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

[sharon sanders]

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.

[Ronan Kelly]

Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1

Agreed 100%.

[Roehl_JC]

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.

[Sally Furniss]

Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1

Submit to Genbank, please.

[Niko]

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.

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!

[mixin]

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]

Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1

Forgive my ignorance

- 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]

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]

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]

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.

[tropical]

Re: Virus Samples Deposited Into GISAID - FluTrackers Opinion on USA Participation for A/H1N1

So it is something like the difference between Microsoft Windows and an open-source system such as Linux.

Hardly,
Microsoft bugs dont kills ...

[JJackson]

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

[gsgs]

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]

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]

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

• 19 APR 2023
• BYMARTIN ENSERINK, JON COHEN

snip

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