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[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]

COVID-19 Genomics UK
New COG-UK logo.jpg
EstablishedApril 2020
FocusCOVID-19 genomic sequencing
Key peopleSharon Peacock
Budget£20 million[1]
Location

In April 2021, COG-UK began the planned transition of sequencing to a national service, with completion by September 2021.[8] COG-UK have stated that their priorities following this transition are data linkage, research and international training.[9]

ImpactEdit

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:[10]

  1. Enabling the identification and monitoring of “Variants of Concern” and “Variants under Investigation” to inform public health actions and policy decisions.[5]
  2. Tracking the introduction and spread of COVID-19 to inform border control, outbreak management and public health policies.[11]
  3. Facilitating key UK COVID-19 studies:
    • The COG-UK HOCI (Hospital-Onset COVID-19 Infections) study [12]
    • The Office of National Statistics (ONS) COVID-19 Infection Survey (CIS) [13]
    • The Real-time Assessment of Community Transmission (REACT) Study [14]
    • The Vivaldi study [15]
    • The Oxford Vaccine trial [16]
    • The Novavax Vaccine trial [17]
  4. Furthering understanding of the biology and evolution of the SARS-CoV-2 virus to guide treatments, vaccine development and diagnostics.[18]
  5. 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.[19]

In April 2021, COG-UK announced their strategic priorities for the following 12 months: [9]

  1. To enhance the value of viral genome sequence data through more extensive data linkage, including human genome data and clinical datasets
  2. To further advance research on SARS-CoV-2 transmission, variants, methods and analysis tools
  3. To coordinate a global SARS-CoV-2 genomics training programme

StructureEdit

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.[20]

Partners in the consortium include the Wellcome Sanger Institute, the Quadram Institute, and 15 more[21] 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.[22]

Key peopleEdit

The executive director of the consortium is Sharon Peacock, a professor and microbiologist at Cambridge University.[23][5] From the start of the pandemic to September 2021, Peacock was on a part-time secondment to Public Health England as Director of Science, where she focused on the development of pathogen sequencing through COG-UK.[24]

DevelopmentsEdit

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)[25] and the COG-UK Mutation Explorer. The SARS-CoV-2 Alpha variant was detected in November 2020 by the COG-UK consortium [4][26] and the variant became the subject of ongoing investigations by the UK public health agencies, coordinated by Public Health England and supported by COG-UK.[27]

By December 2020, the number of sequences uploaded to GISAID by COG-UK was 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[23] and the COG-UK consortium was reported to have understood 'the genetic history of more than 150,000 samples of SARS-CoV-2 virus'.[28]

According to the COG-UK website, by December 2021, the UK had sequenced over 1.8 million SARS-CoV-2 genomes.[29]

Selected publicationsEdit

ReferencesEdit

  1. ^ a b c "UK launches whole genome sequence alliance to map spread of coronavirus". COG-UK Consortium. 23 March 2020. Archived from the original on 25 September 2020. Retrieved 23 December 2020.
  2. ^ Peacock, Sharon (17 December 2020). "A short history of the COVID-19 Genomics UK (COG-UK) Consortium". COG-UK Consortium. Archived from the original on 17 December 2020. Retrieved 19 January 2021.
  3. ^ Gallagher, James (23 March 2020). "Coronavirus to be tracked using its genetic code". www.bbc.co.uk. Retrieved 27 January 2021. The project - called the Covid-19 Genomics UK Consortium - is a collaboration between the NHS, public health agencies and the Wellcome Sanger Institute universities. Business Secretary Alok Sharma said: "This new consortium will bring together the UK's brightest and best scientists to build our understanding of this pandemic, tackle the disease and ultimately, save lives."
  4. ^ a b Wise, Jacqui (16 December 2020). "Covid-19: New coronavirus variant is identified in UK". BMJ. 371: m4857. doi:10.1136/bmj.m4857. ISSN 1756-1833. PMID 33328153.
  5. ^ a b c d Cyranoski, David (15 January 2021). "Alarming COVID variants show vital role of genomic surveillance". Nature. 589 (7842): 337–338. Bibcode:2021Natur.589..337C. doi:10.1038/d41586-021-00065-4. PMID 33452508. S2CID 231621736.
  6. ^ "In tracking Covid mutations, most countries flying blind". www.nst.com.my. 22 January 2021. Retrieved 23 January 2021.
  7. ^ "Bio-Britain is leading the world in the science of Covid". Daily Telegraph. 10 January 2021. Archived from the original on 12 January 2022.
  8. ^ "How SARS-CoV-2 sequencing is becoming a national service". COG-UK consortium. Archived from the original on 25 July 2021.
  9. ^ a b "What next for COG-UK?". Archived from the original on 20 April 2021.
  10. ^ Lo, Stephanie W.; Jamrozy, Dorota (20 July 2020). "Genomics and epidemiological surveillance". Nature Reviews Microbiology. 18 (9): 478. doi:10.1038/s41579-020-0421-0. ISSN 1740-1534. PMC 7371787. PMID 32690878.
  11. ^ Davies, Nicholas G.; Abbott, Sam; Barnard, Rosanna C.; Jarvis, Christopher I.; Kucharski, Adam J.; Munday, James D.; Pearson, Carl A. B.; Russell, Timothy W.; Tully, Damien C.; Washburne, Alex D.; Wenseleers, Tom (9 April 2021). "Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England". Science. 372 (6538): eabg3055. doi:10.1126/science.abg3055. ISSN 0036-8075. PMC 8128288. PMID 33658326.
  12. ^ "COG-UK HOCI". Archived from the original on 5 November 2021.
  13. ^ "COVID-19 Infection Survey". Archived from the original on 1 March 2021.
  14. ^ "Real-time Assessment of Community Transmission (REACT) Study". Archived from the original on 6 July 2020.
  15. ^ "Vivaldi study: results". Archived from the original on 28 May 2021.
  16. ^ 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. ISSN 0140-6736. PMC 8009612. PMID 33798499.
  17. ^ "PREVENT-19: A COVID-19 vaccine candidate clinical trial". Archived from the original on 28 December 2020.
  18. ^ Boshier, Florencia A. T.; Pang, Juanita; Penner, Justin; Parker, Matthew; Alders, Nele; Bamford, Alasdair; Grandjean, Louis; Grunewald, Stephanie; Hatcher, James; Best, Timothy; Dalton, Caroline (2022). "Evolution of viral variants in remdesivir-treated and untreated SARS-CoV-2-infected pediatrics patients". Journal of Medical Virology. 94: 161–172. doi:10.1002/jmv.27285. ISSN 1096-9071. PMC 8426849. PMID 34415583.
  19. ^ 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. ISSN 1474-760X. PMC 8247108. PMID 34210356.
  20. ^ Nov 2020, COG-UK 16. "£12.2 million boost for SARS-CoV-2 real-time genomic surveillance - COG-UK Consortium". www.cogconsortium.uk. Retrieved 19 January 2021.
  21. ^ "UK coronavirus variant: 'we're being sanctioned for transparency'". Daily Telegraph. Archived from the original on 12 January 2022.
  22. ^ "Consortium Partners". COG-UK Consortium. Retrieved 22 December 2020.
  23. ^ a b "How Britain has done so much sequencing of the coronavirus genome". www.economist.com. 16 January 2021. Retrieved 28 February 2021.
  24. ^ "Professor Sharon Peacock - CBE FMedSci | Website and Blog". Sharon Peacock. Retrieved 19 January 2021.
  25. ^ "COVID-19 Genomics UK (COG-UK) Consortium Report #10 -11th August 2020 (see section 'Summary of major tools and pipelines developed by COG-UK')" (PDF). www.cogconsortium.uk. 11 August 2020. Retrieved 23 January 2021.
  26. ^ "The new Covid variants are a peril to us all". www.ft.com.
  27. ^ Dec 2020, COG-UK 14. "Update on new SARS-CoV-2 variant and how COG-UK tracks emerging mutations - COG-UK Consortium". www.cogconsortium.uk. Retrieved 19 January 2021.
  28. ^ Schraer, Rachel (22 December 2020). "Covid: New variant found 'due to hard work of UK scientists'". www.bbc.co.uk. Retrieved 23 January 2021.
  29. ^ "COVID-19 Genomics Consortium". 31 December 2021. Archived from the original on 28 April 2020.

External linksEdit