Research Question: (RQ01):
COG-UK: Can study of the whole virus genome enable scientists to monitor changes at a national scale, reveal how the virus is spreading and whether different strains are emerging?
Ewan Harrison, Michael Chapman, John Danesh
Research Question Narrative:
COVID-19 Genomics UK (COG-UK) Consortium Samples from patients with confirmed cases of COVID-19 will be sent across a network of sequencing centres, which will decode all the genetic information in them.
Support to Answer Question:
Ewan Harrison, HDR UK Cambridge, HDR UK fellow
Intended Research Outcomes:
Viral genome insights to inform clinical care
SAGE Priority Area:
SAGE Priority Question:
Research Funnel Stage:
7 - Analysis, User Management
WHO Priority Area:
Virus natural history, transmission and diagnostics
Data Sourcing Requirements:
Expected data requested: Population clinical datasets (e.g. HES)
BC | INSIGHT platform at Southampton General Hospital - reporting COVID data to PHE contact paul smith - email@example.com
Progress So Far:
Project funding just approved (£20m; UKRI and Wellcome) Challenge: Data linkage and research environment
01/06/2020 Updates and reports from COG-UK can be found via link above.
27/05/2020 Since March 2020, in only eight weeks, COG-UK has generated more than 24,000 SARS-CoV genome sequences from UK samples. These sequences have been analysed and been made available in real time, and collectively represent ~10% of all reported cases in the UK, and greater than half of the total number of SARS-CoV-2 genomes reported globally.
COG-UK reports have covered the number of introductions into the UK, transmission in hospitals and nursing homes, calculation of R, the contribution of spike protein mutations, and variation in diagnostic test primer binding sites.
Major progress has been made in combining SARS-CoV-2 genome data with detailed electronic health record data captured by the NHS and public health agencies. This data will enable researchers to investigate if genetic changes affect how easily the virus is passed on and the severity of the symptoms it causes. Linkage with other large COVID-19 cohorts such as GenOMICC is underway, enabling combined analysis of host and viral genomes.
28/04/2020: 10,567 Viral Sequences now available online This is the largest national repository of viral genome sequences in the world. Continuing to explore linkage to clinical data in each devolved nation.
PPIE Activities So Far:
Hub for data sharing and interoperability
HDR UK community members with skill & will to contribute: firstname.lastname@example.org
Original content: https://web.www.healthdatagateway.org/project/190001