COVID-19 Genomics UK Consortium

COVID-19 Genomics UK

Established	April 2020
Focus	COVID-19 genomic sequencing
Key people	Sharon Peacock
Budget	£20 million[1]
Location	United Kingdom

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^[1][2][3] 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 Alpha variant (at the time, referred to as Variant of Concern 202012/01) in November 2020.^[4] As of January 2021, 45% of all SARS-CoV-2 sequences uploaded to the GISAID sequencing database originated from COG-UK.^[5][6][7]

Strategic Goals[]

Broad sequencing of human pathogenic (disease inducing) viruses serves multiple strategic goals within pandemic response:^[8]

1) It enables emerging new variants of increased transmissibility or severity to be recognized as early as possible. In the case of SARS-CoV-2 Alpha variant, COG-UK reached this target^[4] as a result of international cooperation: Tulio de Oliveira, a computational biologist at the University of KwaZulu-Natal who was involved in the discovery of the SARS-CoV-2 Beta variant ('South African virus variant', N501Y.V2), found indications 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 parts of England, too.^[5]

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 Immune escape variants, and earlier development or adjustment of vaccines that cover strong immunization against these escape-mutations becomes possible. Similar statements hold for the development and usage of monoclonal antibodies. These are only two examples for which 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 … .”^[1]

3) Whole genome sequencing improves the certainty about chains of transmission. A suspected case of contagion between two people can only be confirmed if the viruses infecting these two people 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."^{[4] [9]}

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,^[1] administered by UKRI.^{[citation needed]} 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.^[10]

Partners in the consortium include the Wellcome Sanger Institute, the Quadram Institute, and 15 more^[11] 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.^[12]

Key people[]

The executive director of the consortium is Sharon Peacock, a professor and microbiologist at Cambridge University.^[13][5] 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.^[14]

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).^[15] The SARS-CoV-2 Alpha variant was detected in November 2020 by the COG-UK consortium.^[4][16] The variant is the subject of ongoing investigations by the UK public health agencies, coordinated by Public Health England and supported by COG-UK.^[17] The number of sequences COG-UK have uploaded to GISAID is just under 5% of all UK COVID-19 cases, compared to 3.2% for the United States and 60% for Australia.^[5] Approximately 60% of these were sequenced at the Wellcome Sanger Institute.^[13] 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'.^[18]

Selected publications[]

• Lo, Stephanie W.; Jamrozy, Dorota (20 July 2020). "Genomics and epidemiological surveillance". Nature Reviews. Microbiology: 1. doi:10.1038/s41579-020-0421-0. ISSN 1740-1526. PMC 7371787. PMID 32690878.
• Meredith, Luke W.; Hamilton, William L.; Warne, Ben; Houldcroft, Charlotte J.; Hosmillo, Myra; Jahun, Aminu S.; Curran, Martin D.; Parmar, Surendra; Caller, Laura G.; Caddy, Sarah L.; Khokhar, Fahad A. (1 November 2020). "Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study". The Lancet Infectious Diseases. 20 (11): 1263–1271. doi:10.1016/S1473-3099(20)30562-4. ISSN 1473-3099. PMID 32679081.
• Rambaut, Andrew; Holmes, Edward C.; O’Toole, Áine; Hill, Verity; McCrone, John T.; Ruis, Christopher; du Plessis, Louis; Pybus, Oliver G. (November 2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. ISSN 2058-5276.
• da Silva Filipe, Ana; Shepherd, James G.; Williams, Thomas; Hughes, Joseph; Aranday-Cortes, Elihu; Asamaphan, Patawee; Ashraf, Shirin; Balcazar, Carlos; Brunker, Kirstyn; Campbell, Alasdair; Carmichael, Stephen (January 2021). "Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland". Nature Microbiology. 6 (1): 112–122. doi:10.1038/s41564-020-00838-z. ISSN 2058-5276.
• Thomson, Emma C.; Rosen, Laura E.; Shepherd, James G.; Spreafico, Roberto; da Silva Filipe, Ana; Wojcechowskyj, Jason A.; Davis, Chris; Piccoli, Luca; Pascall, David J.; Dillen, Josh; Lytras, Spyros (January 2021). "Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity". Cell. doi:10.1016/j.cell.2021.01.037. ISSN 0092-8674. PMC 7843029.

References[]

External links[]

• Official website