31 Large scale sequencing of SARS-CoV-2 genomes from one region

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