COVID-19 Genomics UK Consortium

The COVID-19 Genomics UK Consortium (COG-UK) is a group of public health agencies and academic institutions in the United Kingdom created in April 2020 to collect, sequence and analyse genomes of SARS-CoV-2 as part of COVID-19 pandemic response. The consortium comprises the UK's four public health agencies, National Health Service organisations, academic partners and the Wellcome Sanger Institute. The consortium is known for first identifying the SARS-CoV-2 Lineage B.1.1.7 (at the time, referred to as Variant of Concern 202012/01) in November 2020. As of January 2021, 45% of all SARS-CoV-2 sequences uploaded to public databases originate from COG-UK.
Strategic Goals.
Broad sequencing of human pathogenic (disease inducing) viruses serves multiple strategic goals within pandemic response:
1) Emerging new variants of increased transmissibility or severity shall be recognized as early as possible. In the case of the „Kent Variant“ Lineage B.1.1.7 (also/formerly named VOC-202012/01), COG-UK reached this target as a result of international cooperation:
Tulio de Oliveira, a scientist who was involved in the discovery of the South African virus variant N501Y.V2, found incidence that the N501Y mutation accelerates the virus' spread, and shared his findings with Andrew Rambaut. Rambaut immediately searched the British COG-UK data and found the same point mutation in RNA genomes from East Anglia(?), and the English data supported Oliveira's findings — 501Y rapidly became more frequent (as opposed to 501N) in England, too.
Soon, a strict lockdown in the region including Greater London was issued. This probably helped to prevent even more serious consequences of the epidemic. 
2) This method can improve the rapid discovery of emergent Immun-Escape-Variants, and earlier development of vaccines that cover strong immunization against these escape-mutations comes into reach. Similar statements hold for the development and usage of monoclonal antibodies. These are only two examples when decisions about therapy and prevention may depend on the specific virus strain. Patrick Vallance said: “Genomic sequencing … can also help guide treatments in the future … .”
3) Whole genome sequencing improves the certainty about chains of transmission. A suspected case of contagion between two people can only be true if their viruses are identical or nearly identical. In the case of new emerging viruses such as SARS-CoV-2 these data can help to establish knowledge about the routes of transmission, which is vital to guide infectious disease policy-making and for defining the questions for contact tracing.
Sharon Peacock said “Mutations are expected and are a natural part of evolution. Many thousands of mutations have already arisen, and the vast majority have no effect on the virus but can be useful as a barcode to monitor outbreaks.”
Structure.
COG-UK is supported by £20 million funding from the Department of Health and Social Care, UK Research and Innovation (UKRI), and the Wellcome Sanger Institute, administered by UKRI. The consortium was also backed by the Department of Health and Social Care's Testing Innovation Fund on 16 November 2020 to facilitate the genome sequencing capacity needed to meet the increasing number of COVID-19 cases in the UK over the winter period.
Partners in the consortium include the Wellcome Sanger Institute, the Quadram Institute, and 15 more universities including Queen's University Belfast, the University of Birmingham, Cardiff University, the University of Cambridge, the University of Edinburgh, the University of Exeter, the University of Glasgow, the University of Liverpool, Northumbria University, the University of Nottingham, the University of Oxford, the University of Portsmouth, University College London, Imperial College London and the University of Sheffield.
Key people.
The executive director of the consortium is Sharon Peacock, a professor and microbiologist at Cambridge University. Peacock is also on a part-time secondment to Public Health England as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK.
Developments.
During the COVID-19 pandemic, tools developed by the COG-UK consortium have been widely used, including, for example Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN). The SARS-CoV-2 Lineage B.1.1.7 (originally termed Variant of Concern 202012/01) was detected in November 2020 by the COG-UK consortium. The variant is the subject of ongoing investigations by the UK public health agencies, coordinated by Public Health England and supported by COG-UK. The number of sequences COG-UK have uploaded to GISAID is just under 5% of all UK coronavirus infections, compared to 3.2% for the United States and 60% for Australia.
Approximately 60% of these were sequenced at the Wellcome Sanger Institute. By December 2020, the COG-UK consortium was reported to have understood 'the genetic history of more than 150,000 samples of Sars-Cov-2 virus'.