sanders]

New, scientist-run virus database vows to be transparently run and simple to use

Pathoplexus is starting with sequences for Ebola strains and two other risky viruses

• 29 Aug 2024
• 3:35 PM ET
• ByJon Cohen

During the COVID-19 pandemic, researchers had sharp complaints about the main database for sharing SARS-CoV-2 sequences and its overseer, a controlling, secretive businessman with no formal scientific training and a checkered past. Now, a small band of scientists has launched an open-source database for some of the world’s most dangerous viruses that they say will be run by the very researchers who sequence the pathogens and analyze their genomes.

Called Pathoplexus, the database launched this week at first will focus on the Sudan and Zaire strains of Ebola virus, as well as Crimean-Congo hemorrhagic fever virus and West Nile virus. Like similar databases, it hopes to help communities derail outbreaks before they grow, and, if that fails, better respond to epidemics and pandemics. “We believe that building trust through transparency is essential for encouraging broader participation in data sharing,” says Pathoplexus co-founder Anderson Fernandes de Brito, a computational biologist at the University of de São Paulo.

But Pathoplexus aims to stand apart in other ways—especially compared with the Global Initiative on Sharing All Influenza Data (GISAID) database, which has become a central repository of sequences for the viruses that cause COVID-19, influenza, mpox, pneumonia, chikungunya, dengue, and Zika. GISAID has been harshly criticized for concealing its finances and governance, and several scientists have complained about its founder, erstwhile businessman Peter Bogner, and his representatives reprimanding them for how they use the database and even cutting off access during disputes.

more.... https://www.science.org/content/arti...and-simple-use