We sequenced 1500 people with Coronavirus in #Norfolk over the 1st wave & have a paper out today with lots of interesting findings: medrxiv.org/content/10.110…
We found 100 different lineages in circulation in Norfolk, a region of about 1 million people.
Interestingly we found 16 lineages in healthcare workers (& families) which were not observed in patients or in community care. This indicates infection control measures were working.
We sequenced 42% of all Pillar 1 cases, those would have been people who got tested via their hospital, doctor, in care facilities, and staff (plus families of staff).
When I last checked only 5 countries, out of 103, had sequenced more SARS-CoV-2 genomes than have been sequenced in Norfolk for this paper. The UK is the world leader in genomic epidemiology thanks to the enormous effort of over 500 people in @CovidGenomicsUK
From April onwards virtually all the samples in Norfolk had the D614G mutation which is associated with increased transmissibility.
We used the data to discover a lineage which was only found in 6 care facilities, indicating inter care home transmission. Knowing this will help us change how we work for the 2nd wave.
In under 24 hours we sequenced samples from a factory outbreak & confirmed they were all related. It appears to be a recent introduction to the UK from mainland Europe. We are now tracking its spread through the UK.
This work is the combined efforts of over 40 people(@ae_mather @thanhleviet @leomrtns @lizziemeadows @happy_khan @Gemma_L_Kay @tweakyaustin @ThisIsAlp ...) in the East of England lead by @Justin_OGrady & over 500 people in the @CovidGenomicsUK consortium.
A key link was the #NRPBiorepository which allowed us rapidly get anonymised metadata for positive cases, providing context for the genomic data
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