We chat to Justin O'Grady, Andrew Page and Alison Mather about how they went about sequencing 1500 SARS-CoV-2 genomes from one small region in the UK (Norfolk), and how they went about using the data for genomic epidemiology to help get a detailed, near real-time view of the pandemic as it unfolded.
Some of the key points are that in Norfolk and surrounding regions:
100 distinct UK lineages were identified.
16 UK lineages found in key workers were not observed in patients or in community care.
172 genomes from SARS-CoV-2 positive samples sequenced per 100,000 population representing 42.6% of all positive cases.
SARS-CoV-2 genomes from 1035 cases sequenced to a high quality.
Only 5 countries, out of 103, have sequenced more SARS-CoV-2 genomes than have been sequenced in Norfolk for this paper.
Samples covered the entire first wave, March to August 2020.
Stable evolutionary rate of 2 SNPs per month.
D614G mutation is the dominant genotype and associated with increased transmission.
No evidence of reinfection in 42 cases with longitudinal samples.
WGS identified a sublineage associated with care facilities.
WGS ruled out nosocomial outbreaks.
Rapid WGS confirmed the relatedness of cases from an outbreak at a food processing facility.
The manuscript is available from: https://www.medrxiv.org/content/10.1101/2020.09.28.20201475v1
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