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

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

Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. 

The hosts are Dr. Lee Katz from the Centres for Disease Control and Prevention (US), Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Theiagen Genomics (UK) and bring together years of experience in microbial bioinformatics.

The opinions expressed here are our own and do not necessarily reflect the views of Centres for Disease Control and Prevention, University of Oxford or Theiagen Genomics.

Intro music : Werq - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Outro music : Scheming Weasel (faster version) - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Question and comments? microbinfie@gmail.com

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

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