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I have downloaded and analysed the sequences of 832 complete samples from the European Nucleotide Archive but I cannot find a single one that was from the UK. I have also tried Genbank and they do not seem to have any UK ones either. I'm still waiting for my logon for Gisaid - looks like they may have some. Is there anywhere else I can try?

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    $\begingroup$ European Nucleotide Archive has only the genbank sequences but they have a link to download them all. Gisaid refuses to make the sequences at disposal. On bigd.big.ac.cn/ncov/variation/analysis bigd.big.ac.cn/gbrowse/2019-nCoV/… you can find all the high quality sequences in a diff form, except they didn't take the N in account. $\endgroup$
    – reuns
    Apr 19, 2020 at 8:02
  • $\begingroup$ @reuns i think this is a reasonable answer that you could add, probably more helpful than mine. $\endgroup$ Apr 19, 2020 at 15:14
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    $\begingroup$ Thanks for the bigd link. Over 10,000 sequences but unfortunately most of them are stored on Gisaid and they don't let you download these. I thought this information would be in the public domain. $\endgroup$ Apr 19, 2020 at 17:42
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    $\begingroup$ GISAID certainly does allow downloads. You need to register and follow their guidelines for acknowledgement if you publish, but it’s completely false to say they don’t allow downloads. $\endgroup$
    – iayork
    Apr 20, 2020 at 14:54
  • $\begingroup$ Just to clarify, if you go to the bigd link you cannot download any of the sequences held on Gisaid. I'm still waiting to see if my registration for Gisaid gets approved - it's been over a week since I filled in the form. I don't understand why this information is not in the public domain. The irony is that Chine (and most other countries) has been open and shared its genome information with the world, but the UK has not. $\endgroup$ Apr 20, 2020 at 16:01

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Oxford University's Bugbank project is designed to collect SARS-CoV-2 samples (and other microbial cultures) from UK Biobank participants for sequencing. Once completed this data will be available to researchers through the UK Biobank:

We originally developed this system as a pilot study to determine the feasibility of prospective microbiological culture collection from UKB participants to create a microbiological biobank (‘bugbank’) for joint studies of epidemiological, human genetic and pathogen genomic risk factors for infection. In light of the COVID-19 pandemic, we have repurposed the system to provide near-to-real-time data on SARS-CoV-2 positive and negative test results for UKB participants.


* Disclaimer: I have worked on this project.

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    $\begingroup$ Thanks for this. Unfortunately I don't meet the admission criteria - I'm not a researcher, just a curious member of the public. $\endgroup$ Apr 19, 2020 at 17:52

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