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Inspired by amateur variant hunters, I would like to join the Pango lineage proposal community and help contribute to variant surveillance.

However, I cannot seem to get access to GISAID, the platform that exclusively hosts a large share of SARS-CoV-2 sequences from around the world.

I applied/registered for an account back in summer 2022 (almost a year ago) using this form: https://gisaid.org/register/

But since then, nothing has happened. I have send an email and filled out the contact form on the website but never heard back.

I am very confused how GISAID can say they are a "public" database, while at the same time not giving accounts to people like me, not even responding to emails.

How does everyone else get access? Is there a secret email you need to contact? Or do you need to pay? I've read here which describes the founder of GISAID in detail.

Any help would be greatly appreciated!

M__
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AppleBees
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1 Answers1

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I've got a GISAID account and it's subject to an approval process. It was pretty simple and is awarded quickly. There are definitely no fees needed. I personally didn't see the advantages over NCBI's really very impressive SARS-CoV-2 database system and thats what I'd recommend.

Their resource is here: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049&ids=MZ039713%20MZ039682%20OV522182%20

Its perfect for interrogation, it has the full spectrum of epidemiological metadata, and further details are in this post here:

How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?

The Science journal page seemed a very good write up of GISAID BTW.

If you are wanting GISAID for networking, thats a bit tricky because NCBI is not going to do that. You can reapply for GISAID access, but at the time I was much more impressed by NCBI. The speed at which NCBI produced an awesome database was truly jaw-dropping and they'd implemented full pangolineages classification at an early stage. Thus I just use NCBI.

M__
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  • Thanks for the edit @gringer, much appreciated. ".. it has all the data" is good interpretation of what I wrote, but my writing wasn't clear. Specifically, "it has all the epidemiological metadata" is what I intended to say. – M__ May 19 '23 at 21:53