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 '20 at 8:02
  • $\begingroup$ @reuns i think this is a reasonable answer that you could add, probably more helpful than mine. $\endgroup$ – Maximilian Press Apr 19 '20 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. $\endgroup$ – Steve Crawford Apr 19 '20 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 '20 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. $\endgroup$ – Steve Crawford Apr 20 '20 at 16:01

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. $\endgroup$ – Steve Crawford Apr 19 '20 at 17:52

EDIT : the UK put their 10000 sequences (!) there https://www.cogconsortium.uk/data/

Old answer :

At first : play with the nextstrain tree(s), containing most relevant information. http://data.nextstrain.org/ncov_global.json

Then, there you can find the 5067 high quality sequences I extracted from the chinese server one week ago, with most metadata (need to add the sequencing technology, illumina or nanopore). As I said it doesn't take the N in account (fully ambiguous nucleotides), but for the sequence to be classified as high it needs to have few such N. The probability that some N appears at a relevant mutation site is low, but it can happen when looking at to few sequences from a single country (to understand how the epidemic spread). https://urlz.fr/csSg

Gisaid refuses to make the sequences at disposal.

Hope more people will help to build a clean free database.


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