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 Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19 (coronavirus disease 2019), the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus previously had a ...

as part of

COVID-19 pandemic The COVID-19 pandemic, also known as the coronavirus pandemic, is an ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The novel virus was first identif ...

response. The consortium comprises the UK's four public health agencies, National Health Service organisations, academic partners and the

Wellcome Sanger Institute The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust. It is located on the Wellcome Ge ...

. The consortium is known for first identifying the

SARS-CoV-2 Alpha variant The Alpha variant (B.1.1.7) was a Variants of SARS-CoV-2, SARS-CoV-2 variant of concern. It was estimated to be 40–80% more Transmission (medicine), transmissible than the Wild type, wild-type SARS-CoV-2 (with most estimates occupying the ...

(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 the

GISAID GISAID (Global Initiative on Sharing Avian Influenza Data) is a global science initiative and primary source established in 2008 that provides open access to genomic data of influenza viruses and the coronavirus responsible for the COVID-19 pand ...

sequencing database originated from COG-UK. In April 2021, COG-UK began the planned transition of sequencing to a national service, with completion by September 2021. COG-UK have stated that their priorities following this transition are data linkage, research and international training.

Impact

The early and large-scale coordinated national sequencing of SARS-CoV-2 viral genomes, along with the open and rapid sharing of genomic data, had the following impact on the first 12 months of the COVID-19 pandemic response: # Enabling the identification and monitoring of "Variants of Concern" and "Variants under Investigation" to inform public health actions and policy decisions. # Tracking the introduction and spread of COVID-19 to inform border control, outbreak management and public health policies. # Facilitating key UK COVID-19 studies: #* The COG-UK HOCI (Hospital-Onset COVID-19 Infections) study #* The Office of National Statistics (ONS) COVID-19 Infection Survey (CIS) #* The Real-time Assessment of Community Transmission (REACT) Study #* The Vivaldi study #* The Oxford Vaccine trial #* The Novavax Vaccine trial # Furthering understanding of the biology and evolution of the SARS-CoV-2 virus to guide treatments, vaccine development and diagnostics. # Boosting the pandemic response through rapid release of genome data and the development of efficient and cost-effective sequencing protocols and open-access public data analysis tools. In April 2021, COG-UK announced their strategic priorities for the following 12 months: # To enhance the value of viral genome sequence data through more extensive data linkage, including human genome data and clinical datasets # To further advance research on SARS-CoV-2 transmission, variants, methods and analysis tools # To coordinate a global SARS-CoV-2 genomics training programme

Structure

COG-UK is supported by £20 million funding from the

Department of Health and Social Care The Department of Health and Social Care (DHSC) is a department of His Majesty's Government responsible for government policy on health and adult social care matters in England, along with a few elements of the same matters which are not otherwis ...

UK Research and Innovation UK Research and Innovation (UKRI) is a non-departmental public body of the Government of the United Kingdom that directs research and innovation funding, funded through the science budget of the Department for Business, Energy and Industrial Str ...

(UKRI), and the

, 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

, the

Quadram Institute The Quadram Institute is a centre for food and health research, combining Quadram Institute Bioscience (formerly the Institute of Food Research), the Norfolk and Norwich University Hospitals’ endoscopy centre and aspects of the University ...

, and 15 more universities including

Queen's University Belfast , mottoeng = For so much, what shall we give back? , top_free_label = , top_free = , top_free_label1 = , top_free1 = , top_free_label2 = , top_free2 = , established = , closed = , type = Public research university , parent = ...

, the

University of Birmingham , mottoeng = Through efforts to heights , established = 1825 – Birmingham School of Medicine and Surgery1836 – Birmingham Royal School of Medicine and Surgery1843 – Queen's College1875 – Mason Science College1898 – Mason Univers ...

Cardiff University , latin_name = , image_name = Shield of the University of Cardiff.svg , image_size = 150px , caption = Coat of arms of Cardiff University , motto = cy, Gwirionedd, Undod a Chytgord , mottoeng = Truth, Unity and Concord , established = 1 ...

, the

University of Cambridge , mottoeng = Literal: From here, light and sacred draughts. Non literal: From this place, we gain enlightenment and precious knowledge. , established = , other_name = The Chancellor, Masters and Schola ...

, the

University of Edinburgh The University of Edinburgh ( sco, University o Edinburgh, gd, Oilthigh Dhùn Èideann; abbreviated as ''Edin.'' in post-nominals) is a public research university based in Edinburgh, Scotland. Granted a royal charter by King James VI in 15 ...

, the

University of Exeter The University of Exeter is a public university , public research university in Exeter, Devon, England, United Kingdom. Its predecessor institutions, St Luke's College, Exeter School of Science, Exeter School of Art, and the Camborne School of Min ...

, the

University of Glasgow , image = UofG Coat of Arms.png , image_size = 150px , caption = Coat of arms Flag , latin_name = Universitas Glasguensis , motto = la, Via, Veritas, Vita , ...

, the

University of Liverpool , mottoeng = These days of peace foster learning , established = 1881 – University College Liverpool1884 – affiliated to the federal Victoria Universityhttp://www.legislation.gov.uk/ukla/2004/4 University of Manchester Act 200 ...

Northumbria University , mottoeng = A lifetime of learning , established = 1877 - Rutherford College of Technology1969 - Newcastle Polytechnic1992 - gained university status , type = Public , budget = � ...

, the

University of Nottingham The University of Nottingham is a public university, public research university in Nottingham, United Kingdom. It was founded as University College Nottingham in 1881, and was granted a royal charter in 1948. The University of Nottingham belongs t ...

, the

University of Oxford , mottoeng = The Lord is my light , established = , endowment = £6.1 billion (including colleges) (2019) , budget = £2.145 billion (2019–20) , chancellor ...

, the

University of Portsmouth The University of Portsmouth is a public university in Portsmouth, England. It is one of only four universities in the South East England, South East of England rated as Gold in the Government's Teaching Excellence Framework. With approximately 28 ...

University College London , mottoeng = Let all come who by merit deserve the most reward , established = , type = Public research university , endowment = £143 million (2020) , budget = ...

Imperial College London Imperial College London (legally Imperial College of Science, Technology and Medicine) is a public research university in London, United Kingdom. Its history began with Prince Albert, consort of Queen Victoria, who developed his vision for a cu ...

and the

University of Sheffield , mottoeng = To discover the causes of things , established = – University of SheffieldPredecessor institutions: – Sheffield Medical School – Firth College – Sheffield Technical School – University College of Sheffield , type = Pu ...

Key person

The executive director of the consortium is

Sharon Peacock Sharon Jayne Peacock (born 24 March 1959) is a British microbiologist who is Professor of Public Health and Microbiology in the Department of Medicine at the University of Cambridge. Peacock also sits on Cambridge University Council. Peacock ...

, a professor and microbiologist at

Cambridge University , mottoeng = Literal: From here, light and sacred draughts. Non literal: From this place, we gain enlightenment and precious knowledge. , established = , other_name = The Chancellor, Masters and Schola ...

. From the start of the pandemic to September 2021, Peacock was on a part-time secondment to

Public Health England Public Health England (PHE) was an executive agency of the Department of Health and Social Care in England which began operating on 1 April 2013 to protect and improve health and wellbeing and reduce health inequalities. Its formation came as a ...

as Director of Science, where she focused 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 The Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) is a software tool developed by Dr. Áine O'Toole and members of the Andrew Rambaut laboratory, with an associated web application developed by the Centre for Genomic Patho ...

(PANGOLIN) and th
COG-UK Mutation Explorer
The

was detected in November 2020 by the COG-UK consortium and the variant became the subject of ongoing investigations by the UK public health agencies, coordinated by

and supported by COG-UK. By December 2020, the number of sequences uploaded to

by COG-UK was just under 5% of all UK COVID-19 cases, compared to 3.2% for the

United States The United States of America (U.S.A. or USA), commonly known as the United States (U.S. or US) or America, is a country primarily located in North America. It consists of 50 states, a federal district, five major unincorporated territorie ...

and 60% for

Australia Australia, officially the Commonwealth of Australia, is a Sovereign state, sovereign country comprising the mainland of the Australia (continent), Australian continent, the island of Tasmania, and numerous List of islands of Australia, sma ...

. Approximately 60% of these were sequenced at the

and the COG-UK consortium was reported to have understood 'the genetic history of more than 150,000 samples of SARS-CoV-2 virus'. According to the COG-UK website, by December 2021, the UK had sequenced over 1.8 million SARS-CoV-2 genomes.

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 An International Standard Serial Number (ISSN) is an eight-digit serial number used to uniquely identify a serial publication, such as a magazine. The ISSN is especially helpful in distinguishing between serials with the same title. ISSNs ...

1740-1526. PMC&nbs
7371787

PMID PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintain the ...

&nbs
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.

1473-3099.

&nbs
32679081
* 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. * Emary, Katherine R. W.; Golubchik, Tanya; Aley, Parvinder K.; Ariani, Cristina V.; Angus, Brian; Bibi, Sagida; Blane, Beth; Bonsall, David; Cicconi, Paola; Charlton, Sue; Clutterbuck, Elizabeth A. (10 April 2021). "Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial". ''The Lancet''. 397 (10282): 1351–1362. doi:10.1016/S0140-6736(21)00628-0.

0140-6736. PMC 8009612.

33798499. * Nicholls, Samuel M.; Poplawski, Radoslaw; Bull, Matthew J.; Underwood, Anthony; Chapman, Michael; Abu-Dahab, Khalil; Taylor, Ben; Colquhoun, Rachel M.; Rowe, Will P. M.; Jackson, Ben; Hill, Verity (1 July 2021). "CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance". ''Genome Biology''. 22 (1): 196. doi:10.1186/s13059-021-02395-y.

1474-760X. PMC 8247108.

34210356. * Vöhringer, Harald S.; Sanderson, Theo; Sinnott, Matthew; De Maio, Nicola; Nguyen, Thuy; Goater, Richard; Schwach, Frank; Harrison, Ian; Hellewell, Joel; Ariani, Cristina V.; Gonçalves, Sonia (December 2021). "Genomic reconstruction of the SARS-CoV-2 epidemic in England". ''Nature''. 600 (7889): 506–511. doi:10.1038/s41586-021-04069-y.

1476-4687. PMC 8674138.

34649268.

References

External links

* {{COVID-19 pandemic in the United Kingdom, Crown Dependencies and British Overseas Territories COVID-19 pandemic in the United Kingdom 2020 establishments in the United Kingdom College and university associations and consortia in the United Kingdom Genetics in the United Kingdom Genetics or genomics research institutions Medical responses to the COVID-19 pandemic Organizations established for the COVID-19 pandemic Technology consortia United Kingdom responses to the COVID-19 pandemic