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?
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.
- Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank (2020) *
* Disclaimer: I have worked on this project.
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.